title: hESC cells, KRT18P37 KO, Hi-C rep2

city: Beijing

first: Liu

last: He

address: No. 5, Dongdan Sanjo, Dongcheng District

institute: Peking Union Medical College

description: Library name: sample2

data_processing:
The Hic-Pro (v3.1.0) was used for Hi-C data analysis. Clean reads were mapped to human genome hg19 with default parameters, and then uniquely mapped reads were used to build contact pairs, and then valid pairs were used to build contact matrix in 10kb resolution. Hic-Pro (v3.1.0) raw matrix was then converted matrices into .h5 format files with hicConvertFormat subcommand in HiCExplorer (v3.4.3). Different samples’s matrix was then normalized by hicNormalize subcommand in HiCExplorer (v3.4.3) with parameters ‘--normalize smallest’ and then corrected with ‘--filterThreshold -3 5 --iterNum 20’ of hicCorrectMatrix subcommand. Then the matrix was then converted into .hic format for Visualization using FanC (v0.9.24). Insulation scores and TAD boundary strengths were calculated by FanC (v0.9.24) with parameter -w 1mb.
Assembly: hg19
Supplementary files format and content: .hic file include contact matrix of each sample

extract_protocol:
1) Lyse cells by grinding and lysing in an ice bath of lysate to obtain nuclei samples; 2) Restriction enzyme (DpnII) digestion was followed to break the original genomic DNA structure to form a molecular group in units of "protein-DNA cross-linking complex"; 3) Cleave the cleavage site using dNTP-labeled repair enzymes with biotin labeling; 4) Using DNA ligase treatment, the flat ends of DNA molecules on the same "protein-DNA crosslinking complex" were connected to each other, so that the DNA fragment reconstructs the structure based on spatial location to form Hi-C molecules. The junction of the reconstituted molecule would be marked with biotin; 5) Protease 65°C high temperature treatment, unlink protein cross-linking and release DNA, and then use phenolic chloroform extraction to obtain Hi-C characteristic DNA molecules;6) Remove unsuccessfully ligated DNA fragment ends using T4 DNA polymerase exonuclease activity to eliminate residual biotin labeling. 7) Fragmented DNA molecules were interrupted using ultrasound, followed by terminal repair, A-tail ligation, streptavidin-activated magnetic beads to retrieve biotin marker molecules, sequencing linker ligation, PCR enrichment for library preparation, and finally recovered the fragments of interest using AMPure XP beads or agarose gel electrophoresis to obtain the final Hi-C library.
Hi-C

value: human embryonic stem cells

value: KRT18P37 knock out


title: hESC cells, KRT18P37 KO, Hi-C rep1

status: Public on Oct 01 2025

type: SRA

country: China

description: Library name: sample1

library_source: genomic

molecule: genomic DNA

organism: Homo sapiens

tag: cell line

tag: cell type

tag: genotype


title: PRO-seq K562 1h 250 nM  Rep2

city: Cuernavaca

first: Mario

last: Zurita

state: Morelos

address: Av. Universidad 2001

country: Mexico

institute: Instituto de Biotecnología - UNAM

description:
Library name: Sample 4
PROseq_1h250nM_TPL_fwd.bw
PROseq_1h250nM_TPL_rv.bw

library_source: transcriptomic

data_processing:
Alignment: bowtie2, using default parameters
Differential expression analysis: DESeq2
Assembly: hg19
Supplementary files format and content: bigwig file corresponding to each PRO-Seq sample
Library strategy: PRO-Seq

molecule: nuclear RNA

growth_protocol: K562 cells were maintained at 37°C in a humidified 5% CO2 and cultured with RPMI medium supplemented with 10% FBS

extract_protocol:
PRO-seq was performed following the protocol published in Mahat, DB., et al., 2016, Nature Protocols
Libraries were prepared using the TruSeq Small RNA kit

treatment_protocol: K562 cells were counted and seeded at a confluency of 500,000 cells per ml. DMSO or Triptolide were added to the media according to the concentration indicated in the sample name

value: WT

tag: treatment

value: 1h 250 nM Triptolide


title: liverTissue_scRNA-seq_well8

city: Chapel Hill

first: Karen

middle: L

last: Mohlke

state: NC

address: 120 Mason Farm Road

department: Genetics

country: USA

institute: University of North Carolina at Chapel Hill

description:
Library name: well8_scRNA
Each well consists of nuclei that were multiplexed across 5 separate liver donors. The 5 donors were later dimultiplexed using genotype data. Note that the well*_raw_feature_bc_matrix.h5 files contain both RNA and ATAC counts (corresponding to cellranger-arc peak calls), but we did not use the ATAC counts in this file. Rather, we used our own peak calling.

library_source: transcriptomic single cell

data_processing:
Alignment of scATAC-seq and scRNA-seq reads, gene count matrix generation, and ATAC fragment file generation was performed using CellRanger-arc v2.0.0.
We performed genotype-based donor deconvolution and singlet identification for barcodes with >= 1,000 RNA UMI using demuxlet as implemented in popscle. Please see the associated manuscript for details.
We applied the following quality control filters to select high quality nuclei from the set of singlet barcodes. For RNA, we selected barcodes with ≥1,000 UMI, ≥500 expressed genes, and ≤10% of reads mapping to the mitochondrial chromosome using Seurat v5. For ATAC, we counted reads into a set of bulk liver tissue ATAC peaks mapped in 138 individuals and selected barcodes with >500 fragments in peaks, >15% fragments overlapping peaks, and transcription start site (TSS) enrichment >2 (calculated from EnsDb.Hsapiens.v86) using Signac. We used DecontX to minimize ambient RNA contamination.
Following decontamination, we merged corrected count matrices from all batches and identified clusters. To account for batch effects, we used Harmony41 implemented in the Seurat IntegrateLayers function applied to 50 decontaminated RNA PCs, recalculated clusters and UMAP projections, and annotated clusters. To obtain more granular cell type annotation, we used Azimuth42 in R with the supplied liver dataset as the reference to transfer annotations to our gene expression data.
To generate cell type peaks, we generated pseudobulk BAM files for each cell type and donor combination by subsetting the Cell Ranger ATAC-seq BAM files and selecting non-duplicate reads with high mapping quality to primary nuclear chromosomes using samtools v1.17. Due to low read depth, we merged BAM files across donors within a cell type using samtools prior to peak calling. We called peaks for each cell type using MACS2 v2016-02-15. We removed peaks overlapping ENCODE exclusion regions43 using BEDTools. We used ataqv v1.0.0 to calculate quality metrics of the pseudobulk datasets, including transcription start site (TSS) enrichment and percentage of reads overlapping peaks. We generated a single peak set by merging peaks across cell types using BEDTools.
Assembly: GRCh38
Supplementary files format and content: well*_atac_fragments.tsv.gz is the ATAC fragments file produced by CellRanger-arc. CellRanger adjusts the start and stop coordinates of the fragment to correspond tot he Tn5 transposase cut sites. well*_atac_fragments.tsv.gz.tbi is the associated tabix index of the fragments file.
Supplementary files format and content: well*_per_barcode_metrics.csv.gz is the barcode-level quality metrics file produced by CellRanger-arc.
Supplementary files format and content: well*_raw_feature_bc_matrix.h5 contains the raw gene expression count matrix produced by CellRanger-arc in h5 format. Note that there is also an ATAC count matrix in this file that was generated using CellRanger peaks. However, we did not use this ATAC count matrix because we performed our own peak calling.
Supplementary files format and content: mergedConsensusPeaks_peaksCalledOnMergedBams_autosomalOnly_withCellTypeOverlap.bed.gz contains the set of merged ATAC peaks across cell types. The first three columns are peak chromosome, start, and stop coordinates (GRCh38). The 4th column is an arbitrary peak ID. The 5th column contains the list of cell types in which the peak was found.
Supplementary files format and content: allwells_RNA-ATAC-jointpass-UMI1000-harmonized_WNN_azimuth.rds contains the Seurat object containing RNA and ATAC count matrices for the nuclei that passed QC. The file contains several assays corresponding to gene expression, DecontX-filtered gene expression, and ATAC counts in the merged cell type peaks.

molecule: polyA RNA

source_name: liver tissue

extract_protocol:
We isolated frozen human liver tissue from ~12 mg pieces. We pooled aliquots from sets of five individuals, pulverized using a cell crusher (CellCrusher), lysed cells in ice-cold lysis buffer (10 mM Tris-HCl [pH 7.4], 10 mM NaCl, 3 mM MgCl2, 1% BSA, 0.1% Tween-20, 0.1% Nonidet P40, 0.01% digitonin, 1mM dithiothreitol, 0.04 U/ul RNase inhibitor) with vigorous shaking for 5 min at 4°C, and homogenized using a 2-mL dounce with 10 strokes of the loose pestle followed by 30 strokes of the tight pestle. We centrifuged the homogenized samples at 500 x g for 5 min at 4°C, resuspended in 1 mL ice-cold wash buffer (10 mM Tris-HCl [pH 7.4], 10 mM NaCl, 3 mM MgCl2, 1% BSA, 0.1% Tween-20, 1 mM dithiothreitol, 0.04 U/ul RNase inhibitor), sequentially filtered through 70 um, 30 um, and 20 um filters, centrifuged at 500 x g for 5 min at 4°C, and resuspended in 300 ul wash buffer. We then washed nuclei suspensions twice by layering over 300 ul of 1.5 M sucrose and centrifuging at 1,000 x g for 10 min at 4°C. We resuspended final nuclei pellets in 1 mL wash buffer, centrifuged at 500 x g for 5 min at 4°C, and resuspended in 35 ul of diluted nuclei buffer (1X 10x Genomics Nuclei Buffer, 1 mM dithiothreitol, 1 U/ul RNase inhibitor).
We performed single-nucleus chromatin accessibility and gene expression profiling using the 10x Genomics Chromium Controller and Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Reagent Bundle following the manufacturer’s instructions. Briefly, we stained nuclei with acridine orange and propidium iodide (Logos Biosystems PN-F23001) and assessed for viability, concentration, and singleness using a LUNA-FL Dual Fluorescence Cell Counter (Logos Biosystems). We loaded 20,000 nuclei per inlet on a Chromium Controller instrument (10x Genomics). We purified sequencing libraries using SPRIselect beads, visualized using the Bioanalyzer High Sensitivity DNA chip, and quantified via KAPA Library Quantification Kit for Illumina Platforms (Roche PN-KK4824). We separately pooled ATAC and RNA sequencing libraries, spiked with 1% PhiX sequencing control (Illumina)

tag: tissue

value: liver tissue

tag: batch


title: Normal_2_5_5_6

city: Guangzhou

first: Lin

last: Li

address: Shatai South Road

department: Pathophysiology

institute: Southern Medical University

description: Sample 828

data_processing:
Illumina CASAVA version 1.8 were used to the basecalling.
For bisulfite-seq data, Trim Galore (v0.3.3) was used to remove the first 6 bases of random primer, adaptor sequences and low quality bases; for RNA-seq data, each single cell was separated by unique cell barcode, then template switch oligo (TSO), ployA tails, adaptors and low quality bases were removed.
For bisulfite-seq data, clean reads were first mapped to human reference genome hg19 with Bismark (v0.7.6) in paired-end and non-directional module, and then the unmapped reads were realigned to the same reference genome in single-end and non-directional module; for RNA-seq data, clean reads were mapped to human genome hg19 with Tophat (v2.0.14), and then unique UMI counts were calculated by HTSeq.
WCG and GCH methylation level of cytosines was estimated using comstomized scripts.
Genome_build: hg19
Supplementary_files_format_and_content: UMI_count.txt files include UMI counts of RefSeq genes. While WCG.txt and GCH.txt files include the read counts of cytosines in WCG and GCH context respectively. The columns in WCG.txt or GCH.txt files represent "chr" "position" "unmethylated read counts" "methylated read counts".

source_name: testis

extract_protocol:
An individual cell was picked into the cell lysis buffer with vitro methylation (IVM) mixture containing 4 U RNase inhibitor (TAKARA, Cat. 2313B), 0.25% IGEPAL CA-630 (SIGMA, Cat. I3021), 1X GC reaction buffer and 2 U M. CviPI (NEB, Cat. M0227L). After gently vortexed for 10 sec, the cell lysate was incubated at 37 °C for 20 min and then at 65 °C for 25 min. Then, the cell lysate could be directly processed for RNA/DNA separation or stored at -80 °C.
For RNA part, a modified Smart-seq2 protocol was applied for single-cell RNA-seq. For DNA part, Bisulfite-converted DNA was amplified with biotinylated random primer and klenow exo– polymerase (NEB, M0212L) for 7 rounds and excess primer was removed by exonuclease I (NEB, M0293L). After second strands synthesis, the library was amplified by KAPA HiFi HotStart ReadyMix (Kapa Biosystems, KK2602) for 14 cycles.

tag: gender

value: male

tag: age

tag: condition

value: Normal

tag: testis

value: testis


title: liverTissue_scRNA-seq_well7

description:
Library name: well7_scRNA
Each well consists of nuclei that were multiplexed across 5 separate liver donors. The 5 donors were later dimultiplexed using genotype data. Note that the well*_raw_feature_bc_matrix.h5 files contain both RNA and ATAC counts (corresponding to cellranger-arc peak calls), but we did not use the ATAC counts in this file. Rather, we used our own peak calling.


title: Normal_3_1_12_7

description: Sample 837


title: liverTissue_scATAC-seq_well7

description:
Library name: well7_scATAC
Each well consists of nuclei that were multiplexed across 5 separate liver donors. The 5 donors were later dimultiplexed using genotype data. Note that the well*_raw_feature_bc_matrix.h5 files contain both RNA and ATAC counts (corresponding to cellranger-arc peak calls), but we did not use the ATAC counts in this file. Rather, we used our own peak calling.

