title: RNAseq_Kdm6bWT_p30_rep3

description:
Library name: Sample 15
DGE_emx1_kdm6b_p30.txt


title: B_W_M_4_3

status: Public on May 04 2026

type: SRA

city: Freising

first: Ralph

last: Hückelhoven

address: Emil-Ramann-Str. 2

department: Chair of Phytopathology

country: Germany

institute: Technische Universität München

description: Library name: 56_S24_R1_001

library_source: transcriptomic

data_processing:
nf‐core/rnaseq (v3.17.0) using Nextflow  (v24.04.4) for processing the raw reads
3’UTR regions of the last exon extended either by 3 kb or until the following gene
FastQC (v0.12.1) for raw read quality control
Trim Galore (v0.6.10) with Cutadapt (v4.9) for adapter trimming and filtering
STAR (v2.7.11b) was used for read alignment
Salmon (v1.10.3) for transcript quantification
Assembly: The Morex V3 genome (Mascher et al., 2021) was merged with the F. culmorum genome FusCulm_01 (GenBank assembly GCA_003033665.1) to improve mapping accuracy and count Fusarium RNA read counts.
Supplementary files format and content: The HordeumVulgareV3.salmon.gene-counts.csv is a comma-separated table containing the mapped salmon gene-counts for Hordeum vulgare after running the nf-core/rnaseq pipeline.
Supplementary files format and content: The sampleInformation.csv is a comma-separated table explaining the the abbreviations used for the sample names.

molecule: polyA RNA

organism: Hordeum vulgare

source_name: spike tissue

growth_protocol: The plants were grown under controlled conditions in a greenhouse cabin on flooding tables at the Plant Technology Center of the Technical University of Munich. 3-litre pots with a peat substrate (Einheitserde C700, Stender, Germany) were used to grow five seeds each at a temperature of 18/16 °C day/night, with additional lighting for 16 hours per day and a relative air humidity of 60%.

extract_protocol:
Spike material was ground in liquid nitrogen, and extraction of total RNA was performed with 100 mg of each sample using the GeneMATRIX Universal RNA Purification Kit (EURx Molecular Biology Products), following the manufacturer’s instructions.
Libraries for 3’-RNA-sequencing (Moll et al., 2014) were prepared using the QuantSeq 3’mRNA-Seq Library Prep Kit (Lexogen, Austria) according to the manufacturer’s instructions. Library sizes were quantified with a Qubit Fluorometer 2.0 and a Qubit DNA High Sensitivity Assay Kit. Ready-to-load pools of cDNA libraries were determined with qPCR. An Agilent 2010 Electrophoresis Bioanalyzer with the High Sensitivity DNA Assay was used to check the integrity and mRNA fragment size distribution of each library.

treatment_protocol: For artificial infection, three isolates of F. culmorum, Fc002, Fc03, and Fc06 from the fungal culture collection of the Chair of Phytopathology, Technical University of Munich (Hofer et al., 2016; Hoheneder et al., 2022; Linkmeyer et al., 2013) were used. The fungi were grown on potato dextrose agar at 21°C, 60% relative humidity, and a 12 h cycle of UV plus white light and darkness. Fungal inoculum in the form of a spore solution was prepared in autoclaved tap water containing 1 ml/l Tween 80® and was adjusted to a spore concentration of 50,000 conidia/ml containing equal amounts of spores from each strain. Mock treatment consisted of autoclaved tap water and 1 ml/l Tween 80. Barley spikes were sprayed with either F. culmorum spore solution or mock solution until run-off around mid-flowering (GS 65) and afterwards covered and sealed in plastic bags for 2 days to ensure 99% relative air humidity. Treated spikes were sampled 4 and 7 days post inoculation and immediately frozen in liquid nitrogen. For each cultivar, treatment, and time point, four replicates were collected, each consisting of four pooled spikes.

tag: tissue

value: spike tissue

tag: genotype

value: Barke

tag: treatment

value: watered+mock


title: B_W_M_4_4

description: Library name: 68_S30_R1_001


title: RNAseq_Kdm6bWT_p30_rep4

city: East Lansing

first: Jin

last: He

state: Michigan

address: 603 Wilson Road, Biochem Bldg. Rm. 410

country: USA

institute: Michigan State Univeristy

description:
Library name: Sample 16
DGE_emx1_kdm6b_p30.txt

data_processing:
Reads were aligned to the mouse reference genome (UCSC mm9) using HISAT2
The mapped reads were normalized to reads as Reads Per Kilobase of transcript per Million mapped reads (RPKM).
The differential gene expression was calculated by Cuffdiff program and the statistic cutoff for identification of differential gene expression is q < 0.05 and 2-fold RPKM change between samples.
Assembly: mm9
Supplementary files format and content: DGE_emx1_kdm6b_p1.txt
Supplementary files format and content: DGE_emx1_kdm6b_p30.txt

molecule: total RNA

organism: Mus musculus

source_name: mouse cortex

extract_protocol:
RNA was extracted and purified from cells using QI shredder (Qiagen) and RNeasy (Qiagen) spin columns.
Total RNA was extracted using per the manufacturer’s instructions. RNA-seq libraries were  repared from total RNA using the VAHTS Universal V10 RNA-seq Library Prep Kit for Illumina (Vazyme). Adapter-ligated cDNA was PCR-amplified and size-selected magnetic beads. DNA was measured by an Invitrogen Qubit fluorometer. Libraries were sequenced on AVITI or NovaSeq 6000 sequencer at the Michigan State University Genomics Core.

value: mouse cortex

value: wild-type


title: sample22, HIV negative, invasive cervical carcinoma

city: Accra

first: Charles

middle: Ochieng'

last: Olwal

address: WACCBIP, Volta Road, University Of Ghana

department: Department of Biochemistry, Cell and Molecular Biology

country: Ghana

institute: West African Centre for Cell Biology of Infectious Pathogens

description:
Library name: Sample 22
Column name in raw_counts.txt: CK-21-01

data_processing:
Raw fastq files were subjected to quality control using the FastQC and trimmed using Cutadapt to filter out poor-quality reads and adapters. After trimming, we mapped the reads to the human reference genome (hg38) using STAR package. We counted the reads per transcript using featureCount of the Subread package to generate a count matrix data.
Assembly: Reads were mapped to human reference genome (hg38) curated by the University of California, Santa Cruz
Supplementary files format and content: The processed data included a count matrix data in text format

organism: Homo sapiens

source_name: Cervical

extract_protocol:
RNA was extracted using an automated nucleic acid extraction system (TANBead maelstrom 9600) and TANBead® Nucleic Acid Extraction Kit (Ref #W665S66) following manufacturers instructions.
RNA libraries for RNA-seq were prepared using NEBNext® Ultra™ II RNA Library Prep Kit for Illumina® together with the NEBNext rRNA Depletion Kit version 2 following manufacturers protocols.

value: Cervical

tag: cell type

value: Epithelial cells


title: ENY2_6h_aux_1

city: Bethesda

first: Caroline

last: Esnault

state: md

address: 9000 Rockville Pike,

institute: NICHD NIH

description:
Library name: ENY2_6h_aux_1
Ribo-Zero-depleted

library_source: other

data_processing:
Raw fastq files were processed through lcdb-wf v1.10.3rc (https://github.com/lcdb/lcdb-wf) for QC filtering, adapter trimming, mapping and quantification in genes. Briefly, fastq files were trimmed from adapters with cutadapt v4.4; trimmed reads were mapped to hg38 with hisat2 v2.2.1 with parameter --no-unal then sorted with samtools sort v1.16.1; duplicate reads were marked with picard MarkDuplicates v2.27.5; reads in genes were quantified with subread featurecounts v2.0.3.
Assembly: hg38
Supplementary files format and content: featurecounts_set*.txt files contain raw counts in genes.

molecule: other

growth_protocol: The human colorectal cancer cell line DLD-1 was cultured in DMEM (Life Technologies) supplemented with heat-inactivated 10% FBS (Atlanta Biologicals), antibiotics (100 IU/ml penicillin and 100 μg/ml streptomycin), and 2 mM GlutaMAX (Life Technologies) in 5% CO2 atmosphere at 37°C.

extract_protocol:
RNA was extracted with Qiagen RNAeasy Plus Mini Kit. Extracted RNA was analyzed for 260/280 and RIN value was assessed on Bioanalyzer 2100 (Agilent), samples with RIN value more than 9 were proceeded for the library construction using Illumina TruSeq Stranded Total RNA Library Preparation Kit (Illumina) according to manufacturer’s instructions.
1-4 ug of total RNA samples  were depleted for ribosomal RNA (Set 2021) before library construction using Ribo-Zero™ Gold Kit H/M/R Kit (Illumina) or purified with PolyA extraction (Set 2024), and then purified mRNAs were constructed to RNA-Seq libraries with specific barcodes using illumina TruSeq Stranded mRNA Library Prep Kit. All the RNA-Seq libraries were pooled together and sequenced using illumina NovaSeq 6000 to generate approximately ~40 million 2x100 paired-end reads for each sample.

treatment_protocol: AID-GANP, AID-ENY2, AID-PCID2, AID-CETN2, AID-CETN2_3 cells were untreated or treated with 1 mM IAA, Sigma, I5148-10G. AID-SAC3D1 and AID-LENG8 cells were treated with DMSO (1:1000) or 1 uM 5-Ph-IAA, BioAcademia.

tag: cell line

tag: condition

tag: strain

tag: batch


title: sample21, HIV positive, invasive cervical carcinoma

description:
Library name: Sample 21
Column name in raw_counts.txt: CC-21-081


title: RNAseq_Kdm6bWT_p30_rep2

description:
Library name: Sample 14
DGE_emx1_kdm6b_p30.txt


title: sample20, HIV positive, precancerous cervical lesion

description:
Library name: Sample 20
Column name in raw_counts.txt: CC-21-080


title: RNAseq_Kdm6bWT_p30_rep1

description:
Library name: Sample 13
DGE_emx1_kdm6b_p30.txt


title: B_W_M_4_1

description: Library name: 37_S17_R1_001


title: PCID2_untreated_3

description:
Library name: PCID2_untreated_3
Ribo-Zero-depleted

value: untreated


title: CETN2_2h_aux_2

description:
Library name: CETN2_2h_aux_2
Ribo-Zero-depleted


title: ENY2_untreated_2

description:
Library name: ENY2_untreated_2
Ribo-Zero-depleted


title: sample18, HIV positive, precancerous cervical lesion

description:
Library name: Sample 18
Column name in raw_counts.txt: CC-21-077


title: B_W_Fc_7_3

description: Library name: 101_S57_R1_001

value: watered+inoculated


title: B_W_Fc_7_2

description: Library name: 99_S55_R1_001


title: sample16, HIV positive, precancerous cervical lesion

description:
Library name: Sample 16
Column name in raw_counts.txt: CC-21-075


title: CETN2_2h_aux_1

description:
Library name: CETN2_2h_aux_1
Ribo-Zero-depleted


title: B_W_M_4_2

description: Library name: 50_S21_R1_001


title: CLP, Bexarotene, replicate 3

city: Gent

first: Steven

last: Timmermans

address: Technologiepark 71

country: Belgium

institute: VIB-UGent

description:
Library name: Sample 12
CLP_BEX-3

data_processing:
Reads were quality checked with fastQC and preprocessed (adapter removal) with TRIMMOMATIC v0.34 (ILLUMINACLIP & MINLEN filters)
Reads were mapped to the mm39 reference genome with STAR (2.7.10b) and the gencode M30 and read counts were directly obtained using the "--quantMode GeneCounts" parameter for STAR
Differnatial gene expression was determined using DESeq2
Assembly: mm39
Supplementary files format and content: tab delimited count matrix with the raw counts per sample

source_name: liver

growth_protocol: Male C57BL/6J mice were purchased from Janvier. All mice were housed in individually ventilated cages at standard housing conditions (22 °C, 14/10 h light/dark cycle) with food (chow diet consisting of 18% proteins, 4.5% fibers, 4.5% fat, 6.3% ashes, Provimi Kliba SA) and water ad libitum in a specific pathogen free facility.

