title: 20276-plus-cyto_ADT

source_name: Male, 25, non-diabetic, islet, cytokine treated, antibody tags

value: pancreatic islet

value: Male

tag: disease state

value: non-diabetic

value: cytokine treated

value: ADT

value: TotalSeq™-A0008 anti-human CD273  (B7-DC, PD-L2), TotalSeq™-A0022 anti-human CD137L (4-1BB Ligand), TotalSeq™-A0031 anti-human CD40, TotalSeq™-A0032 anti-human CD154, TotalSeq™-A0071 anti-human CD194 (CCR4), TotalSeq™-A0124 anti-human CD31 (PECAM1), TotalSeq™-A0129 anti-human CD140b (PDGFRβ), TotalSeq™-A0140 anti-human CD183 (CXCR3), TotalSeq™-A0143 anti-human CD196 (CCR6), TotalSeq™-A0145 anti-human CD103 (Integrin αE), TotalSeq™-A0151 anti-human CD152 (CTLA-4), TotalSeq™-A0152 anti-human CD223 (LAG-3), TotalSeq™-A0153 anti-human KLRG1 (MAFA-L), TotalSeq™-A0154 anti-human CD27, TotalSeq™-A0155 anti-human CD107a (LAMP-1), TotalSeq™-A0156 anti-human CD95 (Fas), TotalSeq™-A0158 anti-human CD134 (OX40), TotalSeq™-A0159 anti-human HLA-DR, TotalSeq™-A0169 anti-human CD366 (Tim-3), TotalSeq™-A0174 anti-human CD58 (LFA-3), TotalSeq™-A0176 anti-human CD39, TotalSeq™-A0177 anti-human CD178 (Fas-L), TotalSeq™-A0219 anti-human CD119 (IFN-γ R α chain), -TotalSeq™-A0360 anti-human CD357 (GITR), TotalSeq™-A0368 anti-human CD226 (DNAM-1), TotalSeq™-A0579 anti-human CD9, TotalSeq™-A0584 anti-human TCR Vα24-Jα18 (iNKT cell), TotalSeq™-A0597 anti-human CD209 (DC-SIGN), TotalSeq™-A0804 anti-human CD186 (CXCR6), TotalSeq™-B0005 anti-human CD80, TotalSeq™-B0006 anti-human CD86, TotalSeq™-B0007 anti-human CD274 (B7-H1, PD-L1), TotalSeq™-B0048 anti-human CD45, TotalSeq™-B0053 anti-human CD11c, TotalSeq™-B0085 anti-human CD25, TotalSeq™-B0088 anti-human CD279 (PD-1), TotalSeq™-B0100 anti-human CD20, TotalSeq™-B0139 anti-human TCR γ/δ, TotalSeq™-B0146 anti-human CD69, TotalSeq™-B0147 anti-human CD62L, TotalSeq™-B0148 anti-human CD197 (CCR7), TotalSeq™-B0161 anti-human CD11b, TotalSeq™-B0165 anti-human CD314 (NKG2D), TotalSeq™-B0168 anti-human CD57 Recombinant, TotalSeq™-B0171 anti-human CD278 (ICOS), TotalSeq™-B0224 anti-human TCR α/β, TotalSeq™-B0355 anti-human CD137 (4-1BB), TotalSeq™-B0386 anti-human CD28, TotalSeq™-B0390 anti-human CD127 (IL-7Rα), TotalSeq™-B0034 anti-human CD3, TotalSeq™-B0050 anti-human CD19, TotalSeq™-B0063 anti-human CD45RA, TotalSeq™-B0072 anti-human CD4, TotalSeq™-B0080 anti-human CD8a, TotalSeq™-B0081 anti-human CD14, TotalSeq™-B0083 anti-human CD16, TotalSeq™-B0084 anti-human CD56 (NCAM) Recombinant, TotalSeq™-B0089 anti-human TIGIT (VSTM3), TotalSeq™-B0087 anti-human CD45RO, TotalSeq™-B0159 anti-human HLA-DR, TotalSeq™-A0575 anti-human CD49a (ITGA1)


title: Sample 43T Tumor tissue

status: Public on May 29 2025

type: SRA

city: Lyon

first: Massimiliano

last: Cocca

address: 151 Cours Albert Thomas

country: France

institute: Université Claude Bernard Lyon 1, Inserm UMR 1350 - PaThLiv

library_source: transcriptomic

data_processing:
Sequence reads were processed using an internal pipeline developed with the snakemake framework. Reads were trimmed using the fastp software and QC was carried on using fastp and FastQC softaware.
Trimmed sequence reads were aligned to GRCh38 using STAR aligner.
Raw gene expression counts were generated by STAR and RSEM using default parameters.
Assembly: GRCh38
Supplementary files format and content: Tab delimited files including raw counts for each sample

molecule: total RNA

organism: Homo sapiens

source_name: Liver

extract_protocol:
RNA was extracted with the RNAeasy mini kit (Qiagen, #74104) and treated with the RNAse Free DNAse set (Qiagen, #79254) and controlled for quality on a Bioanalyzer (Agilent)
libraries were prepared using the TruSeq® Stranded RNA HT (w/Ribo-Zero™) kit to increases the depth of sequencing.

value: HBV-related HCC

tag: tissue

value: Liver

tag: tissue type

value: Tumor tissue


title: ej2j2_4,  ej2 j2 tomato double mutant Inflorescence meristems

city: Cold Spring Harbor

first: Zachary

last: Lippman

state: New York

address: 1 Bungtown Rd

department: Plant Biology

country: USA

institute: Cold Spring Harbor Laboratory

description: Library name: 1883-4

data_processing:
Reads were trimmed with Trimmomatic (ILLUMINACLIP:TruSeq2-PE.fa:2:30:10:1:FALSE LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36) and aligned to the cDNA annotation of reference genome sequence of tomato (SL4.0) using STAR v2.6.1.d. Normalization and quantification of individual transcript expression was done in R by calculating transcripts per million (TPM).
Assembly: Tomato Heinz SL4.00
Supplementary files format and content: csv file, include TPM values for each sample

organism: Solanum lycopersicum

source_name: Inflorescence meristems

growth_protocol: Inflorescence meristems were collected from n = 4 plants at 8 weeks old under stereoscope magnification.

extract_protocol:
TRIzol (Invitrogen) and a Direct-zol RNA Miniprep kit with on-column DNA digestion (Zymo Research)
TruSeq V2 RNA-Seq prep kit (Illumina)

value: Inflorescence meristems

tag: genotype

value: ej2 j2


title: S4 2W ANT CON-2

city: Beijing

first: Ye-guang

last: Chen

address: Tsinghua Road, Medical Building

department: School of life science

country: China

institute: Tsinghua University

description:
SMAD4-2W results_ant_con-ko.csv
C18S4-2W-con-72-ant

data_processing:
RNA-seq reads were aligned to the reference genome GRCm38 using the STAR software.
Then the differential expression analysis was effectuated employing DESeq2 software.
For functional enrichment analyses, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were conducted, utilizing ClusterProfiler software.
Assembly: mm10

organism: Mus musculus

source_name: Stomach

extract_protocol:
Total RNA was isolated from mouse gastric epithelial cells from Ctrl, ALK3 KO or Smad4 KO mice at 2 week or 4 week after the administration of tamoxifen using TRIzol Reagent (Life Technologies) according to the manufacturer’s instructions.
The library were prepared for sequecing using NEBNext Ultra RNA library Prep Kit for Illumina.

treatment_protocol: Mice were crossed with the mice expressing cre-recombinase and treated with four consecutive daily doses of tamoxifen (Sigma, 100 mg/kg) in corn oil.

value: Stomach

tag: cell line

value: tissue

tag: cell type

value: epithelial cell and stromal cell

value: wild type

tag: treatment

value: Tamoxifen injection


title: SA +Stress

city: San Diego

first: Hung

last: Chan

state: CA

address: 9452 Medical Center Drive,ACTRI Bldg, L1W420

institute: UCSD

description: 10X Genomics

library_source: transcriptomic single cell

data_processing:
Cell Ranger (10X Genomics) with default parameters was used to perform sample demultiplexing ,barcode processing, alignment to the mm10 reference genome, and gene counting
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: skin

extract_protocol:
Single-cell suspensions generated from mouse skin
10X Genomics 3’ V3.1

value: skin

value: whole tissues

value: wild-type

value: SA infection +restraint stress


title: AK3 4W ANT KO-2

description:
ALK3-4W results_ant_con-ko.csv
KO-ant2

value: ALK3 knockout


title: active tuberculosis patient 3

city: Shah Alam, Selangor, Malaysia

first: Yang

last: Jun

state: selangor

address: setia alam

country: Malaysia

institute: UiTM

description:
Library name: Sample 3
sample3

data_processing:
High-quality clean data were obtained by processing fastq-format data with Trimmomatic (v0.30).
removing adapter sequences
discarding 5' or 3' end bases containing Ns or with quality values below 20
removing bases with an average quality score below 20 using a sliding window of 4 bp
eliminating reads shorter than 18 bp after trimming.
Assembly: hg38
Supplementary files format and content: CSV file include the known miRNA in each sequencing sample.
Supplementary files format and content: CSV file include the novel miRNA in each sequencing sample.

source_name: blood

growth_protocol: Fresh whole-blood samples (5 mL) were collected in EDTA-coated anticoagulant tubes from both HCs and patients with active TB (ATB).

extract_protocol:
Total RNA was extracted using the Total RNA Extraction Kit (Thermo Fisher Scientific Inc., MA, USA), following the manufacturer’s instructions. RNA quantity and quality were determined using the Nanodrop 2000 (Thermo Fisher Scientific, MA, USA) and Agilent 2100 Bioanalyzer systems (Agilent Technologies). Only samples with an RNA Integrity Number (RIN) above 7 were utilized to construct a high-quality total RNA sequencing (RNA-seq) library.
For library preparation, 1 μg of total RNA or 10 ng of small RNA was used. The 3’ SR Adaptor for Illumina was attached to the small RNA using a 3’ ligation enzyme. To prevent adaptor-dimer formation, excess 3’ SR Adaptor was hybridized with the SR RT Primer for Illumina. The 5’ SR Adaptor for Illumina was then attached to the small RNA using a 5' ligation enzyme, and first-strand cDNA was synthesized using ProtoScript II Reverse Transcriptase. Each sample was amplified by PCR using P5 and P7 primers, and the PCR products were purified using DNA clean beads. The purified products, ranging from 140 to 160 bp, were recovered and cleaned using PAGE, and validated with an Agilent 2100 Bioanalyzer. Libraries with different indexes were multiplexed, and the qualified libraries were sequenced on the Illumina MGI2000 System (MGI Tech Co., Ltd, China) using paired-end PE150.

treatment_protocol: Samples were immediately centrifuged at 4℃ and 3000×g for 15 minutes to separate the plasma, which was then stored at -80℃ until RNA extraction.

value: blood

value: serum

tag: subject status

value: active tuberculosis

value: infect differentiation

tag: time

value: cough 4 weeks


title: HS-IU_1700

city: Wenzhou

first: Tong

last: Yin

address: Luchengqu Guantanglu38-9

institute: Zhejiang Key Laboratory of Dairy Cattle Genetic Improvement and Milk Quality Researc

description: Library name: HS-IU_1700

data_processing:
we clipped adaptors for RNA reads and discarded short reads (< 36 bp) and reads with poor quality (< 20) applying the software package cutadapt V4.2. In the second step, we assessed the quality of the RNA reads for each sample using FastQC V0.12.1, and found that all samples past the per base sequence quality. Afterwards, the reference genome sequences and the annotation file according to bovine assembly ARS-UCD1.2 were provided to generate the genome index files using the software package STAR V2.7.11a. Finally, the RNA-seq reads were mapped to the reference genome based on the index and genome files generated in the previous step and the number of reads per gene were counted for each sample using the flag “--quantMode GeneCounts” with STAR. After combining the reads per gene for all samples, we identified 23,010 genes with nonzero RNA-seq reads.
Assembly: bovine assembly ARS-UCD1.2
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

organism: Bos taurus

source_name: Whole Blood

extract_protocol:
Total RNA was isolated using the Zymo directZol Mini Prep kit by homogenizing 100 ul of RLT cell suspension in 900 ul TriZOL reagent supplemented with 20 ul 1-Thioglycerol. 200 ng of total RNA were captured on oligo-dT beads and reverse transcribed directly on the beads.
Libraries were prepared using the Lexogen SENSE mRNA-seq Library Prep Kit V2 (Lexogen, Greenland, NH, USA).