library_source: genomic single cell


title: liverTissue_scATAC-seq_well6

description:
Library name: well6_scATAC
Each well consists of nuclei that were multiplexed across 5 separate liver donors. The 5 donors were later dimultiplexed using genotype data. Note that the well*_raw_feature_bc_matrix.h5 files contain both RNA and ATAC counts (corresponding to cellranger-arc peak calls), but we did not use the ATAC counts in this file. Rather, we used our own peak calling.


title: Normal_2_5_5_4

description: Sample 827


title: Normal_2_5_5_1

description: Sample 826


title: liverTissue_scRNA-seq_well6

description:
Library name: well6_scRNA
Each well consists of nuclei that were multiplexed across 5 separate liver donors. The 5 donors were later dimultiplexed using genotype data. Note that the well*_raw_feature_bc_matrix.h5 files contain both RNA and ATAC counts (corresponding to cellranger-arc peak calls), but we did not use the ATAC counts in this file. Rather, we used our own peak calling.


title: liverTissue_scATAC-seq_well5

description:
Library name: well5_scATAC
Each well consists of nuclei that were multiplexed across 5 separate liver donors. The 5 donors were later dimultiplexed using genotype data. Note that the well*_raw_feature_bc_matrix.h5 files contain both RNA and ATAC counts (corresponding to cellranger-arc peak calls), but we did not use the ATAC counts in this file. Rather, we used our own peak calling.


title: Normal_2_4_9_7

description: Sample 824


title: Normal_2_4_9_6

description: Sample 823


title: liverTissue_scRNA-seq_well5

description:
Library name: well5_scRNA
Each well consists of nuclei that were multiplexed across 5 separate liver donors. The 5 donors were later dimultiplexed using genotype data. Note that the well*_raw_feature_bc_matrix.h5 files contain both RNA and ATAC counts (corresponding to cellranger-arc peak calls), but we did not use the ATAC counts in this file. Rather, we used our own peak calling.


title: liverTissue_scATAC-seq_well4

description:
Library name: well4_scATAC
Each well consists of nuclei that were multiplexed across 5 separate liver donors. The 5 donors were later dimultiplexed using genotype data. Note that the well*_raw_feature_bc_matrix.h5 files contain both RNA and ATAC counts (corresponding to cellranger-arc peak calls), but we did not use the ATAC counts in this file. Rather, we used our own peak calling.


title: Normal_2_4_9_5

description: Sample 822


title: PRO-seq K562 1h 1 uM  Rep1

description:
Library name: Sample 7
PROseq_1h1uM_TPL_fwd.bw
PROseq_1h1uM_TPL_rv.bw

value: 1h 1 micromolar Triptolide


title: liverTissue_scATAC-seq_well3

description:
Library name: well3_scATAC
Each well consists of nuclei that were multiplexed across 5 separate liver donors. The 5 donors were later dimultiplexed using genotype data. Note that the well*_raw_feature_bc_matrix.h5 files contain both RNA and ATAC counts (corresponding to cellranger-arc peak calls), but we did not use the ATAC counts in this file. Rather, we used our own peak calling.


title: Normal_2_4_9_3

description: Sample 820


title: Normal_2_4_9_4

description: Sample 821


title: liverTissue_scRNA-seq_well3

description:
Library name: well3_scRNA
Each well consists of nuclei that were multiplexed across 5 separate liver donors. The 5 donors were later dimultiplexed using genotype data. Note that the well*_raw_feature_bc_matrix.h5 files contain both RNA and ATAC counts (corresponding to cellranger-arc peak calls), but we did not use the ATAC counts in this file. Rather, we used our own peak calling.


title: liverTissue_scATAC-seq_well8

description:
Library name: well8_scATAC
Each well consists of nuclei that were multiplexed across 5 separate liver donors. The 5 donors were later dimultiplexed using genotype data. Note that the well*_raw_feature_bc_matrix.h5 files contain both RNA and ATAC counts (corresponding to cellranger-arc peak calls), but we did not use the ATAC counts in this file. Rather, we used our own peak calling.


title: liverTissue_scATAC-seq_well2

description:
Library name: well2_scATAC
Each well consists of nuclei that were multiplexed across 5 separate liver donors. The 5 donors were later dimultiplexed using genotype data. Note that the well*_raw_feature_bc_matrix.h5 files contain both RNA and ATAC counts (corresponding to cellranger-arc peak calls), but we did not use the ATAC counts in this file. Rather, we used our own peak calling.


title: Normal_2_5_6_3

description: Sample 830


title: Normal_2_4_9_1

description: Sample 818


title: Normal_2_4_8_8

description: Sample 817


title: Normal_2_5_5_7

description: Sample 829


title: Normal_2_4_9_2

description: Sample 819


title: liverTissue_scRNA-seq_well1

description:
Library name: well1_scRNA
Each well consists of nuclei that were multiplexed across 5 separate liver donors. The 5 donors were later dimultiplexed using genotype data. Note that the well*_raw_feature_bc_matrix.h5 files contain both RNA and ATAC counts (corresponding to cellranger-arc peak calls), but we did not use the ATAC counts in this file. Rather, we used our own peak calling.


title: Normal_2_4_8_6

description: Sample 815


title: Normal_2_4_8_3

description: Sample 813


title: Normal_2_4_8_7

description: Sample 816


title: liverTissue_scATAC-seq_well1

description:
Library name: well1_scATAC
Each well consists of nuclei that were multiplexed across 5 separate liver donors. The 5 donors were later dimultiplexed using genotype data. Note that the well*_raw_feature_bc_matrix.h5 files contain both RNA and ATAC counts (corresponding to cellranger-arc peak calls), but we did not use the ATAC counts in this file. Rather, we used our own peak calling.


title: Normal_2_4_8_5

description: Sample 814


title: Normal_2_4_9_8

description: Sample 825


title: Normal_2_4_7_8

description: Sample 811


title: Normal_2_4_8_1

description: Sample 812


title: Tumor_EOC_155

city: Göteborg

first: Ella

last: Ittner

address: Medicinaregatan 1F

department: Department of Oncology

country: Sweden

institute: University of Gothenburg

description:
Library name: EOC_155
Paired-end strand-specific RNA libraries

data_processing:
Quality control of FASTQ files using FastQC
Removal of adapter sequences and PolyG-tails using the bbduk tool
FASTQ files were mapped to the human reference genome hg38 using the STAR aligner and the resulting BAM-file was name-sorted
Quantification and count matrix generation via featurecounts
Assembly: GRCh38.p13
Supplementary files format and content: The processed data file "GEO_countsraw_EOC.txt" is given in text format and contains all 146 samples

molecule: total RNA

source_name: primary invasive EOC tumor

extract_protocol:
Total RNA was extracted from fresh-frozen tumor tissue using the RNeasy Lipid Tissue Mini Kit (Qiagen). Quality control of the extracted RNA was conducted using the 4200 Tapestation system (Agilent) and the Qubit RNA HS Assay Kit (ThermoFisher Scientific)
Sequencing libraries were prepared from 100 ng total RNA using the Illumina Stranded Total RNA library preparation kit with Ribo-Zero Plus treatment (cat# 20040525/20040529, Illumina Inc.). Unique dual indexes (cat# 20040553/20040554, Illumina Inc.) were used. The library preparation was performed according to the manufacturers’ protocol (# 1000000124514).

value: primary invasive EOC tumor

tag: histotype

value: HGSC

value: III

tag: age at diagnosis


title: Tumor_EOC_154

description:
Library name: EOC_154
Paired-end strand-specific RNA libraries

value: CCC


title: Tumor_EOC_152

description:
Library name: EOC_152
Paired-end strand-specific RNA libraries

value: MC

value: IV


title: Normal_2_4_7_6

description: Sample 810


title: liverTissue_scRNA-seq_well4

description:
Library name: well4_scRNA
Each well consists of nuclei that were multiplexed across 5 separate liver donors. The 5 donors were later dimultiplexed using genotype data. Note that the well*_raw_feature_bc_matrix.h5 files contain both RNA and ATAC counts (corresponding to cellranger-arc peak calls), but we did not use the ATAC counts in this file. Rather, we used our own peak calling.


title: Normal_2_4_7_5

description: Sample 809


title: Tumor_EOC_151

description:
Library name: EOC_151
Paired-end strand-specific RNA libraries


title: Tumor_EOC_150

description:
Library name: EOC_150
Paired-end strand-specific RNA libraries

value: EC


title: liverTissue_scRNA-seq_well2

description:
Library name: well2_scRNA
Each well consists of nuclei that were multiplexed across 5 separate liver donors. The 5 donors were later dimultiplexed using genotype data. Note that the well*_raw_feature_bc_matrix.h5 files contain both RNA and ATAC counts (corresponding to cellranger-arc peak calls), but we did not use the ATAC counts in this file. Rather, we used our own peak calling.