extract_protocol:
Total RNA was isolated with Aurum Total RNA mini Kit (Bio-Rad) following the manufacturer’s instructions
Library preparation was done using the illumina truseq stranded library kit for sequencing with a NovaSeq 6000 instrument  according the the manufacturer's instructions

treatment_protocol: Mice were subjected to Sham or CLP and 6h after the surgery were injected with DMSO (vehicle) or bexarotene (10 mg/kg), sampeling was performed 2 hours after DMSO or Bexarotene injection

value: liver

value: WT

value: CLP + BEX(10 mg/kg)

tag: treatment time


title: CLP, Bexarotene, replicate 2

description:
Library name: Sample 11
CLP_BEX-2


title: CLP, DMSO control, replicate 3

description:
Library name: Sample 9
CLP_DMSO-3

value: CLP + DMSO


title: B_W_Fc_7_1

description: Library name: 93_S49_R1_001


title: B_W_Fc_7_4

description: Library name: 103_S59_R1_001


title: ENY2_untreated_1

description:
Library name: ENY2_untreated_1
Ribo-Zero-depleted


title: CLP, Bexarotene, replicate 1

description:
Library name: Sample 10
CLP_BEX-1


title: CETN2_2h_aux_3

description:
Library name: CETN2_2h_aux_3
Ribo-Zero-depleted


title: B_W_Fc_4_4

description: Library name: 61_S28_R1_001


title: B_W_Fc_4_3

description: Library name: 58_S25_R1_001


title: CETN2_untreated_1

description:
Library name: CETN2_untreated_1
Ribo-Zero-depleted


title: CLP, DMSO control, replicate 1

description:
Library name: Sample 7
CLP_DMSO-1


title: Sham, Bexarotene, replicate 2

description:
Library name: Sample 5
sham_BEX-2

value: SHAM + BEX(10 mg/kg)


title: CITEseq:ieILC1 HTO

city: STANFORD

first: Imran

middle: Ahammad

last: Mohammad

state: CA

address: lokey stem cell research building, 2165, 265 Campus Drive, Palo Alto, CA 94305

department: OHNS

institute: Stanford University

description:
Library name: ieILC1_HTO
HTO library

data_processing:
Single-cell gene and protein expression matrices were obtained using Cellranger (v6.1.2, 10x Genomics)
Assembly: hg38
Supplementary files format and content: tsv files and matrix files
Library strategy: CITE-seq

molecule: protein

source_name: Cultured cells

extract_protocol:
Live cells were sorted, pooled in equal numbers from each condition, and loaded onto the 10X Genomics chip.
Single-cell processing and library preparation were done using the 10X Genomics Chromium Next GEM Single Cell 3’ Gene Expression and Feature Barcode Kit. Libraries were sequenced with 2x150 bp reads on the NovaSeq (Illumina).

value: Cultured cells

value: NK cells


title: ENY2_untreated_3

description:
Library name: ENY2_untreated_3
Ribo-Zero-depleted


title: CITEseq:ieILC1 ADT

description:
Library name: ieILC1_ADT
ADT library


title: sample19, HIV positive, precancerous cervical lesion

description:
Library name: Sample 19
Column name in raw_counts.txt: CC-21-079


title: CLP, DMSO control, replicate 2

description:
Library name: Sample 8
CLP_DMSO-2


title: Sham, DMSO control, replicate 3

description:
Library name: Sample 3
sham_DMSO-3

value: SHAM + DMSO


title: sample12, HIV positive, normal cervix

description:
Library name: Sample 12
Column name in raw_counts.txt: CC-21-071


title: CETN2_untreated_2

description:
Library name: CETN2_untreated_2
Ribo-Zero-depleted


title: B_W_Fc_4_2

description: Library name: 40_S19_R1_001

value: spike tissue


title: B_W_Fc_4_1

description: Library name: 39_S18_R1_001

value: Barke


title: B_D_M_7_3

description: Library name: 96_S52_R1_001

value: drought+mock


title: CETN2_untreated_3

description:
Library name: CETN2_untreated_3
Ribo-Zero-depleted


title: Sham, Bexarotene, replicate 3

description:
Library name: Sample 6
sham_BEX-3


title: Sham, Bexarotene, replicate 1

description:
Library name: Sample 4
sham_BEX-1


title: sample14, HIV positive, invasive cervical carcinoma

description:
Library name: Sample 14
Column name in raw_counts.txt: CC-21-073


title: B_D_M_7_4

description: Library name: 98_S54_R1_001


title: Sham, DMSO control, replicate 1

description:
Library name: Sample 1
sham_DMSO-1


title: CITEseq:ieILC1 GEX

description:
Library name: ieILC1_GEX
GEX library


title: TGFb_induced_DP_rep2

description: Library name: TGFb_induced_DP_rep2

library_source: genomic

data_processing:
Data analysis was conducted using the nf-core ATAC-seq pipeline (nf-core/atacseq: '2.0') with default parameters.
Assembly: hg38
Supplementary files format and content: count file

molecule: genomic DNA

extract_protocol:
Sorted NK cells from different populations (50,000 cells) were processed using the Diagenode ATAC-seq kit. Nuclei preparation, tagmentation, and library amplification were done according to the manufacturer’s instructions.
Libraries were sequenced in 50 bp paired-end reads.


title: Sham, DMSO control, replicate 2

description:
Library name: Sample 2
sham_DMSO-2


title: sample11, HIV positive, normal cervix

description:
Library name: Sample 11
Column name in raw_counts.txt: CC-21-070


title: sample9, HIV negative, normal cervix

description:
Library name: Sample 9
Column name in raw_counts.txt: CC-21-065


title: sample13, HIV positive, precancerous cervical lesion

description:
Library name: Sample 13
Column name in raw_counts.txt: CC-21-072


title: B_D_M_7_2

description: Library name: 95_S51_R1_001


title: B_D_M_7_1

description: Library name: 92_S48_R1_001


title: TGFb_induced_DP_rep1

description: Library name: TGFb_induced_DP_rep1


title: sample17, HIV positive, precancerous cervical lesion

description:
Library name: Sample 17
Column name in raw_counts.txt: CC-21-076


title: HNSCC_induced_DP_rep2

description: Library name: HNSCC_induced_DP_rep2


title: sample8, HIV negative, normal cervix

description:
Library name: Sample 8
Column name in raw_counts.txt: CC-21-054


title: sample7, HIV negative, normal cervix

description:
Library name: Sample 7
Column name in raw_counts.txt: CC-21-049


title: B_D_M_4_2

description: Library name: 52_S23_R1_001


title: sample5, HIV negative, normal cervix

description:
Library name: Sample 5
Column name in raw_counts.txt: CC-21-041


title: sample10, HIV positive, normal cervix

description:
Library name: Sample 10
Column name in raw_counts.txt: CC-21-069


title: sample15, HIV positive, precancerous cervical lesion

description:
Library name: Sample 15
Column name in raw_counts.txt: CC-21-074


title: HNSCC_induced_DN_rep2

description: Library name: HNSCC_induced_DN_rep2


title: B_D_M_4_4

description: Library name: 66_S29_R1_001


title: sample4, HIV positive, normal cervix

description:
Library name: Sample 4
Column name in raw_counts.txt: CC-21-031


title: HNSCC_induced_DN_rep1

description: Library name: HNSCC_induced_DN_rep1


title: BMDC, C. albicans (Hyphae) treatment, 2

city: Kyoto

first: Masaki

last: Tajima

address: Yoshidakonoe cho

country: Japan

institute: Kyoto University

description: Library name: Hyphae_2

data_processing:
RNA-seq
Raw data (raw reads) of fastq format were firstly processed through fastp software. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Assembly: Mus Musculus(GRCm38/mm10)
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
Supplementary files format and content: tab-delimited text file includes FPKM values for each sample

source_name: Bone marrow derived dendritic cells

growth_protocol: Bone marrow cells from mouse femurs were cultured in the presence of recombinant mouse GM-CSF (20 ng/mL) for 6 days, supplemented with fresh media on day3. On day 6, the cells were treated with indicated treatment.

extract_protocol:
RNA was isolated using ISOGEN with Spin Column kit according to the instruction provided by the manufacturer (Nippongene).
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis.

treatment_protocol: BMDCs were stimulated with Zymosan Depleted (100 microg/mL), heat killed C. albicans (Yeast; 1x10^5/mL), or heat killed C. albicans (Hyphae; 1x10^5/mL).

value: Bone marrow derived dendritic cells

value: C. albicans Hyphae


title: BMDC, C. albicans (Hyphae) treatment, 1

description: Library name: Hyphae_1


title: BMDC, C. albicans (Hyphae) treatment, 3

description: Library name: Hyphae_3


title: B_D_M_4_3

description: Library name: 59_S26_R1_001


title: sample3, HIV negative, normal cervix

description:
Library name: Sample 3
Column name in raw_counts.txt: CC-21-030

value: Cervical


title: BMDC, C. albicans (Yeast) treatment, 1

description: Library name: Yeast_1

value: C. albicans Yeast


title: sample1, HIV positive, normal cervix

description:
Library name: Sample 1
Column name in raw_counts.txt: CC-21-016

value: Epithelial cells


title: CTRL_rep1

description: Library name: CTRL_rep1


title: A549 transduced with Ad5 expressing SARS-CcV-2 nucleocapsid

city: Wuhan

first: Haiyun

last: Yu

state: other

address: 13 Hangkong Road, Baofeng Street

department: Department of Pathogen Biology

country: China

institute: Huazhong University of Science and Technology Tongji Medical College

description: 1 mg total RNA with RNA integrity number > 7.0

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl script.
Trimmed sequence reads were mapped to reference genome Homo sapiens Ensembl v96 using HISAT2 (v2.0.5) package
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Differential expression analysis of two conditions was performed using the edgeR R package (3.18.1). The p values were adjusted using the Benjamini & Hochberg method. Corrected p-value of 0.05 and absolute fold change of 2 were set as the threshold for significantly differential.  expression.
Gene Ontology (GO) Biological Process (BP) terms of these differentially expressed genes were also annotated (corrected p-value less than 0.05) by the clusterProfiler R package, in which gene length bias was corrected.
Assembly: Homo sapiens Ensembl v96
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: A549 cells

growth_protocol: A549 human lung carcinoma cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using TRIzol reagent. 1 ug total RNA with RNA integrity number > 7.0  was used for the construction of sequencing libraries.
Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer's recommendations and index codes were added to attribute sequences to each sample.

value: A549 cells

value: Human lung carcinoma cells

value: Ad5 transduction and expression of SARS-CoV-2 nucleocapsid


title: CTRL_rep2

description: Library name: CTRL_rep2


title: BMDC, C. albicans (Yeast) treatment, 3

description: Library name: Yeast_3

value: WT


title: sample6, HIV negative, normal cervix

description:
Library name: Sample 6
Column name in raw_counts.txt: CC-21-045


title: HNSCC_induced_DP_rep1

description: Library name: HNSCC_induced_DP_rep1


title: BMDC, C. albicans (Yeast) treatment, 2

description: Library name: Yeast_2


title: B_D_Fc_7_4

description: Library name: 104_S60_R1_001

value: drought+inoculated


title: 4-cell embryo, Slbp knockdown (siRNA), n=4

city: Worcester

first: Oliver

last: Rando

state: MA

address: 364 Plantation St.

department: BMB

institute: UMass Chan Medical School

description: Library name: Slbp-i-48hpf

data_processing:
StringTie 2.2.1 for TPM and SAILOR for edits.
Assembly: mm10
Supplementary files format and content: TPM (txt files) and SAILOR edits (bed files).

source_name: 4-cell embryo

extract_protocol:
Smart-seq3 polyA mRNA with TCL buffer and RNA XP beads.
Smart-seq3 and Nextera XT library prep kit.

value: 4-cell embryo

value: FVB/NJ

value: Slbp siRNA and histone-GFP mRNA microinjection at zygote stage

value: 4-cell stage


title: B_D_Fc_7_3

description: Library name: 102_S58_R1_001

value: spike tissue


title: BMDC, No treatment, 3

description: Library name: None_3


title: B_D_M_4_1

description: Library name: 51_S22_R1_001

value: Barke


title: 4-cell embryo, Ybx1 knockdown (siRNA), n=5

description: Library name: Ybx1-i-48hpf

value: Ybx1 siRNA and histone-GFP mRNA microinjection at zygote stage


title: A549 transduced with Ad5 empty vector

value: Ad5 transduction


title: B_D_Fc_7_2

description: Library name: 100_S56_R1_001


title: 4-cell embryo, Rps2 knockdown (siRNA), n=5

description: Library name: Rps2-i-48hpf

value: Rps2 siRNA and histone-GFP mRNA microinjection at zygote stage


title: BMDC, No treatment, 2

description: Library name: None_2

value: Bone marrow derived dendritic cells


title: 1821_Braak_II

city: Watertown

first: Mahlon

last: Collins

address: 490 Arsenal Way Suite 110

institute: Parallel Squared Technology Institute

description: Library name: sample_1821

data_processing:
fastp (default options; trim adapters and generate QC report): ‘fastp’
salmon (read mapping and quantification): salmon index -t gentrome.fa.gz -d decoys.txt -p 4 -i salmon_index --gencode
DESeq2 (differential abundance testing)
Assembly: GRCh38 (Homo_sapiens.GRCh38.dna.primary_assembly.fa.gz)
Supplementary files format and content: .sf quantification files from Salmon

source_name: brain

extract_protocol:
total RNA extraction of Brodmann area 9 dorsolateral prefrontal cortex (approx. 50 mg; Monarch Total RNA miniprep kit [NEB #T2010]) according to manufacturer’s instructions
mRNA library preparation (poly A enrichment)