value: Whole Blood

tag: age

value: Dam

value: no heat stress

tag: batch


title: HS-IU_1725

description: Library name: HS-IU_1725


title: S4 2W CP KO-1

description:
SMAD4-2W results_cp_con-ko.csv
C18S4-2W-ko-92-cp

value: Stomach

value: tissue

value: Smad4 knockout


title: HS-IU_1662

description: Library name: HS-IU_1662


title: Sample 113T Tumor tissue

value: HBV-related HCC

value: Liver

value: Tumor tissue


title: AK3 4W ANT KO-1

description:
ALK3-4W results_ant_con-ko.csv
KO-ant1

value: epithelial cell and stromal cell

value: Tamoxifen injection


title: active tuberculosis patient 1

description:
Library name: Sample 1
sample1


title: Sample FS2_NT Normal liver tissue

value: control

value: Normal liver tissue


title: Sample 43NT Non tumor tissue

value: Non tumor tissue


title: HS-IU_1622

description: Library name: HS-IU_1622


title: Sample FS1_NT Normal liver tissue


title: AK3 4W ANT CON-1

description:
ALK3-4W results_ant_con-ko.csv
CON-ant1

value: wild type


title: HS-IU_1577

description: Library name: HS-IU_1577


title: Donor 2 (s2), Mock, 72h, 2° Experiment

city: Roma

first: Giuseppe

middle: Rubens

last: Pascucci

state: RM

address: Viale Regina Elena, 291

department: Center for Life Nano Science

country: Italy

institute: Istituto Italiano di Tecnologia

description: this second experiment evaluates the impact of interferon (IFN alfa-2a) on viral infection

library_source: genomic

data_processing:
The ATAC-sequencing reads quality was assessed with FastQC v0.11.9 (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). Reads were aligned to the reference genome hg19 using bowtie v2.3.5.1 (Langmead 2012) with default parameters.
The conversion from sam to bam file was performed through the view function of SAMtools v1.7 (Li 2009). BAM files were deduplicated with GATK v4.1.9.0 (https://doi.org/10.1093/bioinformatics/btp616) markDuplicates with default parameters, sorted, and indexed with SAMtools v1.7 sort functions. Peaks were called by MACS2 v2.2.6 (https://doi.org/10.1186/gb-2008-9-9-r137) with parameters --format AUTO --nomodel --shift -100 --extsize 200 -B --SPMR --call-summit -q 0.01 -g hs.
BigWig (bw) files were obtained from the BedGraph (bdg) files applying the bedGraphToBigWig v4 (Kent 2010) tool with default parameters. Finally, all peaks matching blacklisted regions (downloaded from https://www.encodeproject.org/files/ENCFF001TDO/@@download/ ENCFF001TDO.bed.gz) were removed with the function intersect of bedtools suite v2.29.2 (Quinlan 2010).
Assembly: hg19
Supplementary files format and content: standard bigwig and narrow/broad peak

molecule: genomic DNA

growth_protocol: PHHs were prepared using the protocol described in Le Cluyse & Alexandre (2010) with minor modifications. Liver samples are first perfused in Solution I (NaCl 58,44 M, KCl 74,56 M, Na2HPO4, 2H2O 177,99 M, Hepes 0,6%, EGTA 0,5 mM; pH7,4) and then in Solution II (NaCl 58,44 M, KCl 74,56 M, Na2HPO4, 2H2O 177,99 M, Hepes 0,6%, CaCl2 110 M) containing 0,4 mg/ml of collagenase from Clostridium histolyticum (Sigma-Aldrich, #C5138). Cells are seeded at 2,5x10^5 cells per cm² on collagen type IV (Corning, #354236) pretreated plates and cultured overnight in William’s medium (Life Technologies, #22551-089) supplemented with 10% Fetal Clone II (GE Healthcare), 1% penicillin/streptomycin (Invitrogen, #15140122), 1% Glutamax X100 (Invitrogen, #35050038), 5 µg/ml Insulin (Sigma–Aldrich, #I9278) and 5×10-7 M hydrocortisone (Upjohn Laboratories). PHHs are then extensively washed in serum-free medium, kept in serum-free medium for 24 hours to counter-select the growth of contaminating fibroblast and endothelial cells, and then plated in complete William’s medium.

extract_protocol:
50 000 HBV or MOCK infected cells harvested 2- and 72-hours post-infection were used for the transposase reaction, which was carried out essentially as described in Buenrostro et al. (2015). PHHs were trypsinized (Trypsine 0,5% EDTA; Invitrogen, #25300054) at 37°C and the reaction was stopped by adding cell cultured medium on ice. After a wash in cold PBS 1X (Eurobio, #CS1PBS01KBP) cells were centrifugated at 500g for 5 minutes at 4°C, the pellets resuspend the in 50 µl of cold nuclei lysis buffer (10mM Tris-HCL [pH7,4], 10mM NaCl, 3mM MgCl2, 0,1% NP-40). After 30 minutes, the cells were centrifuged at 500g, for 5 minutes at 4°C, the supernatants removed and pelleted nuclei used for the tagmentation protocol. Briefly, pellets were resuspended in the transposase reaction mix: 25 μL 2xTD buffer (Illumina Cat. FC-121-1030), 2.5 μL Tn5 transposase (Nextera Illumina) and 22.5 μL nuclease-free water) for 40 min at 37 °C and then was purified on Qiagen MinElute columns.
Libraries fragments were amplified using 1× NEBNext High fidelity 2x PCR masterMix (M0541) and 1,25 μM of custom Nextera PCR primers using the following PCR conditions: 72 °C for 5 min; 98 °C for 30 s; and thermocycling at 98 °C for 10 s, 63 °C for 30 s and 72 °C for 1 min. Library amplification were monitored by qPCR on 1/10 of the reaction after 5 cycles in order to avoid saturation and the risk of GC and size bias. Libraries were typically amplified for a total of 10–15 cycles followed by size-selection using AMPure beads and library quality control by Bioanalyzer (Agilent). Each ATAC-sequencing library was pair-end sequenced (150 cycles) to an average of 70 million reads per sample using a NextSeq V2 high output sequencing kit on NextSeq 500 Illumina platform.

treatment_protocol: The HBV inoculum used in this study was prepared from HepAD38 cells as previously described (Ladner et al., 1997). HepAD38 is an HepG2-derived stable cell line Carrying a 1.3 HBV transgene (genotype D, serotype ayw) under the control of a tet-off promoter. HepAD38 cells were cultured in HYPERFlask® (Corning, #10020) coated with type IV collagen (Corning, #354236) in 550 ml of complete DMEM-F12 medium supplemented with 10% decomplemented FBS (Gibco, #10270-106), 1% penicillin/streptomycin (Invitrogen, #15140122) and 1% sodium-pyruvate (Invitrogen, #11360039). Supernatants (550 ml/flask) were harvested twice a week for at 3-4 months, clarified first through 0.45 μm and then 0.22 µm filters (Millipore, #10785534) and precipitated overnight at 4 °C with 8% PEG-8000 (Sigma–Aldrich, #1546605), The precipitates were centrifuged at 3500 g for 1 hour and the pellets resuspended in Opti-MEM (Invitrogen, #31985070) to achieve a 50 to 100 fold concentration. After DNA extraction (QIAmp Ultrasens Virus kit, Qiagen) the HBV inoculum was tittered by qPCR using serial dilutions of an HBV plasmid to build a standard curve. Primers are detailed in Supplementary Figure 1. All viral preparations were tested for the presence of endotoxins (Lonza Verviers, Belgium). PHHs were treated with 2% of DMSO (Sigma–Aldrich, #D2650) for 24 hours before infection and then incubated for 16 h with an HBV inoculum produced in HepAD38 cells at a multiplicity of infection of 250 vge (virus genome equivalents) per cell, in presence of 4% PEG-8000 (Polyethylene glycol, Sigma–Aldrich, #1546605). IFN alfa-2a treatment (Roferon-A, Roche) on PHH was administered post infection (1000 UI/ml) and renewed every 48h until the desired time points (1000 UI/ml). Cells were treated with Deferasirox 50 μM and 100μM at 24h, 96h and 6 days post infection.

value: Primary Human Hepatocytes (PHHs)

value: Control sample


title: healthy control 2

description:
Library name: Sample 5
sample5

value: blood

value: serum

value: healthy control

value: infect differentiation


title: AK3 4W CP KO-2

description:
ALK3-4W results_cp_con-ko.csv
KO-cp2

value: Stomach

value: tissue

value: ALK3 knockout


title: Donor 1 (s1), Mock, 72h, 2° Experiment

value: Liver


title: HS-IU_1568

description: Library name: HS-IU_1568

value: Whole Blood

value: Dam

value: heat stress


title: HS-IU_1538

description: Library name: HS-IU_1538

value: no heat stress


title: Donor 2 (s2), INF, 72h, 2° Experiment

value: HBV infected treated with interferon


title: AK3 4W CP CON-2

description:
ALK3-4W results_cp_con-ko.csv
CON-cp2

value: epithelial cell and stromal cell

value: Tamoxifen injection


title: active tuberculosis patient 2

description:
Library name: Sample 2
sample2

value: active tuberculosis

value: cough 5 weeks


title: AK3 4W ANT CON-2

description:
ALK3-4W results_ant_con-ko.csv
CON-ant2

value: wild type


title: AK3 4W CP KO-1

description:
ALK3-4W results_cp_con-ko.csv
KO-cp1


title: HS-IU_1467

description: Library name: HS-IU_1467


title: AK3 2W ANT KO-2

description:
ALK3-2W results_ant_con-ko.csv
C18AK3-2W-ko-142-ant


title: Sample 113NT Non tumor tissue

value: HBV-related HCC

value: Non tumor tissue


title: AK3 4W CP CON-1

description:
ALK3-4W results_cp_con-ko.csv
CON-cp1


title: Donor 2 (s2), HBV, 72h, 2° Experiment

value: Primary Human Hepatocytes (PHHs)

value: HBV infected


title: HS-IU_1463

description: Library name: HS-IU_1463


title: Donor 1 (s1), HBV, 72h, 2° Experiment


title: HS-IU_1460

description: Library name: HS-IU_1460


title: H2023_ mimic miR223_B

type: RNA

city: San Giovanni Rotondo (FG)

first: Fabrizio

last: Bianchi

state: Outside U.S. & Canada

address: Viale Padre Pio 7

institute: Fondazione IRCCS Casa Sollievo della Sofferenza

hyb_protocol: Samples were then hybridized ON using using the Affymetrix GeneChip Hybridization Oven 640 (Thermo Fisher Scientific)

scan_protocol: Samples were whashed, stained, and scanned using a Fluidic Station 450 and Scanner 3000 7G (Thermo Fisher Scientific)

data_processing: Quality control and normalization of Affymetrix .CEL files were performed using TAC software (v4.0; Thermo Fisher Scientific) by performing “Gene level SST-RMA” summarization method with human genome version hg38 (NCBI-Genome Reference Consortium Human Build 38).

label: biotin

source_name: H2023 transfected with mimic miR-223-3p

label_protocol: RNA samples have been amplified, fragmented, and labeled for array hybridization according to the manufacturer’s instruction (Thermo Fisher Scientific).

growth_protocol: H2023 adenocarcinoma cell line were maintained in RPMI (Gibco; Invitrogen) with 10% FBS, and 1% penicillin/streptomycin (Gibco; Invitrogen) at 37°C in a humidified incubator with 5% CO2. Cells were plated at a specific concentration to reach a ~80% confluency before processing.

extract_protocol: Total RNA was purified from cells using guanidinium thiocyanate-phenol-chloroform extraction (TriZol-LS and QIazol, Thermo Fisher Scientific) followed by miRNeasy Mini Kit (Qiagen) to cleanup samples.

treatment_protocol: Reverse transfection was performed using Lipofectamine RNAiMAX (ThermoFisher Scientific) according to the manufacturer’s instructions. Briefly, cells were plated in a 6-well with 0.5 nM of miR-223-3p Mimic (Qiagen), or with 0.5 nM of miR-29a-3p Mimic (Qiagen), or with 0.5 nM of miR-223-3p Inhibitor (Qiagen), or with 0.5 nM of miR-29a-3p Inhibitor (Qiagen), or with 0.5 nM recommended All Stars negative control siRNA (cat. 1027281, Qiagen).  Cell culture media was replaced with fresh complete media at 24h post-transfection.

tag: tumor type

value: adenocarcinoma

value: Lung


title: H2023_ mimic miR29a_B

source_name: H2023 transfected with mimic miR-29a-3p


title: AK3 2W ANT CON-2

description:
ALK3-2W results_ant_con-ko.csv
C18AK3-2W-con-164-ant

value: Stomach

value: tissue


title: Donor 2 (s2), Mock, 72h, replicate 2

value: Liver

value: Control sample


title: flagellin treated mice

city: COLLEGE STATION

first: Yan

last: Zhang

state: Texas

address: 206 olsen blvd

institute: Texas A&M University

data_processing:
Seurat v5.0.2 in R v4.3.4
Assembly: mm10
Supplementary files format and content: Tap-separate files

organism: Mus

source_name: lung

extract_protocol:
Mouse lungs were dissected, minced,  placed in gentleMACS c-tubes and digested in  2 mg/mL collagenase A in DMEM. RNA was harvested following manufacture's protocols.
Single cell RNA sequencing libraries were generated using the 10x Genomics Next GEM Single Cell 5’ Reagent Kit v2 (dual index).