title: Tumor_EOC_149

description:
Library name: EOC_149
Paired-end strand-specific RNA libraries


title: Normal_2_4_7_3

description: Sample 807


title: Tumor_EOC_148

description:
Library name: EOC_148
Paired-end strand-specific RNA libraries


title: Normal_2_4_7_4

description: Sample 808


title: Tumor_EOC_147

description:
Library name: EOC_147
Paired-end strand-specific RNA libraries


title: Normal_2_4_7_2

description: Sample 806


title: Tumor_EOC_144

description:
Library name: EOC_144
Paired-end strand-specific RNA libraries

source_name: borderline EOC tumor

value: borderline EOC tumor

value: BOT


title: Normal_2_4_6_5

description: Sample 802


title: Normal_2_4_6_7

description: Sample 804


title: Tumor_EOC_142

description:
Library name: EOC_142
Paired-end strand-specific RNA libraries


title: Normal_2_4_6_2

description: Sample 800


title: Tumor_EOC_141

description:
Library name: EOC_141
Paired-end strand-specific RNA libraries


title: Tumor_EOC_146

description:
Library name: EOC_146
Paired-end strand-specific RNA libraries


title: Tumor_EOC_153

description:
Library name: EOC_153
Paired-end strand-specific RNA libraries


title: Tumor_EOC_143

description:
Library name: EOC_143
Paired-end strand-specific RNA libraries


title: Normal_2_4_6_6

description: Sample 803


title: Tumor_EOC_140

description:
Library name: EOC_140
Paired-end strand-specific RNA libraries


title: Normal_2_4_6_4

description: Sample 801


title: Normal_2_4_5_7

description: Sample 797


title: Tumor_EOC_139

description:
Library name: EOC_139
Paired-end strand-specific RNA libraries


title: Tumor_EOC_137

description:
Library name: EOC_137
Paired-end strand-specific RNA libraries


title: Normal_2_4_5_6

description: Sample 796


title: Normal_2_4_5_8

description: Sample 798


title: Normal_2_4_6_1

description: Sample 799


title: Tumor_EOC_136

description:
Library name: EOC_136
Paired-end strand-specific RNA libraries


title: Tumor_EOC_156

description:
Library name: EOC_156
Paired-end strand-specific RNA libraries


title: Tumor_EOC_135

description:
Library name: EOC_135
Paired-end strand-specific RNA libraries


title: Normal_2_4_5_4

description: Sample 794


title: Tumor_EOC_134

description:
Library name: EOC_134
Paired-end strand-specific RNA libraries


title: Normal_2_4_6_8

description: Sample 805


title: Normal_2_4_5_3

description: Sample 793


title: Normal_2_4_5_2

description: Sample 792


title: Normal_2_4_5_1

description: Sample 791


title: Tumor_EOC_131

description:
Library name: EOC_131
Paired-end strand-specific RNA libraries

source_name: benign EOC tumor

value: benign EOC tumor

value: BENIGN


title: Normal_2_4_4_7

description: Sample 790


title: Tumor_EOC_129

description:
Library name: EOC_129
Paired-end strand-specific RNA libraries


title: Normal_2_4_4_6

description: Sample 789


title: Normal_2_4_4_4

description: Sample 788


title: Tumor_EOC_138

description:
Library name: EOC_138
Paired-end strand-specific RNA libraries


title: Normal_2_4_4_1

description: Sample 786


title: Tumor_EOC_128

description:
Library name: EOC_128
Paired-end strand-specific RNA libraries


title: Normal_2_4_4_2

description: Sample 787


title: Tumor_EOC_127

description:
Library name: EOC_127
Paired-end strand-specific RNA libraries


title: Normal_2_4_5_5

description: Sample 795


title: Tumor_EOC_133

description:
Library name: EOC_133
Paired-end strand-specific RNA libraries


title: Normal_2_4_3_5

description: Sample 783


title: Tumor_EOC_122

description:
Library name: EOC_122
Paired-end strand-specific RNA libraries


title: Tumor_EOC_123

description:
Library name: EOC_123
Paired-end strand-specific RNA libraries


title: Normal_2_4_3_3

description: Sample 781


title: Normal_2_4_3_7

description: Sample 784


title: Normal_2_4_3_4

description: Sample 782


title: Tumor_EOC_120

description:
Library name: EOC_120
Paired-end strand-specific RNA libraries


title: Tumor_EOC_132

description:
Library name: EOC_132
Paired-end strand-specific RNA libraries


title: Normal_2_4_3_1

description: Sample 779


title: Tumor_EOC_119

description:
Library name: EOC_119
Paired-end strand-specific RNA libraries


title: Normal_2_4_2_8

description: Sample 778


title: Tumor_EOC_124

description:
Library name: EOC_124
Paired-end strand-specific RNA libraries


title: Normal_2_4_3_8

description: Sample 785


title: Normal_2_4_2_7

description: Sample 777


title: Tumor_EOC_125

description:
Library name: EOC_125
Paired-end strand-specific RNA libraries


title: Tumor_EOC_118

description:
Library name: EOC_118
Paired-end strand-specific RNA libraries


title: Tumor_EOC_121

description:
Library name: EOC_121
Paired-end strand-specific RNA libraries


title: Tumor_EOC_126

description:
Library name: EOC_126
Paired-end strand-specific RNA libraries


title: Tumor_EOC_117

description:
Library name: EOC_117
Paired-end strand-specific RNA libraries


title: Tumor_EOC_116

description:
Library name: EOC_116
Paired-end strand-specific RNA libraries


title: Normal_2_4_2_4

description: Sample 775


title: Normal_2_4_2_6

description: Sample 776


title: Normal_2_4_3_2

description: Sample 780


title: Tumor_EOC_115

description:
Library name: EOC_115
Paired-end strand-specific RNA libraries


title: Normal_2_4_2_3

description: Sample 774


title: Tumor_EOC_114

description:
Library name: EOC_114
Paired-end strand-specific RNA libraries


title: Tumor_EOC_130

description:
Library name: EOC_130
Paired-end strand-specific RNA libraries

value: LGSC


title: Normal_2_4_2_2

description: Sample 773


title: Tumor_EOC_113

description:
Library name: EOC_113
Paired-end strand-specific RNA libraries


title: Tumor_EOC_112

description:
Library name: EOC_112
Paired-end strand-specific RNA libraries


title: Normal_2_4_2_1

description: Sample 772


title: Normal_2_4_12_7

description: Sample 771


title: Tumor_EOC_109

description:
Library name: EOC_109
Paired-end strand-specific RNA libraries


title: Normal_2_4_12_4

description: Sample 768


title: Normal_2_4_12_5

description: Sample 769


title: Tumor_EOC_108

description:
Library name: EOC_108
Paired-end strand-specific RNA libraries


title: Normal_2_4_12_3

description: Sample 767


title: Tumor_EOC_110

description:
Library name: EOC_110
Paired-end strand-specific RNA libraries


title: Normal_2_4_12_6

description: Sample 770


title: Normal_2_4_12_2

description: Sample 766


title: Normal_2_4_12_1

description: Sample 765


title: Tumor_EOC_104

description:
Library name: EOC_104
Paired-end strand-specific RNA libraries


title: Normal_2_4_11_8

description: Sample 764


title: Tumor_EOC_105

description:
Library name: EOC_105
Paired-end strand-specific RNA libraries


title: Tumor_EOC_107

description:
Library name: EOC_107
Paired-end strand-specific RNA libraries


title: Normal_2_4_11_7

description: Sample 763


title: Tumor_EOC_106

description:
Library name: EOC_106
Paired-end strand-specific RNA libraries


title: Normal_2_4_11_6

description: Sample 762


title: Tumor_EOC_102

description:
Library name: EOC_102
Paired-end strand-specific RNA libraries


title: Tumor_EOC_101

description:
Library name: EOC_101
Paired-end strand-specific RNA libraries


title: Normal_2_4_11_5

description: Sample 761


title: Normal_2_4_11_4

description: Sample 760


title: Tumor_EOC_100

description:
Library name: EOC_100
Paired-end strand-specific RNA libraries


title: Tumor_EOC_99

description:
Library name: EOC_99
Paired-end strand-specific RNA libraries


title: Normal_2_4_11_1

description: Sample 758


title: Tumor_EOC_111

description:
Library name: EOC_111
Paired-end strand-specific RNA libraries


title: Normal_2_4_11_3

description: Sample 759


title: Tumor_EOC_98

description:
Library name: EOC_98
Paired-end strand-specific RNA libraries


title: Normal_2_4_10_7

description: Sample 756


title: Normal_2_4_10_8

description: Sample 757


title: Tumor_EOC_96

description:
Library name: EOC_96
Paired-end strand-specific RNA libraries


title: Normal_2_4_10_6

description: Sample 755


title: Tumor_EOC_97

description:
Library name: EOC_97
Paired-end strand-specific RNA libraries


title: Normal_2_4_10_5

description: Sample 754


title: Tumor_EOC_94

description:
Library name: EOC_94
Paired-end strand-specific RNA libraries


title: Tumor_EOC_95

description:
Library name: EOC_95
Paired-end strand-specific RNA libraries


title: Tumor_EOC_92

description:
Library name: EOC_92
Paired-end strand-specific RNA libraries


title: Tumor_EOC_90

description:
Library name: EOC_90
Paired-end strand-specific RNA libraries


title: Normal_2_4_10_4

description: Sample 753


title: Tumor_EOC_89

description:
Library name: EOC_89
Paired-end strand-specific RNA libraries


title: Normal_2_3_9_8

description: Sample 750


title: Normal_2_4_10_1

description: Sample 751


title: Normal_2_4_10_3

description: Sample 752


title: Tumor_EOC_87

description:
Library name: EOC_87
Paired-end strand-specific RNA libraries


title: Normal_2_3_9_7

description: Sample 749


title: Tumor_EOC_88

description:
Library name: EOC_88
Paired-end strand-specific RNA libraries


title: Tumor_EOC_86

description:
Library name: EOC_86
Paired-end strand-specific RNA libraries


title: Tumor_EOC_84

description:
Library name: EOC_84
Paired-end strand-specific RNA libraries


title: Tumor_EOC_85

description:
Library name: EOC_85
Paired-end strand-specific RNA libraries


title: Normal_2_3_9_3

description: Sample 745


title: Tumor_EOC_83

description:
Library name: EOC_83
Paired-end strand-specific RNA libraries


title: Tumor_EOC_103

description:
Library name: EOC_103
Paired-end strand-specific RNA libraries


title: Normal_2_3_9_6

description: Sample 748


title: Tumor_EOC_82

description:
Library name: EOC_82
Paired-end strand-specific RNA libraries


title: Normal_2_3_9_1

description: Sample 743


title: Normal_2_3_8_8

description: Sample 742


title: Tumor_EOC_80

description:
Library name: EOC_80
Paired-end strand-specific RNA libraries


title: Normal_2_3_9_2

description: Sample 744


title: Normal_2_3_8_6

description: Sample 741


title: Tumor_EOC_81

description:
Library name: EOC_81
Paired-end strand-specific RNA libraries


title: Tumor_EOC_79

description:
Library name: EOC_79
Paired-end strand-specific RNA libraries


title: Normal_2_3_8_4

description: Sample 740


title: Tumor_EOC_78

description:
Library name: EOC_78
Paired-end strand-specific RNA libraries


title: Tumor_EOC_77

description:
Library name: EOC_77
Paired-end strand-specific RNA libraries


title: Normal_2_3_8_3

description: Sample 739


title: Tumor_EOC_76

description:
Library name: EOC_76
Paired-end strand-specific RNA libraries


title: Normal_2_3_7_8

description: Sample 736


title: Tumor_EOC_75

description:
Library name: EOC_75
Paired-end strand-specific RNA libraries


title: Normal_2_3_8_1

description: Sample 737


title: Tumor_EOC_74

description:
Library name: EOC_74
Paired-end strand-specific RNA libraries


title: Normal_2_3_9_4

description: Sample 746


title: Normal_2_3_7_4

description: Sample 733


title: Normal_2_3_9_5

description: Sample 747


title: Tumor_EOC_69

description:
Library name: EOC_69
Paired-end strand-specific RNA libraries


title: Tumor_EOC_72

description:
Library name: EOC_72
Paired-end strand-specific RNA libraries


title: Normal_2_3_7_6

description: Sample 735


title: Tumor_EOC_70

description:
Library name: EOC_70
Paired-end strand-specific RNA libraries


title: Normal_2_3_7_1

description: Sample 730


title: Tumor_EOC_73

description:
Library name: EOC_73
Paired-end strand-specific RNA libraries


title: Normal_2_3_7_2

description: Sample 731


title: Normal_2_3_7_3

description: Sample 732


title: Normal_2_3_7_5

description: Sample 734


title: Tumor_EOC_71

description:
Library name: EOC_71
Paired-end strand-specific RNA libraries


title: Tumor_EOC_68

description:
Library name: EOC_68
Paired-end strand-specific RNA libraries


title: Tumor_EOC_67

description:
Library name: EOC_67
Paired-end strand-specific RNA libraries


title: Normal_2_3_6_6

description: Sample 727


title: Normal_2_3_6_5

description: Sample 726


title: Tumor_EOC_66

description:
Library name: EOC_66
Paired-end strand-specific RNA libraries


title: Tumor_EOC_65

description:
Library name: EOC_65
Paired-end strand-specific RNA libraries


title: Tumor_EOC_64

description:
Library name: EOC_64
Paired-end strand-specific RNA libraries


title: Normal_2_3_6_7

description: Sample 728


title: Normal_2_3_6_2

description: Sample 725


title: Normal_2_3_8_2

description: Sample 738


title: Tumor_EOC_61

description:
Library name: EOC_61
Paired-end strand-specific RNA libraries


title: Normal_2_3_6_1

description: Sample 724


title: Normal_2_3_5_6

description: Sample 723


title: Tumor_EOC_62

description:
Library name: EOC_62
Paired-end strand-specific RNA libraries


title: Normal_2_3_5_5

description: Sample 722


title: Tumor_EOC_63

description:
Library name: EOC_63
Paired-end strand-specific RNA libraries


title: Normal_2_3_6_8

description: Sample 729


title: Tumor_EOC_60

description:
Library name: EOC_60
Paired-end strand-specific RNA libraries


title: Tumor_EOC_59

description:
Library name: EOC_59
Paired-end strand-specific RNA libraries


title: Normal_2_3_5_4

description: Sample 721


title: Normal_2_3_4_8

description: Sample 718


title: Normal_2_3_5_1

description: Sample 719


title: Tumor_EOC_58

description:
Library name: EOC_58
Paired-end strand-specific RNA libraries


title: Normal_2_3_5_2

description: Sample 720


title: Tumor_EOC_53

description:
Library name: EOC_53
Paired-end strand-specific RNA libraries


title: Tumor_EOC_56

description:
Library name: EOC_56
Paired-end strand-specific RNA libraries


title: Normal_2_3_4_7

description: Sample 717


title: Tumor_EOC_55

description:
Library name: EOC_55
Paired-end strand-specific RNA libraries


title: Normal_2_3_4_2

description: Sample 713


title: Normal_2_3_4_1

description: Sample 712


title: Tumor_EOC_52

description:
Library name: EOC_52
Paired-end strand-specific RNA libraries


title: Normal_2_3_4_3

description: Sample 714


title: Tumor_EOC_50

description:
Library name: EOC_50
Paired-end strand-specific RNA libraries


title: Tumor_EOC_51

description:
Library name: EOC_51
Paired-end strand-specific RNA libraries


title: Normal_2_3_4_4

description: Sample 715


title: Tumor_EOC_48

description:
Library name: EOC_48
Paired-end strand-specific RNA libraries


title: Tumor_EOC_47

description:
Library name: EOC_47
Paired-end strand-specific RNA libraries


title: Tumor_EOC_49

description:
Library name: EOC_49
Paired-end strand-specific RNA libraries


title: Tumor_EOC_46

description:
Library name: EOC_46
Paired-end strand-specific RNA libraries


title: Normal_2_3_3_8

