title: Whole blood, RhCMV 68-1 Rh156,108 miR126 Gag/RTN/Pol, day 126, 30306

description: Library name: G225_O07_ABL3_30306_D126


title: MDA-MB-231 cells, Luc-3D, 1

status: Public on Aug 01 2025

type: SRA

city: Minneapolis

first: Allison

last: Makovec

address: 425 E River Parkway

country: USA

institute: University of Minnesota

description: Library name: M_L_1_3D

library_source: transcriptomic

data_processing:
Reads were trimmed for low quality and adaptors using Trimmomatic. Sequences were mapped to the human reference genome (GRCh38.110) using HISAT2 and sorted using SAMTools. Raw gene counts were generated with featureCounts and converted to normalized oounts and variance stabilizing transformed (VST) normalized counts using DESeq2. Genes with zero expression across all samples were filtered out and duplicate gene names were made unique.
Assembly: GRCh38.110
Supplementary files format and content: comma-separated value files includes DESeq2 normalized count values for each 2D sample
Supplementary files format and content: comma-separated value files includes DESeq2 VST normalized count values for each 2D sample
Supplementary files format and content: comma-separated value files includes DESeq2 normalized count values for each 3D sample
Supplementary files format and content: comma-separated value files includes DESeq2 VST normalized count values for each 3D sample

molecule: total RNA

organism: Homo sapiens

source_name: Breast tissue

growth_protocol: The human breast cancer cell lines MDA-MB-231 and HCC1806 were cultured in RPMI medium 1640, supplemented with 10% FBS , 0.2% GlutaMax, and 1% Penicillin Streptomycin grown at 37° C and 5% CO2.

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen)
RNA library preparation was completed by Novogene

tag: tissue

value: Breast tissue

tag: cell line

tag: cell type

value: Triple-negative breast cancer

tag: genotype

value: Luciferase overexpression


title: BRCA-B3G

city: Lausanne

first: Aspram

last: Minasyan

address: Bugnon 25A

country: Switzerland

institute: Ludwig Institute for Cancer Research / CHUV

library_source: transcriptomic single cell

data_processing:
Barcoded 3’GEX libraries and CML were pooled and sequenced on an on Illumina HiSeq 4000 or NovaSeq6000 system, following 10X Genomics recommendations. GEX libraries were sequenced to a median depth of 20,000 unique reads per cell and CMO libraries were sequenced to a median depth of 5’000 unique reads per cell.
Alignment, barcode and UMI counting were performed using mm10-2020-A reference genome and cellranger-6.1.1 multi from 10x Genomics and processed in Seurat R package. Barcodes that were not mapped to any of the CMO libraries, were pooled together for each corresponding group as a pseudo-mouse.
The cell populations and states were annotated as described in the methods section of the Ghisoni et al. manuscript.
Assembly: mm10-2020-A
Supplementary files format and content: RDS object

organism: Mus musculus

source_name: tumour (C57BL/6NHsd female mice)

extract_protocol:
Cells were counted on the ADAM automated cell counter and viability was estimated with the AccuStain solution kit (NanoEntek). Samples were labeled and multiplexed by group, allowing to be pooled in a single GEM for encapsulation. Cell labeling was performed according to the Cell multiplexing oligo labeling protocol from 10x Genomics (CG00391).
libraries were generated using the Chromium Next GEM Single Cell 3’ Library and Gel beads kit v3.1 according to the manufacturer’s instructions

value: tumour (C57BL/6NHsd female mice)

value: ID8 tumour cells


title: S2133_00176_R1_S44

city: New York

first: James

last: Krueger

state: NY

address: 1230 York Avenue

department: Center for Clinical and Translational Science

institute: The Rockefeller University

description: Column 'S2133_00176' in counts.matrix

data_processing:
Adapter & low quality reads removal with cutadapt v2.0
Alignment with star v2.4.2a
quantification with featureCount (subread v1.5.0.post3)
Assembly: GRCh37
Supplementary files format and content: counts.matrix contains gene counts of each sample

source_name: SKIN

extract_protocol: RNA-Seq

value: SKIN

tag: disease

value: HC

tag: treatment

tag: timepoint

tag: group

value: Normal


title: MDA-MB-231 cells, C5-3D, 3

description: Library name: M_C5_3_3D

value: CREB5 overexpression


title: Whole blood, RhCMV 68-1 Rh156,108 miR126 Gag/RTN/Pol, day 126, 28299

first: Michael

last: Gale

state: Minnesota

address: 689 23rd Ave SE

department: Microbiology and Immunology

description: Library name: G223_O07_ABL3_28299_D126

data_processing:
Trimgalorev0.6.4 used to remove low quality reads and bases
Filtered out globin and rRNA reads using bowtie2v2.4.2
Aligned reads with STARv2.710b
Assembly: Rhesus macaques version10 Ensembl annoation v111
Supplementary files format and content: text file of counts for each sample

organism: Macaca mulatta

source_name: Whole blood

extract_protocol:
Isolation of RNA from Whole Blood Using the RNAdvance Blood Kit – for NHP samples
mRNA Library Prep for RNA from Whole Blood using KAPA HyperPrep Reagents

treatment_protocol: A prime and boost of one of the 3 modified RhCMV/SIV vectors were given to female rhesus macaques

value: Whole blood

value: RhCMV 68-1 Rh156,108 miR126 Gag/RTN/Pol

tag: time

value: day 126

tag: animal id

tag: Sex

value: female

tag: treatment outcome

value: Nonprotected


title: MDA-MB-231 cells, C5-3D, 2

description: Library name: M_C5_2_3D


title: MDA-MB-231 cells, C5-3D, 1

description: Library name: M_C5_1_3D


title: BRCA-A3G


title: S2133_00185_R1_S41

description: Column 'S2133_00185' in counts.matrix


title: S2133_00181_R1_S60

description: Column 'S2133_00181' in counts.matrix


title: HCC1806 cells, C5-3D, 1

description: Library name: H_C5_1_3D


title: Whole blood, RhCMV 68-1 Gag/RTN/Pol, day 7, 35895

description: Library name: G221_O07_ABL3_35895_D7

value: RhCMV 68-1 Gag/RTN/Pol

value: day 7

value: Protected


title: HCC1806 cells, Luc-2D, 3

description: Library name: H_L_3_2D

value: Breast tissue


title: Whole blood, RhCMV 68-1 Gag/RTN/Pol, day 7, 35887

description: Library name: G220_O07_ABL3_35887_D7

value: Uninfected


title: S2133_00196_R1_S61

description: Column 'S2133_00196' in counts.matrix


title: Whole blood, RhCMV 68-1 Gag/RTN/Pol, day 7, 35896

description: Library name: G222_O07_ABL3_35896_D7


title: MDA-MB-231 cells, Luc-3D, 3

description: Library name: M_L_3_3D

value: Triple-negative breast cancer

value: Luciferase overexpression


title: sen1-md  8 hours

city: Stony Brook

first: Nancy

last: Hollingsworth

address: 306 Life Sciences Building

department: Biochemistry and Cell Biology

institute: Stony Brook University

description: Library name: B08

data_processing:
Sequencing data (Fastq files) were mapped the S. cerevisiae SK1 genome using Bowtie 1.1.2.
Samtools were used to convert SAM files to BAM format and then sorted.
Cufflinks was used to calculate FPKM values.
Assembly: Yeast PacBio 2016 was the SK1 reference genome (https://yjx1217.github.io/Yeast_PacBio_2016/data/ )(YUE et al. 2017;doi:10.1038/ng.3847)
Supplementary files format and content: Processed data files are text files containing fpkm values.

molecule: polyA RNA

organism: Saccharomyces cerevisiae

growth_protocol: Cells were grown in Yeast extract, peptone, acetate to an OD = to 3.0 X 10^7 cells/ml

extract_protocol:
RNA was isolated using the Qiagen Rneasy kit.
Sequencing libraries were prepared using the NEBNext Ultra RNA Library kit, PolyA according to the manufacturer's specifications.

treatment_protocol: Cells were pelleted, washed with water and resuspended in volume of 2% potassium acetate to induce sporulation.

value: yeast diploid

value: 8  hours after transfer to Sporulation medium at 30ºC


title: BRCA-ACM

description: CMO

value: tumour (C57BL/6NHsd female mice)