value: lung

value: pulmonary lung cells

value: WT

value: LFN-flagellin/PA


title: PBS treated mice

value: PBS


title: H2023_CTRL mimic_B

source_name: H2023 transfected with mimic control


title: HS-IU_1457

description: Library name: HS-IU_1457

value: Whole Blood

value: Dam

value: no heat stress


title: H2023_ mimic miR29a_A


title: H2023_CTRL mimic_A


title: Donor 2 (s2), Mock, 72h, replicate 1


title: HS-IU_1439

description: Library name: HS-IU_1439


title: AK3 2W ANT CON-1

description:
ALK3-2W results_ant_con-ko.csv
C18AK3-2W-con-144-ant

value: epithelial cell and stromal cell

value: wild type

value: Tamoxifen injection


title: Donor 1 (s1), INF, 72h, 2° Experiment

value: Primary Human Hepatocytes (PHHs)

value: HBV infected treated with interferon


title: fbf-1-3

city: Jerusalem

first: Yonatan

last: Tzur

address: Givat-Ram

country: Israel

institute: Hebrew University of Jerusalem

description: Library name: Fbf_1_S3_R1_001.fastq

data_processing:
Reads  alignment to the C. elegans genome version WBcel235 using STAR  version 2.7.9a
Raw counts per gene were calculated using featureCounts from Subread version 2.0.1
Normalization and differential expression were calculated with Deseq2 version 1.34.0
Assembly: WBcel235
Supplementary files format and content: Excel file with the analysis results. Columns include general gene details (A-B), raw counts for each sample (C-H), normalized counts (I-N), the DESeq2 calculated baseMean (O), the DESeq2 calculated log2FoldChange (P), the DESeq2 calculated lfcSE (Q), the final decision of significance for upregulation in the mutant background (U) and downregulation (V), germline enriched genes as defined in {Reinke, 2004 #3460} (W) and genes bound by FBF-2 as defined in {Porter, 2019 #8095} (X)

molecule: polyA RNA

organism: Caenorhabditis elegans

source_name: fbf-1 Adult worms

growth_protocol: Solid media

extract_protocol:
TRIzol  + Zymo Research Direct-zol RNA miniprep plus kit
KAPA standard mRNA-Seq kit

tag: developmental stage

value: Adult

value: whole worm


title: HS-IU_1516

description: Library name: HS-IU_1516

value: heat stress


title: AK3 2W CP KO-2

description:
ALK3-2W results_cp_con-ko.csv
C18AK3-2W-ko-142-cp

value: Stomach

value: tissue

value: ALK3 knockout


title: MOLM13_H3K27me3_Pos

city: Farmington

first: Harshpreet

last: Chandok

state: CT

address: 10 Discovery Dr

institute: The Jackson Laboratory

data_processing:
Reads were originally aligned to the genome using Bowtie v2.3.5 with the following parameters: -local-very-sensitive -local-no-unal-no-mixed-no-discordant -phred33 -l 10 -X 700 -k1 -N1
PCR Duplicates were rmoved using Picared tools v1.96 using MarkDuplicates
Bam files with unique reads were generated using Samtools v1 and fragments <40 or >1000bp were filtered out, and those regions were compared agianst a blacklist from ENCODE, as well as mitochondrial reads were filtered out.
bigwig files were created with bedGraphToBigWig and the MACS v2.1 package command broadPeak was used to call peaks with a p value cutoff of 1e-8 and broad p value cutoff 1e-4 in general.
HOMERv4 was used to annotate peaks proximal to genes using annotatePeaks.pl utiliing the h38 genome and binding motifs were also identified using HOMER's findMotifsGenome.pl Afterwards PRM-normlized bigwigs were created with bedGraphToBiGWig and bamCoverage to vizualize identified binding sites
Assembly: hg19 and hg38
Supplementary files format and content: Annotated_overlapPeaks.xlsx
Supplementary files format and content: narrowPeaks (samples CHN-13* and CHH-14* do not have a narrowPeak file since they are negative and positive controls respectively)
Library strategy: Cut&Run

growth_protocol: MOLM13 cells were maintained in RPMI-1640 media suppleented with 10% fetal bovine serum (FBS) and 1% Penicillin/Streptomycin in a humidified incubator at 5%CO2 at 37ºC

extract_protocol:
Nuclei were isolated and subjected to the Cut&Run reaction using the CUTANA™ Cut&Run Kit from Epicypher by following the manufacturer's protocol.
Genomic DNA Isolated from the CUT&Run Kit were used for library preparation for the Cut&Run Library kit following the manufactuer's protocol. The library quality was assessed using a High Sensiviity Bioanalyzer and libraries with different barcodes were pooled and sequenced on an Illumina NovaSeq X

treatment_protocol: All cDNA constructs were cloned into a lentiviral fector (EF1α-IRES-Puromycin-T2A-ZsGreen) , with 3X FLAG-Tagsand spin infections were performed at 32ºC at 1500 RCF for 60min with 5µg/mL polybrene and lentiviral supernatants. Cells were FACS Sorted and on million cells per replicate were isolated for library preparation.

value: Acute Myeloid Leukemia

value: WT


title: fbf-1-2

description: Library name: Fbf_1_S11_R1_001.fastq


title: AK3 2W ANT KO-1

description:
ALK3-2W results_ant_con-ko.csv
C18AK3-2W-ko-114-ant


title: AK3 2W CP KO-1

description:
ALK3-2W results_cp_con-ko.csv
C18AK3-2W-ko-114-cp


title: MOLM13_IgG_Neg


title: fbf-1-1

description: Library name: Fbf_1_S12_R1_001.fastq


title: Donor 2 (s2), HBV, 72h, replicate 2

value: Liver

value: HBV infected


title: AK3 2W CP CON-2

description:
ALK3-2W results_cp_con-ko.csv
C18AK3-2W-con-164-cp


title: fbf-1 3xlnc -3

description: Library name: Fbf_1xtriple_1_S2_L001_R1_001.fastq

source_name: fbf-1  3xlnc Adult worms

value: fbf-1 linc-4; linc-29; linc-7


title: Donor 2 (s2), HBV, 72h, replicate 1


title: MOLM13_OE_FLAG-RUNX1DelC_Rep3

value: Lentiviral infection and overexpression


title: AK3 2W CP CON-1

description:
ALK3-2W results_cp_con-ko.csv
C18AK3-2W-con-144-cp

value: epithelial cell and stromal cell


title: fbf-1 3xlnc -2

description: Library name: Fbf_1xtriple_2_S3_L001_R1_001.fastq


title: Donor 1 (s1), HBV, 72h, replicate 2


title: H2023_ mimic miR223_A

value: adenocarcinoma

value: Lung


title: MOLM13_OE_FLAG-RUNX1DelC_Rep2


title: TDC sorted from spleens pooled from 6 naive Zbtb46-GFP mice, replicate 3

city: Milano

first: Michela

last: Riba

address: via Olgettina 60

department: COSR, Center for Omics Sciences

institute: IRCCS, Ospdale San Raffaele

data_processing:
COSR Center (Center for Omics Science, Ospedale San Raffaele custom pipeline
Quality checks have been done on raw data using FastQC and MultiQC
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trimmomatic
Trimmed sequence reads were mapped to Hg38 using STAR
Read count extraction has been made using Rsubread library, featureCounts function
Assembly: Hg38
Supplementary files format and content: text file contains raw counts data for all the samples

source_name: Primary TDC

growth_protocol: 3*106 cells/ml of RPMI+10%FBS

extract_protocol:
RNA was extracted using ReliaPrep™ RNA Miniprep Systems (Promega, Madison, WI, USA) following manufacturer protocol
RNA libraries for RNA-seq were prepared using Lexogen Stranded Quantseq following manufacturer's protocols.

value: Primary TDC

value: Homozygous Zbtb46-GFP

value: Naive mice of 8 weeks of age


title: MOLM13_OE_FLAG-RUNX1DelC_Rep1


title: fbf-1 3xlnc -1

description: Library name: Fbf_1xtriple_3_S4_L001_R1_001.fastq

value: Adult

value: whole worm


title: Donor 1 (s1), Mock, 72h, replicate 2

value: Primary Human Hepatocytes (PHHs)

value: Control sample


title: 3xlnc-3

data_processing:
Reads  alignment to the C. elegans genome version WBcel235 using STAR  version 2.7.9a
Raw counts per gene were calculated using featureCounts from Subread version 2.0.1
Normalization and differential expression were calculated with Deseq2 version 1.34.0
Assembly: WBcel235
Supplementary files format and content: Excel file with the DESeq2 analysis results. Columns include general gene details (A-B), raw counts for each sample (C-G), normalized counts (I-N), the DESeq2 calculated baseMean (O), the DESeq2 calculated lfcMLE (Q), the final decision of significance for upregulation in the mutant background (U) and downregulation (V), germline enriched genes as defined in {Reinke, 2004 #3460} (W) and genes bound by FBF-2 as defined in {Porter, 2019 #8095}

source_name: 3xlnc Adult worms

value: linc-4; linc-29; linc-7


title: MOLM13_OE_FLAG-RUNX1C_Rep3

value: Acute Myeloid Leukemia

value: RUNX1C OE


title: Conventional T cells sorted from spleens pooled from 6 naive Zbtb46-GFP mice, replicate 3

source_name: Primary T cell

value: Primary T cell


title: Donor 1 (s1), Mock, 72h, replicate 1

value: Liver


title: Donor 2 (s2), Mock, 2h, replicate 2


title: TDC sorted from spleens pooled from 6 naive Zbtb46-GFP mice, replicate 2


title: Conventional DC sorted from spleens pooled from 6 naive Zbtb46-GFP mice, replicate 3

source_name: Primary DC

value: Primary DC


title: 3xlnc-2


title: Donor 1 (s1), HBV, 72h, replicate 1

value: HBV infected


title: MOLM13_OE_FLAG-RUNX1C_Rep1

value: Lentiviral infection and overexpression


title: fbf-2-3

source_name: fbf-2 Adult worms


title: Donor 2 (s2), Mock, 2h, replicate 1

source_name: Liver


title: Conventional T cells sorted from spleens pooled from 6 naive Zbtb46-GFP mice, replicate 2


title: 3xlnc-1


title: Conventional DC sorted from spleens pooled from 6 naive Zbtb46-GFP mice, replicate 2


title: MOLM13_OE_FLAG-RUNX1B_Rep3

value: RUNX1B OE


title: MOLM13_OE_FLAG-RUNX1C_Rep2


title: Donor 1 (s1), Mock, 2h, replicate 1


title: MOLM13_OE_FLAG-RUNX1B_Rep2


title: MOLM13_OE_FLAG-RUNX1B_Rep1


title: Donor 1 (s1), Mock, 2h, replicate 2


title: fbf-2-2


title: Donor 2 (s2), HBV, 2h, replicate 2


title: Donor 2 (s2), HBV, 2h, replicate 1


title: TDC sorted from spleens pooled from 5 naive Zbtb46-GFP mice, replicate 1


title: Conventional T cells sorted from spleens pooled from 5 naive Zbtb46-GFP mice, replicate 1


title: fbf-2-1


title: WT-3

source_name: N2 Wild type Adult worms

value: Wild type


title: Donor 1 (s1), HBV, 2h, replicate 2


title: Conventional DC sorted from spleens pooled from 5 naive Zbtb46-GFP mice, replicate 1


title: WT-2


title: MOLM13_OE_FLAG-RUNX1A_Rep2

value: RUNX1A OE


title: ad-egfp4

city: Shanghai

first: Lianju

last: Li

state: China

address: Xujiahui Road

institute: Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases

data_processing:
Paired-end sequence files (fastq) were mapped to the reference genome. Gene abundance was expressed as fragments per kilobase of exon per million reads mapped (FPKM). Differential expression analysis for mRNA was performed using R package edgeR.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample .

source_name: Mouse hepatoma

extract_protocol:
Total RNA was isolated using RNeasy mini kit (Qiagen, Germany).
Paired-end libraries were synthesized using the TruSeq™ RNA Sample Preparation Kit (Illumina, USA). In brief, the mRNA was fragmented into small pieces following purification with poly-T oligo-attached magnetic beads. The cleaved RNA fragments were copied into first strand cDNA and the second strand cDNA was synthesized using DNA Polymerase I and RNase H. These cDNA fragments went through the end repair process, addition of a ‘A’ base, and ligation of adapters. The products were purified and enriched to creat the final cDNA library.

value: Mouse hepatoma

value: ad-egfp


title: WT-1

value: Adult


title: MOLM13_OE_FLAG-RUNX1A_Rep3


title: MOLM13_OE_FLAG-RUNX1A_Rep1


title: ΔnsdD, Conidia 2 days [NdC_6]

city: Madison

first: Heungyun

middle: Harrison

last: Moon

state: WI

address: 1550 Linden drive

department: Bacteriology

institute: University of Wisconsin-Madison

data_processing:
Mapping of the clean reads to the genome was carried out using Tophat2 (version 2.0.12, Veg and Asex samples) and hisat2 (version 2.1, conidia samples).
Gene expression level was processed using HTSeq (version 0.6.1, Veg and Asex samples) and FeatureCounts (version 1.5.0, conidia samples).
Assembly: GCF_000149205.2
Supplementary files format and content: tab-delimited text files include associated peak information for each sample

organism: Aspergillus nidulans

source_name: Conidia

growth_protocol: The fungal strains were inoculated into liquid or solid 1% glucose minimal medium (GMM) with appropriate supplements and incubated at 37 °C for 2 days. The conidia were collected in phosphate-buffered saline (PBS) from the entire plate and counted using a hemocytometer. To collect vegetatively growing cells, 5×105 conidia·ml-1 were inoculated into 100 ml liquid GMM and incubated for 36 hr at 37 °C, 220 rpm. To obtain asexually developing cells, postdevelopmental induction was performed as previously described in Seo et al. (2003). Briefly, 2×106 conidia·ml-1 were inoculated into 100 ml liquid GMM and cultured for 18 hr at 37 °C. Cultured mycelia were harvested and transferred on fresh solid GMM. The plates were air exposed and grown for 24 hr for asexual developmental induction.

extract_protocol:
Total RNA isolation and Northern blot analyses were carried out as described (Seo et al., 2003; Han et al., 2004).
DNA libraries were prepared using TruSeq ChIP library Preparation Kit (Illumina) and sequenced using an Illumina NovaSeq 6000 platform.