value: brain


title: sample2, HIV positive, normal cervix

description:
Library name: Sample 2
Column name in raw_counts.txt: CC-21-022

value: Cervical

value: Epithelial cells


title: 4-cell embryo, Ybx3 knockdown (siRNA), n=4

description: Library name: Ybx3-i-48hpf

value: Ybx3 siRNA and histone-GFP mRNA microinjection at zygote stage


title: B_D_Fc_7_1

description: Library name: 90_S46_R1_001


title: B_D_Fc_4_2

description: Library name: 48_S20_R1_001


title: 4-cell embryo, Rbfox2 knockdown (siRNA), n=4

description: Library name: Rbfox2-i-48hpf

value: Rbfox2 siRNA and histone-GFP mRNA microinjection at zygote stage


title: B_D_Fc_4_4

description: Library name: 69_S127_R1_001


title: BMDC, ZD treatment, 1

description: Library name: ZD_1

value: WT

value: Zymosan Depleted


title: BMDC, ZD treatment, 3

description: Library name: ZD_3


title: 4-cell embryo, Pcbp1 knockdown (siRNA), n=4

description: Library name: Pcbp1-i-48hpf

value: 4-cell embryo

value: Pcbp1 siRNA and histone-GFP mRNA microinjection at zygote stage


title: 4-cell embryo, Rps3 knockdown (siRNA), n=4

description: Library name: Rps3-i-48hpf

value: FVB/NJ

value: Rps3 siRNA and histone-GFP mRNA microinjection at zygote stage


title: B_D_Fc_4_1

description: Library name: 42_S126_R1_001

value: spike tissue

value: drought+inoculated


title: 4-cell embryo, Mrps22 knockdown (siRNA), n=5

description: Library name: Mrps22-i-48hpf

value: Mrps22 siRNA and histone-GFP mRNA microinjection at zygote stage

value: 4-cell stage


title: BMDC, ZD treatment, 2

description: Library name: ZD_2


title: scRNA-seq of KPC tumor from Porcn WT mice

city: Seoul

first: Yi Rang

address: 101 Daehak-ro, Jongno-gu

country: South Korea

institute: Seoul National University Hospital

description:
Library name: WT
10x Genomics Chromium 3' v3.1, n=5 pooled

library_source: transcriptomic single cell

data_processing:
Sequencing data were processed using Cell Ranger (v3.1.3, 10x Genomics) for alignment to the mm10 reference genome, filtering, and quantification of gene expression. UMAP was used for dimensionality reduction and clustering. Differentially expressed genes (DEGs) were identified with a threshold of |log2FC| > 0.25 and adjusted p-value < 0.05.
Assembly: Mouse mm10
Supplementary files format and content: Processed data are provided as 10x Genomics Cell Ranger output format (barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz).

source_name: Pancreatic tumor

growth_protocol: Mice were bred and maintained under specific pathogen-free (SPF) conditions at the Seoul National University Hospital and College of Medicine animal facility. Animals were housed with free access to food and water and fed a standard lab chow diet.

extract_protocol:
KPC tumors were excised from WT (n=5) and KO (n=5) mice, with samples from each genotype pooled separately. Tumors were minced and enzymatically digested with Collagenase V (1.5 mg/mL) and DNase I (0.1 mg/mL) at 37°C for 30 minutes. The single-cell suspension was filtered, red blood cells were lysed using ACK buffer, and viable single cells were enriched for downstream single-cell RNA-sequencing.
Single-cell RNA libraries were prepared using the Chromium Next GEM Single Cell 3’ RNA library v3.1 (10x Genomics) following the manufacturer’s instructions. Libraries were sequenced on an Illumina NovaSeq 6000 platform.

treatment_protocol: Mice bearing orthotopic KPC pancreatic tumors were euthanized 21 days after tumor implantation for single-cell RNA-sequencing. KPC tumors were harvested from macrophage-specific Porcn knockout mice (Csf1r-Cre;Porcnfl/fl) and littermate control mice

value: Pancreatic tumor

value: Tumor-infiltrating cells

value: Porcnfl/fl (WT)

value: Orthotopic KPC implantation (106 cells)


title: B_D_Fc_4_3

description: Library name: 60_S27_R1_001

value: Barke


title: 4-cell embryo, Igf2bp1 knockdown (siRNA), n=5

description: Library name: Igf2bp1-i-48hpf

value: Igf2bp1 siRNA and histone-GFP mRNA microinjection at zygote stage


title: A_W_M_7_2

description: Library name: 81_S38_R1_001

value: Avalon

value: watered+mock


title: A_W_M_7_4

description: Library name: 86_S42_R1_001


title: BMDC, No treatment, 1

description: Library name: None_1

value: Bone marrow derived dendritic cells

value: WT


title: scRNA-seq of KPC tumor from Porcn KO mice

description:
Library name: KO
10x Genomics Chromium 3' v3.1, n=5 pooled

value: Csf1r-Cre;Porcnfl/fl (KO)


title: A_W_M_7_1

description: Library name: 77_S34_R1_001


title: A_W_M_7_3

description: Library name: 82_S39_R1_001


title: A_W_M_4_4

description: Library name: 32_S15_R1_001


title: 4-cell embryo, Hnrnpa1 knockdown (siRNA), n=5

description: Library name: Hnrnpa1-i-48hpf

value: 4-cell embryo

value: FVB/NJ

value: Hnrnpa1 siRNA and histone-GFP mRNA microinjection at zygote stage


title: 4-cell embryo, Magoh knockdown (siRNA), n=3

description: Library name: Magoh-i-48hpf

value: Magoh siRNA and histone-GFP mRNA microinjection at zygote stage


title: A_W_M_4_3

description: Library name: 27_S12_R1_001

value: spike tissue


title: A_W_M_4_2

description: Library name: 23_S10_R1_001


title: 4-cell embryo, Elavl1 knockdown (siRNA), n=4

description: Library name: Elavl1-i-48hpf

value: Elavl1 siRNA and histone-GFP mRNA microinjection at zygote stage

value: 4-cell stage


title: A_W_M_4_1

description: Library name: 13_S5_R1_001


title: 4-cell embryo, Hnrnpa2b1 knockdown (siRNA), n=5

description: Library name: Hnrnpa2b1-i-48hpf

value: Hnrnpa2b1 siRNA and histone-GFP mRNA microinjection at zygote stage


title: WT_biol rep 1

city: Charleston

first: Vamsi

last: Gangaraju

address: 173 Ashley Ave

institute: Medical University of South Carolina

description: Library name: Sample 1

data_processing:
Sequencing adapaters were trimmed using Cutadapt and reads shorter than 25 nucleotides were discarded. Reads were then mapped to the mm10 genome using BWA and aslignment files were processed to BAM files.
BAM files were used as input for MACS2 to detect peaks.
Assembly: mm10
Supplementary files format and content: Tab-delimited txt files containing peaks from MACS2

source_name: tumor

extract_protocol:
EL4 tumor cells were injected into WT and Sphk2 KO mice. After 14 days, tumor-derived MDSCs (FACS-sorted Gr1+CD11b+ cells from ascitic fluid) were collected from WT and Sphk2 KO mice and used for making ATAC-seq libraries. We used 2 × 10^4 MDSCs and modified the concentration of the Tn5 enzyme for the transposase reaction (PMID: 35454405).
NEBNext Ultra II DNA Library Prep Kit for Illumina from NEB was used to prepare libraries following manufacturer's protocol.

value: tumor

value: Myeloid Derived Supressor Cells


title: WT_biol rep 2

description: Library name: Sample 2


title: Sphk2 KO_biol rep 2

description: Library name: Sample 4

value: Sphk2 KO


title: 4-cell embryo, Ddx39a knockdown (siRNA), n=4

description: Library name: Ddx39a-i-48hpf

value: Ddx39a siRNA and histone-GFP mRNA microinjection at zygote stage


title: Sphk2 KO_biol rep 1

description: Library name: Sample 3


title: A_W_Fc_7_4

description: Library name: 87_S43_R1_001

value: Avalon

value: watered+inoculated


title: Ippocampus, female mouse, 2 months, lead+manganese 4

city: Catania

first: Grete Francesca

last: Privitera

address: Via Santa Sofia

department: Department of Clinical and Experimental Medicine

country: Italy

institute: University of Catania

description: Library name: PMF4

data_processing:
Raw seqeunce were trimmed with TrimGalore (v.0.6.9) for adaptor sequence/low-quality sequence.
Trimmed sequence reads were mapped to GRCm39 employing STAR (v.2.7.10b).
Rew read counts have been extracted using featurecounts (v.2.0.6).
Data Normalization and Gene differential expression calculation have been done on R (v.4.4.2) with packages Limma and EdgeR.
Assembly: GRCm39
Supplementary files format and content: tab-delimited text file including raw counts for each Sample

source_name: Brain (hippocampus)

extract_protocol:
RNA was extracted using the Qiagen All Prep DNA/RNA purification kit. 500 ng total RNA were used for the construction of sequencing libraries.
Next generation sequencing experiments were performed by Genomix4life S.R.L. (Baronissi, Salerno, Italy). RNA concentration in each sample was assayed with a Nanodrop One (Thermo Fisher) and its quality assessed with the TapeStation 4200 (Agilent Technologies). Indexed libraries were prepared from 200 ng/ea purified RNA with Illumina Stranded mRNA Prep according to the manufacturer’s instructions. Libraries were quantified using the TapeStation 4200 (Agilent Technologies) and and Qubit fluorometer (Invitrogen Co.), then pooled such that each index-tagged sample was present in equimolar amounts, with final concentration of the pooled samples of 5nM. The pooled samples were subject to cluster generation and sequencing using an Illumina Novaseq6000 System (Illumina) in a 2x100 paired-end format. The raw sequence files generated (.fastq files) underwent quality control analysis using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc).

treatment_protocol: Pb (100 ppm),  Mn (2g/L), Pb + Mn  in drinking water to dams 2 weeks before mating till weaning (postnatal day 21) for a total of 8 weeks.

value: Brain (hippocampus)

tag: Sex

value: F

tag: age

value: 2 months

value: Pb + Mn


title: Ippocampus, female mouse, 2 months, lead+manganese 5

description: Library name: PMF5


title: 4-cell embryo, Cnot8 knockdown (siRNA), n=3

description: Library name: Cnot8-i-48hpf

value: 4-cell embryo

value: FVB/NJ

value: Cnot8 siRNA and histone-GFP mRNA microinjection at zygote stage


title: 4-cell embryo, Carm1 knockdown (siRNA), n=4

description: Library name: Carm1-i-48hpf

value: Carm1 siRNA and histone-GFP mRNA microinjection at zygote stage


title: Ippocampus, female mouse, 2 months, lead+manganese 3

description: Library name: PMF3


title: A_W_Fc_7_3

description: Library name: 80_S37_R1_001

value: spike tissue


title: Ippocampus, female mouse, 2 months, lead+manganese 2

description: Library name: PMF2


title: Ippocampus, female mouse, 2 months, lead+manganese 6

description: Library name: PMF6


title: A_W_Fc_7_2

description: Library name: 78_S35_R1_001


title: 4-cell embryo, Alyref knockdown (siRNA), n=4

description: Library name: Alyref-i-48hpf

value: Alyref siRNA and histone-GFP mRNA microinjection at zygote stage

value: 4-cell stage


title: A_W_Fc_7_1

description: Library name: 74_S32_R1_001


title: Ippocampus, female mouse, 2 months, lead+manganese 1

description: Library name: PMF1


title: 4-cell embryo, scrRNA02 (control), n=3

description: Library name: scrRNA02-48hpf

value: scrRNA02 (control) siRNA and histone-GFP mRNA microinjection at zygote stage


title: A_W_Fc_4_4

description: Library name: 22_S9_R1_001


title: 4-cell embryo, scrRNA01 (control), n=14

description: Library name: scrRNA01-48hpf

value: scrRNA01 (control) siRNA and histone-GFP mRNA microinjection at zygote stage


title: 2-cell embryo, Ybx3-rABE, n=4

description: Library name: Ybx3-rABE-30hpf

source_name: 2-cell embryo

value: 2-cell embryo

value: Ybx3-rABE mRNA microinjection at zygote stage

value: 2-cell stage


title: Ippocampus, female mouse, 2 months, manganese 5

description: Library name: MF5

value: Mn


title: Ippocampus, female mouse, 2 months, manganese 6

description: Library name: MF6

value: Brain (hippocampus)


title: Ippocampus, female mouse, 2 months, manganese 3

description: Library name: MF3

value: F


title: A_W_Fc_4_1

description: Library name: 15_S6_R1_001

value: Avalon

value: watered+inoculated


title: A_W_Fc_4_2

description: Library name: 20_S7_R1_001


title: A_D_M_7_4

description: Library name: 85_S157_R1_001

value: drought+mock


title: 4-cell embryo, Slbp-rABE, n=3

description: Library name: Slbp-rABE-48hpf

value: 4-cell embryo

value: FVB/NJ

value: Slbp-rABE mRNA microinjection at zygote stage


title: Ippocampus, female mouse, 2 months, manganese 1

description: Library name: MF1

value: 2 months


title: A_W_Fc_4_3

description: Library name: 21_S8_R1_001

value: spike tissue


title: Ippocampus, female mouse, 2 months, manganese 2

description: Library name: MF2


title: 4-cell embryo, Rps3-rABE, n=5

description: Library name: Rps3-rABE-48hpf

value: Rps3-rABE mRNA microinjection at zygote stage

value: 4-cell stage


title: A_D_M_7_3

description: Library name: 83_S40_R1_001


title: Ippocampus, female mouse, 2 months, lead 6

description: Library name: PF6

value: Pb


title: 2-cell embryo, control rABE, n=3

description: Library name: rABE-30hpf

value: 2-cell embryo

value: rABE (control) mRNA microinjection at zygote stage


title: A_D_M_7_2

description: Library name: 79_S36_R1_001


title: 4-cell embryo, Rps2-rABE, n=5

description: Library name: Rps2-rABE-48hpf

value: Rps2-rABE mRNA microinjection at zygote stage


title: Ippocampus, female mouse, 2 months, manganese 4

description: Library name: MF4

value: Mn


title: Peripheral DNA from patient MO48

type: genomic

city: L'Hospitalet

first: Josep

last: Jimenez-Chillaron

state: Barcelona

address: c/ Feixa Llarga s/n, Pavello de Govern, 4a planta, Biophysics Unit

department: Physiological Sciences

country: Spain

institute: University of Barcelona

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridized to human Methylation 750K arrays (Illumina) using standard manufacturer protocols.