value: ID8 tumour cells


title: S2133_00192_R1_S40

description: Column 'S2133_00192' in counts.matrix

value: SKIN

value: HC

value: Normal


title: HCC1806 cells, Luc-2D, 1

description: Library name: H_L_1_2D


title: sen1-md  9 hours

description: Library name: B09

value: 9 hours after transfer to Sporulation medium at 30ºC


title: sen1-md  7 hours

description: Library name: B07

value: 7 hours after transfer to Sporulation medium at 30ºC


title: S2133_00180_R1_S8

description: Column 'S2133_00180' in counts.matrix


title: Whole blood, RhCMV 68-1 Gag/RTN/Pol, day 7, 31687

description: Library name: G218_O07_ABL3_31687_D7

value: Whole blood

value: female


title: HCC1806 cells, Luc-2D, 2

description: Library name: H_L_2_2D


title: S2133_00199_R1_S49

description: Column 'S2133_00199' in counts.matrix


title: Whole blood, RhCMV 68-1 Gag/RTN/Pol, day 7, 32607

description: Library name: G219_O07_ABL3_32607_D7

value: RhCMV 68-1 Gag/RTN/Pol

value: day 7


title: sen1-md 5 hours

description: Library name: B05

value: 5 hours after transfer to Sporulation medium at 30ºC


title: S2133_00193_R1_S1

description: Column 'S2133_00193' in counts.matrix


title: S2133_00183_R1_S2

description: Column 'S2133_00183' in counts.matrix


title: sen1-md  6 hours

description: Library name: B06

value: 6 hours after transfer to Sporulation medium at 30ºC


title: S2133_00184_R1_S3

description: Column 'S2133_00184' in counts.matrix


title: HCC1806 cells, C5-2D, 2

description: Library name: H_C5_2_2D

value: Breast tissue

value: Triple-negative breast cancer

value: CREB5 overexpression


title: HCC1806 cells, C5-2D, 3

description: Library name: H_C5_3_2D


title: Whole blood, RhCMV 68-1 Rh156,108 miR126 Gag/RTN/Pol, day 126, 30277

description: Library name: G224_O07_ABL3_30277_D126

value: RhCMV 68-1 Rh156,108 miR126 Gag/RTN/Pol

value: day 126

value: Nonprotected


title: MDA-MB-231 cells, Luc-2D, 3

description: Library name: M_L_3_2D

value: Luciferase overexpression


title: sen1-md  3 hours

description: Library name: B03

value: yeast diploid

value: 3 hours after transfer to Sporulation medium at 30ºC


title: MDA-MB-231 cells, Luc-2D, 1

description: Library name: M_L_1_2D


title: S2133_00200_R1_S28

description: Column 'S2133_00200' in counts.matrix

value: SKIN

value: HC

value: Normal


title: MDA-MB-231 cells, Luc-2D, 2

description: Library name: M_L_2_2D


title: sen1-md  2 hours

description: Library name: B02

value: 2 hours after transfer to Sporulation medium at 30ºC


title: S2133_00194_R1_S24

description: Column 'S2133_00194' in counts.matrix


title: S2133_00191_R1_S11

description: Column 'S2133_00191' in counts.matrix


title: Whole blood, RhCMV 68-1 Gag/RTN/Pol, day 7, 31432

description: Library name: G208_O07_ABL3_31432_D7

value: Whole blood

value: RhCMV 68-1 Gag/RTN/Pol

value: female


title: Whole blood, RhCMV 68-1 Gag/RTN/Pol, day 7, 31450

description: Library name: G209_O07_ABL3_31450_D7

value: day 7

value: Protected


title: Whole blood, RhCMV 68-1 Gag/RTN/Pol, day 3, 35896

description: Library name: G200_O07_ABL3_35896_D3

value: day 3


title: sen1-md  4 hours

description: Library name: B04

value: 4 hours after transfer to Sporulation medium at 30ºC


title: MDA-MB-231 cells, C5-2D, 3

description: Library name: M_C5_3_2D

value: Breast tissue

value: Triple-negative breast cancer

value: CREB5 overexpression


title: Whole blood, RhCMV 68-1 Gag/RTN/Pol, day 7, 30653

description: Library name: G207_O07_ABL3_30653_D7


title: MDA-MB-231 cells, C5-2D, 2

description: Library name: M_C5_2_2D


title: Whole blood, RhCMV 68-1 Gag/RTN/Pol, day 3, 35887

description: Library name: G198_O07_ABL3_35887_D3

value: Uninfected


title: Whole blood, RhCMV 68-1 Gag/RTN/Pol, day 7, 31670

description: Library name: G211_O07_ABL3_31670_D7


title: Whole blood, RhCMV 68-1 Gag/RTN/Pol, day 3, 35895

description: Library name: G199_O07_ABL3_35895_D3


title: S2133_00186_R1_S33

description: Column 'S2133_00186' in counts.matrix


title: SEN1  9 hours

description: Library name: A09

value: yeast diploid

value: 9 hours after transfer to Sporulation medium at 30ºC


title: S2133_00178_R1_2_S12

description: Column 'S2133_00178' in counts.matrix

value: SKIN


title: SEN1  8 hours

description: Library name: A08

value: 8  hours after transfer to Sporulation medium at 30ºC


title: Whole blood, RhCMV 68-1 Gag/RTN/Pol, day 3, 32607

description: Library name: G197_O07_ABL3_32607_D3


title: sen1-md  0 hours

description: Library name: B00

value: 0 hours after transfer to Sporulation medium at 30ºC


title: Whole blood, RhCMV 68-1 Gag/RTN/Pol, day 3, 31687

description: Library name: G196_O07_ABL3_31687_D3


title: S2133_00195_R1_S9

description: Column 'S2133_00195' in counts.matrix

value: HC

value: Normal


title: S2133_00187_R1_S7

description: Column 'S2133_00187' in counts.matrix


title: S2133_00189_R1_S6

description: Column 'S2133_00189' in counts.matrix


title: SEN1  7 hours

description: Library name: A07

value: 7 hours after transfer to Sporulation medium at 30ºC


title: SEN1  5 hours

description: Library name: A05

value: 5 hours after transfer to Sporulation medium at 30ºC


title: Whole blood, RhCMV 68-1 Gag/RTN/Pol, day 3, 31670

description: Library name: G189_O07_ABL3_31670_D3

value: Whole blood

value: RhCMV 68-1 Gag/RTN/Pol

value: female


title: Whole blood, RhCMV 68-1 Gag/RTN/Pol, day 3, 31450

description: Library name: G187_O07_ABL3_31450_D3

value: day 3

value: Protected


title: S2133_00168_R1_S38

description: Column 'S2133_00168' in counts.matrix

value: Psoriasis

value: Ixekizumab 80mg Q2W

value: BL

value: LS


title: sorted KIR+CD8, pool 2

city: PITTSBURGH

first: Jing

last: Li

state: PA

address: 5117 Centre Ave 2.26b

institute: University of Pittsburgh

data_processing:
BD Rhapsody data underwent processing using the Seven Bridges Genomics cloud platform (San Francisco, CA) along with the BD Rhapsody Targeted Analysis Pipeline that incorporates V(D)J processing. After processing, the data was imported into SeqGeq version 1.6.0 (BD, Ashland, OR), which included a CSV file containing all the data, as well as CSV files identifying the Sample Tag and V(D)J calls. Subsequently, the Lex BDSMK plug-in was executed to separate the Sample Tags, followed by the VDJ Explorer to identify clones. Standard data analysis procedures, such as filtering, log-normalization, variable gene selection, dimensionality reduction, and clustering, were performed utilizing the Seurat 3.0 package. Differential expression analysis was carried out using the Wilcoxon rank-sum test implemented in the Seurat package’s “FindAllMarkers” function. Significant DEGs were defined as those with a log fold change >0.5 and Bonferroni-corrected P < 0.05.
Assembly: We used the BD Rhapsody customerized library. Please see the attached reference files for alignment.
Supplementary files format and content: csv files including raw counts for each library
Supplementary files format and content: csv files including sample tag calls for each library
Supplementary files format and content: csv files including VDJ calls for each library

source_name: peripheral blood

extract_protocol:
Sorted cells were captured with beads in  microwell plate using the BD Rhapsody Cartridge Reagent Kit (no. 633731).
Library preparation were completed using the BD Rhapsody cDNA Kit (no. 633773) and BD Rhapsody™ TCR/BCR Multiomic Assay for Targeted kit (no. 666622). Briefly, cells captured by beads went through cell lysis, bead retrieval, cDNA synthesis, template switching and Klenow extension, and library preparation following the BD Rhapsody protocol. Libraries were prepared for sample tags, targeted mRNA, and TCR-seq.

value: peripheral blood


title: S2133_00198_R1_S39

description: Column 'S2133_00198' in counts.matrix

value: SKIN


title: SEN1  6 hours

description: Library name: A06

value: yeast diploid

value: 6 hours after transfer to Sporulation medium at 30ºC


title: hiPSC-CM, MYH7 H251N HET & WT, Day 30, Gene-Expression, replicate 2

city: STANFORD

first: Paul

last: Heinrich

address: 265 CAMPUS DRIVE

department: Cardiovascular Insititute

institute: Stanford University

description:
GE FASTQ-files contain Gene Expression Library data, FB FASTQ-files contain Feature Barcode Library (R2;5P(BC)); Demultiplexing Instructions (Clone/Corresponding_oligo); (4/GAATCGTGATTCTTC), (3/GCAGGAGGTATCAAT), (85/ACATGGTCAACGCTG)
D30CM_MYH7_G256E_H251N_G256EIso.rds

data_processing:
scRNA seq data underwent sample demultiplexing, alignment, filtering, barcode processing, and gene counting using cellranger (10X). Seurat-Object was genererated and single cells were filtered for QC markers such as gene- and feature count as well as mitochnodrial gene ratio. Details can be found in the methods of the manuscript
Assembly: GRCh38-3.0.0
Supplementary files format and content: RDS (Seurat object)

source_name: H251N Clone 3, H251N Clone 4, H251N Clone 85

growth_protocol: hiPSCs were maintained and directed for cardiac differentiation using Wnt-modulating small-molecule-based protocol. Full protocol can be found in the Method section of the manuscript.

extract_protocol:
Detailed protocol can be found in the Method section of the manuscript. Briefly, differentiated cardiomyocytes on differentiation day 30 were harvested and labeled with sample-specific hashtag oligonucleotides according to the manufacturer's protocol (10X Single Cell 3' v3.1 chemistry with CellPlex feature barcoding technology, CG000388 Rev A).
The labeled hiPSC-CMs underwent emulsion-based single cell encapsulation process using 10X Chromium machine, followed by single cell mRNA library construction. The library was constructed using the manufacturer's protocol (10X Single Cell 3' v3.1 chemistry with feature barcoding technology,  CG000388 Rev A). Briefly, the labeled hiPSC-CMs 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 reversetranscribed 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 appropriate 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. Sample 1 has single index, samples 2-7 have dual index.

treatment_protocol: Samples 2 and 3 were treated with 1uM Isoproterenol for 5 days

value: iPSC-Cardiomyocytes


title: hiPSC-CM, MYH7 H251N HET & WT, Day 30, FB-Expression, replicate 1

value: H251N Clone 3, H251N Clone 4, H251N Clone 85


title: sorted KIR+CD8, pool 1


title: S2133_00090_R1_S3

description: Column 'S2133_00090' in counts.matrix

value: Guselkumab 100mg


title: Whole blood, RhCMV 68-1 Gag/RTN/Pol, day 0, 35896

description: Library name: G178_O07_ABL3_35896_D0

value: day 0


title: hiPSC-CM, MYH7 H251N HET & WT, Day 30, FB-Expression, replicate 2


title: S2133_00004_R1_S1

description: Column 'S2133_00004' in counts.matrix


title: SEN1  3 hours

description: Library name: A03

value: 3 hours after transfer to Sporulation medium at 30ºC


title: MDA-MB-231 cells, C5-2D, 1

description: Library name: M_C5_1_2D

value: Breast tissue

value: Triple-negative breast cancer

value: CREB5 overexpression


title: Whole blood, RhCMV 68-1 Gag/RTN/Pol, day 3, 31432

description: Library name: G186_O07_ABL3_31432_D3

value: Whole blood

value: RhCMV 68-1 Gag/RTN/Pol

value: day 3

value: female

value: Nonprotected


title: Whole blood, RhCMV 68-1 Gag/RTN/Pol, day 3, 30653

description: Library name: G185_O07_ABL3_30653_D3

value: Protected


title: SEN1  2 hours

description: Library name: A02

value: 2 hours after transfer to Sporulation medium at 30ºC


title: S2133_00147_R1_S27

description: Column 'S2133_00147' in counts.matrix

value: SKIN

value: Psoriasis

value: LS


title: sorted KIR+CD8, pool 3

value: peripheral blood


title: S2133_00130_R1_S36

description: Column 'S2133_00130' in counts.matrix

value: Guselkumab 100mg

value: BL


title: Whole blood, RhCMV 68-1 Gag/RTN/Pol, day 0, 35895

description: Library name: G177_O07_ABL3_35895_D0

value: day 0


title: hiPSC-CM, MYH7 H251N HET & WT, Day 30, Gene-Expression, replicate 1

value: H251N Clone 3, H251N Clone 4, H251N Clone 85

value: iPSC-Cardiomyocytes


title: MCF7_INPUT

city: Amsterdam

first: Wilbert

last: Zwart

state: Noord-Holland

address: Plesmanlaan 121

department: Oncogenomics

country: Netherlands

institute: Netherlands Cancer Institute

library_source: genomic

data_processing:
Reads were aligned to the human genome build Hg38/GRCh38 using BWA
Reads with a mapping quality (MAPQ) < 20 were removed from further analysis and duplicates were marked by PICARD/GATK markDuplicates
Enrichment over input control was determined using MACS2 (q < 0.001, narrowPeak mode). Only peaks not overlapping with the ENCODE hg38/GRCh38 blacklisted regions, were retained.
Assembly: hg38/GRCh38
Supplementary files format and content: .bed, narrowPeaks

molecule: genomic DNA

source_name: Breast cancer

growth_protocol: MCF7 cells have been cultured in DMEM + 10% FBS + 1% Pen/Strep, at 5% CO2 and 37°C.

extract_protocol:
Chromatin immunoprecipitation followed by sequencing (ChIP)-seq was performed as previously described (Schmidt, D. et al. Methods 48, 240–248 (2009). In brief, cells were fixed in 1% formaldehyde for 10 min and quenched with 0.125M glycine. Nuclear lysates were extracted as previously described and sonicated for 15 cycles (30 sec on/30 sec off) using the Bioruptor® Pico (B01060001, Diagenode). Per ChIP, 50 µL of magnetic Protein A beads (10008D, Thermo Fisher Scientific) were conjugated to 5µL of ERa, TRIM24, H3K23ac, and H3K27ac antibodies.
Illumina

treatment_protocol: None (full media condition)

value: Breast cancer

value: WT

value: Full-media


title: Whole blood, RhCMV 68-1 Gag/RTN/Pol, day 0, 35887

description: Library name: G176_O07_ABL3_35887_D0

value: Whole blood

value: RhCMV 68-1 Gag/RTN/Pol

value: Uninfected


title: MCF7_TRIM24_rep3


title: hiPSC-CM, MYH7 G256E HET & WT Iso treated, Day 30, FB-Expression, replicate 2

description:
GE FASTQ-files contain Gene Expression Library data, FB FASTQ-files contain Feature Barcode Library (R2;5P(BC)); Demultiplexing Instructions (Clone/Corresponding_oligo); (113/CATGCCAATAGAGCG), (174/ATGAGGAATTCCTGC), (102/CGCGATATGGTCGGA), (141/CCGTCGTCCAAGCAT), (157/AACGTTAATCACTCA)
D30CM_MYH7_G256E_H251N_G256EIso.rds

source_name: G256E Clone 113, G256E Clone 174, G256E Clone 102, G256E Clone 157, G256E Clone 141

value: 5 days of 1uM Isopreterenol


title: MCF7_TRIM24_rep2


title: hiPSC-CM, MYH7 G256E HET & WT Iso treated, Day 30, Gene-Expression, replicate 2

value: G256E Clone 113, G256E Clone 174, G256E Clone 102, G256E Clone 157, G256E Clone 141


title: Whole blood, RhCMV 68-1 Gag/RTN/Pol, day 0, 32607

description: Library name: G175_O07_ABL3_32607_D0

value: female

value: Protected


title: S2133_00153_R1_S51

description: Column 'S2133_00153' in counts.matrix

value: SKIN

value: Psoriasis

value: LS


title: SEN1  4 hours

description: Library name: A04

value: yeast diploid

value: 4 hours after transfer to Sporulation medium at 30ºC


title: S2133_00117_R1_S39

description: Column 'S2133_00117' in counts.matrix

value: Guselkumab 100mg


title: MCF7_TRIM24_rep1


title: hiPSC-CM, MYH7 G256E HET & WT Iso treated, Day 30, FB-Expression, replicate 1

description:
GE FASTQ-files contain Gene Expression Library data, FB FASTQ-files contain Feature Barcode Library (R2;5P(BC)); Demultiplexing Instructions (Clone/Corresponding_oligo); (113/AAGATGAGGTCTGTG), (174/GCAGGAGGTATCAAT), (102/CGGATTCCACATCAT), (141/GTTGATCTATAACAG), (157/AAGCTCGTTGGAAGA)
D30CM_MYH7_G256E_H251N_G256EIso.rds

value: iPSC-Cardiomyocytes


title: Whole blood, RhCMV 68-1 Gag/RTN/Pol, day 0, 31687

description: Library name: G174_O07_ABL3_31687_D0

value: day 0


title: hiPSC-CM, MYH7 G256E HET & WT Iso treated, Day 30, Gene-Expression, replicate 1


title: S2133_00054_R1_S47

description: Column 'S2133_00054' in counts.matrix


title: hiPSC-CM, MYH7 G256E HET & WT, Day 30, FB-Expression, replicate 1

description:
GE FASTQ-files contain Gene Expression Library data, FB FASTQ-files contain Feature Barcode Library (R2;5P(BC)); Demultiplexing Instructions (Clone/Corresponding_oligo) (113/GTCAACTCTTTAGCG), (174/GTATTCCCTCAGTCA), (157/AAGGCAGACGGTGCA), (102/GGCTGCGCACCGCCT)
D30CM_MYH7_G256E_H251N_G256EIso.rds