description: Sample 711


title: Tumor_EOC_44

description:
Library name: EOC_44
Paired-end strand-specific RNA libraries


title: Normal_2_3_3_6

description: Sample 709


title: Normal_2_3_3_4

description: Sample 707


title: Tumor_EOC_43

description:
Library name: EOC_43
Paired-end strand-specific RNA libraries


title: Normal_2_3_3_3

description: Sample 706


title: Tumor_EOC_57

description:
Library name: EOC_57
Paired-end strand-specific RNA libraries


title: Normal_2_3_4_5

description: Sample 716


title: Tumor_EOC_42

description:
Library name: EOC_42
Paired-end strand-specific RNA libraries


title: Normal_2_3_3_2

description: Sample 705


title: Normal_2_3_2_7

description: Sample 703


title: Tumor_EOC_40

description:
Library name: EOC_40
Paired-end strand-specific RNA libraries


title: Tumor_EOC_41

description:
Library name: EOC_41
Paired-end strand-specific RNA libraries


title: Tumor_EOC_39

description:
Library name: EOC_39
Paired-end strand-specific RNA libraries


title: Normal_2_3_3_7

description: Sample 710


title: Tumor_EOC_37

description:
Library name: EOC_37
Paired-end strand-specific RNA libraries


title: Tumor_EOC_36

description:
Library name: EOC_36
Paired-end strand-specific RNA libraries


title: Normal_2_3_2_4

description: Sample 700


title: Normal_2_3_2_6

description: Sample 702


title: Tumor_EOC_38

description:
Library name: EOC_38
Paired-end strand-specific RNA libraries


title: Normal_2_3_2_5

description: Sample 701


title: Tumor_EOC_35

description:
Library name: EOC_35
Paired-end strand-specific RNA libraries


title: Tumor_EOC_33

description:
Library name: EOC_33
Paired-end strand-specific RNA libraries


title: Normal_2_3_12_8

description: Sample 696


title: Normal_2_3_2_1

description: Sample 697


title: Tumor_EOC_32

description:
Library name: EOC_32
Paired-end strand-specific RNA libraries


title: Tumor_EOC_34

description:
Library name: EOC_34
Paired-end strand-specific RNA libraries


title: Normal_2_3_3_5

description: Sample 708


title: Tumor_EOC_31

description:
Library name: EOC_31
Paired-end strand-specific RNA libraries


title: Normal_2_3_2_2

description: Sample 698


title: Tumor_EOC_29

description:
Library name: EOC_29
Paired-end strand-specific RNA libraries


title: Normal_2_3_12_4

description: Sample 692


title: Normal_2_3_12_6

description: Sample 694


title: Normal_2_3_12_5

description: Sample 693


title: Tumor_EOC_30

description:
Library name: EOC_30
Paired-end strand-specific RNA libraries


title: Tumor_EOC_28

description:
Library name: EOC_28
Paired-end strand-specific RNA libraries


title: Tumor_EOC_26

description:
Library name: EOC_26
Paired-end strand-specific RNA libraries


title: Normal_2_3_12_3

description: Sample 691


title: Normal_2_3_12_2

description: Sample 690


title: Normal_2_3_2_3

description: Sample 699


title: Tumor_EOC_27

description:
Library name: EOC_27
Paired-end strand-specific RNA libraries


title: Normal_2_3_12_1

description: Sample 689


title: Normal_2_3_11_6

description: Sample 688


title: Normal_2_3_2_8

description: Sample 704


title: Tumor_EOC_25

description:
Library name: EOC_25
Paired-end strand-specific RNA libraries


title: Tumor_EOC_22

description:
Library name: EOC_22
Paired-end strand-specific RNA libraries


title: Tumor_EOC_23

description:
Library name: EOC_23
Paired-end strand-specific RNA libraries


title: Normal_2_3_11_5

description: Sample 687


title: Normal_2_3_12_7

description: Sample 695


title: Normal_2_3_11_2

description: Sample 685


title: Tumor_EOC_18

description:
Library name: EOC_18
Paired-end strand-specific RNA libraries


title: Tumor_EOC_17

description:
Library name: EOC_17
Paired-end strand-specific RNA libraries


title: Normal_2_3_11_3

description: Sample 686


title: Normal_2_3_11_1

description: Sample 684


title: Normal_2_3_10_6

description: Sample 682


title: Tumor_EOC_14

description:
Library name: EOC_14
Paired-end strand-specific RNA libraries


title: Tumor_EOC_16

description:
Library name: EOC_16
Paired-end strand-specific RNA libraries


title: Tumor_EOC_15

description:
Library name: EOC_15
Paired-end strand-specific RNA libraries


title: Normal_2_3_10_7

description: Sample 683


title: Tumor_EOC_12

description:
Library name: EOC_12
Paired-end strand-specific RNA libraries


title: Normal_2_3_10_3

description: Sample 679


title: Normal_2_3_10_5

description: Sample 681


title: Tumor_EOC_10

description:
Library name: EOC_10
Paired-end strand-specific RNA libraries


title: Normal_2_3_10_4

description: Sample 680


title: Normal_2_3_10_2

description: Sample 678


title: Normal_2_2_9_5

description: Sample 676


title: Tumor_EOC_11

description:
Library name: EOC_11
Paired-end strand-specific RNA libraries


title: Normal_2_2_9_3

description: Sample 675


title: Tumor_EOC_6

description:
Library name: EOC_6
Paired-end strand-specific RNA libraries


title: Normal_2_2_8_7

description: Sample 673


title: Normal_2_2_8_8

description: Sample 674


title: Tumor_EOC_13

description:
Library name: EOC_13
Paired-end strand-specific RNA libraries


title: Tumor_EOC_8

description:
Library name: EOC_8
Paired-end strand-specific RNA libraries


title: Normal_2_2_8_4

description: Sample 672


title: Tumor_EOC_3

description:
Library name: EOC_3
Paired-end strand-specific RNA libraries


title: Tumor_EOC_4

description:
Library name: EOC_4
Paired-end strand-specific RNA libraries


title: Tumor_EOC_2

description:
Library name: EOC_2
Paired-end strand-specific RNA libraries


title: Normal_2_2_8_1

description: Sample 670


title: Tumor_EOC_1

description:
Library name: EOC_1
Paired-end strand-specific RNA libraries


title: Normal_2_2_7_8

description: Sample 669


title: LAD2_EGFP_Control_rep2

city: Shiwa-gun

first: Tatsuki

middle: R

last: Kataoka

state: Iwate

address: 1-1-1, Idaidori, Yahaba-cho

country: Japan

institute: Iwate Medical University

description:
Library name: LAD2_Sample8
Column name in raw_counts_All_Samples.txt: EGFP_Veh_rep2

data_processing:
Ubuntu 22.04 LTS with Miniconda3
Trimmomatic (v0.39) was used for quality timming and adaptor removal.
STAR (v2.7.11a) was used for human genome alignment.
RSEM (v1.3.3) was used to quantify gene expression levels.
Assembly: GRCh38.p14
Supplementary files format and content: tub determined txt file includes raw counts for each Sample
Supplementary files format and content: other tub files include TPM values for each Sample.

growth_protocol: LAD2 cells were maintained in StemPro-34 (STEMCELL) medium supplemented with L-glutamine (2 mM), peniciline (100 units/mL), streptomycin (100 mg/mL) and recombinant human SCF (100 ng/mL, Nacalaitesque) in humidified atomosphere with 5% CO2 at 37℃.

extract_protocol:
RNA was harvested with RNA Premium Kit (FastGene). 1.3 ug of total RNA was used for the construction of sequencing library.
RNA libraries for RNA-seq were performed using NEBNext Ultra II Directional RNA Library Prep Kit (New England Biolab) following manufacture's instruction.

treatment_protocol:
To establish GnRHR-expressing mast cell line, LAD2 cells were toransformed with lentiviral particles. Lentiviral particle were constructed and packaged by VectorBuilder (EGFP control: VB010000-9298rtf, GnRHR express: VB900002-2070ngh).
A total of 3 × 10^5 cells of EGFP control or GnRHR-expressing LAD2 were incubated in a culture medium composed of 0.1 % (v/v) DMSO or 1 µM of the GnRH agonist; leuprorelin for 72 hours.

value: Tumor cells

value: EGFP control

value: DMSO


title: Normal_2_2_7_6

description: Sample 668

value: male

value: Normal

value: testis


title: Tumor_EOC_9

description:
Library name: EOC_9
Paired-end strand-specific RNA libraries

value: primary invasive EOC tumor


title: LAD2_EGFP_Control_rep1

description:
Library name: LAD2_Sample7
Column name in raw_counts_All_Samples.txt: EGFP_Veh_rep2


title: Normal_2_3_10_1

description: Sample 677


title: Normal_2_2_7_4

description: Sample 667


title: Tumor_EOC_7

description:
Library name: EOC_7
Paired-end strand-specific RNA libraries

value: III


title: LAD2_EGFP_Trearted_rep2

description:
Library name: LAD2_Sample6
Column name in raw_counts_All_Samples.txt: EGFP_Leu_rep2

value: GnRH agonist


title: Normal_2_2_7_3

description: Sample 666


title: LAD2_EGFP_Trearted_rep1

description:
Library name: LAD2_Sample5
Column name in raw_counts_All_Samples.txt: EGFP_Leu_rep1


title: LAD2_GnRHR_Treated_rep2

description:
Library name: LAD2_Sample2
Column name in raw_counts_All_Samples.txt: GnRHR_Leu_rep2

value: Forced GnRHR expression


title: Normal_2_2_6_5

description: Sample 662


title: Normal_2_2_7_2

description: Sample 665


title: LAD2_GnRHR_Control_rep2

description:
Library name: LAD2_Sample4
Column name in raw_counts_All_Samples.txt: GnRHR_Veh_rep2


title: Normal_2_2_6_7

description: Sample 663


title: Normal_2_2_6_8

description: Sample 664


title: LAD2_GnRHR_Control_rep1

description:
Library name: LAD2_Sample3
Column name in raw_counts_All_Samples.txt: GnRHR_Veh_rep1


title: Normal_2_2_5_8

description: Sample 661


title: UBTF_PDX-1_eltanexor

city: Memphis

first: Jeffery

last: Klco

state: TN

address: 262 Danny Thomas Place

department: Pathology

institute: St Jude Children's Research Hospital

description:
Library name: 3093454_SJAML015373_R23-HMP20_PDX_FMZVC_IDJ22_BM_elta
10X 3' GEX library preparation

data_processing:
Data processing and downstream analysis were carried out using the R programming environment (v4.0.2), leveraging the Seurat package (v4.1.0). To ensure data quality, count matrices from patient-derived samples were merged, and cells were filtered based on gene detection thresholds (minimum of 200 genes per cell) and mitochondrial transcript content (cells with >15% mitochondrial reads were excluded). Normalization was performed by scaling feature counts to 2,000 counts per cell, followed by log transformation. JackStraw analysis was applied to determine significant principal components, and uniform manifold approximation and projection (UMAP) was performed using the top 20 principal components (dims = 1:20, n.neighbors = 5L, min.dist = 0.05). Cell clusters were defined using the FindNeighbors and FindClusters functions (resolution = 0.3) and annotated based on enrichment in eltanexor versus vehicle treated populations. Differential gene expression analysis was performed using the Wilcoxon rank-sum test with Bonferroni correction.
Assembly: GRCh38
Supplementary files format and content: Cell Ranger text output files for individual samples containing single cell data (barcodes, genes, matrix)

source_name: human derived xenograft

growth_protocol: xenograft was expanded in NSG-SGM3 mice

extract_protocol:
For single-cell barcoding, gene expression libraries were constructed using the 10x Genomics Chromium Controller
Sequencing was performed on an Illumina NovaSeq 6000 using the SP Reagent Kit v1.5. Raw sequencing data in FASTQ format were processed using Cell Ranger (v3.0) with alignment to the GRCh38/hg38 human genome

treatment_protocol: The treatment group received eltanexor (KPT-8602) (Selleckchem, S8397) at 10 mg/kg by oral gavage daily (5 days on, 2 days off). The compound was suspended in 0.5% methylcellulose (type 400 cPs)/1.0% Tween 80 in ultrapure water, at 1 mg/mL for a 10 mg/kg free base.  equivalent dose as a 10 mL/kg oral gavage. This solvent was used as vehicle control

value: human derived xenograft

value: human leukemia cells

value: UBTF-TD

value: eltanexor 10 mg/kg


title: Normal_2_2_8_2

description: Sample 671


title: LAD2_GnRHR_Treated_rep1

description:
Library name: LAD2_Sample1
Column name in raw_counts_All_Samples.txt: GnRHR_Leu_rep1


title: Normal_2_2_5_6

description: Sample 659


title: Normal_2_2_5_7

description: Sample 660


title: UBTF-TD PDX-1 cells, rep2, eltanexor_25nM, XPO1

description: Library name: 2692290_SJAML015373_X8-FMZVC_ID147_PDX_Elta_25nM-XPO1-AB1

data_processing:
To obtain quality reads, raw reads were processed and trimmed with Trim_galore (v0.4.4) from cutadapt (DOI: 10.14806ej.17.1.200) and FASTQC analysis. A default quality score cutoff of Q20 is used.  Quality trimmed reads were then mapped to "hg38+rDNA” (DOI: 10.1101/2022.11.10.514243) genome build by bwa (v0.7.12-r1039) and converted to a bam file by samtools (v1.2).
Duplicate reads were marked with biobambam2 (v2.0.87, DOI: 10.1186/175109473-9-13). Uniquely mapped and properly paired reads were then extracted with samtools (v1.2, "-F 1804 -q 1") and sorted by read name using biobambam2 (v2.0.87)
bedtools(v2.17.0, PMID: 20110278) were used to convert bam file to bedpe file as fragments. Fragments with size shorter than 2000bp were extracted and center 80bp of each fragment were used to generate bigwig track files by UCSC tools (v4) and visualized using IGV (v2.16.0).
Narrow peaks were called with MACS2 (v2.1.1.20160309, parameters "-q 0.05") and broad peaks were called by SICER (v1.1, parameters "hg38 1 200 fragmentsize 0.86 600 0.00001").
To perform statistical test between experimental groups, fragments for each reference peak were counted with intersect command from pybedtools (v0.9.1). Next, the number of raw reads mapping per peak were converted to FPKM unit (Fragments Per Kilo base per Million mapped reads), and TMM (trimmed mean of M-values) from edgeR package. Next, we used limma-voom approach to assess the significance of differential peak binding.  Significant peaks were defined by log2FC < -1 or > 1 and FDR < 0.05.
Assembly: hg38+ custom rDNA build from  DOI:  https://doi.org/10.1101/2022.11.10.514243
Supplementary files format and content: bigwig files
Library strategy: CUT&Run

source_name: Human UBTF-TD Patient Derived Xenograft sample

growth_protocol: cbCD34+ cells were growin in SFEM II supplemented with pen-strep, I-glutamine, and recombinant human SCF, FLT-3, TPO and IL-6 (all 50ng/mL PeproTech),  500nM (#72332, STEMCELL Technologies) for UM729, and 500nM SR-1 (1µmol/L, #72344, STEMCELL Technologies), PDX cells were grown in AML media which is StemSpan™ SFEM II (StemCell Technologies 09655) supplemented with human cytokines IL-6 (10ng/mL, PeproTech, 200-06), FLT-3 ligand (50ng/mL, PeproTech, 300-19), IL-3 (10ng/mL, PeproTech, 200-03), and human SCF (50ng/mL, PeproTech, 300-07)

extract_protocol:
CUT&RUN was performed following the kit from EpiCypher (cat# 14-1048)
CUT&RUN DNA libraries were made following NEBNext Ultra II DNA Library Prep Kit for Illumina (cat# E7103), PCR amplification was done for 12 cycles

value: UBTF-TD PDX-1 cells

tag: chip antibody

value: XPO1 (Cell Signaling Technologies, 46249)

value: eltanexor 25nM


title: Normal_2_2_5_4

description: Sample 658


title: UBTF-TD PDX-1 cells, rep2, eltanexor_25nM, UBTF

description: Library name: 2692289_SJAML015373_X8-FMZVC_ID147_PDX_Elta_25nM-UBTF-AB2