scan_protocol: The arrays were scanned using the Illumina iScan system, by using the default Illumina scanner settings.

data_processing: Raw IDAT files were processed using the minfi R package.

label: Cy3 and Cy5

source_name: Peripheral blood

label_protocol: Standard Illumina protocol.

extract_protocol: DNA was extracted from peripheral blood by using the DNeasy Blood & Tissue Kit (QIAGEN), by following the standard manufacturer prcedure.

value: Peripheral blood

value: Female

tag: disease state

value: Obesity


title: Ippocampus, female mouse, 2 months, lead 5

description: Library name: PF5

value: Brain (hippocampus)

value: F


title: A_D_M_7_1

description: Library name: 73_S31_R1_001

value: Avalon

value: drought+mock


title: Ippocampus, female mouse, 2 months, lead 4

description: Library name: PF4


title: Ippocampus, female mouse, 2 months, lead 3

description: Library name: PF3


title: Peripheral DNA from patient MO52

value: Male


title: Peripheral DNA from patient SA37


title: A_D_M_4_3

description: Library name: 25_S11_R1_001


title: A_D_M_4_4

description: Library name: 31_S14_R1_001


title: Peripheral DNA from patient SA10


title: 4-cell embryo, Pcbp1-rABE, n=5

description: Library name: Pcbp1-rABE-48hpf

value: 4-cell embryo

value: FVB/NJ

value: Pcbp1-rABE mRNA microinjection at zygote stage


title: 4-cell embryo, Mrps22-rABE, n=6

description: Library name: Mrps22-rABE-48hpf

value: Mrps22-rABE mRNA microinjection at zygote stage

value: 4-cell stage


title: Ippocampus, female mouse, 2 months, lead 2

description: Library name: PF2

value: 2 months

value: Pb


title: A_D_M_4_2

description: Library name: 12_S4_R1_001

value: spike tissue


title: 4-cell embryo, Igf2bp1-rABE, n=4

description: Library name: Igf2bp1-rABE-48hpf

value: Igf2bp1-rABE mRNA microinjection at zygote stage


title: A_D_M_4_1

description: Library name: 2_S1_R1_001


title: Ippocampus, female mouse, 2 months, lead 1

description: Library name: PF1


title: 4-cell embryo, Magoh-rABE, n=5

description: Library name: Magoh-rABE-48hpf

value: Magoh-rABE mRNA microinjection at zygote stage


title: Peripheral DNA from patient SA12

value: Peripheral blood


title: Peripheral DNA from patient MO47

value: Female

value: Obesity


title: 4-cell embryo, Rbfox2-rABE, n=4

description: Library name: Rbfox2-rABE-48hpf

value: Rbfox2-rABE mRNA microinjection at zygote stage


title: A_D_Fc_7_4

description: Library name: 88_S44_R1_001

value: Avalon

value: drought+inoculated


title: Ippocampus, female mouse, 2 months, control 6

description: Library name: CF6

value: Brain (hippocampus)

value: F

value: control


title: 4-cell embryo, Hnrnpa2b1-rABE, n=4

description: Library name: Hnrnpa2b1-rABE-48hpf

value: 4-cell embryo

value: FVB/NJ

value: Hnrnpa2b1-rABE mRNA microinjection at zygote stage


title: 4-cell embryo, Hnrnpa1-rABE, n=5

description: Library name: Hnrnpa1-rABE-48hpf

value: Hnrnpa1-rABE mRNA microinjection at zygote stage

value: 4-cell stage


title: Ippocampus, female mouse, 2 months, control 5

description: Library name: CF5

value: 2 months


title: Peripheral DNA from patient MO42


title: A_D_Fc_7_3

description: Library name: 84_S41_R1_001

value: spike tissue


title: Ippocampus, female mouse, 2 months, control 4

description: Library name: CF4


title: 4-cell embryo, Elavl1-rABE, n=3

description: Library name: Elavl1-rABE-48hpf

value: Elavl1-rABE mRNA microinjection at zygote stage


title: A_D_Fc_7_2

description: Library name: 76_S33_R1_001


title: Ippocampus, female mouse, 2 months, control 3

description: Library name: CF3


title: 4-cell embryo, Ddx39a-rABE, n=5

description: Library name: Ddx39a-rABE-48hpf

value: Ddx39a-rABE mRNA microinjection at zygote stage


title: A_D_Fc_7_1

description: Library name: 75_S79_R1_001


title: 4-cell embryo, Cnot8-rABE, n=4

description: Library name: Cnot8-rABE-48hpf

value: Cnot8-rABE mRNA microinjection at zygote stage


title: Ippocampus, female mouse, 2 months, control 2

description: Library name: CF2


title: A_D_Fc_4_4

description: Library name: 35_S16_R1_001


title: Peripheral DNA from patient MO29

value: Peripheral blood

value: Male

value: Obesity


title: 4-cell embryo, Carm1-rABE, n=7

description: Library name: Carm1-rABE-48hpf

value: Carm1-rABE mRNA microinjection at zygote stage


title: Peripheral DNA from patient MO44


title: Ippocampus, female mouse, 2 months, control 1

description: Library name: CF1

value: Brain (hippocampus)


title: A_D_Fc_4_3

description: Library name: 30_S13_R1_001

value: Avalon

value: drought+inoculated


title: Ippocampus, male mouse, 2 months, lead+manganese 6

description: Library name: PMM6

value: M

value: Pb + Mn


title: A_D_Fc_4_2

description: Library name: 10_S3_R1_001


title: Peripheral DNA from patient MO53


title: Ippocampus, male mouse, 2 months, lead+manganese 5

description: Library name: PMM5


title: Peripheral DNA from patient MO30

value: Female


title: Peripheral DNA from patient MO36


title: Peripheral DNA from patient MO41


title: 4-cell embryo, Alyref-rABE, n=4

description: Library name: Alyref-rABE-48hpf

value: 4-cell embryo

value: FVB/NJ

value: Alyref-rABE mRNA microinjection at zygote stage


title: Peripheral DNA from patient SA11


title: HT29-Pani10

city: Tours

first: FREDERIC

last: PICOU

address: 10 blvd Tonnelle

department: Hematology

country: France

institute: CHU de Tours

description:
Library name: HT Pani 10
HT29all.csv

data_processing:
Data were processed using R version 3.6.1, via DESeq2 pipeline.
Assembly: GRCh38 Genome Reference Consortium Human
Supplementary files format and content: Data were processed using R version 3.6.1, via DESeq2 pipeline.
Supplementary files format and content: P-value between control and experimenl condition <0,05 are considered, and abs(FC)>2.

source_name: Colon

growth_protocol: Cells were cultured for 48h in presence or absence of antibody, in DMEM+10%FBS, 37°, 5%CO2.

extract_protocol:
miRNA were extracted using Nucleozol RNA purification kit (Macherey-Nagel) and validated using Bioanalyzer (Agilent).
libraries were elaborated using Qiaseq miRNA library kit (Qiagen) / QiaseqmiRNA 48 index (Qiagen)

treatment_protocol: Cells were treated for 48h, with 10 or 100µg/ml of cetuximab or panituximab.

value: Colon

value: colon cancer

value: WT

value: panituximab


title: Ippocampus, male mouse, 2 months, lead+manganese 4

description: Library name: PMM4

value: 2 months


title: Kidney, Tcf21, KO, Rep2

city: Chicago

first: Yalu

last: Zhou

state: IL

address: 303 E Superior St

department: Department of Medicine

institute: Northwestern University

description:
Library name: Sample 4
10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: kidney

extract_protocol:
1.5 kidneys from 4 male mice (2 Tcf21-KO mice, 1 Cre+ ctrl, and 1 Cre- ctrl) were harvested to obtain kidney single cell suspensions. Kidneys were minced with a razor blade and then digested in 0.3 mg/mL liberase TM, 10 µg/mL hyaluronidase, and 20 µg/mL DNAseI at 37°C x 40 min in an Eppendorf Thermomixer. The resulting cell suspension was treated with RBC lysis buffer and then incubated with 0.05% trypsin EDTA at 37°C x 30 min with shaking. 10% FBS in 1X PBS (without calcium/magnesium) was added to inactivate the trypsin. Cells were pelleted and resuspended in 0.01% BSA in 1X PBS (without calcium/magnesium). The suspension was then sequentially filtered through 100 µm and 40 µm strainers. Finally, cell number and viability were deternined by AOPI fluorescent staining using the Nexcelom Cellometer Auto2000.
To recover 20,000 cells per sample, 29,000 cells from each of the 4 samples were loaded into the Chromium X Controller (10X Genomics, PN-1000328) on a Chromium GEM-X Single cell 3’ Chip Kit v4 (10x Genomics, PN-1000215). Samples were processed to generate single cell gel beads in emulsion (GEM) according to the manufacturer’s protocol. The cDNA and libraries were generated using the GEM-X Single cell 3’ Kit v4 (10x Genomics, PN-1000691) and Dual Index Kit TT Set A (10X Genomics, PN-1000215) according to the manufacturer’s manual. Quality control for constructed libraries was performed by the Agilent Bioanalyzer High Sensitivity DNA kit (Agilent Technologies, 5067-4626) and Qubit DNA HS assay kit for qualitative and quantitative analyses, respectively.

value: kidney

value: mixed background

value: 2-3 weeks


title: Peripheral DNA from patient MO39

value: Peripheral blood

value: Male

value: Obesity


title: HT29-Pani100

description:
Library name: HT Pani 100
HT29all.csv


title: Peripheral DNA from patient MO32


title: Kidney, Tcf21, KO, Rep1

description:
Library name: Sample 3
10x Genomics


title: eCPC

city: London

first: Fiona

last: Lewis-McDougall

address: Charterhouse Square

country: United Kingdom

institute: Queen Mary University of London

description:
Library name: eCPC
RNA-seq

data_processing:
Data processing was performed by Novogene Ltd.
Assembly: hg38
Supplementary files format and content: Raw gene counts for all samples generated by Novogene.

source_name: Patient-derived

growth_protocol: eCPCs and iPSC-CPCs were cultured on CELLstart™ (Thermo Fisher Scientific)-coated cultureware in growth medium, which is composed of (1:1) Dulbecco’s MEM/Ham’s F12 (DMEM/F12; Sigma-Aldrich) and Neurobasal A medium (Thermo Fisher Scientific) containing 10% Stemulate® pooled human platelet lysate (Cook medical, USA), 2mM L-alanyl-L-glutamine (Thermo Fisher Scientific), B27 and N2 supplements (Thermo Fisher Scientific), leukemia inhibitory factor (LIF) (10ng/ml; Millipore), bFGF (10ng/ml; Peprotech), EGF (20ng/ml; Peprotech), insulin-transferrin-selenite (ITS; Thermo Fisher Scientific), 1% penicillin/streptomycin (Thermo Fisher Scientific), 0.1% gentamicin (Thermo Fisher Scientific), and 0.1% Fungizone™ (Thermo Fisher Scientific) in a humidified hypoxic incubator at 37°C, 5% CO2, 2% O2.

extract_protocol:
RNA was extracted by directly lysing cells on the inserts using RLT lysis buffer from the Qiagen RNeasy Mini Kit, according to the manufacturer’s instructions.
Library preparation and paired-end 150 bp sequencing (PE150) were performed by Novogene Ltd.