value: 2 days

value: Conidia

value: {delta}nsdD


title: Donor 3 (s3), Mock, 72h

description: 72h Mock s3

data_processing:
The sequencing quality of each sample was assessed with FASTQC v.0.11.9.
RNA-seq reads were independently aligned against the Ensamble hg19 reference transcriptome and quantified using Kallisto v.0.46.2 with the -b 60 parameter and Sleuth v.0.30.0
Assembly: hg19
Supplementary files format and content: TPM_Transcripts_Level_Sleuth.txt is a tab-delimited text file that include normalized TPM values of all samples

growth_protocol: PHHs were prepared using the protocol described in Le Cluyse & Alexandre (2010) with minor modifications. Liver samples are first perfused in Solution I (NaCl 58,44 M, KCl 74,56 M, Na2HPO4, 2H2O 177,99 M, Hepes 0,6%, EGTA 0,5 mM; pH7,4) and then in Solution II (NaCl 58,44 M, KCl 74,56 M, Na2HPO4, 2H2O 177,99 M, Hepes 0,6%, CaCl2 110 M) containing 0,4 mg/ml of collagenase from Clostridium histolyticum (Sigma-Aldrich, #C5138). Cells are seeded at 2,5x10^5 cells per cm² on collagen type IV (Corning, #354236) pretreated plates and cultured overnight in William’s medium (Life Technologies, #22551-089) supplemented with 10% Fetal Clone II (GE Healthcare), 1% penicillin/streptomycin (Invitrogen, #15140122), 1% Glutamax X100 (Invitrogen, #35050038), 5 µg/ml Insulin (Sigma–Aldrich, #I9278) and 5×10-7 M hydrocortisone (Upjohn Laboratories). PHHs are then extensively washed in serum-free medium, kept in serum-free medium for 24 hours to counter-select the growth of contaminating fibroblast and endothelial cells, and then plated in complete William’s medium. PHHs were treated with 2% of DMSO (Sigma–Aldrich, #D2650) for 24 hours before infection and then incubated for 16 h with an HBV inoculum produced in HepAD38 cells at a multiplicity of infection of 250 vge (virus genome equivalents) per cell, in presence of 4% PEG-8000 (Polyethylene glycol, Sigma–Aldrich, #1546605).

extract_protocol:
Total cellular RNA was extracted with the Extract-All reagent (Eurobio, #GEXEXT040U) following the manufacturer’s protocol. Extracted RNA was treated for 1 h at 37 °C with RNAse-free DNase I (Invitrogen, #AM2222), which was subsequently inactivated at 70 °C for 20 min. RNA reverse transcription was performed using the Superscript® IV RT kit (Invitrogen, #18090010), according to manufacturer's instructions.
mRNA libraries were prepared using the TruSeq® Stranded RNA HT (w/Ribo-Zero™) kit to increases the depth of sequencing. Each library was pair-end and was sequenced using 75x2 cycles on a NextSeq 500 Illumina platform.

treatment_protocol: The HBV inoculum used in this study was prepared from HepAD38 cells as previously described (Ladner et al., 1997). HepAD38 is an HepG2-derived stable cell line Carrying a 1.3 HBV transgene (genotype D, serotype ayw) under the control of a tet-off promoter. HepAD38 cells were cultured in HYPERFlask® (Corning, #10020) coated with type IV collagen (Corning, #354236) in 550 ml of complete DMEM-F12 medium supplemented with 10% decomplemented FBS (Gibco, #10270-106), 1% penicillin/streptomycin (Invitrogen, #15140122) and 1% sodium-pyruvate (Invitrogen, #11360039). Supernatants (550 ml/flask) were harvested twice a week for at 3-4 months, clarified first through 0.45 μm and then 0.22 µm filters (Millipore, #10785534) and precipitated overnight at 4 °C with 8% PEG-8000 (Sigma–Aldrich, #1546605), The precipitates were centrifuged at 3500 g for 1 hour and the pellets resuspended in Opti-MEM (Invitrogen, #31985070) to achieve a 50 to 100 fold concentration. After DNA extraction (QIAmp Ultrasens Virus kit, Qiagen) the HBV inoculum was tittered by qPCR using serial dilutions of an HBV plasmid to build a standard curve. Primers are detailed in Supplementary Figure 1. All viral preparations were tested for the presence of endotoxins (Lonza Verviers, Belgium).

value: Primary Human Hepatocytes (PHHs)

value: Control sample


title: ad-egfp3


title: ad-egfp2


title: ΔnsdD, Conidia 2 days [NdC_3]


title: Donor 1 (s1), HBV, 2h, replicate 1


title: ATAC EYFP-PHF13-d24-40d272-280-rep4

city: Berlin

first: Alexandre

middle: P

last: Magalhaes

address: Ihnestrasse 63-73

country: Germany

institute: Max Planck Institute for Molecular Genetics

description: Library name: ATAC-mut2-R4

data_processing:
ATAC-seq fastq files were processed nf-core/atacseq pipeline. In breaf, cutadapt is used to trim adaptors and BWA was used to align fastq files to hg38 genome, picard was used to remove duplicates and low quanlity alignements and bedtools was used to generate bedgraf files thatw were converted to bigwig files
Assembly: hg38
Supplementary files format and content: bigwig coverage files bin at 50bp without extention and smothing for ATAC-seq

growth_protocol: The U2OS cell line was cultured under standard conditions at 37°C with 5% CO₂. The cells were maintained in DMEM pre-supplemented with D-glucose, L-glutamine, sodium pyruvate and further supplemented with 10% FBS and 1x HEPES

extract_protocol:
ATAC-seq - Following sorting, nuclei were isolated using the Nuclei EZ Prep Kit following the manufacturer's instructions for suspension cells. The isolated nuclei were stored at -80°C in RTL buffer supplemented with 2M dithiothreitol (DTT). DNA was extracted from the nuclei employing the ATACeasy Plus Mini Kit, following the manufacturer's guidelines.
ATAC-seq - DNA was purified using Zymo DNA Clean & Concentrator Kit and eluted with 20 µl of elution buffer. The resulting DNA was amplified using NEBNext High-Fidelity 2x PCR Master Mix and a unique combination of Barcoded PCR Primer ( sequences provided in Buenrostro et al. 2013)

treatment_protocol: Transfection was carried out using a 1 DNA: 4 Fugene 4K reagent ratio, following the manufacturer's instructions.


title: Donor 2 (s2), Mock, 72h

description: 72h Mock s2


title: ad-egfp1


title: Donor 3 (s3), HBV, 72h

description: 72h HBV s3


title: ΔnsdD, Conidia 2 days [NdC_1]


title: ad-dyrk1b4


title: wild-type, Conidia 2 days [NWC_3]

value: wild-type


title: ATAC EYFP-rep4

description: Library name: ATAC-ctrl-R4

value: EYFP


title: ATAC EYFP-PHF13-d24-40-rep4

description: Library name: ATAC-2440-R4


title: wild-type, Conidia 2 days [NWC_6]


title: ad-dyrk1b2


title: wild-type, Conidia 2 days [NWC_2]


title: ATAC EYFP-PHF13-rep4

description: Library name: ATAC-wt-R4


title: Donor 1 (s1), HBV, 72h

description: 72h HBV s1

value: Liver


title: ATAC EYFP-PHF13-dPEST2-rep3

description: Library name: ATAC-dPEST2-R3


title: Donor 3 (s3), Mock, 2h

description: 2h Mock s3


title: ATAC EYFP-PHF13-d24-40d232-238-rep4

description: Library name: ATAC-mut1-R4


title: Donor 1 (s1), Mock, 72h

description: 72h Mock s1


title: scRNA-seq-organoids-mouse stomach-NRC

description: scRNA-seq

data_processing:
Raw reads were aligned to the different species genome (Human: GRCh38/hg38, Mouse: GRCm38/mm10), and Cell Ranger (v3.1.0) was used to estimate unique molecular identifiers (UMIs).
Raw aligned features were loaded and processed using the Seurat package (v4.0.2)
Low-quality cells were filtered if they expressed no more than 200 genes or with more than 20% of mitochondrial genes
Assembly: Human: GRCh38/hg38, Mouse: GRCm38/mm10
Supplementary files format and content: text files

source_name: Gastric organoids

growth_protocol: Organoids were embedded in Matrigel and seeded on 48- or 24- well plate. After Matrigel polymerization, the CM medium (Advanced DMEM/F12 supplemented with Penicillin/Streptomycin, GlutaMAX, N2, B27, and N-acetylcysteine containing 50 ng/mL EGF, 100 ng/mL Noggin, 500 ng/mL R-spondin1, 5 μM CHIR, 10 nM Gastrin, 10 μM SB431542, 100 ng/mL FGF10 and 10 μM Y27632) was added and refreshed every 2 days.

extract_protocol:
Gastric glands and organoids were isolated and digested with EDTA and Tryple, alive cells were sorted by flow cytometry. Single cell suspensions were captured using the 10X Genomics Chromium
ScRNA-seq libraries were generated using the Chromium Single Cell 3’ Reagent Ki V3 (10X Genomics). The libraries were sequenced as paired-end with Illumina Novaseq 6000.

treatment_protocol: Organoids were treated with CM and differentiation medium for 2 days.

value: Gastric organoids

tag: group

value: Treated with Noggin Rspondin1 A8301and CHIR 2 days


title: ad-dyrk1b1


title: Donor 2 (s2), Mock, 2h

description: 2h Mock s2


title: ATAC EYFP-PHF13-d24-40d272-280-rep3

description: Library name: ATAC-mut2-R3


title: ΔnsdD, Asex 24 hr [NdA_3]

source_name: Asexually developing cells

value: 24 hours

value: Asexually developing cells


title: ΔnsdD, Asex 24 hr [NdA_2]


title: ΔnsdD, Asex 24 hr [NdA_1]


title: Donor 1 (s1), Mock, 2h

description: 2h Mock s1


title: scRNA-seq-organoids-mouse stomach-EB

description: scRNA-seq

value: Wild type

value: Treated with EGF and BMP4 2 days


title: ad-dyrk1b3

value: Mouse hepatoma


title: Donor 2 (s2), HBV, 72h

description: 72h HBV s2

value: HBV infected


title: Donor 3 (s3), HBV, 2h

description: 2h HBV s3


title: ATAC EYFP-PHF13-d24-40d232-238-rep3

description: Library name: ATAC-mut1-R3


title: ATAC EYFP-PHF13-d24-40-rep3

description: Library name: ATAC-2440-R3


title: scRNA-seq-organoids-mouse stomach-BI

description: scRNA-seq

value: Treated with BMP4 and ISX-9 2 days


title: ATAC EYFP-PHF13-rep3

description: Library name: ATAC-wt-R3


title: Donor 2 (s2), HBV, 2h

description: 2h HBV s2


title: scRNA-seq-organoids-mouse stomach-WT

description: scRNA-seq

value: Untreated


title: wild-type, Asex 24 hr [NWA_3]


title: Donor 1 (s1), HBV, 2h

description: 2h HBV s1


title: wild-type, Asex 24 hr [NWA_2]


title: ATAC EYFP-rep3

description: Library name: ATAC-ctrl-R3


title: RNA-seq-organoids-mouse NRCA-2

description: RNA-Seq

data_processing:
RNA-seq reads were aligned to the human or mouse genome available in Ensembl (release 95) with HISAT2 (v2.1.0)
StringTie (v1.3.3b) for transcript assembly
The quantitative gene expression (FPKM) was obtained with Ballgown
Assembly: Human: hg38, Mouse: mm10
Supplementary files format and content: csv

extract_protocol:
Organoids were digested with Tryple and alive cells were sorted by flow cytometry. Total RNA was extracted with RNeasy Mini Kit (QIAGEN) according to the manufacturer’s instructions.
The library were prepared for sequecing using NEBNext Ultra RNA library Prep Kit for Illumina.

tag: strategy


title: wild-type, Asex 24 hr [NWA_1]


title: ATAC EYFP-PHF13-dPEST2-rep2

description: Library name: ATAC-dPEST2-R2


title: HIPSCI_ATAC_Yoch6_rep3

city: Göttingen

first: Ufuk

last: Günesdogan

address: Justus-von-Liebig Weg 11

institute: University of Goettingen

description: Library name: Yoch6_P5

data_processing:
ATAC-seq data analysis quality check of paired-end was done using FastQC v0.11.5 (www. bioinformatics.babraham.ac.uk/projects/fastqc).
Nextera Transposase adapter and low-quality bases were eliminated using Cutadapt v1.1787.
After trimming, reads were mapped to human genome GRCh38 assembly using bowtie2 v2.3.4.288.
Mapped pairs were further filtered to maintain mapping quality above 20, using custom scripts and SAMtools v1.989.
PCR duplicates and mitochondrial reads were removed by picard (https://broadinstitute.github.io/picard/) and samtools as well as reads blacklisted by The Encyclopedia of DNA Elements (ENCODE) project.
Peaks of accessible chromatin were identified for each sample using MACS2 v2.1.291 with the following settings: -f BEDPE --keep-dup. Coverage tracks requiring bigwig files and heatmaps were generated using deepTools v3.3.192.
Assembly: GRCh38
Supplementary files format and content: bigwig coverage files of merged replicates

source_name: hiPSC

extract_protocol:
ATAC-seq libraries were generated as described in (Corces et al. 2017), with minor modifications. After washing once with 1X DPBS (Life Technologies; 14190144), hiPSCs were harvested with accutase (StemCell Technologies; 07922) by incubation for 5 min at 37°C. After accutase neutralisation with TeSR-E8 medium, cells were centrifuged at 300 x g for 3 min at RT. After resuspension in 1X DPBS, 50,000 cells underwent centrifugation at 500 x g for 5 min at 4°C in a swing arm rotor centrifuge, then lysis in 50µl of cold ATAC Resuspension Buffer (10mM Tris-HCl pH 7.5, 10mM NaCl, 3mM MgCl2) containing 0.1% IGEPAL-630, 0.1% Tween-20, and 0.01% digitonin for 3 min on ice. The lysate was then topped up with 1ml cold ATAC Resuspension Buffer containing 0.1% Tween-20 and centrifuged at 500 x g for 10 min at 4°C in a swing arm rotor centrifuge.
The pellet was then resuspended in 50µl of transposition mixture (1X Illumina Tagment DNA Buffer and 100nM Illumina TDE1 Tagment DNA Enzyme transposase (Illumina; 20034197), 0.33X DPBS, 0.1% Tween-20, 0.01% digitonin) and incubated at 37°C for 30 min with 1000 RPM mixing. After undergoing purification with the Zymo DNA Clean & Concentrator-5 kit (Zymo Research; D4003), samples were eluted in 21µl of elution buffer, and combined with 2.5µl of 25µM i5 primer, 2.5µl of 25µM i7 primer, and 25µl 2X NEBNext High-Fidelity 2X PCR Master Mix (NEB; M0541S). A PCR was then performed with the following conditions: 72°C for 5 min, 98°C for 30 sec, 8 cycles of [98°C for 10 sec, 63°C for 30 sec, 72°C for 1 min]. The samples then underwent a second Zymo DNA Clean & Concentrator-5 purification and were eluted in 30µl of elution buffer prior to a 1.2X AMPure XP bead (Beckman Coulter; A63881) cleanup. Following QC on a Bioanalyzer, libraries were multiplexed and sequenced (paired-end 50bp) using a HiSeq 2000 instrument (Illumina).