value: Human UBTF-TD Patient Derived Xenograft sample

value: UBTF (Abcam, ab244287)


title: UBTF-TD PDX-1 cells, rep2, DMSO, XPO1

description: Library name: 2692288_SJAML015373_X7-FMZVC_ID147_PDX_DMSO-XPO1-AB1

value: DMSO


title: Normal_2_2_5_2

description: Sample 656

value: male


title: Normal_2_2_5_3

description: Sample 657

value: Normal


title: UBTF-TD PDX-1 cells, rep2, DMSO, UBTF

description: Library name: 2692287_SJAML015373_X7-FMZVC_ID147_PDX_DMSO-UBTF-AB2


title: Normal_2_2_5_1

description: Sample 655

value: testis


title: UBTF-TD PDX-2 cells, rep2, eltanexor_25nM, XPO1

description: Library name: 2692286_SJAML074163_X5-D4H9T_ID709_PDX_Elta_25nM-XPO1-AB1

value: UBTF-TD PDX-2 cells


title: UBTF-TD PDX-2 cells, rep2, DMSO, XPO1

description: Library name: 2692284_SJAML074163_X4-D4H9T_ID709_PDX_DMSO-XPO1-AB1


title: Normal_2_2_4_6

description: Sample 653


title: Normal_2_2_4_3

description: Sample 651


title: Normal_2_2_4_2

description: Sample 650


title: UBTF-TD PDX-2 cells, rep1, DMSO, XPO1

description: Library name: 2668739_SJAML074163_X2-D4H9T_ID784_PDX_24hrs_DMSO-XPO1-AB1


title: UBTF-TD PDX-2 cells, rep1, eltanexor_25nM, XPO1

description: Library name: 2668741_SJAML074163_X3-D4H9T_ID784_PDX_24hrs_Elta_25nM-XPO1-AB1


title: Normal_2_2_4_1

description: Sample 649


title: UBTF-TD PDX-2 cells, rep2, DMSO, UBTF

description: Library name: 2692283_SJAML074163_X4-D4H9T_ID709_PDX_DMSO-UBTF-AB2


title: Normal_2_2_3_5

description: Sample 647


title: Normal_2_2_3_3

description: Sample 646


title: UBTF-TD PDX-1 cells, rep1, eltanexor_25nM, UBTF

description: Library name: 2668734_SJAML015373_X5-FMZVC_ID45_PDX_24hrs_Elta_25nM-UBTF-AB2


title: UBTF-TD PDX-2 cells, rep1, DMSO, UBTF

description: Library name: 2668738_SJAML074163_X2-D4H9T_ID784_PDX_24hrs_DMSO-UBTF-AB2


title: UBTF_PDX-1_Vehicle

description:
Library name: 3093452_SJAML015373_R21-HMP20_PDX_FMZVC_IDJ01_BM_veh
10X 3' GEX library preparation

value: vehicle


title: Normal_2_2_2_8

description: Sample 644


title: UBTF-TD PDX-1 cells, rep1, DMSO, XPO1

description: Library name: 2668733_SJAML015373_X4-FMZVC_ID45_PDX_24hrs_DMSO-XPO1-AB1


title: Normal_2_2_3_6

description: Sample 648


title: Normal_2_2_2_7

description: Sample 643


title: UBTF-TD PDX-1 cells, rep1, DMSO, UBTF

description: Library name: 2668732_SJAML015373_X4-FMZVC_ID45_PDX_24hrs_DMSO-UBTF-AB2


title: Normal_2_2_2_5

description: Sample 642


title: Normal_2_2_4_8

description: Sample 654


title: Normal_2_2_2_2

description: Sample 641


title: cord-blood CD34+ cells, MPC-FKBP12-UBTF-TD54, rep2, dTAG_1uM, XPO1

description: Library name: 2657721_SJNORM077216_C68_cbCD34_FKBP12_TD54_dTAG_1uM_24hr_rep2_XPO1_AB1

source_name: cord-blood CD34+ cells

value: cord-blood CD34+ cells


title: cord-blood CD34+ cells, MPC-FKBP12-UBTF-TD54, rep2, DMSO, XPO1

description: Library name: 2657700_SJNORM077216_C58_cbCD34_FKBP12_TD54_DMSO_rep2_XPO1_AB1


title: Normal_2_2_12_6

description: Sample 639


title: cord-blood CD34+ cells, MPC-FKBP12-UBTF-TD54, rep1, dTAG_1uM, XPO1

description: Library name: 2590385_SJNORM077216_C31_CD34_MPC_FKBP12_TD54_5E_dTAG_13_1uM_rep1_XPO1_AB1


title: Normal_2_2_4_5

description: Sample 652


title: UBTF-TD PDX-2 cells, rep1, eltanexor_25nM, UBTF

description: Library name: 2668740_SJAML074163_X3-D4H9T_ID784_PDX_24hrs_Elta_25nM-UBTF-AB2


title: UBTF-TD PDX-1 cells, rep1, eltanexor_25nM, XPO1

description: Library name: 2668735_SJAML015373_X5-FMZVC_ID45_PDX_24hrs_Elta_25nM-XPO1-AB1


title: cord-blood CD34+ cells, MPC-FKBP12-UBTF-TD54, rep1, DMSO, XPO1

description: Library name: 2657699_SJNORM077216_C57_cbCD34_FKBP12_TD54_DMSO_rep1_XPO1_AB1


title: cord-blood CD34+ cells, MPC-FKBP12-UBTF-TD54, rep2, eltanexor_25nM, HA

description: Library name: 2657717_SJNORM077216_C66_cbCD34_FKBP12_TD54_Elta_25nM_24hr_rep2_HA_AB3

value: HA (Cell Signaling Technologies, 3724)


title: Normal_2_2_12_2

description: Sample 636


title: Normal_2_2_11_7

description: Sample 634


title: Normal_2_2_12_4

description: Sample 638


title: cord-blood CD34+ cells, MPC-FKBP12-UBTF-TD54, rep1, eltanexor_25nM, HA

description: Library name: 2657716_SJNORM077216_C65_cbCD34_FKBP12_TD54_Elta_25nM_24hr_rep1_HA_AB3


title: Normal_2_2_12_1

description: Sample 635


title: Normal_2_2_12_3

description: Sample 637


title: cord-blood CD34+ cells, MPC-FKBP12-UBTF-TD54, rep1, eltanexor_25nM, XPO1

description: Library name: 2657722_SJNORM077216_C65_cbCD34_FKBP12_TD54_Elta_25nM_24hr_rep1_XPO1_AB1


title: cord-blood CD34+ cells, MPC-FKBP12-UBTF-TD54, rep1, dTAG_1uM, HA

description: Library name: 2657715_SJNORM077216_C64_cbCD34_FKBP12_TD54_dTAG_1uM_24hr_rep1_HA_AB3


title: Normal_2_2_3_1

description: Sample 645


title: cord-blood CD34+ cells, MPC-FKBP12-UBTF-TD54, rep2, DMSO, HA

description: Library name: 2643834_SJNORM077216_C44_CD34_MPC_FKBP12_TD54_5E_DMSO_rep1_HA_AB3


title: cord-blood CD34+ cells, MPC-FKBP12-UBTF-TD54, rep2, eltanexor_25nM, XPO1

description: Library name: 2657723_SJNORM077216_C66_cbCD34_FKBP12_TD54_Elta_25nM_24hr_rep2_XPO1_AB1


title: Normal_2_2_11_6

description: Sample 633


title: cord-blood CD34+ cells, MPC-FKBP12-UBTF-TD54, rep1, DMSO, HA

description: Library name: 2657696_SJNORM077216_C57_cbCD34_FKBP12_TD54_DMSO_rep1_HA_AB3


title: Normal_2_2_11_2

description: Sample 630


title: Normal_2_2_11_4

description: Sample 631


title: Normal_2_2_11_5

description: Sample 632


title: cord-blood CD34+ cells, MPC-nHA-UBTF-TD48, rep3, H3K27ac

description: Library name: 3177780_SJNORM094202_C2-TD48_JK47_D45-H3K27Ac-AB5

value: H3K27ac (Cell Signaling Technologies,  8173)


title: cord-blood CD34+ cells, MPC-nHA-UBTF-TD48, rep3, HA

description: Library name: 3177779_SJNORM094202_C2-TD48_JK47_D45-HA-AB3


title: Normal_2_2_10_5

description: Sample 629


title: Normal_2_2_1_7

description: Sample 628


title: Normal_2_2_1_6

description: Sample 627


title: cord-blood CD34+ cells, MPC-nHA-UBTF-TD48, rep2, H3K27ac

description: Library name: 3177777_SJNORM094196_C2-TD48_JK30_D45-H3K27Ac-AB5


title: cord-blood CD34+ cells, MPC-FKBP12-UBTF-TD54, rep2, dTAG_1uM, HA

description: Library name: 2643846_SJNORM077216_C48_CD34_MPC_FKBP12_TD54_5E_dTAG_13_1uM_rep2_HA_AB3


title: Normal_2_2_1_5

description: Sample 626


title: cord-blood CD34+ cells, MPC-nHA-UBTF-TD48, rep2, HA

description: Library name: 3177776_SJNORM094196_C2-TD48_JK30_D45-HA-AB3


title: cord-blood CD34+ cells, MPC-nHA-UBTF-TD48-NES-M, rep1, H3K27ac

description: Library name: 3177775_SJNORM094190_C2-TD48-NES-Mutation_JK27_D45-H3K27Ac-AB5


title: Normal_2_1_9_7

description: Sample 624


title: cord-blood CD34+ cells, MPC-nHA-UBTF-TD48, rep1, HA

description: Library name: 3177772_SJNORM094189_C2-TD48_JK27_D45-HA-AB3


title: Normal_2_1_9_5

description: Sample 622


title: cord-blood CD34+ cells, MPC-nHA-UBTF-TD48, rep1, H3K27ac

description: Library name: 3177773_SJNORM094189_C2-TD48_JK27_D45-H3K27Ac-AB5


title: cord-blood CD34+ cells, MPC-nHA-UBTF-TD48-NES-M, rep3, H3K27ac

description: Library name: 3177782_SJNORM094203_C2-TD48-NES-Mutation_JK47_D45-H3K27Ac-AB5


title: cord-blood CD34+ cells, MPC-nHA-UBTF-TD48-NES-M, rep3, HA

description: Library name: 3177781_SJNORM094203_C2-TD48-NES-Mutation_JK47_D45-HA-AB3


title: Normal_2_1_6_6

description: Sample 620


title: Normal_2_1_6_4

description: Sample 619


title: cord-blood CD34+ cells, MPC-nHA-UBTF-TD84-NES-M, rep3, H3K27ac

description: Library name: 3145811_SJNORM093891_C2-TD84-8Ala-JK37_D50-H3K27Ac-AB5


title: cord-blood CD34+ cells, MPC-nHA-UBTF-TD84-NES-M, rep2, H3K27ac

description: Library name: 3145809_SJNORM093890_C2-TD84-8Ala-JK35_D50-H3K27Ac-AB5


title: cord-blood CD34+ cells, MPC-nHA-UBTF-TD84-NES-M, rep2, HA

description: Library name: 3145808_SJNORM093890_C2-TD84-8Ala-JK35_D50-HA-AB3


title: cord-blood CD34+ cells, MPC-nHA-UBTF-TD84-NES-M, rep3, HA

description: Library name: 3145810_SJNORM093891_C2-TD84-8Ala-JK37_D50-HA-AB3


title: cord-blood CD34+ cells, MPC-nHA-UBTF-TD84-NES-M, rep1, H3K27ac

description: Library name: 3145807_SJNORM093889_C2-TD84-8Ala-JK34_D50-H3K27Ac-AB5


title: Normal_2_1_5_1

description: Sample 616


title: Normal_2_1_6_3

description: Sample 618


title: cord-blood CD34+ cells, MPC-nHA-UBTF-TD84-NES-M, rep1, HA

description: Library name: 3145806_SJNORM093889_C2-TD84-8Ala-JK34_D50-HA-AB3


title: cord-blood CD34+ cells, MPC-nHA-UBTF-TD48-NES-M, rep2, H3K27ac

description: Library name: 3177778_SJNORM094230_C1-TD48-NES-Mutation_JK30_D45-H3K27Ac-AB5


title: Normal_2_1_5_8

description: Sample 617


title: Normal_2_1_4_5

description: Sample 615


title: cord-blood CD34+ cells, MPC-nHA-UBTF-TD84, rep3, H3K27ac

description: Library name: 3145799_SJNORM093885_C2-TD84-JK37_D50-H3K27Ac-AB5


title: Normal_2_1_3_6

description: Sample 614


title: Normal_2_2_1_4

description: Sample 625


title: cord-blood CD34+ cells, MPC-nHA-UBTF-TD84, rep3, HA

description: Library name: 3145798_SJNORM093885_C2-TD84-JK37_D50-HA-AB3


title: Normal_2_1_9_6

description: Sample 623


title: Normal_2_1_7_1

description: Sample 621


title: Normal_2_1_3_4

description: Sample 613


title: cord-blood CD34+ cells, MPC-nHA-UBTF-TD48-NES-M, rep1, HA

description: Library name: 3177774_SJNORM094190_C2-TD48-NES-Mutation_JK27_D45-HA-AB3