treatment_protocol: CPCs were compared to 1) Human iPSCs, which were cultured in on recombinant human vitronectin and maintained in feeder-free, serum-free E8 Flex medium and 2) Human  iPSC-derived cardiomyocytes (hiPSC-CMs) generated using a protocol adapted from Burridge et al. (2015). Briefly, hiPSC-CMs were generated in CDM3 medium consisting of RPMI 1640 supplemented with 75 mg/mL recombinant human albumin (Merck) and 64 mg/mL L-ascorbic acid 2-phosphate (Merck). Differentiation was induced by treating cells with 6 μM CHIR99021 (Cambridge Bioscience) for 48 hours. On day 2, the medium was replaced with CDM3 containing 2 μM Wnt-C59, and from day 4 onward, cells were maintained in CDM3 alone, with media changes performed every two days.

value: endogenous cardiac progenitor cells

value: eCPC


title: Ippocampus, male mouse, 2 months, lead+manganese 3

description: Library name: PMM3

value: Brain (hippocampus)

value: M

value: Pb + Mn


title: Peripheral DNA from patient SA32


title: Ippocampus, male mouse, 2 months, lead+manganese 2

description: Library name: PMM2


title: HT29-Ctx10

description:
Library name: HT Ctx 10
HT29all.csv

value: cituximab


title: Kidney, Cre, Positive control

description:
Library name: Sample 2
10x Genomics

value: control


title: NeonatalhiPSC_CM

description:
Library name: NeonatalhiPSC_CM
RNA-seq

value: human induced pluripotent stem cell-derived cardiomyocytes

value: cardiomyocyte differentiation

value: Neonatal


title: Peripheral DNA from patient MO45


title: HT29-Ctx100

description:
Library name: HT Ctx 100
HT29all.csv

value: Colon

value: colon cancer

value: WT


title: Kidney, Cre, Negative control

description:
Library name: Sample 1
10x Genomics

value: kidney

value: mixed background

value: 2-3 weeks


title: Ippocampus, male mouse, 2 months, manganese 6

description: Library name: MM6

value: 2 months

value: Mn


title: HT29-Ct

description:
Library name: HT control
HT29all.csv


title: A_D_Fc_4_1

city: Freising

first: Ralph

address: Emil-Ramann-Str. 2

institute: Technische Universität München

description: Library name: 5_S2_R1_001

data_processing:
nf‐core/rnaseq (v3.17.0) using Nextflow  (v24.04.4) for processing the raw reads
3’UTR regions of the last exon extended either by 3 kb or until the following gene
FastQC (v0.12.1) for raw read quality control
Trim Galore (v0.6.10) with Cutadapt (v4.9) for adapter trimming and filtering
STAR (v2.7.11b) was used for read alignment
Salmon (v1.10.3) for transcript quantification
Assembly: The Morex V3 genome (Mascher et al., 2021) was merged with the F. culmorum genome FusCulm_01 (GenBank assembly GCA_003033665.1) to improve mapping accuracy and count Fusarium RNA read counts.
Supplementary files format and content: The HordeumVulgareV3.salmon.gene-counts.csv is a comma-separated table containing the mapped salmon gene-counts for Hordeum vulgare after running the nf-core/rnaseq pipeline.
Supplementary files format and content: The sampleInformation.csv is a comma-separated table explaining the the abbreviations used for the sample names.

source_name: spike tissue

extract_protocol:
Spike material was ground in liquid nitrogen, and extraction of total RNA was performed with 100 mg of each sample using the GeneMATRIX Universal RNA Purification Kit (EURx Molecular Biology Products), following the manufacturer’s instructions.
Libraries for 3’-RNA-sequencing (Moll et al., 2014) were prepared using the QuantSeq 3’mRNA-Seq Library Prep Kit (Lexogen, Austria) according to the manufacturer’s instructions. Library sizes were quantified with a Qubit Fluorometer 2.0 and a Qubit DNA High Sensitivity Assay Kit. Ready-to-load pools of cDNA libraries were determined with qPCR. An Agilent 2010 Electrophoresis Bioanalyzer with the High Sensitivity DNA Assay was used to check the integrity and mRNA fragment size distribution of each library.

value: spike tissue

value: Avalon

value: drought+inoculated


title: Peripheral DNA from patient MO31

value: Peripheral blood

value: Female

value: Obesity


title: NeonatalhiPSC

description:
Library name: NeonatalhiPSC
RNA-seq

value: human induced pluripotent stem cell


title: alveolar macrophage, HDAC1-2-cKO-C

city: Beijing

first: wenlong

last: Lai

address: Tsinghua university

department: School of medicine

institute: Tsinghua University

data_processing:
The raw data obtained was filtered by removing low quality reads and adapter reads
The clean reads were aligned to the reference genome mm10 (NCBI assembly of the mouse genome) by using Bowtie2 and BWA
The gene expression levels of each sample were calculated by using RSEM and normalized by calculation of the FPKM (Fragments Per Kilobase of transcript per Million fragments mapped) value.
Differential expressed genes for each pairwise comparison were defined as q-value < 0.05 and absolute value of log2 fold change ≥ 0.847.
Genome_build: mouse (mm10)
Supplementary_files_format_and_content: Tab-delimited text files include counts and FPKM values for every gene in each Sample.

source_name: alveolar macrophage

extract_protocol:
Total RNA from alveolar macrophage was extracted by Trizol reagent according to the manufacturer’s instructions. Purified mRNA was fragmented by adding an appropriate amount of the interrupting reagent under high-temperature conditions, and the cDNA was synthesized using the fragmented mRNA as a template. The fragment size was then selected and amplified by PCR, then the constructed library was qualified with Agilent 2100 Bioanalyzer and ABI StepOne Plus Real-Time PCR System and conducted sequencing.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: lung

value: alveolar macrophage

value: CD11c-Cre HDAC1f/fHDAC2f/f


title: Peripheral DNA from patient MO27


title: 4-cell embryo, control rABE, n=22

description: Library name: rABE-48hpf

value: 4-cell embryo

value: FVB/NJ

value: rABE (control) mRNA microinjection at zygote stage

value: 4-cell stage


title: alveolar macrophage, HDAC1-2-cKO-B


title: Peripheral DNA from patient MO28


title: HCT116-Pani100

description:
Library name: HCT Pani 100
HCT116all.csv

value: Colon

value: colon cancer

value: WT

value: panituximab


title: Ippocampus, male mouse, 2 months, lead+manganese 1

description: Library name: PMM1

value: Brain (hippocampus)

value: M

value: 2 months

value: Pb + Mn


title: NeonhiPSC_CPC

description:
Library name: NeonhiPSC_CPC
RNA-seq

value: human induced pluripotent stem cell-derived cardiac progenitor cells

value: CPC differentiation

value: Neonatal


title: alveolar macrophage, HDAC1-2-cKO-A

value: lung

value: alveolar macrophage


title: Peripheral DNA from C12

value: Peripheral blood

value: Male

value: Lean Control


title: Peripheral DNA from C16


title: C4hiPSC_CM

description:
Library name: C4hiPSC_CM
RNA-seq

value: human induced pluripotent stem cell-derived cardiomyocytes

value: cardiomyocyte differentiation


title: HCT116-Ctx10

description:
Library name: HCT Ctx 10
HCT116all.csv

value: Colon

value: colon cancer

value: cituximab


title: Ippocampus, male mouse, 2 months, manganese 3

description: Library name: MM3

value: Brain (hippocampus)

value: Mn


title: Peripheral DNA from C8


title: alveolar macrophage, WT-C

value: wildtype


title: C2hiPSC_CM

description:
Library name: C2hiPSC_CM
RNA-seq


title: HCT116-Pani10

description:
Library name: HCT Pani 10
HCT116all.csv

value: WT

value: panituximab


title: Peripheral DNA from patient MO34

value: Female

value: Obesity


title: Ippocampus, male mouse, 2 months, manganese 2

description: Library name: MM2

value: M

value: 2 months


title: Ippocampus, male mouse, 2 months, manganese 4

description: Library name: MM4


title: C4hiPSC_CPC

description:
Library name: C4hiPSC_CPC
RNA-seq

value: human induced pluripotent stem cell-derived cardiac progenitor cells

value: CPC differentiation


title: alveolar macrophage, WT-B

value: lung

value: alveolar macrophage


title: Ippocampus, male mouse, 2 months, manganese 1

description: Library name: MM1


title: alveolar macrophage, WT-A


title: Peripheral DNA from C13

value: Peripheral blood

value: Male

value: Lean Control


title: Peripheral DNA from C14


title: C2hiPSC_CPC

description:
Library name: C2hiPSC_CPC
RNA-seq


title: Monocyte short-read RNA-Seq, 3h LPS in vitro activation, healthy volunteer 8

city: Utrecht

first: Jorg

last: van Loosdregt

address: Lundlaan 6

country: Netherlands

institute: UMC Utrecht

description: Library name: HC8LPS

data_processing:
For short-read RNA-Seq, libraries were sequenced at the Utrecht Sequencing Facility using the Nextseq500 platform (Illumina), which produced single end reads of 75 bp. For Native RNA-Seq, Raw data was interpreted by Nanopore Technologies sequencing base calling software (basecRAWller) and reads that passed minimum quality were kept for the analysis.
Short-reads were trimmed using Trim Galore and aligned and counted to the reference genome using STAR. Long-reads aligned to the reference genome using minimap2 and were quantified using flair. Both data were also quantified using salmon.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file including raw counts per gene/isoform (STAR and flair)
Supplementary files format and content: tab-delimited tekt file including raw abundances per isoform (salmon)

source_name: PBMC

extract_protocol:
Monocytes were lysed in TRIzol LS reagent (Thermo Fisher) directly or after LPS activation. RNA was isolated using the Dynabead mRNA Purification Kit (Thermo Fisher) according to the manufacturer's protocol. For short-read RNA-Seq, the concentration of RNA was quantified using a Qubit RNA HS assay and Qubit fluorometer (Thermo Fisher). For Native RNA-Seq, 1 μM mRNA per sample was loaded on MinION flowcells and ran for approximately two hours at the Utrecht Sequencing Facility.
For short-read RNA-Seq, polyadenylated messenger RNA was isolated using Poly(A) beads (NEXTflex), and sequencing libraries were made using the Rapid Directional RNA-seq kit (NEXTflex).

treatment_protocol: Human peripheral blood mononuclear cells (PBMCs) were obtained from healthy donor blood in sodium heparin tubes and isolated using Ficoll-paque plus (Cytiva, Marlborough, MA, USA) density gradient media. Primary human CD14+ monocytes were isolated from PBMC using automatic magnetic-activated cell sorting (MACS, Miltenyi Biotech, Bergisch Gladbach, Germany) using human CD14+ monocyte isolation kit (Miltenyi Biotec, Bergisch Gladbach, Germany) according to the manufacturers protocol. Ex vivo samples were collected at this stage, to avoid any stimulation from in vitro culture. Primary monocytes were cultured in Roswell Park Memorial Institute (RPMI) 1640 medium (Thermo Fisher, Hampton, NH, USA) supplemented with 10% heat-inactivated fetal calf serum (Sigma-Aldrich, St. Louis, MI, USA), 1% L-glutamine (Life Technologies, Carlsbad, CA, USA), 100 U/mL of penicillin and 100 mg/mL of streptomycin (Gibco, New York, NY, USA). Cells were cultured at 37 °C in 5% CO2m and stimulated with 100 ng/ml LPS (Sigma-Aldrich) for 3 hours in culture medium.

value: PBMC

value: Human monocytes (CD14 +)

value: LPS


title: Ippocampus, male mouse, 2 months, lead 6

description: Library name: PM6

value: Brain (hippocampus)

value: Pb


title: Ippocampus, male mouse, 2 months, manganese 5

description: Library name: MM5

value: Mn


title: Monocyte short-read RNA-Seq, 3h LPS in vitro activation, healthy volunteer 7

description: Library name: HC7LPS


title: Ippocampus, male mouse, 2 months, lead 5

description: Library name: PM5


title: Peripheral DNA from patient MO18

value: Female


title: HCT116-Ct

description:
Library name: HCT control
HCT116all.csv

value: Colon

value: colon cancer

value: WT


title: Ippocampus, male mouse, 2 months, lead 4

description: Library name: PM4

value: M

value: 2 months


title: Monocyte short-read RNA-Seq, 3h LPS in vitro activation, healthy volunteer 6

description: Library name: HC6LPS


title: BCI_R2

city: Montreal

first: Sonia

middle: Victoria

last: del Rincon

state: QC

address: E-537, 3755 Chemin de la Côte-Ste-Catherine

country: Canada

institute: McGill University

description:
Library name: B4_BCI_R2
BelvaCobiINK_2

data_processing:
nf-core/rnaseq pipeline v3.8.1 was used to perform quality control, trimming and alignment on raw paired-end fastq reads, followed by reference genome-guided transcriptome assembly and gene expression quantification.
Assembly: GRCh38
Supplementary files format and content: (WM3406_rawcounts.csv) containing gene-level raw counts.
Supplementary files format and content: Rows represent genes (gene symbols), columns represent individual samples.