source_name: G256E Clone 113, G256E Clone 174, G256E Clone 102, G256E Clone 157


title: Whole blood, RhCMV 68-1 Gag/RTN/Pol, day 0, 31670

description: Library name: G167_O07_ABL3_31670_D0


title: SEN1  0 hours

description: Library name: A00

value: 0 hours after transfer to Sporulation medium at 30ºC


title: MCF7_ERa_rep2

value: Breast cancer

value: WT

value: Full-media


title: MCF7_ERa_INPUT


title: S2133_00033_R1_S58

description: Column 'S2133_00033' in counts.matrix

value: BL


title: hiPSC-CM, MYH7 G256E HET & WT, Day 30, Gene-Expression, replicate 1

value: G256E Clone 113, G256E Clone 174, G256E Clone 102, G256E Clone 157


title: Whole blood, RhCMV 68-1 Gag/RTN/Pol, day 0, 31450

description: Library name: G165_O07_ABL3_31450_D0

value: Whole blood

value: RhCMV 68-1 Gag/RTN/Pol


title: S2133_00071_R1_S22

description: Column 'S2133_00071' in counts.matrix

value: Ixekizumab 80mg Q2W


title: S2133_00097_R1_S4

description: Column 'S2133_00097' in counts.matrix

value: SKIN


title: Whole blood, RhCMV 68-1 Gag/RTN/Pol, day 0, 30653

description: Library name: G163_O07_ABL3_30653_D0

value: female

value: Protected


title: HL-60 RIP-Seq input

city: Boston

first: Annalisa

last: Di Ruscio

address: 3 Blackfan Circle, Center of Life Science, Room 407

institute: Beth Israel Deaconess Medical Center, Harvard Medical School

data_processing:
Raw reads were trimmed using fastp with the flags: “LeadMinTrimQual: 3 TrailMinTrimQual: 3 avgMinQual: 15 minReadLength: 40 palindromeClipTreshold: 30 seedMisMatches: 2 simpleClipThreshold: 10 windowSize: 4”. After cleanup, reads were aligned to hg38  uisng hisat2 (v2.1) with options: --rna-strandness FR –no-mixed –no-discordant”. Bam file sorting and indexing was performed using samtools (v1.12). Reads overalapping promoter RNAs were counted using featureCounts (subread-2.0.1) with options set to: “-p -B -O -F 'SAF' -s 1”.  The resulting count matrix was imported into R and for each promoter RNA the following statistics have been computed: number of reads in the RIP, normalized number of reads in the input, Fold enrichment (ratio between RIP and normalized input), P-Value of the test reads using a hypergeometric distribution, adjusted P-Value using Benjamini & Hochberg correction. Transcripts were retained if displaying at least a fold enrichment of 10 and an adjusted p-value ≤ 0.05.  Bam coverage maps were generated using bamCoverage from deeptools (v3.5.1) with options set to: “ --effectiveGenomeSize 2913022398 –normalizeUsing BPM –smoothLength 5 -bs 1 --ignoreDuplicates –exactScaling –filterRNAstrand=[forward|reverse]. Bigwig files of log2(IP/input) signal were generated using bamCompare from deeptools (v3.5.1) with options set to: “--operation log2 --ignoreDuplicates --scaleFactorsMethod None --normalizeUsing RPKM --effectiveGenomeSize 2913022398 --extendReads --binSize 6 --exactScaling --skipNAs --smoothLength 18 –ignoreDuplicates”.
Assembly: hg38
Supplementary files format and content: bigWig coverage files

molecule: nuclear RNA

growth_protocol: The human leukemia cell line HL-60 was obtained from ATCC and grown in glutamine containing medium in the absence of antibiotics, at 37 °C in a humidified atmosphere with 5% CO2.

extract_protocol: Nascent RNA/DNA capture was performed using Click-iT® Nascent RNA Capture Kit (ThermoFisher) according to the manufacturer’s instructions with minor modifications. Briefly, 1. Labeling the cells with EU/EdU. 200 mM EU or 30 mM EdU stock solutions were added to the cells, to a final concentration 0.5 mM or 30 uM, respectively. 2. Incubation. The cells were incubated for 1 or 2 hours. 3. RNA/DNA isolation. The cells were harvested and the RNA/DNA were isolated and dissolved in 14 uL of H2O. 4. Biotinylation of RNA/DNA by Click reaction. Click-iT reaction cocktail (50 uL per reaction) was prepared accordingly to manufacturer’s instructions: a mixture containing 1x Click-iT EU buffer; 2 mM CuSO4; 1 mM Biotin azide; 13.25 uL of the isolated RNA; 10 mM Click-iT® reaction buffer additive 1; 12 mM Click-iT reaction buffer additive 2 was prepared. After adding each component, the reaction cocktail was gently mixed by vortexing. The addition of the Click-iT reaction buffer additive 1 stock initiates the click reaction between the EU-RNA/EdU-DNA and biotin azide. Afterwards the Click-iT reaction buffer additive 2 is added and incubated for 30 minutes with gentle vortexing. 5. RNA/DNA precipitation. 1 uL of UltraPure Glycogen, 55 uL of 7 M ammonium acetate, and 750 uL of chilled 100% ethanol were added to the click reaction, incubated at –70°C for at least 30 minutes and after centrifugation the pellet was dissolved in 125 uL of H2O. 6. Binding biotinylated RNA/DNA to Dynabeads MyOne Streptavidin T1 magnetic beads. The RNA/DNA binding reaction mixture included: 125 uL 2xClick-iT RNA binding buffer; 2 uL Ribonuclease Inhibitor or 2 uL of water for DNA; 125 uL of the isolated biotinylated RNA/DNA. The RNA binding reaction mixture was heated at 68–70°C for 5 minutes and 50 uL of bead suspension added into the heated RNA binding reaction mixture. The tube containing the RNA/DNA binding reaction was incubated at r.t. for 30 min while gently vortexing to prevent the beads from settling. The beads were immobilized using the magnet and washed 5 times with 500 uL of Click-iT reaction wash buffer 1 and 5 times with 500 uL of Click-iT reaction wash buffer 2. Finally, the beads were resuspended in 50 uL of Click-iT reaction wash buffer 2 and the captured RNA immediately processed to cDNA synthesis. The captured DNA was released into 50 uL of boiling water and used in qPCR analyses. RIP-Seq - Immunoprecipitated RNA were processed for sequencing as described by Di Ruscio et al.(Di Ruscio et al., 2013) with some modifications. RNAs were depleted of ribosomal RNA with Ribo-ZeroTM Magnetic Gold Kit. Double stranded cDNA libraries were constructed using ScriptSeq v2 RNA-Seq Library Preparation Kit. The libraries were subjected to final size-selection in 3% agarose gels. 250-500 bp fragments were excised and recovered using the Qiaquick Gel Extraction Kit (Qiagen). RNA-Seq - RNA was extracted with TRI Reagent (MRC). RNA samples were treated with DNase I (10 U of DNase I (Roche) per 3 ug of total RNA; 37ºC for one hour; in the presence of RNase A inhibitor).   RIP-Seq - Immunoprecipitated RNA were processed for sequencing as described by Di Ruscio et al.(Di Ruscio et al., 2013) with some modifications. RNAs were depleted of ribosomal RNA with Ribo-ZeroTM Magnetic Gold Kit. Double stranded cDNA libraries were constructed using ScriptSeq v2 RNA-Seq Library Preparation Kit. The libraries were subjected to final size-selection in 3% agarose gels. 250-500 bp fragments were excised and recovered using the Qiaquick Gel Extraction Kit (Qiagen). RNA-Seq - RNA was extracted with TRI Reagent (MRC). RNA samples were treated with DNase I (10 U of DNase I (Roche) per 3 ug of total RNA; 37ºC for one hour; in the presence of RNase A inhibitor). RNAs were depleted of ribosomal RNA with Ribo-Zero Magnetic Gold Kit. Double stranded cDNA libraries were constructed using ScriptSeq v2 RNA-Seq Library Preparation Kit. The libraries were subjected to final size-selection in 3% agarose gel. 250-500 bp fragments were excised and recovered using the Qiaquick Gel Extraction Kit (Qiagen). Libraries were sequenced on a Hi-Seq-2000 Illumina. ChIP-Seq – ChIP libraries’ construction was performed as described (Mikkelsen et al., 2008) and paired-end sequenced on NextSeq500 platform, at a reading length of 36 nucleotides. Nanopore RNA-Seq - Total nuclera RNA was  isolated after one hour from the release of the S-phase using TRI Reagent (MRC) according to manufacturer’s istructions. RNA sample was  depleted of ribosomal RNA with Ribo-ZeroTM Magnetic Gold Kit. The Polyadenylated RNAs were enriched using oligod(T)25 magnetic beads (NEB S1419S). The remaining polyA minus RNAs wer polyadenylated using TdT (NEB M0315S). The resulting RNA from both fractions, polyA plus and minus were subjected to library preparation using the Direct RNA sequencing kit (SQK-RNA002, Oxford Nanopore Technologies, UK)  according to manufacturer’s istructions. Libraries were sequenced on PromethIon device using R10.4 flow cells.

treatment_protocol: Double Thymidine block (early S-phase block) was carried out as described (Di Ruscio et al., 2013). Briefly, HL-60 cells were grown overnight to 70-80% confluence, washed twice with 1xPBS and cultured in DMEM (10% FCS) + 2.5 mM Thymidine for 18 h (first block). Thymidine was washed out with 1xPBS and cells were grown in DMEM (10% FCS). After 8 hrs cells were cultured in the presence of thymidine for 18 h (second block) and then released as described (Di Ruscio et al., 2013). Synchrony was monitored by flow cytometry analysis of propidium iodide-stained cells using a LSRII flow cytometer (BD Biosciences) at the Harvard Stem Cell Institute/Beth Israel Deaconess Center flow cytometry facility. DRB and Actinomycin D treatments were carried out as described (Di Ruscio et al., 2013). Briefly, after release from double thymidine block, HL-60 cells were treated with 100 μM of 5,6-Dichlorobenzimidazole 1-β–D-ribofuranoside (DRB)(Mitchell and Fraser, 2008) (Sigma Aldrich) or 0.8 μM of Actinomycin D (Sigma Aldrich) as indicated at each time point.

value: Human Caucasian promyelocytic leukaemia

tag: rip antibody

value: none (input)


title: 70,M,scRNAseq

city: Guangzhou

first: Dandan

last: Zong

address: No.106, Zhongshan 2nd Road

country: China

institute: Guangdong Provincial People’s Hospital

description: 10x Genomics

data_processing:
the raw data was analyzed using 10x cellranger
Assembly: hg38，mm10
Supplementary files format and content: Tab-separated text files include count values, features and barcodes

source_name: Normal thyroid tissue

extract_protocol:
cells were trypsined and filtered using a 0.4uM filter in order to obtain a mix composed of single cells.
the single cell mixture was processed using the 10X Chromium Single Cell 3' Reagent Kits User Guide

value: Normal thyroid tissue

tag: age

value: 70 years

value: Male

value: NO


title: MCF7_ERa_rep1

value: Breast cancer


title: Whole blood, RhCMV 68-1 Gag/RTN/Pol, day 0, 31432

description: Library name: G164_O07_ABL3_31432_D0

value: day 0

value: Nonprotected


title: S2133_00074_R1_S20

description: Column 'S2133_00074' in counts.matrix

value: Psoriasis

value: LS


title: 73,M,scRNAseq

description: 10x Genomics

value: 73 years


title: Whole blood, RhCMV 68-1 HLAE supertope Rh156,108 miR126, day 7, 33495

description: Library name: G083_O07_ABL3_33495_D7

value: Whole blood

value: day 7


title: HL-60 RIP-Seq TIP60

value: Rabbit polyclonal TIP60 (home made)


title: S2133_00132_R1_S29

description: Column 'S2133_00132' in counts.matrix

value: SKIN

value: Guselkumab 100mg


title: HL-60 RIP-Seq H2A.Z

value: Human Caucasian promyelocytic leukaemia

value: H2A.Z (Abcam ab4174)


title: Whole blood, RhCMV 68-1 HLAE supertope Rh156,108 miR126, day 7, 32931

description: Library name: G082_O07_ABL3_32931_D7

value: female

value: Protected


title: 29,M,scRNAseq

description: 10x Genomics

value: Normal thyroid tissue

value: 29 years

value: Male


title: 30,F,,scRNAseq

description: 10x Genomics

value: 30 years

value: Female

value: NO


title: Whole blood, RhCMV 68-1 HLAE supertope Rh156,108 miR126, day 7, 32886

description: Library name: G081_O07_ABL3_32886_D7


title: S2133_00012_R1_S21

description: Column 'S2133_00012' in counts.matrix

value: Psoriasis

value: BL

value: LS


title: WT_glycerol_3

city: Novato

first: Fan

last: Zheng

state: California

address: 8001 Redwood Blvd, Novato, CA 94945

institute: BUCK INSTITUTE FOR RESEARCH ON AGING

description:
Library name: G_3
Yeast BY4741 grown in SC medium with [glucose/glycerol] as carbon source, RNA extracted and sequenced as paired-end.

data_processing:
Raw sequencing reads (FASTQ format) were quality filtered and adapter-trimmed using fastp (v0.20.1). Clean reads were aligned to the Saccharomyces cerevisiae reference genome (SGD R64-2-1) using HISAT2 (v2.2.1). Read counts per gene were quantified using featureCounts (v2.0.1) based on gene annotations from SGD. TPM and FPKM values were calculated for downstream expression analysis.
Assembly: Saccharomyces cerevisiae S288C (R64-2-1)
Supplementary files format and content: Processed data file includes a raw read count matrix (tab-delimited text) and a normalized expression matrix (e.g., DESeq2-normalized counts) across all samples.