value: hiPSC


title: RNA-seq-organoids-mouse NRCA-1

description: RNA-Seq


title: ΔnsdD, Vege 36 hr [NdV_3]

source_name: vegetatively grown cells

value: 36 hours

value: vegetatively grown cells

value: {delta}nsdD


title: HIPSCI_ATAC_Yoch6_rep2

description: Library name: Yoch6_P4


title: ATAC EYFP-PHF13-d24-40d272-280-rep2

description: Library name: ATAC-mut2-R2


title: RNA-seq-organoids-mouse ISX9-1

description: RNA-Seq

value: Treated with Isx-9 2 days


title: ΔnsdD, Vege 36 hr [NdV_2]


title: HIPSCI_ATAC_Yoch6_rep1

description: Library name: Yoch6_P3


title: RNA-seq-organoids-mouse ISX9-2

description: RNA-Seq


title: ATAC EYFP-PHF13-d24-40d232-238-rep2

description: Library name: ATAC-mut1-R2


title: ΔnsdD, Vege 36 hr [NdV_1]


title: HIPSCI_ATAC_Wibj2_rep3

description: Library name: Wibj2_P5


title: ATAC EYFP-PHF13-d24-40-rep2

description: Library name: ATAC-2440-R2


title: wild-type, Vege 36 hr [NWV_3]

value: wild-type


title: RNA-seq-organoids-mouse EB-2

description: RNA-Seq


title: RNA-seq-organoids-mouse EB-1

description: RNA-Seq


title: ATAC EYFP-rep2

description: Library name: ATAC-ctrl-R2

value: EYFP


title: HIPSCI_ATAC_Wibj2_rep2

description: Library name: Wibj2_P4


title: wild-type, Vege 36 hr [NWV_2]


title: ATAC EYFP-PHF13-rep2

description: Library name: ATAC-wt-R2


title: wild-type, Vege 36 hr [NWV_1]


title: ATAC EYFP-PHF13-dPEST2-rep1

description: Library name: ATAC-dPEST2-R1


title: RNA-seq-organoids-mouse BMP4-1

description: RNA-Seq

value: Treated with BMP4 2 days


title: HIPSCI_ATAC_Sojd3_rep3

description: Library name: Sojd3_P5


title: ATAC EYFP-PHF13-d24-40d272-280-rep1

description: Library name: ATAC-mut2-R1


title: HIPSCI_ATAC_Wibj2_rep1

description: Library name: Wibj2_P3


title: RNA-seq-organoids-mouse BMP4-2

description: RNA-Seq


title: RNA-seq-organoids-mouse BI-2

description: RNA-Seq


title: HIPSCI_ATAC_Sojd3_rep2

description: Library name: Sojd3_P4


city: 91400 Orsay

first: Florent

last: Dumont

state: Ile de France

address: 17 avenue des sciences

institute: Université Paris-Saclay

description:
Library name: s10
s10 right ventricular tissue from Sham pig

data_processing:
bcl2fastq2-2.18.12 (demultiplex)
Cutadapt 1.15 (adapter trimming)
FastQC v0.11.5 (quality control)
Rsubread v2.8.1 align
Rsubread v2.8.1 featureCounts
edgeR v3.36.0 TMM (normalization)
limma 3.50.0 (linearization)
Assembly: Sscrofa11.1
Supplementary files format and content: tabular CPM TMM quantile normalized CPM (Count per Million)
Supplementary files format and content: GEO_B117_processed_10_15638.tsv

organism: Sus scrofa

source_name: RV

extract_protocol:
RNAeasy Mini Kit (QIAGEN)
TruSeq Stranded Total RNA library prep kit (Illumina)

treatment_protocol: Right ventricular biopsies collected from 5 CTEPH pigs and 5 sham pigs.

value: RV

value: SHAM


title: ATAC EYFP-PHF13-d24-40d232-238-rep1

description: Library name: ATAC-mut1-R1


description:
Library name: s9
s9 right ventricular tissue from CTEPH pig

value: CTEPH


description:
Library name: s8
s8 right ventricular tissue from Sham pig


title: RNA-seq-organoids-mouse con-2

description: RNA-Seq

value: Wild type


title: ATAC EYFP-PHF13-d24-40-rep1

description: Library name: ATAC-2440-R1


description:
Library name: s7
s7 right ventricular tissue from Sham pig


title: ATAC EYFP-PHF13-rep1

description: Library name: ATAC-wt-R1


title: HIPSCI_ATAC_Qolg1_rep3

description: Library name: Qolg1_P5


title: HIPSCI_ATAC_Qolg1_rep2

description: Library name: Qolg1_P4


title: RNA-seq-organoids-mouse con-1

description: RNA-Seq


description:
Library name: s6
s6 right ventricular tissue from Sham pig


title: ATAC EYFP-rep1

description: Library name: ATAC-ctrl-R1


title: RNA EYFP-PHF13-dPEST2-rep3

description: Library name: RNA-dPEST2-R4

data_processing:
RNA-seq fastq files were processed with in-house scripts. In breaf, Trimtomatic was used to trim and cut adaptors and STAR was used to align and counts files to hg38 genome.
Assembly: hg38
Supplementary files format and content: STAR count table for RNA-seq

molecule: nuclear RNA

extract_protocol:
RNA-seq - Following sorting, nuclei were isolated using the Nuclei EZ Prep Kit following the manufacturer's instructions for suspension cells. The isolated nuclei were stored at -80°C in RTL buffer supplemented with 2M dithiothreitol (DTT). RNA was extracted from the nuclei employing the RNeasy Plus Mini Kit, following the manufacturer's guidelines.
RNA-seq - Library preparation was conducted with the Illumina Stranded mRNA Prep Kit per the manufacturer's protocol.


title: RNA-seq-organoids-mouse NRC-2

description: RNA-Seq

value: Treated with Noggin Rspondin1 and CHIR 2 days


title: HIPSCI_ATAC_Qolg1_rep1

description: Library name: Qolg1_P3


title: HIPSCI_ATAC_Podx1_rep3

description: Library name: Podx1_P6


description:
Library name: s4
s4 right ventricular tissue from CTEPH pig


description:
Library name: s5
s5 right ventricular tissue from CTEPH pig


title: RNA-seq-organoids-mouse NRC-1

description: RNA-Seq


title: HIPSCI_ATAC_Podx1_rep2

description: Library name: Podx1_P5


description:
Library name: s3
s3 right ventricular tissue from CTEPH pig


title: RNA-seq-organoids-mouse con-noggin-EGF+BMP4-1

description: RNA-Seq

value: Treated with Noggin and EGF withdrawal and add BMP4 2 days


title: HIPSCI_ATAC_Podx1_rep1

description: Library name: Podx1_P4


title: RNA EYFP-PHF13-d24-40d232-238-rep3

description: Library name: RNA-mut1-R4


description:
Library name: s2
s2 right ventricular tissue from Sham pig


title: RNA-seq-organoids-mouse con-noggin+BMP4-1

description: RNA-Seq

value: Treated with Noggin withdrawal and add BMP4 2 days


title: RNA-seq-organoids-mouse con-noggin-2

description: RNA-Seq

value: Treated with Noggin withdrawal 2 days


title: RNA EYFP-PHF13-d24-40-rep3

description: Library name: RNA-2440-R4


title: HIPSCI_ATAC_Letw5_rep3

description: Library name: Letw5_P6


title: RNA-seq-organoids-mouse BI-1

description: RNA-Seq

value: Treated with BMP4 and ISX-9 2 days


title: HIPSCI_ATAC_Sojd3_rep1

description: Library name: Sojd3_P3

value: hiPSC


description:
Library name: s1
s1 right ventricular tissue from CTEPH pig


title: HIPSCI_ATAC_Letw5_rep2

description: Library name: Letw5_P5


title: RNA-seq-organoids-mouse con-noggin-1

description: RNA-Seq


title: RNA EYFP-PHF13-rep3

description: Library name: RNA-wt-R4


title: VGLL_7

type: genomic

first: Simone

last: Schmid

address: Charitéplatz 1

department: Department of Neuropathology

institute: Charité-Universitätsmedizin Berlin

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450k or 850k Beadchip using standard Illumina protocol

scan_protocol: Arrays were scanned on the iscan instument acording to standarad protocol

data_processing:
Standard R packages minfi, Rtsne, conumee
Average Beta and Detection P value

label: Cy3 and Cy5

source_name: Tumor

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from human tumor samples using Maxwell RSC FFPE Plus DNA Purification Kit (Promega, USA) according to standard instructions


title: subcutaneous_graft

city: TianJin

first: Liu

last: Chang

address: Weijin Road

institute: Nankai University

description: subcutaneous graft

data_processing:
The sequencing data were processed using an open-source pipeline (https://github.com/MGI-tech-bioinformatics/DNBelab_C_Series_scRNA-analysis-software). Briefly, all samples were performed sample de-multiplexing, barcode processing, and single-cell 3' unique molecular identifier (UMI) counting with default parameters. Processed reads were then aligned to GRCm39 genome reference using STAR (2.7.2b). Valid cells were automatically identified based on the UMI number distribution of each cell by using the “barcodeRanks” function of the DropletUtils tool to remove background beads and the beads that had UMI counts less than the threshold value. Finally, we used PISA to calculate the gene expression of cells and create a gene x cell matrix for each library.
Assembly: GRCm39
Supplementary files format and content: Tab-separated values files and matrix files

source_name: gonad

extract_protocol:
The fresh kidney capsule graft and subcutaneous graft were cut into approximately 1mm3 pieces and washed with 4ml cold PBS solution 3 times. Then the samples were minced into small pieces, and enzymatically digested using the MACS Tumor Dissociation Kit (Miltenyi Biotec) for 30 min with agitation, according to the manufacturer’s instructions. The dissociated cells were subsequently passed through a 70-μm and 40-µm cell-strainer (Miltenyi Biotec) and centrifuged at 300g for 10 min. After removing the supernatant, the pelleted cells were suspended in red blood cell lysis buffer (Tiangen Biotech #RT122-1) and incubated at 4°C for 10 min to lyse red blood cells. The cell pellets were re-suspended in washing buffer (0.04% bovine serum albumin [BSA] in Dulbecco’s phosphate-buffered saline [DPBS]) after washing two times with washing buffer. The final cell concentration was adjusted to 1,000 cells/μL (viability≥80%) in all samples by using Countess™ 3 Automated Cell Counter (Life).
DNBelab C Series High-throughput Single-Cell RNA Library (940-000519-00) was utilized for scRNA-seq library preparation. In brief, Briefly, the cells were diluted to a concentration of 1,000 cells/mL and loaded into the cell reservoir of the microfluidic chip. Barcoded beads and droplet-generation oil were successively added to the beads and oil reservoirs. Encapsulated droplets were generated and collected using a DNBelab C4 /DNBelabTaiM4 system. Beads that captured the mRNA were recovered for reverse transcription (RT). Following polymerase chain reaction (PCR) amplification by polymerase chain reaction, complementary DNA (cDNA) was purified and quan-tified using a Qubit dsDNA kit (Thermo Fisher Scientific). Libraries of 3’-end transcripts were subsequently constructed through cDNA fragmentation, size selection, end repair and A-tailing, adapter ligation, PCR for indexing libraries, and cyclisation of sequencing libraries, according to the manufacturer’s instructions. Sequencing libraries were purified and quantified using the Qubit ssDNA kit (Thermo Fisher Scientific) and Qsep100 (Bioptic).