title: cord-blood CD34+ cells, MPC-nHA-UBTF-TD84, rep2, H3K27ac

description: Library name: 3145797_SJNORM093884_C2-TD84-JK35_D50-H3K27Ac-AB5


title: cord-blood CD34+ cells, MPC-nHA-UBTF-TD84, rep2, HA

description: Library name: 3145796_SJNORM093884_C2-TD84-JK35_D50-HA-AB3


title: Normal_2_1_3_2

description: Sample 612


title: cord-blood CD34+ cells, MPC-nHA-UBTF-TD84, rep1, HA

description: Library name: 3145794_SJNORM093883_C2-TD84-JK34_D50-HA-AB3


title: Normal_2_1_2_2

description: Sample 609


title: Normal_2_1_12_8

description: Sample 608


title: cord-blood CD34+ cells, MPC-nHA-UBTF-TD84, rep1, H3K27ac

description: Library name: 3145795_SJNORM093883_C2-TD84-JK34_D50-H3K27Ac-AB5


title: cord-blood CD34+ cells, MPC-Empty Vector, rep1, HA

description: Library name: 3145792_SJNORM093881_C2-MPC-EV-JK37_D50-HA-AB3


title: Normal_2_1_2_3

description: Sample 610


title: cord-blood CD34+ cells, MPC-Empty Vector, rep1, H3K27ac

description: Library name: 3145793_SJNORM093881_C2-MPC-EV-JK37_D50-H3K27Ac-AB5


title: Normal_2_1_12_2

description: Sample 606


title: Normal_2_1_12_7

description: Sample 607


title: cord-blood CD34+ cells, MPC-Empty Vector, rep1, H3K4me3

description: Library name: 3145791_SJNORM093881_C2-MPC-EV-JK37_D50-H3K4me3-AB12

value: H3K4me3 (EpiCypher, 13-0041)


title: cord-blood CD34+ cells, MPC-Empty Vector, rep1, IgG

description: Library name: 3145790_SJNORM093881_C2-MPC-EV-JK37_D50-IGG-AB14

value: IgG (EpiCypher, 13-0042)


title: Normal_2_1_12_1

description: Sample 605


title: cord-blood CD34+ cells, MPC-nHA-UBTF-TD84-NES-M, rep2, XPO1

description: Library name: 3100814_SJNORM091103_C2-TD-84-NES-mut_JK22_D46-XPO1-AB1


title: cord-blood CD34+ cells, MPC-nHA-UBTF-TD84-NES-M, rep3, XPO1

description: Library name: 3100815_SJNORM091103_C3-TD-84-NES-mut_JK28_D46-XPO1-AB1


title: cord-blood CD34+ cells, MPC-nHA-UBTF-TD84-NES-M, rep1, XPO1

description: Library name: 3100813_SJNORM091103_C1-TD-84-NES-mut_JK18_D46-XPO1-AB1


title: Normal_2_1_11_6

description: Sample 603


title: E. coli TRIC-seq, stationary - Replicate 5 resequenced

city: Amsterdam

first: Gaurav

last: Dugar

address: Science Park 904

department: Bacterial Cell Biology

country: Netherlands

institute: University of Amsterdam

description: Library name: R20S2_re

data_processing:
*library strategy: TRIC-seq
paired-end FASTQ files were pre-processed using fastp (version 1.0.1) for adapter trimming, quality filtering, PCR duplicate removal, and merging of overlapping read pairs
STAR mapper 2.7.11a was used for mapping and extract chimeric reads (RNA-RNA interactions).
Custom scripts used to analyse and visualize RNA-RNA interactions in TRIC-seq can be found at - https://github.com/gdx7/TRIC-seq and https://github.com/gdx7/TRICweb
Assembly: NC_000913.3 (E. coli)
Assembly: CP003725.1 (S. stutzeri)
Assembly: NC_008095.1 (M. xanthus)
Assembly: NC_007795.1 (S. aureus)
Supplementary files format and content: .csv file with mapping statistics and extraction of chimeric reads

organism: Escherichia coli

extract_protocol:
Cells were pelleted, and crosslinks were reversed by incubation with Proteinase K at 65°C for 3 hours. Total RNA was extracted using PCI (Phenol:Chloroform:Isoamyl alcohol for RNA, Carl Roth, #X985.3). The biotinylated chimeric RNAs were captured using MyOne Streptavidin C1 beads (Thermo Fisher, #65002)
The construction of TRIC-seq libraries includes a multi-step in situ protocol involving cell fixation, permeabilization, RNA fragmentation, 3'-end biotin labelling, proximity ligation, followed by RNA purification, enrichment of chimeric junctions, and strand-specific library preparation for sequencing.
directional sequencing library was prepared using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB, #E7760), which employs a dUTP-based method with random hexamers for reverse transcription


title: cord-blood CD34+ cells, MPC-nHA-UBTF-TD84, rep3, XPO1

description: Library name: 3100812_SJNORM091102_C3-TD-84_JK28_D46-XPO1-AB1


title: Normal_2_1_11_5

description: Sample 602


title: E. coli TRIC-seq, stationary - Replicate 4 resequenced

description: Library name: R20S1_re


title: cord-blood CD34+ cells, MPC-nHA-UBTF-TD84, rep2, XPO1

description: Library name: 3100811_SJNORM091102_C2-TD-84_JK22_D46-XPO1-AB1


title: Normal_2_1_2_5

description: Sample 611


title: cord-blood CD34+ cells, MPC-nHA-UBTF-TD84, rep1, XPO1

description: Library name: 3100810_SJNORM091102_C1-TD-84_JK18_D46-XPO1-AB1


title: upf3-3

city: Paris

first: Maxime

last: Wery

address: 26 rue d'Ulm

country: France

institute: Institut Curie

description: Library name: sample9

data_processing:
Reads were trimmed using Trim Galore
Reads were mapped on the N. castellii reference genome (ASM23734v1) including mitochondrial genome (AF437291) and ERCC RNA spike-in sequences using HISAT2 V2.2.0, with default parameters and maximum intron size of 5000.
Gene count was obtained with featureCounts v2.0.0.
Gene count was normalized using estimatesizefactorsformatrix() function from DESeq2 package (R software), using snoRNA counts.
Normalized densities were computed for each sample as : normalized gene count / gene length
Assembly: ASM23734v1
Supplementary files format and content: tab delimited file, containing normalized tag/nt for each sample

organism: Naumovozyma castellii

source_name: Yeast cells

growth_protocol: Cells were grown to mid-log phase (OD600 0.5) at 25°C in rich medium (YPD).

extract_protocol:
Total RNA was extracted using standard hot phenol procedure as described (PMID: 39535701) . Extracted RNA was ethanol-precipitated, resuspended in nuclease-free H2O (Ambion) and quantified using a NanoDrop 2000c spectrophotometer and/or a Qubit fluorometer with the Qubit RNA HS Assay kit (Life Technologies).
For each sample, 1 µg of total RNA was mixed with 2 µl of diluted ERCC RNA spike-in mix (1:100 dilution in nuclease-free H2O; Invitrogen). Ribosomal (r)RNAs were depleted using the Ribominus Eukaryote v2 kit (Ambion). Libraries were prepared using the TruSeq Stranded mRNA Sample Preparation Kit (Illumina) and the IDT for Illumina – TruSeq RNA UD indexes (Illumina).

tag: strain

value: Yeast cells

value: MATalpha ura3-1 ho upf3::kanMX6


title: cord-blood CD34+ cells, MPC-nHA-UBTF-TD54-NES-M, rep3, XPO1

description: Library name: 3100809_SJNORM091101_C3-TD-54-NES-mut_JK28_D46-XPO1-AB1

value: XPO1 (Cell Signaling Technologies, 46249)


title: Normal_2_1_11_2

description: Sample 600


title: cord-blood CD34+ cells, MPC-nHA-UBTF-TD54, rep3, XPO1

description: Library name: 3100806_SJNORM091100_C3-TD-54_JK28_D46-XPO1-AB1


title: Normal_2_1_11_3

description: Sample 601


title: cord-blood CD34+ cells, MPC-nHA-UBTF-TD54, rep1, XPO1

description: Library name: 3100804_SJNORM091100_C1-TD-54_JK18_D46-XPO1-AB1


title: upf3-2

description: Library name: sample8


title: Normal_2_1_10_7

description: Sample 598


title: cord-blood CD34+ cells, MPC-nHA-UBTF-TD54-NES-M, rep1, XPO1

description: Library name: 3100807_SJNORM091101_C1-TD-54-NES-mut_JK18_D46-XPO1-AB1


title: cord-blood CD34+ cells, MPC-nHA-UBTF-TD54, rep2, XPO1

description: Library name: 3100805_SJNORM091100_C2-TD-54_JK22_D46-XPO1-AB1


title: cord-blood CD34+ cells, MPC-nHA-UBTF-TD54-NES-M, rep2, H3K27Ac

description: Library name: 3100797_SJNORM091101_C3-TD-54-NES-mut_JK28_D46-H3K27Ac-AB5


title: upf3-1

description: Library name: sample7


title: Normal_2_1_10_8

description: Sample 599


title: upf2-3

description: Library name: sample6

value: MATalpha ura3-1 ho upf2::kanMX6


title: cord-blood CD34+ cells, MPC-nHA-UBTF-TD54-NES-M, rep2, XPO1

description: Library name: 3100808_SJNORM091101_C2-TD-54-NES-mut_JK22_D46-XPO1-AB1


title: upf2-2

description: Library name: sample5


title: Normal_2_1_11_8

description: Sample 604


title: cord-blood CD34+ cells, MPC-nHA-UBTF-TD54, rep2, H3K27Ac

description: Library name: 3100794_SJNORM091100_C2-TD-54_JK22_D46-H3K27Ac-AB5


title: Normal_2_1_10_6

description: Sample 597


title: Normal_2_1_10_4

description: Sample 596


title: upf2-1

description: Library name: sample4


title: cord-blood CD34+ cells, MPC-nHA-UBTF-TD54-NES-M, rep1, H3K27Ac

description: Library name: 3100796_SJNORM091101_C1-TD-54-NES-mut_JK18_D46-H3K27Ac-AB5


title: cord-blood CD34+ cells, MPC-nHA-UBTF-TD54, rep3, H3K27Ac

description: Library name: 3100795_SJNORM091100_C3-TD-54_JK28_D46-H3K27Ac-AB5


title: cord-blood CD34+ cells, MPC-nHA-UBTF-TD54, rep1, H3K27Ac

description: Library name: 3100793_SJNORM091100_C1-TD-54_JK18_D46-H3K27Ac-AB5


title: Normal_2_1_10_2

description: Sample 595


title: cord-blood CD34+ cells, MPC-nHA-UBTF-TD54-NES-M, rep3, HA

description: Library name: 3100786_SJNORM091101_C3-TD-54-NES-mut_JK28_D46-HA-AB3


title: cord-blood CD34+ cells, MPC-nHA-UBTF-TD54, rep3, HA

description: Library name: 3100783_SJNORM091100_C3-TD-54_JK28_D46-HA-AB3


title: cord-blood CD34+ cells, MPC-nHA-UBTF-TD54-NES-M, rep1, HA

description: Library name: 3100784_SJNORM091101_C1-TD-54-NES-mut_JK18_D46-HA-AB34


title: WT_UPF2_UPF3_3

description: Library name: sample3

value: MATalpha ura3-1 ho


title: WT_UPF2_UPF3_1

description: Library name: sample1


title: cord-blood CD34+ cells, MPC-nHA-UBTF-TD54, rep2, HA

description: Library name: 3100782_SJNORM091100_C2-TD-54_JK22_D46-HA-AB3


title: cord-blood CD34+ cells, MPC-nHA-UBTF-TD54, rep1, HA

description: Library name: 3100781_SJNORM091100_C1-TD-54_JK18_D46-HA-AB3


title: WT_UPF2_UPF3_2

description: Library name: sample2


title: UBTF-TD84-NES-M, RNA-seq, Rep1

description: Library name: SJNORM093889_C1_TD_84_8Ala_NES_M_JK16_D50

data_processing:
RNA-Seq reads were mapped to GRCh38/hg38 human genome assembly using STAR v2.7.9a
Gene expression count matrix was generated using RSEM (v1.3.0)
The count data were transformed to log2-counts per million (log2CPM) using Voom method available from R package Limma (v3.50.3). Limma was also used to perform differential expression analysis between DMSO and dTAG-13 treated samples.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file for log2-counts per million (log2CPM) , one gene per row and one sample per column.

source_name: cord-blood CD34+ Cells expressing nHA-UBTF-TD84-NES-M

extract_protocol:
RNA was harvested using Quikc-RNA Miniprep Kit (Zymo Research R1055)). RNA was then quantified using the Quant-iT RiboGreen RNA assay (ThermoFisher) and quality checked by the 2100 Bioanalyzer RNA 6000 Nano assay (Agilent) or 4200 TapeStation High Sensitivity RNA ScreenTape assay (Agilent) prior to library generation.
Libraries were prepared from total RNA with the Illumina Stranded Total RNA Prep kit according to the manufacturer’s instructions (Illumina, PN 20072063). Libraries were analyzed for insert size distribution using the 2100 BioAnalyzer High Sensitivity kit (Agilent), 4200 TapeStation D1000 ScreenTape assay (Agilent), or 5300 Fragment Analyzer NGS fragment kit (Agilent). Libraries were quantified using the Quant-iT PicoGreen ds DNA assay (ThermoFisher) or by low pass sequencing with a MiSeq nano kit (Illumina).
Paired end 100 cycle sequencing was performed on a NovaSeq 6000 (Illumina).

value: cord-blood CD34+ Cells

value: expressing nHA-UBTF-TD84-NES-M


title: Normal_1_7_3_2

description: Sample 591

value: male


title: Normal_1_7_3_4

description: Sample 592

value: Normal


title: UBTF-TD84-NES-M, RNA-seq, Rep3

description: Library name: SJNORM093891_C1_TD_84_8Ala_NES_M_JK31_D50


title: Normal_1_7_3_8

description: Sample 593

value: testis


title: upf1_CHX_2

description: Library name: sample5

data_processing:
Reads were trimmed using Trim Galore.
Trimmed reads were mapped to the N. castellii reference genome using Hisat2.
Uniquely mapped reads with a length of 25-35 nt were kept.
Ribotricer v1.3.1 was used to defined translated ORFs and compute phase after pooling all samples.
Assembly: ASM23734v1
Supplementary files format and content: tab delimited file, with read count per ORF for pooled samples and phase score.
Library strategy: Ribo-Seq

molecule: cytoplasmic RNA

growth_protocol: Cells were grown to mid-log phase (OD600 0,5) at 25°C in YPD.