growth_protocol: Saccharomyces cerevisiae wild-type strain BY4741 was cultured in synthetic complete (SC) medium supplemented with either glucose or glycerol as the carbon source overnight.

extract_protocol:
5-10 OD yeast cell were pellet and wash once with ddH20, yeast cells were digested with Lyllazyme (70mg/ml) for 3min at RT and immediately washed by icy digestion buffer. The RNA is extracted with Quick-RNA Miniprep Kit (Zymo).
Library construction was performed by Novogene using a non-strand-specific mRNA-seq protocol with poly(A) enrichment. Libraries were prepared for paired-end 150 bp sequencing on the Illumina NovaSeq X Plus platform. A total of ~6 Gb of raw data was generated per sample.

value: wild-type haploid yeast cell

value: WT

value: Glycerol


title: Whole blood, RhCMV 68-1 HLAE supertope Rh156,108 miR126, day 7, 32751

description: Library name: G080_O07_ABL3_32751_D7

value: Whole blood

value: day 7

value: Nonprotected


title: 26,F,scRNAseq

description: 10x Genomics

value: 26 years


title: 25,M,scRNAseq

description: 10x Genomics

value: 25 years


title: WT_glycerol_2

description:
Library name: G_2
Yeast BY4741 grown in SC medium with [glucose/glycerol] as carbon source, RNA extracted and sequenced as paired-end.


title: Whole blood, RhCMV 68-1 HLAE supertope Rh156,108 miR126, day 7, 32624

description: Library name: G079_O07_ABL3_32624_D7

value: female

value: Protected


title: WT_glycerol_1

description:
Library name: G_1
Yeast BY4741 grown in SC medium with [glucose/glycerol] as carbon source, RNA extracted and sequenced as paired-end.


title: WT_glucose_3

description:
Library name: D_3
Yeast BY4741 grown in SC medium with [glucose/glycerol] as carbon source, RNA extracted and sequenced as paired-end.

value: Glucose


title: tnf_ski_2

city: Iowa City

first: Vinnyfred

last: Vincent

address: 431 Newton Rd

department: Internal Medicine

institute: University of Iowa

data_processing:
The paired-end reads were aligned to the reference human transcriptome (GENCODE 43, GRCh38.p13) and counted using Salmon software
Read count data obtained from Salmon were normalized using DESeq2.
Assembly: GENCODE 43, GRCh38.p13
Supplementary files format and content: comma separated values file contains the normalized counts for each sample

source_name: human umbilical vein endothelial cells

growth_protocol: HUVECs were grown on gelatin-coated cell culture plates in an endothelial  cell growth medium supplemented with FGF, LR3, IGF-1, VEGF165, EGF, heparin, hydrocortisone, L-ascorbic acid, and 10% fetal bovine serum and maintained at 5% CO2, 37°C, and 100% relative humidity

extract_protocol:
Total cellular RNA was isolated using RNAiso Plus mediated cell lysis, chloroform phase separation, and isopropanol precipitation
New England Biolabs (NEB) Ultra II directional RNA-Seq Library Prep kit protocol was used to prepare libraries for total RNA sequencing

treatment_protocol: Tumor necrosis factor-alpha (TNF-α) (10ng/mL) was used, to induce endothelial inflammation, and 5µM AdipoRon, an agonist of adiponectin receptors to study the effect of adiponectin on endothelial cells. A dual inhibitor of sphingosine kinase 1 (SPHK1) and sphingosine kinase 2 (SPHK2), SKI-I was used to inhibit sphingosine kinase activity at 5µM concentration. All the treatments were carried out for 12 hours in starvation medium (basal medium+0.5% bovine serum albumin (BSA)).

value: human umbilical vein endothelial cells

value: tumor necrosis factor alpha and ski-1


title: Whole blood, RhCMV 68-1 HLAE supertope Rh156,108 miR126, day 7, 32319

description: Library name: G078_O07_ABL3_32319_D7


title: S2133_00034_R1_S41

description: Column 'S2133_00034' in counts.matrix

value: SKIN

value: Ixekizumab 80mg Q2W


title: S2133_00058_R1_S43

description: Column 'S2133_00058' in counts.matrix

value: Psoriasis


title: Whole blood, RhCMV 68-1 HLAE supertope Rh156,108 miR126, day 7, 33705

description: Library name: G084_O07_ABL3_33705_D7


title: 73,F,scRNAseq

description: 10x Genomics

value: Normal thyroid tissue

value: 73 years

value: Female

value: NO


title: WT_glucose_2

description:
Library name: D_2
Yeast BY4741 grown in SC medium with [glucose/glycerol] as carbon source, RNA extracted and sequenced as paired-end.

value: wild-type haploid yeast cell

value: WT


title: S2133_00003_R1_S16

description: Column 'S2133_00003' in counts.matrix

value: BL

value: LS


title: HL-60 RIP-Seq acH2A.Z

value: Human Caucasian promyelocytic leukaemia


title: tnf_adiporon_2

value: tumor necrosis factor alpha and adiporon


title: Whole blood, RhCMV 68-1 Rh156,108 miR126 Gag/RTN/Pol, day 7, 35907

description: Library name: G076_O07_ABL3_35907_D7

value: Whole blood

value: RhCMV 68-1 Rh156,108 miR126 Gag/RTN/Pol

value: day 7

value: female

value: Nonprotected


title: S2133_00100_R1_S4

description: Column 'S2133_00100' in counts.matrix

value: SKIN

value: Guselkumab 100mg


title: Whole blood, RhCMV 68-1 Rh156,108 miR126 Gag/RTN/Pol, day 7, 33530

description: Library name: G075_O07_ABL3_33530_D7

value: Protected


title: Hl-60 Nuclear Extract S-Phase 1hr Nanopore polyA(-) RNA-Seq

data_processing:
Basecalling was performed using guppy (Oxford Nanopore Technologies, UK)  v6.1.2 (GPU-based).   Reads were aligned to the hg38 human reference genome using minimap2 (v2.17-r941). Bam coverage maps were generated using bamCoverage from deeptools (v3.5.1) with default parameters.
Assembly: hg38
Supplementary files format and content: bigWig coverage files

extract_protocol:
Nanopore RNA-Seq - Total nuclera RNA was  isolated after one hour from the release of the S-phase using TRI Reagent (MRC) according to manufacturer’s istructions. RNA sample was  depleted of ribosomal RNA with Ribo-ZeroTM Magnetic Gold Kit. The Polyadenylated RNAs were enriched using oligod(T)25 magnetic beads (NEB S1419S). The remaining polyA minus RNAs wer polyadenylated using TdT (NEB M0315S). The resulting RNA from both fractions, polyA plus and minus were subjected to library preparation using the Direct RNA sequencing kit (SQK-RNA002, Oxford Nanopore Technologies, UK)  according to manufacturer’s istructions. Libraries were sequenced on PromethIon device using R10.4 flow cells.
Nascent RNA/DNA capture was performed using Click-iT® Nascent RNA Capture Kit (ThermoFisher) according to the manufacturer’s instructions with minor modifications. Briefly, 1. Labeling the cells with EU/EdU. 200 mM EU or 30 mM EdU stock solutions were added to the cells, to a final concentration 0.5 mM or 30 uM, respectively. 2. Incubation. The cells were incubated for 1 or 2 hours. 3. RNA/DNA isolation. The cells were harvested and the RNA/DNA were isolated and dissolved in 14 uL of H2O. 4. Biotinylation of RNA/DNA by Click reaction. Click-iT reaction cocktail (50 uL per reaction) was prepared accordingly to manufacturer’s instructions: a mixture containing 1x Click-iT EU buffer; 2 mM CuSO4; 1 mM Biotin azide; 13.25 uL of the isolated RNA; 10 mM Click-iT® reaction buffer additive 1; 12 mM Click-iT reaction buffer additive 2 was prepared. After adding each component, the reaction cocktail was gently mixed by vortexing. The addition of the Click-iT reaction buffer additive 1 stock initiates the click reaction between the EU-RNA/EdU-DNA and biotin azide. Afterwards the Click-iT reaction buffer additive 2 is added and incubated for 30 minutes with gentle vortexing. 5. RNA/DNA precipitation. 1 uL of UltraPure Glycogen, 55 uL of 7 M ammonium acetate, and 750 uL of chilled 100% ethanol were added to the click reaction, incubated at –70°C for at least 30 minutes and after centrifugation the pellet was dissolved in 125 uL of H2O. 6. Binding biotinylated RNA/DNA to Dynabeads MyOne Streptavidin T1 magnetic beads. The RNA/DNA binding reaction mixture included: 125 uL 2xClick-iT RNA binding buffer; 2 uL Ribonuclease Inhibitor or 2 uL of water for DNA; 125 uL of the isolated biotinylated RNA/DNA. The RNA binding reaction mixture was heated at 68–70°C for 5 minutes and 50 uL of bead suspension added into the heated RNA binding reaction mixture. The tube containing the RNA/DNA binding reaction was incubated at r.t. for 30 min while gently vortexing to prevent the beads from settling. The beads were immobilized using the magnet and washed 5 times with 500 uL of Click-iT reaction wash buffer 1 and 5 times with 500 uL of Click-iT reaction wash buffer 2. Finally, the beads were resuspended in 50 uL of Click-iT reaction wash buffer 2 and the captured RNA immediately processed to cDNA synthesis. The captured DNA was released into 50 uL of boiling water and used in qPCR analyses. RIP-Seq - Immunoprecipitated RNA were processed for sequencing as described by Di Ruscio et al.(Di Ruscio et al., 2013) with some modifications. RNAs were depleted of ribosomal RNA with Ribo-ZeroTM Magnetic Gold Kit. Double stranded cDNA libraries were constructed using ScriptSeq v2 RNA-Seq Library Preparation Kit. The libraries were subjected to final size-selection in 3% agarose gels. 250-500 bp fragments were excised and recovered using the Qiaquick Gel Extraction Kit (Qiagen). RNA-Seq - RNA was extracted with TRI Reagent (MRC). RNA samples were treated with DNase I (10 U of DNase I (Roche) per 3 ug of total RNA; 37ºC for one hour; in the presence of RNase A inhibitor).   RIP-Seq - Immunoprecipitated RNA were processed for sequencing as described by Di Ruscio et al.(Di Ruscio et al., 2013) with some modifications. RNAs were depleted of ribosomal RNA with Ribo-ZeroTM Magnetic Gold Kit. Double stranded cDNA libraries were constructed using ScriptSeq v2 RNA-Seq Library Preparation Kit. The libraries were subjected to final size-selection in 3% agarose gels. 250-500 bp fragments were excised and recovered using the Qiaquick Gel Extraction Kit (Qiagen). RNA-Seq - RNA was extracted with TRI Reagent (MRC). RNA samples were treated with DNase I (10 U of DNase I (Roche) per 3 ug of total RNA; 37ºC for one hour; in the presence of RNase A inhibitor). RNAs were depleted of ribosomal RNA with Ribo-Zero Magnetic Gold Kit. Double stranded cDNA libraries were constructed using ScriptSeq v2 RNA-Seq Library Preparation Kit. The libraries were subjected to final size-selection in 3% agarose gel. 250-500 bp fragments were excised and recovered using the Qiaquick Gel Extraction Kit (Qiagen). Libraries were sequenced on a Hi-Seq-2000 Illumina. ChIP-Seq – ChIP libraries’ construction was performed as described (Mikkelsen et al., 2008) and paired-end sequenced on NextSeq500 platform, at a reading length of 36 nucleotides. Nanopore RNA-Seq - Total nuclera RNA was  isolated after one hour from the release of the S-phase using TRI Reagent (MRC) according to manufacturer’s istructions. RNA sample was  depleted of ribosomal RNA with Ribo-ZeroTM Magnetic Gold Kit. The Polyadenylated RNAs were enriched using oligod(T)25 magnetic beads (NEB S1419S). The remaining polyA minus RNAs wer polyadenylated using TdT (NEB M0315S). The resulting RNA from both fractions, polyA plus and minus were subjected to library preparation using the Direct RNA sequencing kit (SQK-RNA002, Oxford Nanopore Technologies, UK)  according to manufacturer’s istructions. Libraries were sequenced on PromethIon device using R10.4 flow cells.