value: gonad


title: HIPSCI_ATAC_Letw5_rep1

description: Library name: Letw5_P4


title: RNA EYFP-PHF13-d24-40d272-280-rep2

description: Library name: RNA-mut2-R2


title: IEC4.1_ASO4 + IFNγ 3

city: Chicago

first: Aiyu

last: Gong

state: IL

address: 1735 W. Harrison St

department: MPI

institute: Rush University

description: Gene expression

data_processing:
Base-calling sofeware, version, parameters;
BGI SOAPnuke v1.5.2 software used for basecalling.
Sequencing data filtering:this project uses the filtering software SOAPnuke developed by BGI independently for filtering. Software Information:  SOAPnuke:Version v1.5.2; Parameters -l 15 -q 0.2 -n 0.05
Data filtering steps; 1) Remove the reads containing the adaptor (adaptor pollution); 2) Remove reads whose N content is greater than 5%; 3) Remove low-quality reads (we define reads with bases with a quality score less than 15 as the proportion of total bases in the reads that are greater than 20% as low-quality reads). The filtered "Clean Reads" are saved in FASTQ format.
Read alignment: Align to the reference genome: After getting clean reads, used HISAT to align the clean reads to the reference genome. Software Information: HISAT2;  Version：v2.0.4; Parameters：--sensitive --no-discordant --no-mixed -I 1 -X 1000 -p 8 --rna-strandness RF
Assembly: mm10; Reference species: Species：Mus_musculus; Source：NCBI;  Reference Genome Version：GCF_000001635.26_GRCm38.p6
Supplementary files format and content: tab-delimited text files include gene expression RPKM values level for each Sample

extract_protocol:
IEC 4.1 cells were harvested, and RNA were extract using Rneasy Mini Kit (QIAGEN Cat. No. 74104).  Agilent 2100 or Fragment Analyzer was used to detect thequality of RNA. 2 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using DNBSEQ platform

value: Mouse intestine epithelial cells

value: ASO4 + IFNγ


title: RNA EYFP-PHF13-dPEST2-rep2

description: Library name: RNA-dPEST2-R2


title: HIPSCI_ATAC_Kucg2_rep2

description: Library name: Kucg2_P5


title: VGLL_5


title: IEC4.1_ASO4 + IFNγ 2

description: Gene expression


title: RNA EYFP-PHF13-d24-40d232-238-rep2

description: Library name: RNA-mut1-R2


title: HIPSCI_ATAC_Kucg2_rep1

description: Library name: Kucg2_P4


title: IEC4.1_ASO4 + IFNγ 1

description: Gene expression


title: RNA EYFP-PHF13-d24-40-rep2

description: Library name: RNA-2440-R2


title: HIPSCI_ATAC_Kolf3_rep3

description: Library name: Kolf3_P6


title: HIPSCI_ATAC_Kolf3_rep2

description: Library name: Kolf3_P5


title: VGLL_1


title: IEC4.1_ASO4 2

description: Gene expression


title: RNA EYFP-rep3

description: Library name: RNA-ctrl-R4


title: RNA EYFP-rep2

description: Library name: RNA-ctrl-R2


title: HIPSCI_ATAC_Kolf3_rep1

description: Library name: Kolf3_P4


title: wild-type, anti-FLAG antibody, 2 days [WIP4]

data_processing:
Read sequences were mapped to the genome using bowties2 and Homer was utilized to call peaks.
Identification of NsdD direct targets was done by selecting genes, in which NsdD peaks are found in their promoter regions within the 1.5kb upstream range from the translation start site (TSS).
Assembly: GCF_000149205.2
Supplementary files format and content: tab-delimited text files include associated peak information for each sample

source_name: spores

growth_protocol: The fungal strains were inoculated into liquid or solid 1% glucose minimal medium (GMM) with appropriate supplements and incubated at 37 °C for 2 days. The conidia were collected in phosphate-buffered saline (PBS) from the entire plate and counted using a hemocytometer.

extract_protocol:
To collect samples for ChIP-seq analysis, two-day-old conidia (2×109) of TMK13 were cross-linked with 1% formaldehyde, resuspended in lysis buffer, and homogenized by a mini-beadbeater with 0.5mm zirconia/silica beads. The lysates were then sonicated for five to seven cycles (60 s on, 60 s off) with a sonicator to achieve 150-200 bp size DNA fragments. After centrifugation, the lysates were diluted in the ChIP dilution buffer and applied for ChIP assays using the MAGnify Chromatin Immunoprecipitation System (Invitrogen) follwing the manufacturer’s instruction with a modest modification. The diluted chromatin extracts were incubated with 1 μg of mouse monoclonal Anti-FLAG antibody (Sigma-Aldrich). As negative controls, the chromatin extract was reacted with 1 μg of Anti-rabbit IgG. Initial input DNAs before immunoprecipitation were used as positive controls. The enriched DNA fragments were retrieved and used as a template for ChIP-seq.
DNA libraries were prepared using TruSeq ChIP library Preparation Kit (Illumina) and sequenced using an Illumina NovaSeq 6000 platform.

value: 2 days

value: spores

value: mouse monoclonal anti-FLAG antibody


title: HIPSCI_ATAC_Kolf2_rep3

description: Library name: Kolf2_P5


title: RNA EYFP-PHF13-dPEST2-rep1

description: Library name: RNA-dPEST2-R1


title: HIPSCI_ATAC_Kucg2_rep3

description: Library name: Kucg2_P6


title: wild-type, anti-FLAG antibody, 2 days [WIP3]

value: wild-type


title: kidney_capsule_graft

description: kidney renal capsule graft


title: VGLL_4


title: RNA EYFP-PHF13-d24-40d272-280-rep1

description: Library name: RNA-mut2-R1


title: VGLL_3


title: IEC4.1_ST+ IFNγ 3

description: Gene expression

value: ST+ IFNγ


title: HIPSCI_ATAC_Kolf2_rep2

description: Library name: Kolf2_P4


title: wild-type, anti-FLAG antibody, 2 days [WIP2]


title: IEC4.1_ST+ IFNγ 2

description: Gene expression


title: IEC4.1_ASO4 3

description: Gene expression


title: VGLL_2


title: wild-type, anti-FLAG antibody, 2 days [WIP1]


title: RNA EYFP-PHF13-rep2

description: Library name: RNA-wt-R2


title: IEC4.1_ST+ IFNγ 1

description: Gene expression


title: RNA EYFP-PHF13-d24-40-rep1

description: Library name: RNA-2440-R1


title: RNA EYFP-PHF13-d24-40d232-238-rep1

description: Library name: RNA-mut1-R1


title: HIPSCI_ATAC_Kolf2_rep1

description: Library name: Kolf2_P3


title: IEC4.1_ST 3

description: Gene expression

value: ST


title: NsdD-FLAG strain, anti-FLAG antibody, 2 days [N5ip]

value: NsdD::FLAG expressing strain


title: RNA EYFP-PHF13-rep1

description: Library name: RNA-wt-R1


title: IEC4.1_ASO4 1

description: Gene expression


title: HIPSCI_ATAC_Bima1_rep2

description: Library name: Bima1_P4


title: IEC4.1_ST 2

description: Gene expression


title: NsdD-FLAG strain, anti-FLAG antibody, 2 days [N4ip]


title: RNA EYFP-rep1

description: Library name: RNA-ctrl-R1

value: EYFP


title: HIPSCI_ATAC_Bima1_rep1

description: Library name: Bima1_P3


title: NsdD-FLAG strain, anti-FLAG antibody, 2 days [N2ip]


title: BL/6 NZB Non Lactating F3

status: Public on May 28 2025

city: New York

first: Edmund

middle: C

last: Jenkins

state: NY

address: 1468 Madison Avenue

department: Heme/Onc

institute: Icahn School of Medicine at Mt. Sinai

data_processing:
Fatstq file were aligned using biojupies
Assembly: GRCm38/mm10

source_name: Mammary Gland

extract_protocol:
Snap frozen tissue followe by polyA RNA extraction
polyA isolation

value: Mammary Gland

value: BL/6 NZB


title: IEC4.1_ST 1

description: Gene expression


title: BL/6 NZB Non Lactating F2


title: BL/6 NZB Non Lactating F1


title: BL/6 NZB lactation day 21 F2


title: BL/6 NZB lactation day 21 F3


title: BL/6 NZB lactation day 14 F3


title: BL/6 NZB lactation day 21 F1


title: BL/6 NZB lactation day 14 F1


title: BL/6 NZB lactation day 14 F2


title: BL/6 NZB lactation day 8 F3


title: BL/6 NZB lactation day 8 F2


title: BL/6 NZB lactation day 8 F1


title: BL/6 C57 Non Lactating F3


title: HIPSCI_ATAC_Bima1_rep3

description: Library name: Bima1_P5


title: BL/6 C57 Non Lactating F1


title: BL/6 C57 lactation day 21 F3


title: BL/6 C57 lactation day 21 F1


title: BL/6 C57 lactation day 21 F2


title: BL/6 C57 lactation day 14 F2


title: BL/6 C57 lactation day 14 F1


title: BL/6 C57 lactation day 8 F3


title: BL/6 C57 lactation day 8 F1


title: A375 Vemurafenib Resistant Rep 1

city: Warszawa

first: Tomasz

last: Gambin

address: Nowowiejska 15/19

country: Poland

institute: Warsaw University of Technology

description: Library name: Sample 3

data_processing:
Raw sequencing data were quality checked and aligned using standard pipelines (e.g., STAR for alignment and featureCounts for quantification). Normalization and differential expression analysis were performed using DESeq2. Pathway enrichment was carried out using Enrichr. Visualization and additional analyses (e.g., IC50, QCM-D curves) were performed in R.
Assembly: RNA-seq reads were aligned to the human genome version GRCh38. Gene annotation files (GTF) were downloaded from Ensembl or GENCODE corresponding to the genome build.
Supplementary files format and content: TSV file containing gene symbols and log fold changes after deseq2 analysis

source_name: Skin

growth_protocol: Parental and vemurafenib-resistant A375 human melanoma cells were cultured at 37°C with 5% CO₂ in RPMI-1640 medium (Biowest), supplemented with 10% fetal bovine serum (Gibco) and 1% penicillin/streptomycin (Sigma Aldrich). Cells were passaged weekly using 0.05% trypsin-EDTA.

extract_protocol:
Approximately 1 million cells were harvested per condition after drug treatment. Cells were centrifuged and lysed using RNA Extracol (EURx) according to the manufacturer's protocol. Lysates were stored at −80 °C and shipped on dry ice to the sequencing facility.
RNA samples were processed externally at the Laboratory of Sequencing, Nencki Institute of Experimental Biology, PAS. Libraries were prepared using polyA selection and strand-specific library construction, followed by paired-end sequencing.

treatment_protocol: A375 melanoma cells were cultured in RPMI-1640 supplemented with 10% FBS and 1% penicillin/streptomycin. Vemurafenib resistance was induced in A375 cells by gradual weekly increases of vemurafenib concentration, starting from 0.1 µM and doubling each week to 6.4 µM. For drug treatments, cells were exposed for 24 h to sorafenib (5 µM), pioglitazone (1 µM), or their combination. DMSO (<1%) was used as vehicle control. Treatments were administered 24 h after seeding in either 96-well plates (for viability assays) or polystyrene-coated QCM-D sensors (for glycan analysis).

value: Skin

value: Melanoma cell


title: A375 Vemurafenib Resistant Rep 2

description: Library name: Sample 4


title: BL/6 C57 Non Lactating F2


title: RNA EYFP-PHF13-d24-40d272-280-rep3

description: Library name: RNA-mut2-R4


title: SG040_D28_CD3PosCD8PosCARPos

city: Baltimore

first: Carrie

last: McCracken

state: MD

address: 670 W. Baltimore St.

institute: Institute of Genome Sciences

description: Library name: IL100292463

data_processing:
Reads were assessed for quality, trimmed if PHRED scores fell below 20, and any remaining adapter sequences were removed. Processed paired-end reads were aligned to human reference genome GRCh38 using HISAT2, and counts were generated using the HTseq analysis package. Reads that successfully mapped to the reference genome were used for downstream analyses
Assembly: Human reference (GRCh38)
Supplementary files format and content: htseq output with gene counts for each sample

source_name: Blood

extract_protocol:
Samples were processed using the Qiagen RNeasy Micro kit with an addition of cRNA to aid in RNA precipitation. Kit was followed per manufacturers protocol from there and eluted in 30uL RNase free water.
Samples were processed using  the Takara, SMART-Seq® v4 Ultra® Low Input RNA Kit.  There were no deviations from the manufacture’s protocol.  Final libraries were assessed for quality and quantity on the  Revity Gx touch.

value: Blood


title: large 4N clone derived from DLD1, biological replicate L2

city: Blacksburg

first: Mathew

last: Bloomfield

state: VA

address: 1015 Life Science Circle

department: Biological Sciences

institute: Virginia Tech

description: Library name: DLD1-L2

data_processing:
Raw data were first processed using fastp software to clean the data, which were then mapped to the reference genome using Hisat2 v2.0.5.
Gene expression was quantified using featureCounts v1.5.0-p3, and differential expression analysis was performed using the DESeq2 R package.
Assembly: GRCh38
Supplementary files format and content: Tab-delimited text file includes FPKM values for each sample.

source_name: colon

growth_protocol: All cells were maintained at 37°C and 5% CO2 in media supplemented with 10% fetal bovine serum (FBS; Thermo Fisher Scientific) and 1% anti-biotic and anti-mycotic (Thermo Fisher Scientific).

extract_protocol:
Total RNA was extracted using the RNeasy extraction kit.
mRNA was purified from total RNA using poly-T oligo-attached magnetic beads and sequenced using an Illumina NovaSeq platform. The first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using either dUTP for directional library.