source_name: melanoma

growth_protocol: WM3406 cells were maintained in RPMI supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
Cultured cells were pelleted, and RNA was prepared using the E.Z.N.A. total RNA isolation kit (OMEGA Bio-Tek). RNA concentrations were then quantified using a NanoDrop spectrophotometer (ThermoFisher Scientific)
Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations.

treatment_protocol: We treated NRAS-mutant WM3406 melanoma cell lines with belvarafenib (25 nM), cobimetinib (50 nM), and the mTOR inhibitor sapanisertib (INK128, 25 nM) for 24 h.

value: melanoma

value: metastatic cutaneous melanoma cells

value: NRAS-mutant


title: Peripheral DNA from C15

value: Peripheral blood

value: Male


title: Peripheral DNA from patient MO13

value: Obesity


title: Peripheral DNA from C7

value: Lean Control


title: BCI_R1

description:
Library name: A4_BCI_R1
BelvaCobiINK_1


title: Caco-2 cells, Treatment biol rep 3

city: Macul

first: Omar

last: Porras

state: Santiago

address: El libano 5524

department: INTA

country: Chile

institute: University of Chile

description:
Library name: Treatment biol rep 3
Column name in raw_counts_All_samples.txt: 129

data_processing:
Sequence reads were trimmed with Trim Galore v0.6.10 to obtain high-quality reads
Trimmed sequences aligment was  carried out with STAR v2.5.2b  and mapped to Homo sapiens (GRCh38.p14) reference genome
Assembly: GRCh38.p14
Supplementary files format and content: comma-delimited text file includes raw count for each sample

growth_protocol: Cells were cultured in Minimal Essential Medium supplemented with fetal bovine serum (10%) and penicillin/streptomycin (1%). The cultures were maintained at 37 °C in a humid atmosphere with 5% CO 2 and 95% air. At passage 14, cells were seeded onto 0.4 µm pore-size polycarbonate Transwells (Corning, NY, USA), and the medium was refreshed twice weekly.

extract_protocol:
Each basquet transwell with approximately 1.5 × 10^5 Caco-2 cells were lysed with TRIZOL following the manufacturer's instructions
Libraries were obtained with the MGIEasy RNA Library Prep Kit and the MGIEasy Circularization Module V2.0.

treatment_protocol: SHIME ferments were mixed with culture medium at equal proportions to be added at the apical side of differentiated Caco-2 cells for 7 hours. After this period, apical media were replaced with full-supplemented culture medium. The next day, a second SHIME ferment exposure followed the same procedures described above.

value: Human colon adenocarcinoma

value: SHIME ferment exposure


title: Monocyte short-read RNA-Seq, 3h LPS in vitro activation, healthy volunteer 5

description: Library name: HC5LPS

value: PBMC

value: Human monocytes (CD14 +)

value: LPS


title: Caco-2 cells, Treatment biol rep 1

description:
Library name: Treatment biol rep 1
Column name in raw_counts_All_samples.txt: 127


title: Caco-2 cells, Treatment biol rep 2

description:
Library name: Treatment biol rep 2
Column name in raw_counts_All_samples.txt: 128


title: Ippocampus, male mouse, 2 months, lead 3

description: Library name: PM3

value: Brain (hippocampus)

value: Pb


title: BC_R3

description:
Library name: C2_BC_R3
BelvaCobi_3

value: Belva+cobi


title: Caco-2 cells, Control biol rep 3

description:
Library name: Control biol rep 3
Column name in raw_counts_All_samples.txt: 126

value: WT

value: Control


title: Monocyte short-read RNA-Seq, 3h LPS in vitro activation, healthy volunteer 4

description: Library name: HC4LPS


title: Ippocampus, male mouse, 2 months, lead 2

description: Library name: PM2

value: M

value: 2 months


title: Peripheral DNA from patient MO14


title: Peripheral DNA from C9


title: Caco-2 cells, Control biol rep 2

description:
Library name: Control biol rep 2
Column name in raw_counts_All_samples.txt: 125


title: Peripheral DNA from C11

value: Female


title: Peripheral DNA from C5

value: Peripheral blood


title: BC_R2

description:
Library name: B2_BC_R2
BelvaCobi_2

value: melanoma

value: metastatic cutaneous melanoma cells

value: NRAS-mutant


title: Peripheral DNA from C6

value: Male

value: Lean Control


title: Caco-2 cells, Control biol rep 1

description:
Library name: Control biol rep 1
Column name in raw_counts_All_samples.txt: 124

value: Human colon adenocarcinoma


title: Ippocampus, male mouse, 2 months, lead 1

description: Library name: PM1


title: Ippocampus, male mouse, 2 months, control 6

description: Library name: CM6

value: control


title: Peripheral DNA from C10


title: Monocyte short-read RNA-Seq, 3h LPS in vitro activation, healthy volunteer 2

description: Library name: HC2LPS

value: PBMC

value: Human monocytes (CD14 +)

value: LPS


title: INK128_R3

description:
Library name: C3_INK128_R3
INK_3


title: INK128_R2

description:
Library name: B3_INK128_R2
INK_2


title: Peripheral DNA from patient MO23

value: Obesity


title: Monocyte short-read RNA-Seq, Ex vivo, healthy volunteer 7

description: Library name: HC7exvivo

value: ex vivo


title: Monocyte short-read RNA-Seq, Ex vivo, healthy volunteer 8

description: Library name: HC8exvivo


title: BC_R1

description:
Library name: A2_BC_R1
BelvaCobi_1

value: Belva+cobi


title: Monocyte short-read RNA-Seq, 3h LPS in vitro activation, healthy volunteer 3

description: Library name: HC3LPS


title: Ippocampus, male mouse, 2 months, control 5

description: Library name: CM5

value: Brain (hippocampus)

value: M


title: Monocyte short-read RNA-Seq, Ex vivo, healthy volunteer 6

description: Library name: HC6exvivo


title: Ippocampus, male mouse, 2 months, control 2

description: Library name: CM2

value: 2 months


title: Ippocampus, male mouse, 2 months, control 3

description: Library name: CM3


title: INK128_R1

description:
Library name: A3_INK128_R1
INK_1


title: Astrocytes, HET24

city: Buffalo

first: Henry

middle: G.

last: Withers

state: New York

address: Elm and Carlton Streets

department: Biostatistics and Bioinformatics

institute: Roswell Park Comprehensive Cancer Center

data_processing:
Samples were aligned with STAR (version 2.7.9a) to the mouse genome using reference build GRCm38.p6 and the corresponding GENCODE annotation version M25 (November 2019).
Quality control for raw reads was performed with fastqc. Spliced alignment of the reads to the reference genome was done with STAR mapping tool followed by a second round of quality control using RSeQC software. Mapped reads are quantified at the gene level in a raw counts matrix using featureCounts from Subread using fracOverlap 1 (only entire reads overlapping to annotation feature are counted).
Assembly: GRCm38.p6 and GENCODE annotation M25
Supplementary files format and content: Processed data in supplementary tab-delimited file (.tsv) contains a matrix of raw read counts for each gene_accession number (rows) and sample (columns)

source_name: forebrain

growth_protocol: Bulk forebrain tissue was harvested from mice at embryonic day 16-17.

extract_protocol:
Total RNA was extracted using the miRNeasy Micro Kit (217084, Qiagen).
RNA libraries for RNA-seq were prepared using TruSeq library preparation kit following manufacturer’s protocol.

value: Forebrain

value: Astrocytes

value: Npas+/-


title: Astrocytes, HET5


title: Astrocytes, HET6


title: Ippocampus, male mouse, 2 months, control 4

description: Library name: CM4


title: Astrocytes, WT15

value: Npas+/+


title: Monocyte short-read RNA-Seq, 3h LPS in vitro activation, healthy volunteer 1

description: Library name: HC1LPS


title: Monocyte short-read RNA-Seq, Ex vivo, healthy volunteer 5

description: Library name: HC5exvivo


title: Ippocampus, male mouse, 2 months, control 1

description: Library name: CM1


title: Astrocytes, HET7


title: Astrocytes, WT16


title: DMSO_R1

description:
Library name: A1_DMSO_R1
DMSO_1

value: melanoma

value: metastatic cutaneous melanoma cells

value: NRAS-mutant

value: DMSO


title: Monocyte short-read RNA-Seq, Ex vivo, healthy volunteer 4

description: Library name: HC4exvivo

value: PBMC


title: DMSO_R2

description:
Library name: B1_DMSO_R2
DMSO_2


title: DMSO_R3

description:
Library name: C1_DMSO_R3
DMSO_3


title: Astrocytes, WT41


title: T47D_input

city: Philadelphia

first: Alekh

last: Paranjapye

state: Pennsylvania

address: 3400 Civic Center Blvd

department: Genetics

institute: University of Pennsylvania

data_processing:
Libraries were sequenced on Illumina HiSeq2500 machines.
Data was analyzed using ENCODE (phase-3) transcription factor and histone ChIP-seq pipeline https://github.com/ENCODE-DCC/chip-seq-pipeline2
Genome_build: hg19
Supplementary_files_format_and_content: bigwig, regionPeak

growth_protocol: Cells were grown in indicated medias using standard methods

extract_protocol:
Cells were lysed in lysis buffer (5mM PIPES pH 8.0, 85mM KCL, 0.5% NP-40, 1x Protease Inhibitor Cocktail (Roche)). Nuclei were isolated by centrifugation, lysed in RIPA buffer (1x PBS, 1% NP-40, 0.5% sodium deoxycholate, 0.1% SDS, Protease Inhibitor Cocktail), and sonicated. Protein-DNA complexes were isolated with rabbit anti-KLF5 (Yang Y, et al. Cancer Biol Ther. 2005) [Calu-3 KLF5 Rep1], Santa Cruz sc-398470 [Calu-3 KLF5 Rep2, 16HBE14o- KLF5], Santa Cruz sc-7962 [Calu-3 CEBPB]
DNA ends were blunted using T4 DNA polymerase, Klenow DNA polymerase, and T4 polynucleotide kinase. Next, DNA was incubated with Klenow exo- to add 5’ adenine overhangs. Multiplex adaptors were then ligated to the ends and converted to dsDNA using 5 cycles of PCR. DNA was size-selected to contain fragments between 200 and 300bp and PCR amplified for 5 cycles. DNA was purified with 1.2x AMPure XP beads. Sequencing was performed on an Illumina Hi-Seq.

value: Human luminal A breast epithelial cells

tag: growth media

value: RPMI + 10% FBS + Insulin


title: Astrocytes, WT43


title: Monocyte short-read RNA-Seq, Ex vivo, healthy volunteer 3

description: Library name: HC3exvivo

value: Human monocytes (CD14 +)


title: Monocyte short-read RNA-Seq, Ex vivo, healthy volunteer 2

description: Library name: HC2exvivo

value: ex vivo


title: THP-1-induced macrophages, CST3-/-_3

status: Public on May 03 2026

city: Changzhou

first: Jie

last: Zhao

state: Jiangsu

address: No.68 Gehu Road

institute: The Third Affiliated Hospital of Nanjing Medical University

description: Library name: Sample 6

data_processing:
The sequencing data was filtered with SOAPnuke by  Removing reads containing sequencing adapter
Removing reads whose low-quality base ratio (base quality less than or equal to 15) is more than 20%
Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format
Assembly: GCF_000001405.39_GRCh38.p13

source_name: CST3-/- THP-1 induced macrophages

growth_protocol: THP-1 cell lines were maintained under standard culture conditions in complete RPMI-1640 medium supplemented with fetal bovine serum and antibiotics, at 37°C in a humidified incubator with 5% CO2.

extract_protocol:
Total RNA was extracted from tissues using TRIzol (Invitrogen, Carlsbad, California, USA) according to manual instruction
Library preparation is performed using Optimal Dual-mode mRNA Library Prep Kit (BGI-Shenzhen, China). A certain amount of RNA are denatured at suitable temperature to open the secondary structure, and mRNA is enriched by oligo (dT) attached magnetic beads. After reacting at a suitable temperature for a fixed time period, RNAs are fragmented with fragmentation reagents

treatment_protocol: THP-1 cells (CST3+/+ and CST3−/−) were differentiated into macrophage-like cells by treatment with PMA. After PMA exposure, cells were allowed to adhere and differentiate, followed by a resting period in PMA-free complete medium prior to downstream assays and sample collection.