title: S2133_00165_R1_S17

description: Column 'S2133_00165' in counts.matrix

value: Psoriasis

value: Ixekizumab 80mg Q2W


title: Whole blood, RhCMV 68-1 Rh156,108 miR126 Gag/RTN/Pol, day 7, 33514

description: Library name: G074_O07_ABL3_33514_D7


title: Hl-60 Nuclear Extract S-Phase 1hr Nanopore polyA(+) RNA-Seq


title: ski_1

value: human umbilical vein endothelial cells

value: sphingosine kinase inhibitor (ski-1)


title: Whole blood, RhCMV 68-1 Rh156,108 miR126 Gag/RTN/Pol, day 7, 35908

description: Library name: G077_O07_ABL3_35908_D7


title: adiporon_2

value: adiporon


title: Whole blood, RhCMV 68-1 Rh156,108 miR126 Gag/RTN/Pol, day 7, 32569

description: Library name: G072_O07_ABL3_32569_D7


title: Cisplatin treated kidneys,Cis2

city: Shanghai

first: Bo

last: Deng

address: 639 Zhizaoju Road

department: Division of Nephrology

institute: Shanghai Ninth People's Hospital, School of Medicine, Shanghai Jiaotong University

data_processing:
Raw data were processed through in-house perl scripts. During this process, clean data were obtained after removing low-quality reads and reads containing adapter or ploy-N  from raw data.
Reference genome and gene model annotation files were downloaded from genome website directly
Index of the reference genome was built and clean reads were aligned to the reference genome using HISAT
Assembly: GRCm38.p6
Supplementary files format and content: xls file includes RPKM values for each sample

source_name: kidneys

extract_protocol:
Kidney tissues underwent total RNA extraction through the application of an RNASimple Total RNA Kit (DP419, Tiangen)
RNA libraries for RNA-seq were prepared following manufacturer's protocols

treatment_protocol: Cisplatin-induced AKI was established by cisplatin administration,injected i.p.

value: kidneys

value: WT

value: Cisplatin treat


title: Whole blood, RhCMV 68-1 HLAE supertope Rh156,108 miR126, day 7, 32290

description: Library name: G070_O07_ABL3_32290_D7


title: tnf_adiporon_1

value: tumor necrosis factor alpha and adiporon


title: Whole blood, RhCMV 68-1 HLAE supertope Rh156,108 miR126, day 7, 32240

description: Library name: G069_O07_ABL3_32240_D7

value: Whole blood


title: S2133_00002_R1_S51

description: Column 'S2133_00002' in counts.matrix

value: LS


title: tnf_ski_1

value: tumor necrosis factor alpha and ski-1


title: Cisplatin treated kidneys,Cis3


title: ski_2


title: S2133_00115_R1_S45

description: Column 'S2133_00115' in counts.matrix


title: S2133_00131_R1_S29

description: Column 'S2133_00131' in counts.matrix


title: S2133_00162_R1_S54

description: Column 'S2133_00162' in counts.matrix


title: adiporon_1


title: control_2

value: vehicle


title: WT_glucose_1

description:
Library name: D_1
Yeast BY4741 grown in SC medium with [glucose/glycerol] as carbon source, RNA extracted and sequenced as paired-end.

value: wild-type haploid yeast cell

value: Glucose


title: S2133_00113_R1_S52

description: Column 'S2133_00113' in counts.matrix

value: SKIN

value: Guselkumab 100mg

value: BL


title: S2133_00008_R1_S4

description: Column 'S2133_00008' in counts.matrix

value: Psoriasis

value: Ixekizumab 80mg Q2W


title: S2133_00103_R1_S33

description: Column 'S2133_00103' in counts.matrix


title: control_1

value: human umbilical vein endothelial cells


title: Whole blood, RhCMV 68-1 HLAE supertope Rh156,108 miR126, day 7, 31654

description: Library name: G067_O07_ABL3_31654_D7

value: day 7

value: female

value: Nonprotected


title: S2133_00027_R1_S48

description: Column 'S2133_00027' in counts.matrix


title: Cisplatin treated kidneys,Cis1

value: kidneys

value: WT

value: Cisplatin treat


title: Whole blood, RhCMV 68-1 Rh156,108 miR126 Gag/RTN/Pol, day 7, 32543

description: Library name: G071_O07_ABL3_32543_D7

value: Whole blood

value: RhCMV 68-1 Rh156,108 miR126 Gag/RTN/Pol

value: Protected


title: tnf_2

value: tumor necrosis factor alpha


title: Whole blood, RhCMV 68-1 Rh156,108 miR126 Gag/RTN/Pol, day 7, 32574

description: Library name: G073_O07_ABL3_32574_D7


title: Control kidneys, Ctrl3

value: Control


title: tnf_1


title: Whole blood, RhCMV 68-1 HLAE supertope Rh156,108 miR126, day 7, 31644

description: Library name: G066_O07_ABL3_31644_D7


title: Control kidneys, Ctrl1


title: Huh7 cells

city: Harbin

first: Yucao

last: Sun

state: Heilongjiang Province

address: No.150, Haping Road, Nangang District

institute: Harbin Medical University Cancer Hospital

description: control

data_processing:
clean data (clean reads) were obtained by trimming reads containing adapter, ploy-N or with low quality from raw data
Index of the reference genome was built using hisat2-v2.0.5  and paired-end clean reads were mapped to the reference genome.
Stringtie-1.3.3b ）was used to count the read numbers mapped to each gene. And then FPKM was calculated.It normalizes for both sequencing depth and genome size.
(For samples with biological replicates, edgeR_3.24.3 (lncRNA), DESeq2_R-3.1.2(circRNA)) Differential expression analysis of two conditions/groups (at least two biological replicates per condition/group) was performed using the edgeR.The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate . Genes with an adjusted P-value <0.05 were assigned as differentially expressed ones.
Gene Ontology (GO) enrichment analysis of differentially expressed genes was implemented by the GOseq R package, in which gene length bias was corrected. GO terms with corrected P-value less than 0.05 were considered as significantly enriched GO functions of gene set. KEGG is a database resource for understanding high-level functions and utilities of the biological system, such as the cell, the organism and the ecosystem, from molecularlevel information, especially large-scale molecular datasets generated by genome sequencing and other high-through put experimental technologies (http://www.genome.jp/kegg/). We used KOBAS to test the statistical enrichment of differential expression genes in KEGG pathways.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample ...

growth_protocol: HepG2 and Huh7 cells were matained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37°C。

extract_protocol:
RNA was harvested using Trizol reagent.
A total of 1 µg total RNA per sample was used as input material for the lncRNA library preparation. Strand-specific libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample

value: control


title: Whole blood, IL15, day 21, 39103

description: Library name: G079_O20_Cy_39103_D21

data_processing:
Trimgalorev0.6.10 used to remove low quality reads and bases
Filtered out globin and rRNA reads using bowtie2v2.4.4
Aligned reads with STARv2.7.10b to both rhesus macaque and cynomolgus macaque genomes
Assembly: Macaca fascicularis version 6 Ensembl annoation v110 and Macaca mulatta version 10 Ensembl annoation v110
Supplementary files format and content: Two count matricies one the macaca fascicularis and macaca mulatta

organism: Macaca fascicularis

extract_protocol:
Isolation of RNA from Whole Blood Using the RNAdvance Blood Kit
mRNA Library Prep for RNA from Whole Blood using KAPA HyperPrep Reagents

treatment_protocol: Cynomolgus macaques treated  treated with increasing doses of IL-15/IL-15Ra

value: day 21

value: Male

tag: dose

value: 15 ug/kg IL-15/IL-15Ra


title: S2133_00139_R1_S38

description: Column 'S2133_00139' in counts.matrix

value: SKIN

value: Psoriasis

value: Ixekizumab 80mg Q2W

value: BL

value: LS


title: Whole blood, RhCMV 68-1 HLAE supertope Rh156,108 miR126, day 7, 26712

description: Library name: G064_O07_ABL3_26712_D7

value: day 7

value: female

value: Nonprotected


title: S2133_00060_R1_S7

description: Column 'S2133_00060' in counts.matrix


title: Control kidneys, Ctrl2

value: kidneys

value: WT


title: Whole blood, RhCMV 68-1 HLAE supertope Rh156,108 miR126, day 7, 31893

description: Library name: G068_O07_ABL3_31893_D7

value: Whole blood

value: Protected


title: HepG2 cells

description: control


title: Whole blood, IL15, day 21, 39104

description: Library name: G080_O20_Cy_39104_D21


title: Whole blood, IL15, day 21, 39098

description: Library name: G076_O20_Cy_39098_D21

value: Female


title: S2133_00102_R1_S18

description: Column 'S2133_00102' in counts.matrix


title: Whole blood, IL15, day 21, 39097

description: Library name: G075_O20_Cy_39097_D21


title: S2133_00141_R1_S28

description: Column 'S2133_00141' in counts.matrix


title: Whole blood, RhCMV 68-1 Rh156,108 miR126 Gag/RTN/Pol, day 7, 30438

description: Library name: G062_O07_ABL3_30438_D7

value: RhCMV 68-1 Rh156,108 miR126 Gag/RTN/Pol


title: HUWE1_11

city: Memphis

first: Yong-Dong

last: Wang

state: TN

address: 262 Danny Thomas Pl, MS1135

institute: St. Jude Children's Research Hospital

description: HUWE1 siRNAs set 3 replicate 3

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence and low-quality sequence, then mapped to hg38 whole genome using CLC Genomic Workbench RNA seq tool. TPM for transcripts were reported.
Assembly: hg38
Supplementary files format and content: all.tpm_2 tab-delimited text file includes TPM values for all 12 samples

source_name: human HEK293T cells treated with siRNAs

extract_protocol:
Cells were homogenized in Trizol and RNA extracted by isopropanol precipitation from the aqueous phase. RNA sequencing was performed as previously described from from human HEK293T cells treated with siRNAs targetingUBA1 and E2 ubiquitin-conjugating enzymes compared to control treatment with non-targeting (NT) siRNAs
For sequencing, biological replicates were prepared with the TruSeq stranded mRNA library prep kit (Illumina) and sequenced on the Illumina NovaSeq 6000 platform.

value: human HEK293T cells treated with siRNAs

value: HUWE1 siRNAs


title: S2133_00072_R1_S10

description: Column 'S2133_00072' in counts.matrix


title: S2133_00079_R1_S5

description: Column 'S2133_00079' in counts.matrix


title: Whole blood, RhCMV 68-1 HLAE supertope Rh156,108 miR126, day 7, 27769

description: Library name: G065_O07_ABL3_27769_D7


title: Whole blood, IL15, day 21, 39102

description: Library name: G078_O20_Cy_39102_D21

value: day 21

value: Male

value: 15 ug/kg IL-15/IL-15Ra


title: HepG2 cells treat with SDT+cuproptosis

description: treat(SDT+cuproptosis)

value: SDT+cuproptosis


title: Whole blood, IL15, day 21, 39095

description: Library name: G074_O20_Cy_39095_D21


title: Whole blood, IL15, day 21, 39090

description: Library name: G073_O20_Cy_39090_D21


title: Whole blood, RhCMV 68-1 Rh156,108 miR126 Gag/RTN/Pol, day 7, 30310

description: Library name: G060_O07_ABL3_30310_D7


title: S2133_00092_R1_S42

description: Column 'S2133_00092' in counts.matrix

value: SKIN

value: Psoriasis

value: Ixekizumab 80mg Q2W


title: Huh7 cells treat with SDT+cuproptosis

description: treat(SDT+cuproptosis)