treatment_protocol: Cytokinesis failure was induced in DLD1 cells by adding 1.5 µg/mL DCB to the culture medium for 20 hr. In HCT116 and CAL51, cytokinesis failure was induced by adding 75 µM blebbistatin to the culture medium for 20 hr. Drugs were washed out four times in media. The cells were allowed to recover for 48 hr before performing single cell cloning via limiting dilution in 96-well plates. Wells containing single cells were identified and expanded into clonal cell lines for further screening.

value: colon

value: epithelial

value: 20 hr dihydrocytochalasin


title: large 4N clone derived from DLD1, biological replicate L4

description: Library name: DLD1-L4


title: Human Epidermal Equivalent, N/TERT-1, untreated experiment 1

city: geneva

first: Wolf

middle: Henning

last: Boehncke

address: Rue Michel servet 1

country: Switzerland

institute: Univeristy of Geneva

description: Library name: 1_ctrl2

data_processing:
Reads were generated on an Illumina NovaSeq 6000 sequencer. FastQ reads were mapped to the ENSEMBL reference genome (GRCh38) using STAR, version v.2.7.10b, with standard settings. The transcriptome metrics were evaluated with the Picard tools v. 2.21.6. The table of counts with the number of reads mapping to each gene feature of the UCSC human hg38 reference was prepared with HTSeq v.0.11.3. The differential expression analysis was performed using R/Bioconductor package edgeR v.3.18.1. Briefly, the counts were normalized according to the library size and filtered. The genes were filtered on expression levels. As required by the experimental design, a paired t-test was used to assess the differentially expressed genes (DEG). The DEG p values were corrected for multiple testing errors with a 5% false discovery rate (FDR) according to the correction by Benjamini-Hochberg (BH). Library preparation, sequencing, and read mapping of the reference genome were performed by the Genomics Platform at the University of Geneva, Switzerland.
Assembly: UCSC human hg38 reference
Supplementary files format and content: raw count as .txt; DEG as .csv

source_name: epidermis

extract_protocol:
Total RNA was isolated using the Quick-RNA MiniPrep kit (Zymo Research), according to the manufacturer's protocol.
cDNA libraries were constructed using the Illumina Stranded mRNA lig stranded Kit according to the manufacturer’s protocol.

value: epidermis

value: keratinocyte

value: WT

value: Control


title: Human Epidermal Equivalent, N/TERT-1, untreated experiment 3

description: Library name: 3_ctrl1


title: Human Epidermal Equivalent, N/TERT-1, TGFβ1 treated experiment 3

description: Library name: 3_TGFB1


title: Human Epidermal Equivalent, N/TERT-1, untreated experiment 2

description: Library name: 2_ctrl1


title: scRNA-seq and Cell Hashing, PBMCs, GEX

city: Hod hasheon

first: Noa

last: Tal

address: Kaplan 14

institute: Schneider children hospital

description:
Library name: sample_gex
polyA RNA
GEX (3' mRNA) library: R1 file contains cell barcode and UMI; R2 file conatins transcript

data_processing:
The Cell Ranger multi pipeline (v7.0.1, 10× Genomics) with default settings was used for cell demultiplexing, filtering, barcode counting, and UMI (Unique Molecular Identifier) counting.
Quality control, dimensionality reduction, visualization, and downstream analysis were performed using the R Seurat package (v4.9.9; Satija et al., 2015).
Assembly: GRCh38 reference genome, 2020-A version
Supplementary files format and content: cellRanger output files: rna_barcodes.tsv.gz, rna_features.tsv.gz, rna_matrix.mtx.gz
Supplementary files format and content: cellRanger output files: hto_barcodes.tsv.gz, hto_features.tsv.gz, hto_matrix.mtx.gz

source_name: whole blood

extract_protocol:
Freshly isolated PBMCs were counted, and viability was assessed using trypan blue. Cells were washed and labeled with anti-ꞵ2-microglobulin/anti-CD298 antibodies conjugated to oligonucleotides (TotalSeq-B anti human Hashtag antibodies, Biolegend, Table S3) for 30 min at 4°C according to manufacturer’s instructions. Equal numbers of labeled cells from each sample were mixed and diluted in PBS + 0.04% BSA to a final concentration of 1600 cells/µl. The sample was then immediately processed with the Chromium Next GEM Single Cell 3’ v3.1 kit, with feature barcoding for cell surface proteins, according to the manufacturer protocol.
Single-cell RNA-seq libraries were prepared using the 10X Genomics technology. Final libraries were quantified by qPCR with the NEB-next Library Quant Kit (New England Biolabs), as well as with Qubit and TapeStation. Sequencing was done on a Nova-Seq6000 using SP, 100 cycles kit mode allocating 800M reads in total (Illumina). Fastq files were generated by the usage of bcl2fastq v2.20.0.422.

value: whole blood

value: PBMCs

value: Mixed sample (Healthy Control1, Healthy control2, Patient's Mother, Patient)

tag: library type

value: mRNA


title: SG040_D28_CD3PosCD8NegCARNeg

description: Library name: IL100292462


title: Human Epidermal Equivalent, N/TERT-1, TGFβ1 treated experiment 2

description: Library name: 2_TGFB1


title: scRNA-seq and Cell Hashing, PBMCs, HTO

description:
Library name: sample_hto
Hashtag-derived oligonucleotide (HTO)
HTO library: R1 file contains cell barcode and UMI; R2 file conatins Hashtag Antibody Derived Tag reads

library_source: other

molecule: protein

value: HTO

tag: hto

value: TotalSeq™-B0251 anti-human Hashtag 1, TotalSeq™-B0252 anti-human Hashtag 2,TotalSeq™-B0253 anti-human Hashtag 3, TotalSeq™-B0254 anti-human Hashtag 4


title: Human Epidermal Equivalent, N/TERT-1, TGFβ1 treated experiment 1

description: Library name: 1_TGFB1


title: SG040_D28_CD3PosCD8NegCARPos

description: Library name: IL100292461


title: BL/6 C57 lactation day 8 F2

value: Mammary Gland


title: VB657_CSF

description: Library name: IL6531-001

data_processing:
The demultiplexing, barcoded processing, gene counting, and aggregation were made using the Cell Ranger software v.7.2.0 (https://www.10xgenomics.com/support/software/cell-ranger/latest)
Assembly: Human reference (GRCh38)
Supplementary files format and content: Tab-separated value files and matrix files

source_name: Cerebrospinal Fluid

extract_protocol:
Single cells were encapsulated in Gel-Beads-in emulsion (GEMs) using the 10X Controller with a Chromium Single Cell 3’ NextGEM v3.1 Library and Gel Bead kit (10X Genomics).
Cells were counted on a Countess 3 with Trypan Blue. 16,500 cells were loaded into the Chromium X to target 10,000 cells.  Libraries were generated according to the manufacturers protocol using the 10X NextGEM 3’ v3.1 chemistry (10X Genomics). Libraries were assessed for concentration and fragment size using the DNA High Sensitivity Assay on the GX Touch (Revity).

value: Cerebrospinal Fluid


title: BL/6 C57 lactation day 14 F3


title: small 4N clone derived from DLD1, biological replicate S1

description: Library name: DLD1-S1


title: 2N clone derived from DLD1, biological replicate 2N1

description: Library name: DLD1-2N1


title: 2N clone derived from DLD1, biological replicate 2N2

description: Library name: DLD1-2N2


title: small 4N clone derived from DLD1, biological replicate S2

description: Library name: DLD1-S2


title: A375 Control Rep 2

description: Library name: Sample 2

value: Skin

value: Melanoma cell


title: A375 Control Rep 1

description: Library name: Sample 1


title: parental DLD1 cells

description: Library name: DLD1

value: colon


title: large 4N clone derived from HCT116, biological replicate L2

description: Library name: HCT116-L2

value: colonocyte; epithelial

value: 20 hr blebbistatin


title: large 4N clone derived from HCT116, biological replicate L3

description: Library name: HCT116-L3


title: VB657_PBMC

description: Library name: IL6532-001

value: Blood


title: large 4N clone derived from DLD1, biological replicate L3

description: Library name: DLD1-L3

value: epithelial

value: 20 hr dihydrocytochalasin


title: large 4N clone derived from HCT116, biological replicate L1

description: Library name: HCT116-L1


title: small 4N clone derived from HCT116, biological replicate S1

description: Library name: HCT116-S1


title: small 4N clone derived from HCT116, biological replicate S2

description: Library name: HCT116-S2


title: small 4N clone derived from DLD1, biological replicate S3

description: Library name: DLD1-S3


title: 2N clone derived from HCT116, biological replicate 2N1

description: Library name: HCT116-2N1


title: small 4N clone derived from HCT116, biological replicate S3

description: Library name: HCT116-S3


title: large 4N clone derived from CAL51, biological replicate L3

description: Library name: CAL51-L3

source_name: breast

value: breast

value: triple negative breast cancer cell line


title: parental HCT116 cells

description: Library name: HCT116


title: large 4N clone derived from CAL51, biological replicate L1

description: Library name: CAL51-L1


title: parental CAL51 cells

description: Library name: CAL51


title: 2N clone derived from CAL51, biological replicate 1

description: Library name: CAL51-2N1


title: small 4N clone derived from CAL51

description: Library name: CAL51-S1


title: Remyelination no MG LPC Conc 0 1mM D 3div Rep2

city: Basel

first: Roland

last: Schmucki

address: Grenzacherstrase

institute: F. Hoffmann - La Roche AG

description:
Library name: BioNi37A_3Remyelination_no_MG_LPC_Conc_0_1mM_D_3div_Rep2
PS-22410_refseq_count.gct
PS-22410_refseq_tpm.gct

data_processing:
Basecalls and sample de-multiplexing performed by bcl2fastq conversion with default parameters
Sequenced reads were quality check with fastqc default parameters and then mapped with STAR using default algorithm parameters against hg38
The resulting BAM files were processed with FeatureCounts (Subreads) to yield count data for RefSeq transcript annotations
Transcripts Per Million (TPM) were calculated.
RefSeq annotations from NCBI Homo sapiens Annotation Release RS_2023_10
Assembly: hg38
Supplementary files format and content: PS-22410_refseq_count.gct and PS-13893_refseq_count.gct contain raw read counts per RefSeq gene (Entrezgene ID and gene symbol) in gct format
Supplementary files format and content: PS-22410_refseq_tpm.gct and PS-13893_refseq_tpm.gct contain normalized read counts per RefSeq gene (Entrezgene ID and gene symbol) in gct format

source_name: neural

extract_protocol:
brain organoids with and without microglia were lysed using MagNA Pure DNA Tissue Lysis Buffer  and RNA isolated using the MagNA Pure 96 System (Roche).
10ng of high quality total RNAs were used to prepare sequencing libraries using the Illumina Stranded 28 Total RNA Prep with Ribo-Zero Library Prep Kit (Illumina) according to the manufacturer’s instructions. All libraries were multiplexed into a single pool and sequenced on an Illumina NovaSeq 6000 instrument using an SP flowcell. Raw sequencing data were demultiplexed using the BLC Convert demultiplexing pipeline and each library generated approximately 28 million paired-end 50 bp reads.

value: neural

value: iPSC-derived

tag: Sex

value: female

value: Remyelination control_no_MG


title: Remyelination no MG LPC Conc 0 1mM D 3div Rep3

description:
Library name: BioNi37A_3Remyelination_no_MG_LPC_Conc_0_1mM_D_3div_Rep3
PS-22410_refseq_count.gct
PS-22410_refseq_tpm.gct

tag: tissue


title: Remyelination 10C MG LPC Conc 0 1mM D 3div Rep3

description:
Library name: BioNi37A_6Remyelination_10C_MG_LPC_Conc_0_1mM_D_3div_Rep3
PS-22410_refseq_count.gct
PS-22410_refseq_tpm.gct

value: Remyelination control +MG


title: Remyelination 10C MG LPC Conc 0 1mM D 3div Rep1

description:
Library name: BioNi37A_6Remyelination_10C_MG_LPC_Conc_0_1mM_D_3div_Rep1
PS-22410_refseq_count.gct
PS-22410_refseq_tpm.gct


title: Remyelination 10C MG LPC Conc 0 1mM D 3div Rep2

description:
Library name: BioNi37A_6Remyelination_10C_MG_LPC_Conc_0_1mM_D_3div_Rep2
PS-22410_refseq_count.gct
PS-22410_refseq_tpm.gct


title: LPC Demyelination 10C MG LPC Conc 0 1mM D 3div Rep1

description:
Library name: BioNi37A_5LPC_Demyelination_10C_MG_LPC_Conc_0_1mM_D_3div_Rep1
PS-22410_refseq_count.gct
PS-22410_refseq_tpm.gct

value: Demyelination +MG


title: LPC Demyelination 10C MG LPC Conc 0 1mM D 3div Rep2

description:
Library name: BioNi37A_5LPC_Demyelination_10C_MG_LPC_Conc_0_1mM_D_3div_Rep2
PS-22410_refseq_count.gct
PS-22410_refseq_tpm.gct


title: LPC Demyelination 10C MG LPC Conc 0 1mM D 3div Rep3

description:
Library name: BioNi37A_5LPC_Demyelination_10C_MG_LPC_Conc_0_1mM_D_3div_Rep3
PS-22410_refseq_count.gct
PS-22410_refseq_tpm.gct


title: Remyelination no MG LPC Conc 0 1mM D 3div Rep1

description:
Library name: BioNi37A_3Remyelination_no_MG_LPC_Conc_0_1mM_D_3div_Rep1
PS-22410_refseq_count.gct
PS-22410_refseq_tpm.gct