value: THP-1-induced macrophages

value: PMA induced


title: RNA-seq of chromatin fraction in CTD degradation replicate2

first: Yajing

last: Hao

address: NO.1 Beichen West Road, Chaoyang District

department: Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences

institute: Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation

data_processing:
After obtaining raw RNA-Seq data, we first used Trimmomatic to perform sliding window trimming, cutting the average quality once within the 4-bp window falling below 20 and removing the trimmed read if it had a length less than 38. SortMeRNA (Kopylova et al., 2012) was used to filter ribosomal RNAs with default parameters. We mapped the filtered reads to the genome (genome version mm10) using STAR (Dobin et al., 2013) with parameters --outFilterScoreMinOverLread 0.1, --outFilterMatchNminOverLread 0.1, --outFilterMismatchNmax 4 and --outFilterMultimapNmax 8.
After obtaining the mapping files, we removed the duplicate reads using Picard (http://broadinstitute.github.io/picard/) with parameters MarkDuplicates and REMOVE_DUPLICATES = true. We calculated the gene read counts using FeatureCounts (Liao et al., 2014) and converted them to FPKM using the edgeR (Robinson et al., 2010) package in R language. The bigwig files of each RNA-Seq data set from the sense strand and antisense strand were obtained using bamCoverage from DeepTools with a parameter --binSize 1, --ignoreDuplicates, –minMappingQuality 255 and –normalizeUsing CPM.
The SPI value was calculated as previously described (Herzel and Neugebauer, 2015) and normalized by spike-in, considering that the mouse CTD degron does not affect gene splicing in spike-in cells.
Assembly: mm10
Supplementary files format and content: bw

source_name: mESC cell

growth_protocol: mESCs were cultured in 2i + LIF conditions at 37 °C in a 5% of CO2 incubator. Cells were negative for mycoplasma (tested every three months).

extract_protocol:
Each RNA was extracted using Trizol reagent and coupled with Direct-zol RNA Miniprep kit according to the manufacturer’s instructions.
total RNA with rRNA depleted
RNA-seq libraries were generated using the Illumina TruSeq Stranded Total RNA Library Prep Gold with TruSeq Unique Dual Indexes. Samples were processed following manufacturer’s instructions, except modifying RNA shear time to five minutes. The libraries were multiplexed and sequenced with 100 bp paired end (PE100) to a depth of approximately 30 million reads per library on an Illumina NovaSeq 6000.

treatment_protocol: The cell fractionation was performed as previously described, with additional modifications. Briefly, 5 x 106 cells were gently trypsinized and collected by centrifugation. the cell pellets were rinsed twice with ice-cold 1 x PBS and then were lysed by ice-cold CE buffer (10 mM HEPES [pH 7.5], 0.1 % NP-40, 1 mM EDTA, 1 mM DTT, 60 mM KCl and 340 mM Sucrose) for 5 min on ice. The supernatant (cytoplasmic fraction) was collected by centrifugation. the nuclei pellets were gently rinsed with ice-cold 1 x PBS/1 mM EDTA then gently resuspended in ice-cold glycerol buffer (20 mM Tris-HCl [pH 7.5], 75 mM NaCl, 0.5 mM EDTA, 0.85 mM DTT and 50% glycerol). Gently mix with equal volume of nuclei lysis buffer (10 mM HEPES [pH 7.5], 1.0% NP-40, 0.2 mM EDTA, 1 mM DTT, 7.5 mM MgCl2, 300 mM NaCl and 1 M urea) and incubated on ice for 3 min, then collect the supernatant (nucleoplasm fraction) by centrifugation. the chromatin pellets were gently rinsed twice with ice-cold 1 x PBS/1 mM EDTA and then dissolved with TRIzol reagents (Invitrogen) for extracting chromatin-associated RNA. The purified chromatin-associated RNA was used for RNA-seq library preparation.

value: mESC cell


title: T47D ELF5 ChIP-seq rep3

source_name: T47D ELF5 ChIP-seq

tag: chip antibody


title: RNA-seq of chromatin fraction in control condition replicate1

value: Dox


title: Monocyte short-read RNA-Seq, Ex vivo, healthy volunteer 1

description: Library name: HC1exvivo


title: RNA-seq of chromatin fraction in control condition replicate2


title: RNA-seq of chromatin fraction in CTD degradation replicate1


title: T47D ELF5 ChIP-seq rep2


title: THP-1-induced macrophages, CST3+/+_1

description: Library name: Sample 1

source_name: CST3+/+ THP-1 induced macrophages


title: THP-1-induced macrophages, CST3-/-_1

description: Library name: Sample 4


title: THP-1-induced macrophages, CST3-/-_2

description: Library name: Sample 5


title: Astrocytes, WT5

value: Forebrain


title: THP-1-induced macrophages, CST3+/+_3

description: Library name: Sample 3


title: THP-1-induced macrophages, CST3+/+_2

description: Library name: Sample 2


title: T47D ELF5 ChIP-seq rep1


title: Uninflamed_3

description:
Library name: Sample 5
BD

data_processing:
The BD Rhapsody WTA Analysis Pipeline(version 1.8) was used to create sequencing libraries from single cell transcriptomes without specifying a targeted panel. After sequencing, the analysis pipeline takes the FASTQ files, a reference genome file（human：GRCh38） and a transcriptome annotation file （human:GENCODE v32/Ensembl 98）for sequence alignment.
Assembly: human：GRCh38
Supplementary files format and content: barcodes.tsv, features.tsv,matrix.mtx in a tar archive

source_name: Colon tissues

extract_protocol:
Single-cell RNA-seq experiment was performed by experimental personnel in the laboratory of GENECHEM. The tissues were surgically removed and kept in MACS Tissue Storage Solution (Miltenyi Biotec) until processing. The tissue samples were processed as described below. Briefly, samples were first washed with phosphate-buffered saline (PBS), minced into small pieces (approximately 1mm3) on ice and enzymatically digested with 1 mg/mL collagenase I (Gibco)，1 mg/mL collagenase II，60U/mL Hyaluronidase (Sigma), 10U/mL Liberase (Roche) and 0.02mg/mL DNase I (Roche) for 90 min at 37°C, with agitation . After digestion, samples were sieved through a 100µm and 40µm cell strainer, and centrifuged at 300g for 5 min. After the supernatant was removed, the pelleted cells were suspended in red blood cell lysis buffer (Gibco) to lyse red blood cells. After washing with DPBS containing sample buffer, the cell pellets were re-suspended in DPBS containing sample buffer，stained and counted.
BD Rhapsody system was used to capture the transcriptomic information of single cells. Single-cell capture was achieved by random distribution of a single-cell suspension across >200,000 microwells through a limited dilution approach. Beads with oligonucleotide barcodes were added to saturation so that a bead was paired with a cell in a microwell. The cells were lysed in the microwell to hybridize mRNA molecules to barcoded capture oligos on the beads. Beads were collected into a single tube for reverse transcription and ExoI digestion. Upon cDNA synthesis, each cDNA molecule was tagged on the 5′ end (that is, the 3′ end of a mRNA transcript) with a unique molecular identifier (UMI) and cell barcode indicating its cell of origin. Whole transcriptome libraries were prepared using the BD Rhapsody single-cell whole-transcriptome amplification (WTA) workflow including random priming and extension (RPE), RPE amplification PCR and WTA index PCR. The libraries were quantified using a High Sensitivity D1000 ScreenTape (Agilent）and High Sensitivity D1000 Reagents (Agilent）on a 4150 TapeStation System (Agilent) and the Qubit High Sensitivity DNA assay (Thermo Fisher Scientific). Sequencing was performed by illumina sequencer (Illumina, San Diego, CA) on a 150 bp paired-end run.

treatment_protocol: Inflamed and uninflamed colon tissues from CD patients

value: Colon tissues

value: Uninflamed


title: HUVEC, CD109 siRNA transfection, replicate 2

first: Jeremy

last: Barth

state: SC

address: 173 Ashley Ave, BSB 627

institute: MUSC

description: Library name: 9KD

data_processing:
Fastq files were obtained from the provider and then analyzed using Partek Flow (Illumina) software.
Reads were aligned to hg38 using STAR 2.7.8a
Aligned reads were quantified to annotation model (Partek E/M) built from hg38 Ensembl Transcripts release 111
Normalization and comparative analyses were done with DESeq2. CD109 siRNA transfection (n=3) was compared to scramble control siRNA transfection (n=3).
Assembly: HG38
Supplementary files format and content: Tab delimited text file of DESeq2 normalized counts, FDR step up adjustsed p-value (Benjamini and Hochberg) and log2 fold change

source_name: Human Umbilical Vein Endothelial Cell

growth_protocol: Pooled, multiple donor human umbilical vein endothelial cells (HUVECs) (Lonza, Basel, Switzerland) were maintained at 37°C with 5% CO2 in endothelial basal medium 2 (Lonza) supplemented with EGM-2 SingleQuots growth factors.

extract_protocol:
Total RNA was isolated from n=3 scramble control and CD109 siRNA treated HUVEC cultures using the RNeasy Micro Kit (QIAGEN) with RNase free DNAse digestion (QIAGEN) to prevent genomic DNA contamination according to manufacturer’s protocol.
Total RNA samples were submitted to a commercial provider (Genewiz-Azenta) for paired-end sequencing at 150bp read length and 20-30 M reads per sample.

treatment_protocol: HUVECs were transfected using an Amaxa Nucleofection system as described by the manufacturer. Briefly, 1x106 cells were transfected per cuvette, with 2 uM of siRNA targeting human CD109 (Santa Cruz Biotechnology, sc-44950) or non-specific scramble control siRNA (sc-37007).

value: Human Umbilical Vein Endothelial Cell

tag: sirna transfection


title: HUVEC, CD109 siRNA transfection, replicate 3

description: Library name: 10KD


title: Inflamed_4

description:
Library name: Sample 7
BD

value: Inflamed


title: HUVEC, scramble control transfection, replicate 2

description: Library name: 2CON

value: Scramble control


title: Inflamed_3

description:
Library name: Sample 6
BD


title: HUVEC, scramble control transfection, replicate 3

description: Library name: 5CON


title: HUVEC, CD109 siRNA transfection, replicate 1

description: Library name: 7KD


title: HUVEC, scramble control transfection, replicate 1

description: Library name: 1CON


title: Uninflamed_2

description:
Library name: Sample 3
BD


title: Inflamed_2

description:
Library name: Sample 4
BD


title: Inflamed_1

description:
Library name: Sample 2
BD


title: C1hiPSC_CM

description:
Library name: C1hiPSC_CM
RNA-seq

value: human induced pluripotent stem cell-derived cardiomyocytes

value: cardiomyocyte differentiation


title: BCI_R3

description:
Library name: C4_BCI_R3
BelvaCobiINK_3

value: melanoma

value: metastatic cutaneous melanoma cells

value: NRAS-mutant


title: Uninflamed_1

description:
Library name: Sample 1
BD


title: Patient_41_Visium

city: New York

first: Bettina

last: Nadorp

state: NY

address: 500 1st Ave

department: Medicine/Pathology

institute: NYU Langone Health

description: slide ID: V43L11-065, area: D1

data_processing:
The Spaceranger Software (version 2.1.1, 10x Genomics) was employed to demultiplex and align the raw reads to GRCh38 (version 2020-A). The Seurat R package (version 4.3)30 was used for all downstream analyses. Spots with low-depth coverage (<200 features/spot) were filtered. Individual samples were normalized using SCTransform, merged, and rpca integrated using default parameters with 3000 integration features and dimensions 1-30. 2D UMAP visualization was based on the 30 reciprocal PCA dimensions and 20 nearest neighbors. We then generated a shared nearest neighbor (SNN) graph with 20 nearest neighbors and subsequently clustered the graph (range of resolutions from 0.1-1.5). We used resolution 0.5 to annotate the spot using the healthy donor annotations from Castillo et al., Sci Immunol, 2023.
Assembly: hg38
Supplementary files format and content: tiff image and associated metadata for each sample
Library strategy: Spatial Transcriptomics

source_name: skin with myeloid sarcoma

extract_protocol:
FFPE
We used 10X Visium spatial transcriptomics platform (Visium CytAssist for FFPE Spatial Gene Expression 6.5mm, Human, 4 rxns[1000520], Dual Index Kit TS Set A, 96 rxn [1000251] and Visium CytAssist Spatial Gene Expression Reagent Kits, CG000495 RevE) to characterize the spatial gene expression patterns in four myeloid sarcomas in the skin. We followed all steps outlined in the 10X Genomics CytAssist Visium Protocol with overnight hybridization of ~18h. Tissue preparation, staining, and High-Resolution Scanning were performed by OSUCCC CPDISR. Library generation, FFPE tissue total RNA quality, and sequencing of the resultant CytAssist Visium Spatial Transcriptomic libraries were performed by OSUCCC GSR.

value: skin with myeloid sarcoma


title: Patient_84_Visium

description: slide ID: V43L11-065, area: A1


title: Patient_15_Visium

description: slide ID: V43L11-087, area: D1


title: Pt_52_PB

data_processing:
RNA-seq data were processed using the EnFusion ensemble approach of seven fusion detection algorithms
Transcripts per million (TPM) values were generated from paired-end RNA sequence data using Salmon with bootstrapping set to 100
Assembly: Homo sapiens GRCh38.p12
Supplementary files format and content: HTSeq cov

source_name: peripheral blood

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries. RNA libraries for RNA-seq were prepared using TruSeq Stranded Total with Rebo Zero Gold library preparation kit following manufacturer's protocols.
Tumor derived RNA was subjected to 0.8x SPRI bead cleanup and size selection prior to DNase treatment and ribodepletion prior to using the NEBNext Ultra II Directional kit preparation. The library was constructed for whole transcriptome sequencing (RNA-seq). Paired-end 151-bp reads were generated on the Illumina NovaSeq (Illumina, Inc.)