title: Whole blood, IL15, day 21, 39100

description: Library name: G077_O20_Cy_39100_D21


title: S2133_00104_R1_S44

description: Column 'S2133_00104' in counts.matrix

value: LS


title: Whole blood, RhCMV 68-1 Rh156,108 miR126 Gag/RTN/Pol, day 7, 31374

description: Library name: G063_O07_ABL3_31374_D7

value: day 7

value: female


title: HUWE1_10

description: HUWE1 siRNAs set 3 replicate 2


title: HUWE1_7

description: HUWE1 siRNAs set 2 replicate 3


title: S2133_00065_R1_S40

description: Column 'S2133_00065' in counts.matrix

value: Guselkumab 100mg

value: BL


title: HUWE1_9

description: HUWE1 siRNAs set 3 replicate 1


title: HUWE1_12

description: HUWE1 siRNAs set 3 replicate 4


title: S2133_00066_R1_S25

description: Column 'S2133_00066' in counts.matrix


title: Whole blood, RhCMV 68-1 Rh156,108 miR126 Gag/RTN/Pol, day 7, 30386

description: Library name: G061_O07_ABL3_30386_D7

value: Whole blood

value: Protected


title: HUWE1_8

description: HUWE1 siRNAs set 2 replicate 4


title: S2133_00075_R1_S46

description: Column 'S2133_00075' in counts.matrix


title: Whole blood, IL15, day 17, 39104

description: Library name: G072_O20_Cy_39104_D17

value: day 17


title: S2133_00089_R1_S35

description: Column 'S2133_00089' in counts.matrix


title: Whole blood, RhCMV 68-1 Rh156,108 miR126 Gag/RTN/Pol, day 7, 30277

description: Library name: G058_O07_ABL3_30277_D7

value: RhCMV 68-1 Rh156,108 miR126 Gag/RTN/Pol

value: Nonprotected


title: Whole blood, IL15, day 17, 39103

description: Library name: G071_O20_Cy_39103_D17


title: S2133_00051_R1_S41

description: Column 'S2133_00051' in counts.matrix


title: Whole blood, RhCMV 68-1 Rh156,108 miR126 Gag/RTN/Pol, day 7, 28299

description: Library name: G057_O07_ABL3_28299_D7


title: Whole blood, IL15, day 17, 39098

description: Library name: G068_O20_Cy_39098_D17

value: Female


title: Whole blood, RhCMV 68-1 HLAE supertope Rh156,108 miR126, day 3, 33495

description: Library name: G055_O07_ABL3_33495_D3

value: day 3


title: S2133_00093_R1_S35

description: Column 'S2133_00093' in counts.matrix


title: HUWE1_6

description: HUWE1 siRNAs set 2 replicate 2

value: human HEK293T cells treated with siRNAs

value: HUWE1 siRNAs


title: Whole blood, IL15, day 17, 39102

description: Library name: G070_O20_Cy_39102_D17

value: Male

value: 15 ug/kg IL-15/IL-15Ra


title: Whole blood, RhCMV 68-1 HLAE supertope Rh156,108 miR126, day 3, 33705

description: Library name: G056_O07_ABL3_33705_D3


title: HUWE1_5

description: HUWE1 siRNAs set 2 replicate 1


title: Whole blood, RhCMV 68-1 Rh156,108 miR126 Gag/RTN/Pol, day 7, 30306

description: Library name: G059_O07_ABL3_30306_D7


title: S2133_00109_R1_S58

description: Column 'S2133_00109' in counts.matrix

value: SKIN

value: Psoriasis

value: Ixekizumab 80mg Q2W


title: Whole blood, IL15, day 17, 39097

description: Library name: G067_O20_Cy_39097_D17


title: NT_3

description: non-targeting siRNAs set 2&3 replicate 3

value: non-targeting siRNAs


title: Whole blood, IL15, day 17, 39095

description: Library name: G066_O20_Cy_39095_D17


title: S2133_00055_R1_S36

description: Column 'S2133_00055' in counts.matrix

value: LS


title: NT_2

description: non-targeting siRNAs set 2&3 replicate 2


title: Whole blood, RhCMV 68-1 HLAE supertope Rh156,108 miR126, day 3, 32886

description: Library name: G053_O07_ABL3_32886_D3

value: female


title: Whole blood, RhCMV 68-1 HLAE supertope Rh156,108 miR126, day 3, 32751

description: Library name: G052_O07_ABL3_32751_D3

value: Whole blood


title: S2133_00041_R1_S19

description: Column 'S2133_00041' in counts.matrix


title: Whole blood, RhCMV 68-1 HLAE supertope Rh156,108 miR126, day 3, 32624

description: Library name: G051_O07_ABL3_32624_D3

value: Protected


title: NT_1

description: non-targeting siRNAs set 2&3 replicate 1


title: Whole blood, IL15, day 17, 39100

description: Library name: G069_O20_Cy_39100_D17

value: day 17


title: NT_4

description: non-targeting siRNAs set 2&3 replicate 4


title: S2133_00142_R1_S55

description: Column 'S2133_00142' in counts.matrix

value: Guselkumab 100mg


title: Whole blood, RhCMV 68-1 HLAE supertope Rh156,108 miR126, day 3, 32931

description: Library name: G054_O07_ABL3_32931_D3


title: Whole blood, IL15, day 17, 39090

description: Library name: G065_O20_Cy_39090_D17


title: Whole blood, IL15, day 14, 39104

description: Library name: G064_O20_Cy_39104_D14

value: day 14


title: Whole blood, RhCMV 68-1 Rh156,108 miR126 Gag/RTN/Pol, day 3, 35907

description: Library name: G048_O07_ABL3_35907_D3

value: RhCMV 68-1 Rh156,108 miR126 Gag/RTN/Pol

value: Nonprotected


title: Whole blood, RhCMV 68-1 HLAE supertope Rh156,108 miR126, day 3, 32319

description: Library name: G050_O07_ABL3_32319_D3

value: day 3


title: S2133_00108_R1_S25

description: Column 'S2133_00108' in counts.matrix

value: BL


title: Whole blood, IL15, day 14, 39103

description: Library name: G063_O20_Cy_39103_D14

value: Male


title: RKO cell  shRPLP0P2#1

city: Hangzhou

first: Hang

last: Yuan

address: 158 Shangtang Road, Hangzhou, Zhejiang,China

institute: Zhejiang Provincial People's Hospital

data_processing:
Reads obtained from  the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following  assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt  (https://cutadapt.readthedocs.io/en/stable/, version:cutadapt-1.9).
We aligned reads of all samples to the < research species > reference genome using HISAT2  (https://daehwankimlab.github.io/hisat2/, version:hisat2-2.2.1) package, which initially remove a portion of the reads based  on quality information accompanying each read and then maps the reads to the reference genome. HISAT2 allows multiple  alignments per read (up to 20 by default) and a maximum of two mismatch when mapping the reads to the reference.  HISAT2 build a database of potential splice junctions and confirms these by comparing the previously unmapped reads  against the database of putative junctions.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,  version:stringtie-2.1.6) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a  comprehensive transcriptome using gffcompare software (http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,  version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown  (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all  transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per  million mapped reads) value.
Genes differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR  between two samples). The genes with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change ≥ 2  were considered differentially expressed genes. Differentially expressed genes were then subjected to enrichment analysis  of GO functions and KEGG pathways.
Assembly: Homo_sapiens.GRCh38
Supplementary files format and content: genes_fpkm_expression.xlsx

source_name: RKO

growth_protocol: RKO cells were maintained in RPMI-1640 medium supplemented with 10% fetal bovine serum

extract_protocol:
RNA was extracted using Trizol reagent (thermofisher, 15596018) following the manufacturer's procedure. The total  RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA,  5067-1511) , 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) (Thermo Fisher, CA, USA) with two  rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under  elevated temperature (Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min). Then the  cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen,  cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I  (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA). 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 (NEB,  cat.m0280, USA) 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: RKO

value: colon carcinoma cell line

value: PRLP0P2 knockdown


title: RKO cell  shRPLP0P2#2

value: PRLP0P3 knockdown


title: Whole blood, RhCMV 68-1 Rh156,108 miR126 Gag/RTN/Pol, day 3, 35908

description: Library name: G049_O07_ABL3_35908_D3


title: Whole blood, RhCMV 68-1 Rh156,108 miR126 Gag/RTN/Pol, day 3, 33514

description: Library name: G046_O07_ABL3_33514_D3


title: RKO cell  shControl#2

value: WT


title: RKO cell  shControl#1


title: Whole blood, IL15, day 14, 39100

description: Library name: G061_O20_Cy_39100_D14

value: 15 ug/kg IL-15/IL-15Ra


title: S2133_00021_R1_S32

description: Column 'S2133_00021' in counts.matrix

value: SKIN

value: Psoriasis

value: Ixekizumab 80mg Q2W

value: LS


title: RKO cell  shRPLP0P2#3

value: PRLP0P4 knockdown


title: S2133_00045_R1_S59

description: Column 'S2133_00045' in counts.matrix

value: Guselkumab 100mg


title: Whole blood, IL15, day 14, 39097

description: Library name: G059_O20_Cy_39097_D14

value: Whole blood

value: day 14

value: Female


title: Whole blood, IL15, day 14, 39102

description: Library name: G062_O20_Cy_39102_D14


title: RKO cell  shControl#3


title: S2133_00070_R1_S50

description: Column 'S2133_00070' in counts.matrix


title: Whole blood, RhCMV 68-1 Rh156,108 miR126 Gag/RTN/Pol, day 3, 33530

description: Library name: G047_O07_ABL3_33530_D3

value: RhCMV 68-1 Rh156,108 miR126 Gag/RTN/Pol

value: day 3

value: female

value: Protected


title: Whole blood, IL15, day 14, 39090

description: Library name: G057_O20_Cy_39090_D14


title: S2133_00001_R1_S24

description: Column 'S2133_00001' in counts.matrix


title: ESCC cells, Control

first: Fangfang

last: Chen

state: Guangdong

address: No.132 Waihuandong Road, University Town

department: School of Pharmaceutical Sciences

institute: Sun Yat-sen University

data_processing:
Illumina bcl2fastq 2.0 software used for basecalling
clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Hisat2 can generate a database of splice junctions based on the gene model annotation file
The mapped reads of each sample were assembled using StringTie with default parameters. Then, all transcripts from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software.
RSEM was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Supplementary files format and content: Excel spreadsheet file includes gene name and FPM values for each sample.

source_name: Esophageal cancer cell

growth_protocol: Cells were cultured in complete RPMI-1640 medium supplemented with 10% FBS, 100 IU/mL penicillin and 100 μg/mL streptomycin at 37°C in a humidified atmosphere with 5% CO2.

extract_protocol:
Total RNA was extrated from each cell sample using a RNeasy Mini Kit (Qiagen, USA). A total amount of 1 µg RNA per sample was used as input material for the RNA sample preparations.
Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (CatalogE7530L, NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

treatment_protocol: Cells were infected with Fusobacterium nucleatum at an MOI of 100 for 24 h

value: Esophageal cancer cell

tag: infection

value: PBS


title: S2133_00082_R1_S52

description: Column 'S2133_00082' in counts.matrix

data_processing:
Adapter & low quality reads removal with cutadapt v2.0
Alignment with star v2.4.2a
quantification with featureCount (subread v1.5.0.post3)
Assembly: GRCh37
Supplementary files format and content: counts.matrix contains gene counts of each sample

extract_protocol: RNA-Seq

value: BL


title: Whole blood, IL15, day 14, 39098

description: Library name: G060_O20_Cy_39098_D14

value: 15 ug/kg IL-15/IL-15Ra


title: Whole blood, IL15, day 10, 39104

description: Library name: G056_O20_Cy_39104_D10

value: day 10

value: Male


title: Whole blood, IL15, day 10, 39103

description: Library name: G055_O20_Cy_39103_D10


title: ESCC cells, Fn

value: WT

value: Fn


title: Whole blood, IL15, day 14, 39095

description: Library name: G058_O20_Cy_39095_D14


title: S2133_00159_R1_S2

description: Column 'S2133_00159' in counts.matrix

value: SKIN

value: Psoriasis

value: Ixekizumab 80mg Q2W

value: LS


title: Whole blood, RhCMV 68-1 HLAE supertope Rh156,108 miR126, day 3, 32240

description: Library name: G041_O07_ABL3_32240_D3

data_processing:
Trimgalorev0.6.4 used to remove low quality reads and bases
Filtered out globin and rRNA reads using bowtie2v2.4.2
Aligned reads with STARv2.710b
Assembly: Rhesus macaques version10 Ensembl annoation v111
Supplementary files format and content: text file of counts for each sample

extract_protocol:
Isolation of RNA from Whole Blood Using the RNAdvance Blood Kit – for NHP samples
mRNA Library Prep for RNA from Whole Blood using KAPA HyperPrep Reagents

value: Whole blood

value: Nonprotected


title: Whole blood, RhCMV 68-1 Rh156,108 miR126 Gag/RTN/Pol, day 3, 32574

description: Library name: G045_O07_ABL3_32574_D3

value: RhCMV 68-1 Rh156,108 miR126 Gag/RTN/Pol

value: day 3


title: Whole blood, IL15, day 10, 39102

description: Library name: G054_O20_Cy_39102_D10


title: S2133_00031_R1_S14

description: Column 'S2133_00031' in counts.matrix


title: Whole blood, RhCMV 68-1 Rh156,108 miR126 Gag/RTN/Pol, day 3, 32569

description: Library name: G044_O07_ABL3_32569_D3

value: female

value: Protected


title: Whole blood, RhCMV 68-1 Rh156,108 miR126 Gag/RTN/Pol, day 3, 32543

description: Library name: G043_O07_ABL3_32543_D3


title: S2133_00138_R1_S37

description: Column 'S2133_00138' in counts.matrix


title: SW480-LM3-1

city: jinan

first: liu

last: jialiang

address: wenhuaxi road

institute: shandong university

description:
SQ23025064-LIB-6-1-LIB-B-1
processed data file1.txt

data_processing:
SOAPnuke (V2.1.0) was used to filter the sequencing data as follows:  (1) Reads containing sequencing joints were removed;  (2) Reads with N ratio greater than 0.5% were removed;  (3) Removal of low-quality reads (those with Qphred≤20 bases accounting for more than 50% of the length of the entire reads).  Clean reads are obtained after filtering
Assembly: HISAT2 (V2.1.0) was used to compare clean reads with the reference genome,  and Bowtie2  (V2.3.5) was used to align the quality controlled sequence to the  reference transcription sequence.
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

extract_protocol:
Total RNA was extracted using the Trizol(Invitrogen, CA, USA), RNA purity and integrity was monitored by NanoDrop 2000 spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA) and a Bioanalyzer 2100 system (Agilent  Technologies, CA, USA). RNA contamination was assessed by 1.5% agarose gel.
Oligo(dT)-attached magnetic beads were used to purify mRNA. Purified mRNA  was fragmented into small pieces with fragment buffer at appropriate temperature. Then  First-strand cDNA was generated using random hexamer-primed reverse transcription,  followed by a second-strand cDNA synthesis and purified using AMPure XP Beads.  Afterwards, A-Tailing Mix and RNA Index Adapters were added by incubating to end  cDNA repair. The cDNA fragments obtained from previous steps were amplified by  PCR, and products were purified by Ampure XP Bead, get the final library. After the library was constructed, Qubit 2.0 was used for preliminary  quantification, and the library was diluted to 1.5 ng/μL. Then Agilent 2100 BioAnalyzer  was used to detect the insert size of the library. Qrt-pcr was used to accurately quantify the effective concentration of the library to ensure the quality of the library.