title: LPC Demyelination no MG LPC Conc 0 1mM D 3div Rep3

description:
Library name: BioNi37A_2LPC_Demyelination_no_MG_LPC_Conc_0_1mM_D_3div_Rep3
PS-22410_refseq_count.gct
PS-22410_refseq_tpm.gct

value: Demyelination no MG


title: LPC Demyelination no MG LPC Conc 0 1mM D 3div Rep2

description:
Library name: BioNi37A_2LPC_Demyelination_no_MG_LPC_Conc_0_1mM_D_3div_Rep2
PS-22410_refseq_count.gct
PS-22410_refseq_tpm.gct


title: Control 10C MG Rep2

description:
Library name: BioNi37A_4Control_10C_MG_Rep2
PS-22410_refseq_count.gct
PS-22410_refseq_tpm.gct


title: 2N clone derived from HCT116, biological replicate 2N2

description: Library name: HCT116-2N2


title: large 4N clone derived from CAL51, biological replicate L2

description: Library name: CAL51-L2


title: 2N clone derived from CAL51, biological replicate 2

description: Library name: CAL51-2N2


title: Control no MG Rep3

description:
Library name: BioNi37A_1Control_no_MG_Rep3
PS-22410_refseq_count.gct
PS-22410_refseq_tpm.gct

value: no Demyelination control no MG


title: LPC Demyelination no MG LPC Conc 0 1mM D 3div Rep1

description:
Library name: BioNi37A_2LPC_Demyelination_no_MG_LPC_Conc_0_1mM_D_3div_Rep1
PS-22410_refseq_count.gct
PS-22410_refseq_tpm.gct


title: Control no MG Rep1

description:
Library name: BioNi37A_1Control_no_MG_Rep1
PS-22410_refseq_count.gct
PS-22410_refseq_tpm.gct


title: Control no MG Rep2

description:
Library name: BioNi37A_1Control_no_MG_Rep2
PS-22410_refseq_count.gct
PS-22410_refseq_tpm.gct


title: Remyelination DMSO id112

description:
Library name: Readout_18
PS-13893_refseq_count.gct
PS-13893_refseq_tpm.gct

value: Remyelination control + DMSO +MG


title: Remyelination id109

description:
Library name: Readout_17
PS-13893_refseq_count.gct
PS-13893_refseq_tpm.gct


title: Remyelination DMSO id111

description:
Library name: Readout_11
PS-13893_refseq_count.gct
PS-13893_refseq_tpm.gct


title: Demyelination Control id106

description:
Library name: Readout_16
PS-13893_refseq_count.gct
PS-13893_refseq_tpm.gct


title: Remyelination id108

description:
Library name: Readout_10
PS-13893_refseq_count.gct
PS-13893_refseq_tpm.gct


title: Clemastine 1uM id114

description:
Library name: Readout_12
PS-13893_refseq_count.gct
PS-13893_refseq_tpm.gct

value: Remyelination + Clemastine +MG

tag: dose


title: large 4N clone derived from DLD1, biological replicate L1

description: Library name: DLD1-L1

value: colon

tag: genotype


title: Control 10C MG Rep3

description:
Library name: BioNi37A_4Control_10C_MG_Rep3
PS-22410_refseq_count.gct
PS-22410_refseq_tpm.gct

tag: cell line


title: No Demyelination Control id102

description:
Library name: Readout_8
PS-13893_refseq_count.gct
PS-13893_refseq_tpm.gct

tag: cell type

value: no Demyelination control +MG


title: Demyelination Control id104

description:
Library name: Readout_2
PS-13893_refseq_count.gct
PS-13893_refseq_tpm.gct

tag: treatment


title: Remyelination id107

description:
Library name: Readout_3
PS-13893_refseq_count.gct
PS-13893_refseq_tpm.gct


title: Clemastine 1uM id113

description:
Library name: Readout_5
PS-13893_refseq_count.gct
PS-13893_refseq_tpm.gct


title: No Demyelination Control id101

description:
Library name: Readout_1
PS-13893_refseq_count.gct
PS-13893_refseq_tpm.gct


title: Control 10C MG Rep1

description:
Library name: BioNi37A_4Control_10C_MG_Rep1
PS-22410_refseq_count.gct
PS-22410_refseq_tpm.gct


title: Demyelination Control id105

description:
Library name: Readout_9
PS-13893_refseq_count.gct
PS-13893_refseq_tpm.gct


title: Remyelination DMSO id110

description:
Library name: Readout_4
PS-13893_refseq_count.gct
PS-13893_refseq_tpm.gct


title: Clemastine 1uM id115

description:
Library name: Readout_19
PS-13893_refseq_count.gct
PS-13893_refseq_tpm.gct


title: T148_A_RICH

city: Toronto

first: Jason

last: Moffat

state: Ontario

address: 686 Bay Street

department: Genetics and Genome Biology

country: Canada

institute: Hospital for Sick Children

description:
Library name: Moffat_16
TAZ mutant HAP1 cells cultured in IMEM + 10% FBS

data_processing:
Paired-end reads were aligned with STAR (v2.6.1b) against the hg38 genome build and Gencode v25 gene annotations. (STAR command line parameters:   --outSAMstrandField intronMotif --outSAMtype BAM SortedByCoordinate --quantMode GeneCounts --sjdbGTFfile gencode.v25.annotation.gtf).
Sample-level read count files from STAR were merged with ENSEMBL and Entrez Gene annotations using R
Assembly: hg38
Supplementary files format and content: Tab-delimited read count matrix for each sample

growth_protocol: Cells were cultured in either IMDM (rich) or DMEM (minimal) media supplemented with 10% FBS and 1% Penicillin/Streptomycin and propagated in biological triplicates in 15cm dishes. Cells were lysed directly on dishes on ice with RLT buffer before proceeding to RNA extraction.

extract_protocol:
Cell lysates were first homogenized using QIAshredder columns followed by RNA isolation using the Qiagen RNeasy Plus kit according to manufacturers instructions, including on-column DNase treatment.
Poly(A)-enriched mRNA libraries were prepared as follows. 300ng per sample was processed according to NEBNext Ultra II Directional RNA Library Prep sample preparation protocol (Part # E7760L) with the NEBNext Poly(A) mRNA Magnetic Isolation Module (Part # E7490). 1µL top stock of each purified final library was run on an Agilent TapeStation HS D1000 tape (Agilent). The libraries were quantified using Quant-iT dsDNA HS Assay Kit (ThermoFisher Scientific) and were pooled at equimolar ratios after size adjustment. The final pool was run on an Agilent Bioanalyzer dsDNA High Sensitivity chip and quantified using NEBNext Library Quant Kit for Illumina (NEB). The quantified pool was hybridized at a final concentration of 2.75pM and sequenced paired-end 2x50 bp on the Illumina NovaSeq6000 platform using an S2 flowcell.

value: chronic myelogenous leukemia-derived

value: TAZ knockout (T148)


title: T148_C_MIN

description:
Library name: Moffat_15
TAZ mutant HAP1 cells cultured in DMEM (minimal) + 10% FBS


title: T148_C_RICH

description:
Library name: Moffat_18
TAZ mutant HAP1 cells cultured in IMEM + 10% FBS


title: T148_B_MIN

description:
Library name: Moffat_14
TAZ mutant HAP1 cells cultured in DMEM (minimal) + 10% FBS


title: T148_B_RICH

description:
Library name: Moffat_17
TAZ mutant HAP1 cells cultured in IMEM + 10% FBS


title: No Demyelination Control id103

description:
Library name: Readout_15
PS-13893_refseq_count.gct
PS-13893_refseq_tpm.gct


title: T126_C_RICH

description:
Library name: Moffat_12
TAZ mutant HAP1 cells cultured in IMEM + 10% FBS

value: TAZ knockout (T126)


title: T148_A_MIN

description:
Library name: Moffat_13
TAZ mutant HAP1 cells cultured in DMEM (minimal) + 10% FBS


title: T126_B_RICH

description:
Library name: Moffat_11
TAZ mutant HAP1 cells cultured in IMEM + 10% FBS


title: T126_A_RICH

description:
Library name: Moffat_10
TAZ mutant HAP1 cells cultured in IMEM + 10% FBS


title: T126_C_MIN

description:
Library name: Moffat_09
TAZ mutant HAP1 cells cultured in DMEM (minimal) + 10% FBS


title: T126_B_MIN

description:
Library name: Moffat_08
TAZ mutant HAP1 cells cultured in DMEM (minimal) + 10% FBS


title: WT_C_MIN

description:
Library name: Moffat_03
WT HAP1 cells cultured in DMEM (minimal) + 10% FBS

value: wild-type


title: T126_A_MIN

description:
Library name: Moffat_07
TAZ mutant HAP1 cells cultured in DMEM (minimal) + 10% FBS


title: WT_B_MIN

description:
Library name: Moffat_02
WT HAP1 cells cultured in DMEM (minimal) + 10% FBS


title: WT_C_RICH

description:
Library name: Moffat_06
WT HAP1 cells cultured in IMDM + 10% FBS


title: WT_A_RICH

description:
Library name: Moffat_04
WT HAP1 cells cultured in IMDM + 10% FBS


title: MDAMB231, tramadol0.5

city: Taipei

first: Zih-Syuan

last: Wu

address: No.161, Sec. 6, Minquan E. Rd., Neihu Dist., Taipei City 114201, Taiwan

country: Taiwan

institute: National defense medical center

description: Library name: MDAMB231 tramadol0.5

data_processing:
In order to remove technical sequences, including adapters, polymerase chain reaction (PCR) primers, or fragments thereof, and quality of bases lower than 20, pass filter data of fastq format were processed by Cutadapt (V1.9.1) to be high quality clean data. Firstly, reference genome sequences and gene model annotation files of relative species were downloaded from genome website, such as UCSC, NCBI, ENSEMBL. Secondly, Hisat2 (v2.0.1) was used to index reference genome sequence. Finally, clean data were aligned to reference genome via software Hisat2 (v2.0.1). In the beginning transcripts in fasta format are converted from known gff annotation file and indexed properly. Then, with the file as a reference gene file, HTSeq (v0.6.1) estimated gene and isoform expression levels from the pair-end clean data.
Assembly: hg38
Supplementary files format and content: tab-delimited text file include raw counts for each sample
Supplementary files format and content: tab-delimited text file include FPKM values for each sample

source_name: Homo sapiens

extract_protocol:
RNA was extracted using RNeasy Mini Kit_QIAGEN.
Libraries for polyA+ RNA-Sequencing were prepared from 1 μg RNA per sample using NovaSeq 6000 (Illumina)

value: Homo sapiens

value: breast cancer


title: MDAMB231, o-de0.05

description: Library name: MDAMB231 o-de0.05


title: WT_A_MIN

description:
Library name: Moffat_01
WT HAP1 cells cultured in DMEM (minimal) + 10% FBS


title: MCF-7, o-de0.05

description: Library name: MCF-7 o-de0.05


title: MCF-7, tramadol0.5

description: Library name: MCF-7 tramadol0.5


title: HEK293T 0Q rep 1 (mRNA-seq)

first: Tao

last: Pan

state: Illinois

address: 929 E. 57th Street

department: Biochemistry and Molecular Biology

institute: University of Chicago

description:
Library name: Sample1
0Q_rep1_L1_bc1

data_processing:
Raw sequencing reads were first demultiplexed by barcode sequence using Je demultiplex (PMID: 27717304).
Reads were trimmed using FastP (PMID: 30423086). After trimming, read quality control was assessed with FastQC (www.bioinformatics.babraham.ac.uk/projects/fastqc) to confirm the removal of low-quality bases and adapter sequences.
Trimmed reads were aligned to the mm39 (GRCm39) reference genome using STAR (PMID: 23104886).
Once mapped, reads were counted with the RSEM software (PMID: 21816040). Subsequent differential expression analysis was completed using custom scripts in R.
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: human embryonic kidney cell

growth_protocol: 0Q HEK293T cells were obtained as previously reported (PMID: 29970597). HEK293T cells (ATCC, CRL-11268) were cultured at 37°C in Dulbecco's modified Eagle's medium (DMEM) (Cytiva; SH30022.01) supplemented with 10% volume/volume (v/v) dialyzed fetal bovine serum (Gibco; 26400044) and 1% v/v Penicillin-Streptomycin (Thermo Fisher Scientific; 15070063).

extract_protocol:
Total RNA was extracted from cells using TRIzol reagent (Thermo Fisher Scientific; 15596026)
MSR-seq (PMID 35513407)

treatment_protocol: 100Q cells were obtained by culturing 0Q cells with 1 µM queuine (Toronto Research Chemicals) for 24 hours). Both 0Q and 100Q HEK293T cells were grown in triplicate.

value: human embryonic kidney cell

value: queuine-depleted media


title: HEK293T 100Q rep 1 (mRNA-seq)

description:
Library name: Sample4
100Q_rep1_L1_bc5

value: 100 nM queuine supplement


title: HEK293T 0Q rep 2 (mRNA-seq)

description:
Library name: Sample2
0Q_rep2_L1_bc2


title: HEK293T 0Q rep 3 (mRNA-seq)

description:
Library name: Sample3
0Q_rep3_L1_bc3


title: HEK293T 100Q rep 2 (mRNA-seq)

description:
Library name: Sample5
100Q_rep2_L1_bc6


title: HEK293T 100Q rep 3 (mRNA-seq)

description:
Library name: Sample6
100Q_rep3_L1_bc7


title: WT_B_RICH

description:
Library name: Moffat_05
WT HAP1 cells cultured in IMDM + 10% FBS