extract_protocol:
Cells were lysed and ribosome-protected fragments (RPFs) were prepared as previously described (Andjus et al., 2024), starting from 20 A260 units of extracts.
After rRNA depletion, RPFs were treated with 5 units of Antarctic phosphatase (New England Biolabs), and then with 10 units of T4 polynucleotide kinase (New England Biolabs) in the presence of 1 mM ATP. Phosphorylated RPFs were purified using the RNA Clean & Concentrator-5 kit (Zymo Research) following manufacturer’s instructions, and eluted in 15 µL of nuclease-free H2O. Ribo-seq libraries were constructed using the NEBNext Multiplex Small RNA Library Prep Set for Illumina (New England Biolabs), following manufacturer’s instructions. Amplified libraries were purified using AMPure XP beads (Beckman Coulter), and then on 6% Novex TBE gel (Invitrogen).

treatment_protocol: Cells were treated with CHX for 15 minutes.

value: MATalpha ura3-1 ho upf1::kanMX6

value: CHX


title: UBTF-TD84, RNA-seq, Rep5

description: Library name: SJNORM093884_C1_TD_84_JK30_D50

source_name: cord-blood CD34+ Cells expressing nHA-UBTF-TD84

value: expressing nHA-UBTF-TD84


title: upf1_CHX_3

description: Library name: sample6


title: UBTF-TD84-NES-M, RNA-seq, Rep2

description: Library name: SJNORM093890_C1_TD_84_8Ala_NES_M_JK30_D50


title: upf1_CHX_1

description: Library name: sample4


title: Normal_1_7_2_6

description: Sample 590


title: UBTF-TD84, RNA-seq, Rep2

description: Library name: SJNORM094193_C1_MPC_UBTF_TD84_JK30_D43


title: UBTF-TD84, RNA-seq, Rep6

description: Library name: SJNORM093885_C1_TD_84_JK31_D50


title: cord-blood CD34+ cells, MPC-nHA-UBTF-TD54-NES-M, rep2, HA

description: Library name: 3100785_SJNORM091101_C2-TD-54-NES-mut_JK22_D46-HA-AB3

value: cord-blood CD34+ cells

value: HA (Cell Signaling Technologies, 3724)


title: UBTF-TD84, RNA-seq, Rep3

description: Library name: SJNORM094199_C1_MPC_UBTF_TD84_JK47_D43


title: WT_CHX_3

description: Library name: sample3


title: UBTF-TD84, RNA-seq, Rep1

description: Library name: SJNORM094186_C1_MPC_UBTF_TD84_JK27_D43


title: Normal_2_1_10_1

description: Sample 594


title: UBTF-TD54-NES-M, RNA-seq, Rep4

description: Library name: SJNORM093379_C1-TD-54_JK23_D50

source_name: cord-blood CD34+ Cells expressing nHA-UBTF-TD54-NES-M

value: expressing nHA-UBTF-TD54-NES-M


title: WT_CHX_2

description: Library name: sample2


title: Normal_1_6_9_8

description: Sample 588


title: Normal_1_6_9_7

description: Sample 587


title: UBTF-TD54-NES-M, RNA-seq, Rep3

description: Library name: SJNORM091101_C4_TD_54_NES_mutant_JK18_D50


title: UBTF-TD54-NES-M, RNA-seq, Rep1

description: Library name: SJNORM085159_C1_UBTF_TD54_NES_mut_1


title: Normal_1_6_9_5

description: Sample 586


title: UBTF-TD54-NES-M, RNA-seq, Rep2

description: Library name: SJNORM085158_C4_UBTF_TD54_NES_mut_2


title: WT_CHX_1

description: Library name: sample1


title: UBTF-TD54, RNA-seq, Rep4

description: Library name: SJNORM094198_C1_MPC_UBTF_TD54_JK47_D43


title: Normal_1_6_8_6

description: Sample 585


title: UBTF-TD54, RNA-seq, Rep3

description: Library name: SJNORM094192_C1_MPC_UBTF_TD54_JK30_D43

source_name: cord-blood CD34+ Cells expressing nHA-UBTF-TD54

value: expressing nHA-UBTF-TD54


title: Normal_1_7_2_1

description: Sample 589


title: UBTF-TD54, RNA-seq, Rep1

description: Library name: SJNORM091100_C6_TD_54_JK18_D50


title: UBTF-TD84, RNA-seq, Rep4

description: Library name: SJNORM093883_C1_TD_84_JK16_D50


title: Normal_1_6_8_5

description: Sample 584


title: UBTF-TD54, RNA-seq, Rep2

description: Library name: SJNORM093380_C1_TD_54_JK28_D50


title: Normal_1_6_8_4

description: Sample 583


title: UBTF-TD48-NES-M, RNA-seq, Rep2

description: Library name: SJNORM094203_C1_MPC_UBTF_TD48_NES_M_JK47_D43

source_name: cord-blood CD34+ Cells expressing nHA-UBTF-TD48-NES-M

value: expressing nHA-UBTF-TD48-NES-M


title: UBTF-TD48-NES-M, RNA-seq, Rep3

description: Library name: SJNORM095861_C1-MPC-UBTF-TD48-NES-M_JK30_D43


title: WT_1_CHX

description: Library name: sample7

data_processing:
Adapter sequences were removed using Trim Galore.
Reads were then mapped to the N. castellii and S. pombe reference genomes using version 2.4.1 of Bowtie, with default parameters.
Subsequent analyses used 22–23-nt reads uniquely mapped to the N. castellii genome.
Densities were normalized on the levels of S. pombe centromeric 22–23-nt small RNAs.
Assembly: ASM23734v1 (N. castellii)
Assembly: ASM294v2 (S. pombe)
Supplementary files format and content: tab delimited file, containing normalized counts (tag/nt) for each sample

extract_protocol:
Total RNA was extracted using standard hot phenol procedure as described (PMID: 39535701) . Extracted RNA was ethanol-precipitated, resuspended in nuclease-free H2O (Ambion) and quantified using a NanoDrop 2000c spectrophotometer and/or a Qubit fluorometer with the Qubit RNA HS Assay kit (Life Technologies).
For each condition, small RNA-seq analysis was performed from two biological replicates. Briefly, 25 µg of total RNA were mixed with 1 μg of total RNA from the YAM2400 (WT) strain of S. pombe; the 22–23-nt small RNAs derived from S. pombe centromeric regions are used as RNA spike-in to normalize small RNA-seq signals. Libraries were constructed using the NEBNext Multiplex Small RNA Library Prep Set for Illumina (New England Biolabs), following manufacturer’s instructions, starting from 50-100 ng of small RNAs (<80 nt) purified on 15% TBE–urea polyacrylamide gels.

treatment_protocol: For CHX-treated cells, CHX was added at a final concentration of 100 micrograms per mL for 15 min.


title: WT_2_CHX

description: Library name: sample8


title: UBTF-TD48, RNA-seq, Rep3

description: Library name: SJNORM094202_C1_MPC_UBTF_TD48_JK47_D43

source_name: cord-blood CD34+ Cells expressing nHA-UBTF-TD48

value: expressing nHA-UBTF-TD48


title: dcr1_1_CHX

description: Library name: sample9

value: MATalpha ura3-1 ho dcr1


title: UBTF-TD48-NES-M, RNA-seq, Rep1

description: Library name: SJNORM094190_C1_MPC_UBTF_TD48_NES_M_JK27_D43


title: UBTF-TD48, RNA-seq, Rep2

description: Library name: SJNORM094196_C1_MPC_UBTF_TD48_JK30_D43


title: UBTF-TD48, RNA-seq, Rep1

description: Library name: SJNORM094189_C1_MPC_UBTF_TD48_JK27_D43


title: dcr1_upf1_2

description: Library name: sample6

value: MATalpha ura3-1 ho dcr1 upf1::kanMX6

value: Untreated


title: Normal_1_6_8_2

description: Sample 581


title: UBTF-WT, RNA-seq, Rep5

description: Library name: SJNORM094197_C1_MPC_UBTF_WT_JK47_D43

source_name: cord-blood CD34+ Cells expressing nHA-UBTF-WT

value: cord-blood CD34+ Cells

value: expressing nHA-UBTF-WT


title: UBTF-WT, RNA-seq, Rep4

description: Library name: SJNORM094191_C1_MPC_UBTF_WT_JK30_D43


title: dcr1_upf1_1

description: Library name: sample5


title: Normal_1_6_8_3

description: Sample 582

value: male


title: upf1_2

description: Library name: sample4


title: UBTF-WT, RNA-seq, Rep2

description: Library name: SJNORM082856_C4_UBTF_WT_2


title: Normal_1_6_7_8

description: Sample 580

value: Normal


title: UBTF-WT, RNA-seq, Rep3

description: Library name: SJNORM093882_C1_UBTF_WT_JK37_D50


title: UBTF-WT, RNA-seq, Rep1

description: Library name: SJNORM085158_C2_UBTF_WT_1


title: dcr1_2_CHX

description: Library name: sample10


title: MPC-EV, RNA-seq, Rep3

description: Library name: SJNORM093881_C1_MPC_EV_JK37_D50

source_name: cord-blood CD34+ Cells expressing MPC Empty Vector

value: expressing MPC Empty Vector


title: Normal_1_6_7_7

description: Sample 579

value: testis


title: Normal_1_6_7_6

description: Sample 578


title: MPC-EV, RNA-seq, Rep2

description: Library name: SJNORM085158_C1_MPC_EV_3


title: MPC-EV, RNA-seq, Rep1

description: Library name: SJNORM083481_C3_MPC_EV_1


title: upf1_1

description: Library name: sample3

value: MATalpha ura3-1 ho upf1::kanMX6


title: WT_1

description: Library name: sample1

value: MATalpha ura3-1 ho


title: CLI, replicate 9, RNA-seq

city: Lexington

first: Ahmed

last: Ismaeel

state: Kentucky

address: 900 S Limestone St

department: Physiology

institute: University of Kentucky

description:
Library name: PK39
Zymo-Seq RiboFree Total RNA Library Kit

data_processing:
Read sequences in fastq format were aligned to the human genome (hg38).
Assembly: hg38
Supplementary files format and content: Text document read counts.

source_name: skeletal muscle

extract_protocol:
Total RNA was isolated using the Direct-zol RNA Microprep Kit (Zymo Research, Cat#: R2060) following the manufacturer’s instructions.
Zymo-Seq RiboFree Total RNA Library Kit (Zymo Research, Cat#: R3000) was used for library preparation

value: skeletal muscle


title: dcr1_upf1_2

description: Library name: sample14

value: untreated


title: CLI, replicate 10, RNA-seq

description:
Library name: PK40
Zymo-Seq RiboFree Total RNA Library Kit


title: Normal_1_6_7_2

description: Sample 575

source_name: testis


title: Normal_1_6_7_4

description: Sample 576


title: CLI, replicate 5, RNA-seq

description:
Library name: PK35
Zymo-Seq RiboFree Total RNA Library Kit


title: dcr1_upf1_1

description: Library name: sample13


title: Normal_1_6_6_7

description: Sample 574


title: CLI, replicate 6, RNA-seq

description:
Library name: PK36
Zymo-Seq RiboFree Total RNA Library Kit


title: CLI, replicate 4, RNA-seq

description:
Library name: PK34
Zymo-Seq RiboFree Total RNA Library Kit


title: PRRSV

city: Nanjing

first: Yaotang

last: Wu

address: Nanjing Agricultural University, Wei gang 1

institute: Nanjing Agricultural University

description:
Library name: PRRSV
column name in all_mirna.exp_profile.xls

data_processing:
Subsequently, unique sequences with length in 18~25 nucleotide were mapped to specific species precursors in miRBase 22.0 by BLAST search to identify known miRNAs and novel 3p- and 5p- derived miRNAs. Length variation at both 3' and 5' ends and one mismatch inside of the sequence were allowed in the alignment.
The unique sequences mapping to specific species mature miRNAs in hairpin arms were identified as known miRNAs. The unique sequences mapping to the other arm of known specific species precursor hairpin opposite to the annotated mature miRNA-containing arm were considered to be novel 5p- or 3p-derived miRNA candidates. The remaining sequences were mapped to other selected species precursors (with the exclusion of specific species) in miRBase 22.0 by BLAST search, and the mapped pre-miRNAs were further BLASTed against the specific species genomes to determine their genomic locations.
The above two we defined as known miRNAs. The unmapped sequences were BLASTed against the genomes, and the hairpin RNA structures containing sequences were predicated from the flank 120 nt sequences using RNAfold software (http://rna.tbi.univie.ac. at/cgi-bin/RNAfold.cgi). The criteria for secondary structure prediction were: (1) number of nucleotides in one bulge in stem (≤12) (2) number of base pairs in the stem region of the predicted hairpin (≥16) (3) cutoff of free energy (kCal/mol ≤-15) (4) length of hairpin (up and down stems + terminal loop ≥50) (5) length of hairpin loop (≤200). (6) number of nucleotides in one bulge in mature region (≤4) (7) number of biased errors in one bulge in mature region (≤2) (8) number of biased bulges in mature region (≤2) (9) number of errors in mature region (≤4) (10) number of base pairs in the mature region of the predicted hairpin (≥12) (11) percent of mature in stem (≥80).
Assembly: GCA_037993035.2
Supplementary files format and content: excel,expression profiles

organism: Chlorocebus aethiops

growth_protocol: Marc-145 cells were maintained in RPMI 1640  supplemented with 10% FBS, penicillin (100 U/ml), and streptomycin (100 mg/mL) at 37℃ in a humidified atmosphere with 5% CO2.