value: human colon cancer cells


title: S2133_00163_R1_S59

description: Column 'S2133_00163' in counts.matrix


title: Whole blood, RhCMV 68-1 HLAE supertope Rh156,108 miR126, day 3, 32290

institute: University of Minnesota

description: Library name: G042_O07_ABL3_32290_D3


title: SW480-LM3-2

description:
SQ23025065-LIB-6-2-LIB-B-2
processed data file1.txt


title: S2133_00157_R1_S54

description: Column 'S2133_00157' in counts.matrix

value: BL


title: Whole blood, RhCMV 68-1 HLAE supertope Rh156,108 miR126, day 3, 31644

description: Library name: G038_O07_ABL3_31644_D3


title: Whole blood, IL15, day 10, 39100

description: Library name: G053_O20_Cy_39100_D10

value: 15 ug/kg IL-15/IL-15Ra


title: Whole blood, IL15, day 10, 39098

description: Library name: G052_O20_Cy_39098_D10

value: day 10

value: Female


title: Whole blood, IL15, day 10, 39097

description: Library name: G051_O20_Cy_39097_D10


title: Whole blood, IL15, day 10, 39090

description: Library name: G049_O20_Cy_39090_D10


title: S2133_00129_R1_S58

description: Column 'S2133_00129' in counts.matrix


title: HUWE1siRNA_3

description: HUWE1 siRNAs replicate 3

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence and low-quality sequence, then mapped to hg38 whole genome using CLC Genomic Workbench RNA seq tool. TPM for transcripts were reported.
Assembly: hg38
Supplementary files format and content: all.tpm.txt tab-delimited text file includes TPM values for all 8 samples