value: peripheral blood


title: Pt_58_BM

source_name: bone marrow

value: bone marrow


title: Pt_78_PB


title: Pt_60_PB


title: Pt_54_PB


title: Pt_77_BM


title: Pt_75_BM


title: Patient_43B_Visium

description: slide ID: V43L11-087, area: A1


title: Pt_61_BM


title: Pt_88_MS

source_name: myeloid sarcoma

value: myeloid sarcoma

tag: tissue site

value: cutis


title: Pt_54_BM


title: HCT116-Ctx100

description:
Library name: HCT Ctx 100
HCT116all.csv

source_name: Colon

value: Colon

value: colon cancer

value: WT

value: cituximab


title: Pt_92_MS


title: Pt_91A_MS


title: Pt_62_BM


title: Pt_85A_MS


title: Pt_83_MS


title: Pt_86A_MS


title: Pt_87_MS


title: Pt_81_MS


title: Pt_78_MS


title: Pt_84_MS


title: Pt_77_MS


title: Pt_80A_MS


title: Pt_75_MS


title: Pt_66_MS


title: Pt_62_MS


title: Pt_117_MS

value: Leg mass


title: Pt_114_MS

value: Ear mass


title: Pt_29C_MS

value: supraclavicular


title: Pt_118_MS

value: Duodenal mass


title: Pt_52B_MS


title: Pt_60_MS


title: Pt_68B_MS


title: Pt_61_MS


title: Pt_126_MS

value: left Medial Thigh cytology


title: Pt_42_MS

value: skin


title: Pt_120_MS

value: Right shoulder mass


title: Pt_40A_MS

value: paraspinal soft tissue (March)


title: Pt_128_MS

value: left inferior middle turbinate, nasopharyngeal, left sphenoid-ethmoid, sphenoid


title: Pt_54_MS


title: Pt_119_MS

value: Lung mass


title: Pt_36B_MS

value: subcutateous/LN


title: Pt_110_MS

value: myeloid sarcoma

value: laryngeal mass


title: Pt_41_MS

value: upper chest skin


title: Pt_37_MS

value: sinus mass


title: Pt_43A_MS

value: breast


title: Pt_31B_MS

value: peritoneum (2015)


title: Pt_32_MS

value: spleen


title: Pt_35_MS

value: soft tissue nodule


title: Pt_30_MS

value: parotid


title: Pt_29B_MS

value: tonsil (2014)


title: Pt_26_MS

value: anal skin


title: Pt_13_MS

value: breast mass


title: VSMCs,male,tdTomato

city: Chongqing

first: Qing

middle: Rex

last: Lyu

state: Chongqing

address: #118 Xingguang Avenue

department: Affiliated Chongqing General Hospital

institute: Chongqing University

description: Library name: Male_Red

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.
Assembly: GRCm39
Supplementary files format and content: A txt file includes raw counts for each sample

source_name: Ascending aorta and aortic arches

extract_protocol:
The ascending aorta and aortic arch tissues were minced and digested in an enzyme solution containing DNase I (5 U/mL), collagenase IV (1 mg/mL), and dispase (1 mg/mL) in sequential 30-, 60-, and 90-minute steps, with trituration and cell counting performed between each step. After digestion, the cell suspension was passed through a 30-m cell strainer. After centrifugation, the supernatant was removed, red blood cells were lysed, and the cells were finally resuspended and counted to obtain a single-cell suspension. Next, the prepared single-cell suspensions were subjected to fluorescence-activated cell sorting (FACS) (BD, FACSAria III, U.S.A.) based on GFP and tdTomato fluorescence. Four groups were collected for downstream experiments: GFP-male, tdTomato-male, GFP-female, and tdTomato-female.
The RNA-seq transcriptome library was prepared following SMART-Seq_V4 Ultra Low Input RNA Kit for Sequencing from Clontech (San Diego, CA) using 10ng of total RNA. Reverse transcription (one-strand synthesis) was performed first, and RNA with a polyA tail (major mRNA) was reverse transcribed using Oligo(dT) primer. Three cytosine (C) residues are added to the 3' end of the cDNA strand because of the use of a special active reverse transcriptase (MMLVRT) for reverse transcription. Two strands of cDNA were synthesized with the use of TSO (template-switching oligo) primers, thereby replacing RNA complementary to one strand of cDNA. Then, the cDNA was expanded to ng level by PCR amplification. DNA disruption using a modified, highly active Tn5 transposase was performed while the linker was added to both ends of the cDNA. After the last PCR amplification, the machine was ready for sequencing. After quantified by Qubit 4.0, paired-end RNA-seq sequencing library was sequenced with the NovaSeq X plus sequencer (2 × 150bp read length).

value: Ascending aorta and aortic arches

value: Vascular smooth muscle cells

value: male

tag: sorted population

value: tdTomato


title: VSMCs,male,GFP

description: Library name: Male_Green

tag: tissue

value: GFP


title: Pt_11_MS

value: myeloid sarcoma

value: epidural tumor


title: VSMCs,female,tdTomato

description: Library name: Female_Red

value: female


title: VSMCs,female,GFP

description: Library name: Female_Green


title: Pt_6_MS

value: pelvic/ovary mass


title: Pt_5_MS

value: sigmoid colon


title: Pt_23_MS

value: cervical lymph node


title: Pt_34_MS

value: sacral tumor


title: Tumour, 100 mg/kg STC-15, 48 h, rep5

city: Cambridge

first: Harry

last: Fischl

address: Babraham Research Campus

institute: Storm Therapeutics

description:
Library name: TS48_5
rRNA depleted total RNA-seq

data_processing:
Paired-end RNA-seq fastq files were trimmed of adapters using Trim Galore (Krueger et al., 2023) and then aligned to either the mouse GRCm39 genome using the STAR aligner (Dobin et al., 2013). Normalised bigwig tracks were generated by dividing the signal at each nucleotide by the total genome signal and multiplying by 1 billion.
Assembly: GRCm39
Supplementary files format and content: .bw files show normalized signal for positive and negative strands

source_name: Tumour

growth_protocol: Female C57Bl/6 mice (Envigo UK), were implanted subcutaneously (s.c.) on the left flank with 1x107 MC38 cells in serum free DMEM.  Tumours were measured three times weekly by digital calipers.

extract_protocol:
For RNA-seq, blood and tumour samples for were collected at termination. Up to 500 μL of blood was collected by cardiac puncture, stored in RNAprotect tubes (Qiagen, 76554) and left at RT. Tumours were cut in half, placed in cryovials and snap frozen.
RNA from in vivo whole blood and tumour samples were generated into RNA-seq libraries by Novogene using their rRNA-depletion strand-specific sequencing service. Blood samples were also depleted for Globin RNA. Libraries were sequenced to a depth of greater than 40 million PE150 reads on a NovaSeq X plus Illumina machine. Data from five biological replicates were collected for each in vivo condition.

treatment_protocol: Mice were randomised into 7 groups (5 mice/group). Six groups were orally dosed with 100 mg/kg STC-15 once daily, for sample collection at T=0, T=1h, T=4h, T=12h, T= 48h and T=120h. One group was orally dosed once daily with vehicle control, for sample collection at T=120h. The mice in the T=0 group received 6 treatment doses and were terminated 24h after the 6th dose. The mice in the other groups received 7 treatment doses and were collected at the indicated time following the 7th dose.

value: Tumour

value: C57BL6 murine colon adenocarcinoma cells

value: 100 mg/kg QD STC-15


title: Tumour, 100 mg/kg STC-15, 120 h, rep3

description:
Library name: TS120_3
rRNA depleted total RNA-seq


title: Pt_18_MS

value: frontal brain tumor


title: Pt_15_MS

value: left shin skin


title: Pt_21_MS

value: mesenteric mass


title: Tumour, 100 mg/kg STC-15, 48 h, rep3

description:
Library name: TS48_3
rRNA depleted total RNA-seq


title: Pt_8_BM_CR

value: bone marrow


title: Tumour, 100 mg/kg STC-15, 120 h, rep2

description:
Library name: TS120_2
rRNA depleted total RNA-seq


title: Tumour, 100 mg/kg STC-15, 120 h, rep5

description:
Library name: TS120_5
rRNA depleted total RNA-seq


title: Pt_42_AML_Dx


title: Pt_32_AML_Rl


title: Tumour, 100 mg/kg STC-15, 120 h, rep4

description:
Library name: TS120_4
rRNA depleted total RNA-seq


title: Tumour, 100 mg/kg STC-15, 120 h, rep1

description:
Library name: TS120_1
rRNA depleted total RNA-seq


title: Pt_42_BM


title: Pt_22_MS

value: lung mass


title: Tumour, 100 mg/kg STC-15, 48 h, rep4

description:
Library name: TS48_4
rRNA depleted total RNA-seq


title: Tumour, 100 mg/kg STC-15, 24 h, rep5

description:
Library name: TS24_5
rRNA depleted total RNA-seq


title: Tumour, 100 mg/kg STC-15, 48 h, rep1

description:
Library name: TS48_1
rRNA depleted total RNA-seq


title: Tumour, 100 mg/kg STC-15, 48 h, rep2

description:
Library name: TS48_2
rRNA depleted total RNA-seq


title: Tumour, 100 mg/kg STC-15, 24 h, rep4

description:
Library name: TS24_4
rRNA depleted total RNA-seq


title: Pt_37_BM


title: Tumour, 100 mg/kg STC-15, 24 h, rep2

description:
Library name: TS24_2
rRNA depleted total RNA-seq


title: Pt_40_BM


title: Tumour, 100 mg/kg STC-15, 24 h, rep3

description:
Library name: TS24_3
rRNA depleted total RNA-seq


title: Pt_35_BM


title: Pt_41_BM


title: Pt_36_BM


title: Tumour, 100 mg/kg STC-15, 24 h, rep1

description:
Library name: TS24_1
rRNA depleted total RNA-seq


title: Tumour, 100 mg/kg STC-15, 12 h, rep5

description:
Library name: TS12_5
rRNA depleted total RNA-seq


title: Pt_32_BM


title: Pt_26A_BM


title: Pt_31_BM


title: Tumour, 100 mg/kg STC-15, 12 h, rep2

description:
Library name: TS12_2
rRNA depleted total RNA-seq


title: Tumour, 100 mg/kg STC-15, 12 h, rep4

description:
Library name: TS12_4
rRNA depleted total RNA-seq


title: Tumour, 100 mg/kg STC-15, 12 h, rep1

description:
Library name: TS12_1
rRNA depleted total RNA-seq


title: Tumour, 100 mg/kg STC-15, 4 h, rep4

description:
Library name: TS4_4
rRNA depleted total RNA-seq


title: Tumour, 100 mg/kg STC-15, 4 h, rep5

description:
Library name: TS4_5
rRNA depleted total RNA-seq


title: Pt_21_BM


title: Pt_6_BM


title: Tumour, 100 mg/kg STC-15, 4 h, rep3

description:
Library name: TS4_3
rRNA depleted total RNA-seq


title: Pt_22_BM


title: Pt_23_BM


title: Tumour, 100 mg/kg STC-15, 12 h, rep3

description:
Library name: TS12_3
rRNA depleted total RNA-seq


title: Tumour, 100 mg/kg STC-15, 4 h, rep2

description:
Library name: TS4_2
rRNA depleted total RNA-seq


title: Tumour, 100 mg/kg STC-15, 1 h, rep5

description:
Library name: TS1_5
rRNA depleted total RNA-seq


title: Pt_5_BM


title: Pt_9_BM


title: Pt_16_BM


title: Pt_29_BM


title: Tumour, 100 mg/kg STC-15, 1 h, rep4

description:
Library name: TS1_4
rRNA depleted total RNA-seq


title: Tumour, 100 mg/kg STC-15, 4 h, rep1

description:
Library name: TS4_1
rRNA depleted total RNA-seq


title: Tumour, 100 mg/kg STC-15, 1 h, rep2

description:
Library name: TS1_2
rRNA depleted total RNA-seq


title: Tumour, 100 mg/kg STC-15, 1 h, rep1

description:
Library name: TS1_1
rRNA depleted total RNA-seq


title: Pt_10_BM


title: Pt_20_BM


title: Pt_24_BM


title: Tumour, Vehicle, 120 h, rep5

description:
Library name: TV120_5
rRNA depleted total RNA-seq

value: Vehicle


title: Tumour, Vehicle, 120 h, rep3

description:
Library name: TV120_3
rRNA depleted total RNA-seq


title: Pt_2_BM


title: Pt_10_BM_CR


title: Ct_AML_L


title: Tumour, Vehicle, 120 h, rep4

description:
Library name: TV120_4
rRNA depleted total RNA-seq