extract_protocol:
Total 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.
Approximately 5 µg of total RNA were used to prepare nine small RNA librariesaccording to the protocol of TruSeq Small RNA Sample Prep Kits (Illumina, San Diego, CA, USA). And then the libraries were sequenced by Illumina Hiseq 2500 at the LC-BIO following the vendor’s recommended protocol. Raw reads were subjected to an in-house program, ACGT101-miR (v4.2) to remove adapter dimers, junk, low complexity, common RNA families (rRNA, tRNA, snRNA, snoRNA) and repeats.

value: Renal cell

value: WT

value: PRRSV


title: upf1_2_CHX

description: Library name: sample12

value: CHX


title: Normal_2_2_12_7

description: Sample 640


title: Normal_1_6_6_6

description: Sample 573


title: upf1_1_CHX

description: Library name: sample11


title: HPPRRSV

description:
Library name: HPPRRSV
column name in all_mirna.exp_profile.xls

value: HPPRRSV


title: Normal_1_6_6_4

description: Sample 572


title: WT_2

description: Library name: sample2


title: WT_2_CHX

description: Library name: sample10


title: CLI, replicate 2, RNA-seq

description:
Library name: PK32
Zymo-Seq RiboFree Total RNA Library Kit


title: Blank

description:
Library name: Blank
column name in all_mirna.exp_profile.xls

value: Blank


title: CLI, replicate 1, RNA-seq

description:
Library name: PK31
Zymo-Seq RiboFree Total RNA Library Kit


title: Normal_1_6_7_5

description: Sample 577


title: chow_shFos3

city: Brussels

first: Ao

state: Brussels

address: 808 Route de Lennik

department: Faculty of Medicine

country: Belgium

institute: Université libre de Bruxelles (ULB)

description: Library name: chow_shFos3

data_processing:
FastQC, fastp, Trimmomatic, HISAT2, SAMtools, and featureCounts.
Assembly: Mus_musculus.GRCm38.98.gtf.gz
Supplementary files format and content: Gene count data of 3 Adv-Control and 3 Adv-shRNA-Fos.

organism: Mus musculus

source_name: Liver

extract_protocol:
The total RNA from mouse liver tissues was extracted with the RNeasy Mini Kit (50) (QIAGEN, #74104) and the RNase-Free DNase Set (50) (QIAGEN, #79254).
mRNA library preparation (poly A enrichment)

value: Liver

value: Adv-shRNA-Fos


title: CLI, replicate 8, RNA-seq

description:
Library name: PK38
Zymo-Seq RiboFree Total RNA Library Kit


title: CLI, replicate 7, RNA-seq

description:
Library name: PK37
Zymo-Seq RiboFree Total RNA Library Kit


title: IC-post, replicate 10, RNA-seq

description:
Library name: PK30
Zymo-Seq RiboFree Total RNA Library Kit

value: revascularization


title: Normal_1_6_6_2

description: Sample 570

value: male


title: WT_1_CHX

description: Library name: sample9


title: chow_shFos2

description: Library name: chow_shFos2


title: Normal_1_6_6_1

description: Sample 569

value: Normal


title: IC, replicate 10, RNA-seq

description:
Library name: PK29
Zymo-Seq RiboFree Total RNA Library Kit


title: upf1_3

description: Library name: sample7


title: Normal_1_6_5_8

description: Sample 568


title: IC-post, replicate 9, RNA-seq

description:
Library name: PK28
Zymo-Seq RiboFree Total RNA Library Kit


title: chow_shFos1

description: Library name: chow_shFos1


title: chow_con3

description: Library name: chow_con3

value: Adv-Control


title: upf1_2

description: Library name: sample6


title: Normal_1_6_5_7

description: Sample 567

value: testis


title: CLI, replicate 3, RNA-seq

description:
Library name: PK33
Zymo-Seq RiboFree Total RNA Library Kit


title: upf1_1

description: Library name: sample5

value: MATalpha ura3-1 ho upf1::kanMX6


title: chow_con2

description: Library name: chow_con2


title: IC, replicate 9, RNA-seq

description:
Library name: PK27
Zymo-Seq RiboFree Total RNA Library Kit


title: Normal_1_6_5_6

description: Sample 566


title: IC-post, replicate 8, RNA-seq

description:
Library name: PK26
Zymo-Seq RiboFree Total RNA Library Kit


title: IC, replicate 8, RNA-seq

description:
Library name: PK25
Zymo-Seq RiboFree Total RNA Library Kit


title: WT_4

description: Library name: sample4

value: MATalpha ura3-1 ho


title: Normal_1_6_5_5

description: Sample 565


title: chow_con1

description: Library name: chow_con1


title: Normal_1_6_5_1

description: Sample 564


title: WT_3

description: Library name: sample3


title: mESC cells, AC106872.1-KI-D11 rep1

description: Library name: sample9

data_processing:
Clean reads were mapped to mouse genome version mm10 by STAR (v2.4.0j) with default settings. Aligned reads were then quantified using featureCounts (v1.6.3) with parameter ‘-s 0’. Normalization and differential expression analysis were performed using DESeq2 (v1.26.0).
Assembly: mm10
Supplementary files format and content: text file include raw counts of each sample

source_name: mouse embryonic stem cells

extract_protocol:
mESC was digested into single-cell using 0.05% trypsin-EDTA and centrifuged at 1000 r.p.m. for 5 min. 1 mL Trizol was added to mix the cell pellets, and 200 μL chloroform was added for shaking violently. After centrifuging at 12000 r.p.m., 4℃ for 15 min, the upper water phase was absorbed, and added with equal volume isopropyl alcohol. RNA was precipitated by centrifugation at 12000 r.p.m., 4℃ for 15 min and cleaned with 75% ethanol then dissolved in RNase-free water. RNA concentration was measured using nanodrop.
RNA-seq

value: mouse embryonic stem cells

value: AC106872.1 knock in


title: WT_2

description: Library name: sample2

value: untreated


title: mESC cells, AC106872.1-KI-D11 rep2

description: Library name: sample10


title: IC, replicate 7, RNA-seq

description:
Library name: PK23
Zymo-Seq RiboFree Total RNA Library Kit

value: skeletal muscle


title: Normal_1_6_4_8

description: Sample 563


title: mESC cells, AC106872.1-KI-B9 rep2

description: Library name: sample8

value: AC106872.2 knock in


title: IC-post, replicate 6, RNA-seq

description:
Library name: PK22
Zymo-Seq RiboFree Total RNA Library Kit


title: IC-post, replicate 7, RNA-seq

description:
Library name: PK24
Zymo-Seq RiboFree Total RNA Library Kit


title: WT_1

description: Library name: sample1


title: Normal_1_6_4_6

description: Sample 561


title: upf1_4

description: Library name: sample8


title: S. aureus TRIC-seq, stationary

description: Library name: R22S14

organism: Staphylococcus aureus


title: Normal_1_6_4_5

description: Sample 560


title: IC, replicate 6, RNA-seq

description:
Library name: PK21
Zymo-Seq RiboFree Total RNA Library Kit


title: M. xanthus TRIC-seq, stationary

description: Library name: R22S7

organism: Myxococcus xanthus


title: mESC cells, AC106872.1-KI-B9 rep1

description: Library name: sample7


title: mESC cells, KRT18P67-KI-B5 rep2

description: Library name: sample6

value: KRT18P67 knock in


title: IC-post, replicate 5, RNA-seq

description:
Library name: PK20
Zymo-Seq RiboFree Total RNA Library Kit


title: ngs1/pYL27-4NAG 3

city: Wuhan

first: Xiang-Dong

last: Gao

state: Hubei

address: Luojiashan, Wuchang district

institute: Wuhan University

description:
Library name: Sample 12
raw counts

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using Tophat  v2.1.1 with default  parameters.
The gene expression level was calculated by Cufflinks (v 2.2.1).
Trimmed sequences were mapped
Assembly: NCBI Reference genome (Yarrowia lipolytica CLIB122)
Supplementary files format and content: xlsx format
Supplementary files format and content: raw counts

organism: Yarrowia lipolytica

source_name: yeast strain

growth_protocol: Cells were grown in YNB-GlcNAc to about 0.8 of OD600

extract_protocol:
Total RNA was extracted using Yeast RNA Kit (Omega, China)
RNA libraries were prepared for sequencing using standard Illumina protocols. A total amount of 1 µg RNA per sample was used as input material for RNA sample preparations. Sequencing libraries were generated using TruSeq RNA Library Preparation Kit (Illumina, USA) following manufacturer’s recommendations.

treatment_protocol: No treatment

value: yeast strain

value: ngs1 mutant

value: No


title: mESC cells, KRT18P67-KI-B5 rep1

description: Library name: sample5


title: Normal_1_6_6_3

description: Sample 571


title: IC, replicate 5, RNA-seq

description:
Library name: PK19
Zymo-Seq RiboFree Total RNA Library Kit


title: mESC cells, KRT18P67-KI-C4 rep2

description: Library name: sample4


title: IC-post, replicate 4, RNA-seq

description:
Library name: PK18
Zymo-Seq RiboFree Total RNA Library Kit


title: Normal_1_6_4_1

description: Sample 558


title: ngs1/pYL27-4NAG 1

description:
Library name: Sample 10
raw counts


title: Normal_1_6_4_7

description: Sample 562


title: mESC cells, KRT18P67-KI-C4 rep1

description: Library name: sample3


title: IC, replicate 4, RNA-seq

description:
Library name: PK17
Zymo-Seq RiboFree Total RNA Library Kit


title: Normal_1_6_3_8

description: Sample 557


title: rep1/pYL27-4NAG 3

description:
Library name: Sample 9
raw counts

value: rep1 mutant


title: Normal_1_6_3_7

description: Sample 556


title: Normal_1_6_3_6

description: Sample 555


title: mESC cells, WT rep2

description: Library name: sample2

value: WT


title: IC, replicate 3, RNA-seq

description:
Library name: PK15
Zymo-Seq RiboFree Total RNA Library Kit


title: Viso_3

city: Hangzhou

first: Putao

last: Yuan

address: No. 3, Qingchun Road East

department: Department of Orthopaedic Surgery

institute: Sir Run Run Shaw Hospital, Zhejiang University School of Medicine

description: Library name: Sample6

data_processing:
The raw paired end reads were trimmed and quality controlled by fastp with default parameters
Then clean reads were separately aligned to reference genome with orientation mode using HISAT2 software
The mapped reads of each sample were assembled by StringTie in a reference-based approach.
To identify DEGs ( differential expression genes) between two different samples, the expression level of each transcript was calculated according to the transcripts per million reads (TPM) method
Assembly: genome assembly
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

source_name: Bone marrow

extract_protocol:
Total RNA from each sample was extracted using TRIzol® Reagent according to the manufacturer’s instructions (Invitrogen, Carlsbard, CA, USA) and genomic DNA was removed using DNase I (TaKara, Shiga, Japan)
The RNA-seq transcriptome librariy was prepared following Illumina® Stranded mRNA Prep Ligation from Illumina (San Diego, CA) using 1μg of total RNA.

value: Bone marrow

value: BMMs

value: Bone marrow-derived macrophages

value: Visomitin


title: mESC cells, WT rep1

description: Library name: sample1


title: rep1/pYL27-4NAG 1

description:
Library name: Sample 7
raw counts


title: IC-post, replicate 3, RNA-seq

description:
Library name: PK16
Zymo-Seq RiboFree Total RNA Library Kit

value: revascularization


title: rep1/pYL27-4NAG 2

description:
Library name: Sample 8
raw counts


title: IC-post, replicate 2, RNA-seq

description:
Library name: PK14
Zymo-Seq RiboFree Total RNA Library Kit


title: WT/pYL27-4NAG 3

description:
Library name: Sample 6
raw counts

value: Wild type


title: Viso_2

description: Library name: Sample5


title: ngs1/pYL27-4NAG 2

description:
Library name: Sample 11
raw counts


title: Normal_1_6_4_2

description: Sample 559

value: male

value: Normal

value: testis


title: Normal_1_6_3_5

description: Sample 554


title: IC, replicate 2, RNA-seq

description:
Library name: PK13
Zymo-Seq RiboFree Total RNA Library Kit

value: skeletal muscle


title: Viso_1

description: Library name: Sample4


title: Normal_1_6_3_2

description: Sample 552


title: WT/pYL27-4NAG 1

description:
Library name: Sample 4
raw counts


title: Normal_1_6_3_1

description: Sample 551


title: Con_3

description: Library name: Sample3

value: Control


title: Normal_1_6_3_3

description: Sample 553


title: IC, replicate 1, RNA-seq

description:
Library name: PK11
Zymo-Seq RiboFree Total RNA Library Kit


title: IC-post, replicate 1, RNA-seq

description:
Library name: PK12
Zymo-Seq RiboFree Total RNA Library Kit


title: WT/pYL27 3

description:
Library name: Sample 3
raw counts


title: Con_2

description: Library name: Sample2


title: Normal_1_6_2_7

description: Sample 550


title: WT/pYL27 2

description:
Library name: Sample 2
raw counts


title: Con_1

description: Library name: Sample1


title: WT/pYL27 1

description:
Library name: Sample 1
raw counts


title: Control, replicate 9, RNA-seq

description:
Library name: PK9
Zymo-Seq RiboFree Total RNA Library Kit


title: Normal_1_6_2_6

description: Sample 549


title: Normal_1_6_2_5

description: Sample 548