tag: sirna

value: HUWE1 siRNAs


title: S2133_00155_R1_S12

description: Column 'S2133_00155' in counts.matrix

tag: tissue


title: Whole blood, RhCMV 68-1 Rh156,108 miR126 Gag/RTN/Pol, day 3, 31374

description: Library name: G035_O07_ABL3_31374_D3


title: Whole blood, RhCMV 68-1 Rh156,108 miR126 Gag/RTN/Pol, day 3, 30438

description: Library name: G034_O07_ABL3_30438_D3


title: Whole blood, IL15, day 8, 39103

description: Library name: G047_O20_Cy_39103_D8

value: day 8

value: Male


title: S2133_00081_R1_S8

description: Column 'S2133_00081' in counts.matrix

value: SKIN

value: Psoriasis


title: Whole blood, RhCMV 68-1 Rh156,108 miR126 Gag/RTN/Pol, day 3, 30386

description: Library name: G033_O07_ABL3_30386_D3


title: Whole blood, RhCMV 68-1 Rh156,108 miR126 Gag/RTN/Pol, day 3, 30310

description: Library name: G032_O07_ABL3_30310_D3


title: Whole blood, RhCMV 68-1 HLAE supertope Rh156,108 miR126, day 3, 31893

description: Library name: G040_O07_ABL3_31893_D3


title: Whole blood, IL15, day 8, 39098

description: Library name: G044_O20_Cy_39098_D8


title: non-targeting siRNA_2

description: non-targeting siRNAs replicate 2

tag: cell line

value: non-targeting siRNAs


title: SW480-P-3

description:
SQ23025069-LIB-8-3-LIB-A-3
processed data file1.txt

tag: cell type


title: S2133_00170_R1_S53

description: Column 'S2133_00170' in counts.matrix

value: Guselkumab 100mg

value: LS


title: Whole blood, RhCMV 68-1 HLAE supertope Rh156,108 miR126, day 3, 31654

description: Library name: G039_O07_ABL3_31654_D3

value: Whole blood

value: Nonprotected


title: Whole blood, IL15, day 8, 39097

description: Library name: G043_O20_Cy_39097_D8


title: SW480-P-2

description:
SQ23025068-LIB-8-2-LIB-A-2
processed data file1.txt


title: S2133_00022_R1_S16

description: Column 'S2133_00022' in counts.matrix

value: Ixekizumab 80mg Q2W


title: SW480-LM3-3

description:
SQ23025066-LIB-6-3-LIB-B-3
processed data file1.txt


title: SW480-P-1

description:
SQ23025067-LIB-8-1-LIB-A-1
processed data file1.txt


title: Whole blood, RhCMV 68-1 HLAE supertope Rh156,108 miR126, day 3, 27769

description: Library name: G037_O07_ABL3_27769_D3

value: day 3

value: female


title: Whole blood, IL15, day 10, 39095

description: Library name: G050_O20_Cy_39095_D10


title: S2133_00061_R1_S31

description: Column 'S2133_00061' in counts.matrix


title: HUWE1siRNA_4

description: HUWE1 siRNAs replicate 4


title: S2133_00122_R1_S60

description: Column 'S2133_00122' in counts.matrix


title: Whole blood, RhCMV 68-1 HLAE supertope Rh156,108 miR126, day 3, 26712

description: Library name: G036_O07_ABL3_26712_D3


title: Whole blood, IL15, day 8, 39095

description: Library name: G042_O20_Cy_39095_D8


title: Whole blood, IL15, day 8, 39104

description: Library name: G048_O20_Cy_39104_D8


title: HUWE1siRNA_2

description: HUWE1 siRNAs replicate 2


title: MCF7_TRIM24KO_INPUT

value: Breast cancer

tag: genotype

value: Full-media


title: S2133_00125_R1_S23

description: Column 'S2133_00125' in counts.matrix

tag: disease

value: BL


title: HUWE1siRNA_1

description: HUWE1 siRNAs replicate 1


title: Whole blood, IL15, day 8, 39102

description: Library name: G046_O20_Cy_39102_D8

tag: treatment

value: 15 ug/kg IL-15/IL-15Ra


title: non-targeting siRNA_4

description: non-targeting siRNAs replicate 4


title: S2133_00052_R1_S34

description: Column 'S2133_00052' in counts.matrix

tag: timepoint


title: Whole blood, RhCMV 68-1 HLAE supertope Rh156,108 miR126, day 0, 33705

description: Library name: G028_O07_ABL3_33705_D0

value: day 0

value: Protected


title: Whole blood, IL15, day 8, 39100

description: Library name: G045_O20_Cy_39100_D8

value: day 8

value: Male


title: Whole blood, IL15, day 7, 39104

description: Library name: G040_O20_Cy_39104_D7

value: day 7

value: 10 ug/kg IL-15/IL-15Ra


title: S2133_00038_R1_S39

description: Column 'S2133_00038' in counts.matrix

value: SKIN

value: Psoriasis

value: Guselkumab 100mg

tag: group


title: MCF7_TRIM24KO_H3K27ac_rep3


title: S2133_00026_R1_S27

description: Column 'S2133_00026' in counts.matrix

value: LS


title: non-targeting siRNA_3

description: non-targeting siRNAs replicate 3

value: non-targeting siRNAs


title: S2133_00152_R1_S63

description: Column 'S2133_00152' in counts.matrix


title: Whole blood, RhCMV 68-1 Rh156,108 miR126 Gag/RTN/Pol, day 3, 30277

description: Library name: G030_O07_ABL3_30277_D3

value: Whole blood

value: RhCMV 68-1 Rh156,108 miR126 Gag/RTN/Pol

tag: time

value: day 3

value: Nonprotected


title: Whole blood, IL15, day 7, 39102

description: Library name: G038_O20_Cy_39102_D7

tag: animal id


title: MCF7_TRIM24KO_H3K27ac_rep1

value: Breast cancer

value: Full-media


title: Whole blood, IL15, day 8, 39090

description: Library name: G041_O20_Cy_39090_D8

tag: Sex

value: Female

value: 15 ug/kg IL-15/IL-15Ra


title: Whole blood, RhCMV 68-1 HLAE supertope Rh156,108 miR126, day 0, 32751

description: Library name: G024_O07_ABL3_32751_D0

value: day 0

value: female

tag: treatment outcome


title: Whole blood, IL15, day 7, 39100

description: Library name: G037_O20_Cy_39100_D7

value: day 7

value: Male


title: non-targeting siRNA_1

description: non-targeting siRNAs replicate 1


title: Whole blood, RhCMV 68-1 Rh156,108 miR126 Gag/RTN/Pol, day 3, 30306

description: Library name: G031_O07_ABL3_30306_D3

value: Protected


title: MCF7_NT_H3K27ac_rep3

value: NT


title: Whole blood, RhCMV 68-1 Rh156,108 miR126 Gag/RTN/Pol, day 3, 28299

description: Library name: G029_O07_ABL3_28299_D3


title: S2133_00036_R1_S64

description: Column 'S2133_00036' in counts.matrix

value: SKIN

value: Psoriasis

value: Guselkumab 100mg


title: MCF7_NT_INPUT


title: S2133_00091_R1_S45

description: Column 'S2133_00091' in counts.matrix

value: LS


title: Whole blood, RhCMV 68-1 HLAE supertope Rh156,108 miR126, day 0, 32319

description: Library name: G022_O07_ABL3_32319_D0

value: Whole blood


title: MCF7_NT_H3K27ac_rep1


title: Whole blood, IL15, day 7, 39103

description: Library name: G039_O20_Cy_39103_D7

value: 10 ug/kg IL-15/IL-15Ra


title: S2133_00049_R1_S30

description: Column 'S2133_00049' in counts.matrix

value: Ixekizumab 80mg Q2W


title: MCF7_TRIM24KO_H3K27ac_rep2

value: Breast cancer


title: S2133_00046_R1_S45

description: Column 'S2133_00046' in counts.matrix


title: MCF7_TRIM24KO_H3K23ac_rep3

value: Full-media


title: Whole blood, RhCMV 68-1 HLAE supertope Rh156,108 miR126, day 0, 33495

description: Library name: G027_O07_ABL3_33495_D0


title: Whole blood, RhCMV 68-1 HLAE supertope Rh156,108 miR126, day 0, 32886

description: Library name: G025_O07_ABL3_32886_D0


title: S2133_00120_R1_S17

description: Column 'S2133_00120' in counts.matrix


title: S2133_00030_R1_S21

description: Column 'S2133_00030' in counts.matrix

value: BL


title: Whole blood, IL15, day 7, 39090

description: Library name: G033_O20_Cy_39090_D7

value: Female


title: Whole blood, RhCMV 68-1 HLAE supertope Rh156,108 miR126, day 0, 32931

description: Library name: G026_O07_ABL3_32931_D0

value: day 0


title: Whole blood, IL15, day 7, 39098

description: Library name: G036_O20_Cy_39098_D7


title: S2133_00029_R1_S18

description: Column 'S2133_00029' in counts.matrix


title: MCF7_NT_H3K27ac_rep2


title: Whole blood, RhCMV 68-1 HLAE supertope Rh156,108 miR126, day 0, 32624

description: Library name: G023_O07_ABL3_32624_D0

value: female


title: Whole blood, IL15, day 4, 39104

description: Library name: G032_O20_Cy_39104_D4

value: day 4


title: Whole blood, IL15, day 7, 39097

description: Library name: G035_O20_Cy_39097_D7

value: day 7


title: Whole blood, IL15, day 4, 39103

description: Library name: G031_O20_Cy_39103_D4

value: Male


title: Whole blood, IL15, day 7, 39095

description: Library name: G034_O20_Cy_39095_D7


title: Whole blood, RhCMV 68-1 Rh156,108 miR126 Gag/RTN/Pol, day 0, 35908

description: Library name: G021_O07_ABL3_35908_D0

value: RhCMV 68-1 Rh156,108 miR126 Gag/RTN/Pol

value: Nonprotected


title: S2133_00059_R1_S34

description: Column 'S2133_00059' in counts.matrix

value: SKIN

value: Psoriasis


title: Whole blood, RhCMV 68-1 Rh156,108 miR126 Gag/RTN/Pol, day 0, 35907

description: Library name: G020_O07_ABL3_35907_D0


title: MCF7_TRIM24KO_H3K23ac_rep2


title: S2133_00133_R1_S13

description: Column 'S2133_00133' in counts.matrix

value: LS


title: S2133_00154_R1_S27

description: Column 'S2133_00154' in counts.matrix


title: Whole blood, RhCMV 68-1 Rh156,108 miR126 Gag/RTN/Pol, day 0, 33530

description: Library name: G019_O07_ABL3_33530_D0

value: Whole blood

value: Protected


title: S2133_00057_R1_S31

description: Column 'S2133_00057' in counts.matrix

value: Ixekizumab 80mg Q2W


title: MCF7_TRIM24KO_H3K23ac_rep1

value: Breast cancer


title: MCF7_NT_H3K23ac_rep1

value: NT

value: Full-media


title: S2133_00140_R1_S29

description: Column 'S2133_00140' in counts.matrix


title: Whole blood, IL15, day 4, 39098

description: Library name: G028_O20_Cy_39098_D4

value: Female

value: 10 ug/kg IL-15/IL-15Ra


title: MCF7_TRIM24KO_ERa_rep3


title: MCF7_NT_H3K23ac_rep3


title: Whole blood, RhCMV 68-1 Rh156,108 miR126 Gag/RTN/Pol, day 0, 32574

description: Library name: G017_O07_ABL3_32574_D0

value: day 0

value: female


title: S2133_00121_R1_S17

description: Column 'S2133_00121' in counts.matrix


title: MCF7_NT_H3K23ac_rep2


title: Whole blood, IL15, day 4, 39100

description: Library name: G029_O20_Cy_39100_D4

value: day 4


title: S2133_00009_R1_S21

description: Column 'S2133_00009' in counts.matrix


title: Whole blood, RhCMV 68-1 Rh156,108 miR126 Gag/RTN/Pol, day 0, 32569

description: Library name: G016_O07_ABL3_32569_D0


title: S2133_00094_R1_S3

description: Column 'S2133_00094' in counts.matrix


title: Whole blood, IL15, day 4, 39102

description: Library name: G030_O20_Cy_39102_D4

value: Male


title: MCF7_NT_ERa_rep3


title: Whole blood, RhCMV 68-1 HLAE supertope Rh156,108 miR126, day 0, 32240

description: Library name: G013_O07_ABL3_32240_D0


title: S2133_00067_R1_S25

description: Column 'S2133_00067' in counts.matrix


title: Whole blood, IL15, day 4, 39090

description: Library name: G025_O20_Cy_39090_D4


title: S2133_00023_R1_S10

description: Column 'S2133_00023' in counts.matrix

value: BL


title: Whole blood, RhCMV 68-1 Rh156,108 miR126 Gag/RTN/Pol, day 0, 33514

description: Library name: G018_O07_ABL3_33514_D0

value: RhCMV 68-1 Rh156,108 miR126 Gag/RTN/Pol

value: Nonprotected


title: Whole blood, RhCMV 68-1 Rh156,108 miR126 Gag/RTN/Pol, day 0, 32543

description: Library name: G015_O07_ABL3_32543_D0


title: S2133_00039_R1_S10

description: Column 'S2133_00039' in counts.matrix

value: SKIN

value: Psoriasis


title: MCF7_NT_ERa_rep2


title: Whole blood, IL15, day 4, 39097

description: Library name: G027_O20_Cy_39097_D4

value: Whole blood


title: Whole blood, RhCMV 68-1 HLAE supertope Rh156,108 miR126, day 0, 32290

description: Library name: G014_O07_ABL3_32290_D0


title: Whole blood, IL15, day 4, 39095

description: Library name: G026_O20_Cy_39095_D4


title: MCF7_TRIM24KO_ERa_rep2


title: MCF7_TRIM24KO_ERa_rep1


title: Whole blood, RhCMV 68-1 HLAE supertope Rh156,108 miR126, day 0, 31654

description: Library name: G011_O07_ABL3_31654_D0


title: Whole blood, RhCMV 68-1 HLAE supertope Rh156,108 miR126, day 0, 31893

description: Library name: G012_O07_ABL3_31893_D0

value: Protected


title: S2133_00148_R1_S24

description: Column 'S2133_00148' in counts.matrix

value: Guselkumab 100mg

value: LS


title: MCF7_DMSO_rep3

data_processing:
Sequencing data were aligned to the human reference genome hg38 using HISAT2 (v2.1.0), and the number of reads per gene was measured with HTSeq count (v0.5.3)
Assembly: hg38/GRCh38
Supplementary files format and content: .tsv, gene count values for each sample

growth_protocol: DMEM + 10% FBS + 1% Pen/Strep, cultured at 5% CO2 and 37 °C.

extract_protocol:
Total RNA was extracted using RNeasy Mini kit (Qiagen, Germany) following manufacturer´s instructions.
Illumina

treatment_protocol: MCF7 TRIM24-KO RNA-seq experiments were performed in full-media. MCF7 cells were incubated for 24h with 5μM of dTRIM24 or DMSO in full-media.

value: Breast cancer

value: WT


title: Whole blood, IL15, day 3, 39104

description: Library name: G024_O20_Cy_39104_D3

value: day 3

value: 5 ug/kg IL-15/IL-15Ra


title: MCF7_NT_ERa_rep1

data_processing:
Reads were aligned to the human genome build Hg38/GRCh38 using BWA
Reads with a mapping quality (MAPQ) < 20 were removed from further analysis and duplicates were marked by PICARD/GATK markDuplicates
Enrichment over input control was determined using MACS2 (q < 0.001, narrowPeak mode). Only peaks not overlapping with the ENCODE hg38/GRCh38 blacklisted regions, were retained.
Assembly: hg38/GRCh38
Supplementary files format and content: .bed, narrowPeaks

value: NT

value: Full-media


title: Whole blood, RhCMV 68-1 HLAE supertope Rh156,108 miR126, day 0, 26712

description: Library name: G008_O07_ABL3_26712_D0

value: day 0

value: female


title: Whole blood, RhCMV 68-1 HLAE supertope Rh156,108 miR126, day 0, 27769

description: Library name: G009_O07_ABL3_27769_D0


title: S2133_00146_R1_S32

description: Column 'S2133_00146' in counts.matrix

value: BL


title: MCF7_DMSO_rep1


title: Whole blood, RhCMV 68-1 Rh156,108 miR126 Gag/RTN/Pol, day 0, 31374

description: Library name: G007_O07_ABL3_31374_D0

value: RhCMV 68-1 Rh156,108 miR126 Gag/RTN/Pol


title: Whole blood, IL15, day 3, 39102

description: Library name: G022_O20_Cy_39102_D3

value: Male


title: S2133_00007_R1_S28

description: Column 'S2133_00007' in counts.matrix

value: SKIN


title: MCF7_DMSO_rep2


title: MCF7_dTRIM24_rep3


title: Whole blood, RhCMV 68-1 HLAE supertope Rh156,108 miR126, day 0, 31644

description: Library name: G010_O07_ABL3_31644_D0


title: Whole blood, IL15, day 3, 39098

description: Library name: G020_O20_Cy_39098_D3

value: Female


title: Whole blood, IL15, day 3, 39103

description: Library name: G023_O20_Cy_39103_D3

value: Whole blood


title: Whole blood, RhCMV 68-1 Rh156,108 miR126 Gag/RTN/Pol, day 0, 30438

description: Library name: G006_O07_ABL3_30438_D0

value: Nonprotected


title: S2133_00042_R1_S5

description: Column 'S2133_00042' in counts.matrix

value: Psoriasis

value: Guselkumab 100mg


title: Whole blood, IL15, day 3, 39090

description: Library name: G017_O20_Cy_39090_D3


title: S2133_00005_R1_S11

description: Column 'S2133_00005' in counts.matrix

value: LS


title: Whole blood, IL15, day 3, 39097

description: Library name: G019_O20_Cy_39097_D3


title: Whole blood, RhCMV 68-1 Rh156,108 miR126 Gag/RTN/Pol, day 0, 30306

description: Library name: G003_O07_ABL3_30306_D0

value: Protected


title: S2133_00173_R1_S6

description: Column 'S2133_00173' in counts.matrix


title: Whole blood, RhCMV 68-1 Rh156,108 miR126 Gag/RTN/Pol, day 0, 30386

description: Library name: G005_O07_ABL3_30386_D0


title: MCF7_NT(2)_rep3

value: Breast cancer


title: Whole blood, RhCMV 68-1 Rh156,108 miR126 Gag/RTN/Pol, day 0, 30310

description: Library name: G004_O07_ABL3_30310_D0


title: MCF7_dTRIM24_rep1

value: WT


title: S2133_00015_R1_S62

description: Column 'S2133_00015' in counts.matrix

value: Ixekizumab 80mg Q2W


title: Whole blood, IL15, day 1, 39104

description: Library name: G016_O20_Cy_39104_D1

value: day 1

value: 5 ug/kg IL-15/IL-15Ra


title: Whole blood, IL15, day 3, 39100

description: Library name: G021_O20_Cy_39100_D3

value: day 3


title: MCF7_NT(2)_rep2

value: NT

value: Full-media


title: Whole blood, IL15, day 1, 39103

description: Library name: G015_O20_Cy_39103_D1

value: Male


title: S2133_00149_R1_S47

description: Column 'S2133_00149' in counts.matrix

value: SKIN


title: Whole blood, IL15, day 3, 39095

description: Library name: G018_O20_Cy_39095_D3

value: Female


title: MCF7_NT(2)_rep1


title: Whole blood, IL15, day 1, 39102

description: Library name: G014_O20_Cy_39102_D1

value: Whole blood


title: S2133_00134_R1_S43

description: Column 'S2133_00134' in counts.matrix

value: BL


title: MCF7_dTRIM24_rep2


title: MCF7_NT(1)_rep3


title: Whole blood, RhCMV 68-1 Rh156,108 miR126 Gag/RTN/Pol, day 0, 28299

description: Library name: G001_O07_ABL3_28299_D0

value: RhCMV 68-1 Rh156,108 miR126 Gag/RTN/Pol

value: day 0

value: female

value: Nonprotected


title: Whole blood, IL15, day 1, 39098

description: Library name: G012_O20_Cy_39098_D1


title: PBMCs, IL15, day 10, 34100

description:
Library name: G019_O16_34100_d10_GEMS2_cDNA1_LIB2
!0x Genomics

data_processing:
demuliplexed and aligned data using CellRanger v6.0.1 to the Rhesus macaque genome (Mmul 10)
Assembly: Rhesus macaque genome v10 (Mmul) Ensembl annotation version 100
Supplementary files format and content: barcode, features and matrix files

source_name: PBMCs

extract_protocol:
10x extraction protocol
Chromium Next GEM Single Cell 3’ Reagent Kits v3.1 ; 10X Genomics

treatment_protocol: Rhesus macaques were treated with IL-15/IL-15Rawere collected at 4 time points (baseline, pre IL-15, and days 3, 7 and 10)

value: PBMCs

value: day 10

value: male

value: 15 ug/kg IL-15/IL-15Ra


title: S2133_00171_R1_S37

description: Column 'S2133_00171' in counts.matrix

value: Psoriasis

value: Ixekizumab 80mg Q2W

value: LS


title: S2133_00084_R1_S12

description: Column 'S2133_00084' in counts.matrix

value: Guselkumab 100mg


title: S2133_00098_R1_S42

description: Column 'S2133_00098' in counts.matrix


title: MCF7_NT(1)_rep2

value: Breast cancer

value: NT

value: Full-media


title: Whole blood, IL15, day 1, 39095

description: Library name: G010_O20_Cy_39095_D1

value: Whole blood

value: day 1

value: Female

value: 5 ug/kg IL-15/IL-15Ra


title: Whole blood, RhCMV 68-1 Rh156,108 miR126 Gag/RTN/Pol, day 0, 30277

description: Library name: G002_O07_ABL3_30277_D0

value: RhCMV 68-1 Rh156,108 miR126 Gag/RTN/Pol

value: day 0

value: female


title: Whole blood, IL15, day 1, 39100

description: Library name: G013_O20_Cy_39100_D1

value: Male


title: MCF7_NT(1)_rep1


title: Whole blood, IL15, day 1, 39097

description: Library name: G011_O20_Cy_39097_D1


title: PBMCs, IL15, day 10, 34024

description:
Library name: G018_O16_34024_d10_GEMS1_cDNA1_LIB1
!0x Genomics

value: PBMCs

value: day 10

value: male


title: MCF7_TRIM24KO(B)_rep2


title: MCF7_TRIM24KO(B)_rep3


title: S2133_00040_R1_S48

description: Column 'S2133_00040' in counts.matrix

value: SKIN

value: Psoriasis

value: Ixekizumab 80mg Q2W


title: Whole blood, IL15, day 1, 39090

description: Library name: G009_O20_Cy_39090_D1


title: PBMCs, IL15, day 10, 32062

description:
Library name: G016_O16_32062_d10_GEMS1_cDNA1_LIB1
!0x Genomics

value: 15 ug/kg IL-15/IL-15Ra


title: Whole blood, Control, day 0, 39104

description: Library name: G008_O20_Cy_39104_D0

value: Control

value: 0 ug/kg IL-15/IL-15Ra


title: S2133_00110_R1_S53

description: Column 'S2133_00110' in counts.matrix

value: LS


title: PBMCs, IL15, day 10, 31954

description:
Library name: G020_O16_31954_d10_GEMS1_cDNA1_LIB1
!0x Genomics


title: PBMCs, IL15, day 7, 31954

description:
Library name: G015_O16_31954_d7_GEMS2_cDNA1_LIB1
!0x Genomics

value: day 7

value: 10 ug/kg IL-15/IL-15Ra


title: MCF7_TRIM24KO(B)_rep1

value: Breast cancer

value: Full-media


title: S2133_00096_R1_S8

description: Column 'S2133_00096' in counts.matrix

value: BL


title: S2133_00143_R1_S52

description: Column 'S2133_00143' in counts.matrix


title: Whole blood, Control, day 0, 39103

description: Library name: G007_O20_Cy_39103_D0

value: Whole blood

value: day 0


title: PBMCs, IL15, day 7, 34100

description:
Library name: G014_O16_34100_d7_GEMS2_cDNA1_LIB2
!0x Genomics

value: PBMCs


title: MCF7_TRIM24KO(A)_rep3


title: MCF7_TRIM24KO(A)_rep2


title: Whole blood, Control, day 0, 39102

description: Library name: G006_O20_Cy_39102_D0

value: Male


title: PBMCs, IL15, day 7, 34024

description:
Library name: G013_O16_34024_d7_GEMS1_cDNA1_LIB1
!0x Genomics

value: male


title: PBMCs, IL15, day 10, 33047

description:
Library name: G017_O16_33047_d10_GEMS1_cDNA1_LIB1
!0x Genomics

value: day 10


title: S2133_00124_R1_S12

description: Column 'S2133_00124' in counts.matrix

value: SKIN

value: Psoriasis


title: Whole blood, Control, day 0, 39100

description: Library name: G005_O20_Cy_39100_D0


title: PBMCs, IL15, day 7, 33047

description:
Library name: G012_O16_33047_d7_GEMS1_cDNA1_LIB1
!0x Genomics


title: MCF7_TRIM24KO(A)_rep1


title: S2133_00135_R1_S62

description: Column 'S2133_00135' in counts.matrix

value: Ixekizumab 80mg Q2W


title: S2133_00123_R1_S46

description: Column 'S2133_00123' in counts.matrix