title: Toxoplasma and HFF, total RNA, replicate 2

description: Library name: total_RNA_rep2

data_processing:
Reads from both sequencing runs were treated as single-end for compatibility. Adapters were trimmed with cutadapt (v3.7) and options -u 4 -a NNNNCTGTCTCTTATACACATCTCCGAGC --match-read-wildcards --minimum-length=15 and --nextseq-trim=20 or -q 20 for NovaSeq and HiSeq reads, respectively.
STAR (v2.7.1a) was used to map reads to a metagenome of T. gondii, H. sapiens, size markers, and spike-in sequences with settings --outFilterType BySJout --outSAMattributes All --alignIntronMax 25000 --outSAMtype BAM SortedByCoordinate --outFilterMultimapNmax 1.
A custom Toxoplasma transcriptome annotation was generated to include representative 5′ UTR isoforms expressed in our data. For ToxoDB, Markus et al. 2021 Tz TSS and Bz TSS transcript isoforms, 5′ UTRs were split into windows of three nt with bedtools makewindows, and total RNA coverage was calculated across these windows for each model using bedtools coverage -counts -s. We calculated cumulative read coverage and D for each model, where D is the ks.test statistic from comparison of a normalized, even distribution against read coverage for the model normalized to the UTR length and total cumulative sum. D values were compared for all models for a given gene, and the model with the lowest D value was selected as the representative isoform, except in the following cases: 1) In cases where the difference between D values was less than 0.05, we selected the model with the longest length. 2) In cases where all models had a D value greater than 0.4, the result was deemed inconclusive, and the 5′ UTR was excluded from further analyses. RPKM was calculated from counts generated with featureCounts, and transcripts with RPKM > 5 in both replicates were considered expressed. CDS and 3′ UTR annotations were used directly from ToxoDB models. In cases where there are multiple annotated CDS isoforms, the longest isoform was selected. The GFF file was updated with the new UTRs.
For the H. sapiens transcriptome annotation, canonical transcripts were identified from the UCSC genome browser knownCanonical option, and the H. sapiens transcriptome was filtered to include just the canonical transcript for each gene. The transcript with the longest CDS was selected for genes with multiple canonical transcripts or no canonical transcripts.
The spliced transcriptome fasta for Toxoplasma was created using gffread -w. Genome-aligned reads were re-aligned to spliced H. sapiens and T. gondii transcriptomes with STAR options --outFilterMismatchNmax 2 --outFilterType BySJout --outSAMattributes All --outSAMtype BAM SortedByCoordinate.
Total mRNA and ribosome footprint reads mapping to the CDS of each transcript, excluding the first and last three codons, were counted with featureCounts and parameters GTF.featureType="CDS", useMetaFeatures=F, readShiftType = "downstream", readShiftSize = 12, read2pos = 5, strandSpecific = 1. Ribosome footprint and mRNA RPKM were calculated for each gene using DESeq2, and translation efficiency (ribosome footprint RPKM / mRNA RPKM) was calculated for each biological replicate and the average taken.
Assembly: ToxoDB Release 68 and HostDB Release 68
Supplementary files format and content: CDS_raw_counts.xlsx is an Excel spreadsheet that contains CDS counts (excluding the first and last 3 codons) generated with featureCounts. One tab contains Toxoplasma data and one tab contains host cell data.
Supplementary files format and content: RPKM_and_TE.xlsx is an Excel spreadsheet that contains RPKM values for the CDS of each transcript, and a separate tab with translation efficiency (TE). Separate tabs are provided for Toxoplasma and host data.
Supplementary files format and content: Toxoplasma_gondii_ME49_updated_5UTRs.gff is the GFF that contains updated 5' UTR models and remaning gene annotations from ToxoDB.


title: Healthy donor 2 P6520 CD8SP

status: Public on Jul 15 2025

type: RNA

city: Madrid

first: María

middle: L

last: Toribio

state: Madrid

address: Calle Nicolás Cabrera, 1. Campus Cantoblanco

department: Interactions with the environment

country: Spain

institute: Centro de Biología Molecular Severo Ochoa (CSIC-UAM)

description: Total RNA from CD8 Single Positive stage (CD8SP, CD4- CD8+ CD3+ TCRαβ+) isolated from human postnatal thymus. Healthy donor 2 of 3.

hyb_protocol: Labeled targets from 5 μg of total RNA was used for hybridization on each OSU-CCC miRNA microarray custom version 4, containing 393 mouse, 409 humans and 962 ultraconserved sequences in quadruplicate. All probes on these microarrays are 40-mer oligonucleotides spotted by contacting technologies and covalently attached to a polymeric matrix. The microarrays were hybridized in 6× SSPE (0.9 M sodium chloride/60 mM sodium phosphate/8 mM EDTA, pH 7.4)/30% formamide at 25°C for 18 h, washed in 0.75× TNT (Tris·HCl/sodium chloride/Tween 20) at 37°C for 40 min, and processed by using direct detection of the biotin-containing transcripts by Streptavidin-Alexa647 conjugate.

scan_protocol: Processed slides were scanned by using a Gene Pix 4000B scanner, with the laser set to 635 nm, at power 100 and PMT 80 settings.

data_processing:
Microarray images were analyzed using GenePix Pro 6.0.1.00 (Axon Instruments, Molecular Devices). Average values of the replicate spots of each miRNA were background subtracted; log2-transformed, and normalized using quantiles normalization (Bioconductor). miRNAs were retained when present in at least 20% of samples. All the data analyses were performed using BRB-ArrayTools, v3.6.0, and R v2.3.1 (R Foundation for Statistical Computing) with a P-value <0.05.
The *txt files contain normalized signal intensity

label: Biotin

molecule: total RNA

organism: Homo sapiens

source_name: postnatal thymus

label_protocol: Five micrograms of the test RNAs were labeled with 3′-(N)8-(A)12-biotin-(A)12-biotin-5′] oligonucleotide primer using the SuperScript II RNase H Reverse Transcriptase KIT (Invitrogen).

growth_protocol: Human primary thymocyte populations were purified from fresh pediatric thymus samples (aged 1 month to 4 years) by density centrifugation (Lymphoprep, STEM CELL Technologies), followed by sequential immunomagnetic selection based on cell surface markers (Dynal, Invitrogen and Miltenyi Biotec).

extract_protocol: Total RNA was extracted using TRIzol reagent (Invitrogen). RNA integrity was confirmed using the Agilent 2100 Bioanalyzer (Agilent Technologies).

tag: tissue

value: thymus

tag: t-cell developmental stage


title: S461591_WTA_023

type: SRA

city: Birmingham

first: Claudio

last: Mauro

address: University of Birmingham

department: Institute of Immunology and Immunology

country: United Kingdom

institute: University of Birmingham

library_source: transcriptomic

data_processing:
FASTQ files were processed using the GeoMX NGS pipeline (2.0.0.16) to produce dcc files
dcc files were uploaded to the GeoMx DSP for downstream analysis
Data were filtered using default settings and normalised using Q3 normilisation
Assembly: N/A
Supplementary files format and content: dcc files containing raw counts
Library strategy: Spatial Transcriptomics

source_name: coronary artery

extract_protocol:
5μm thick FFPE slides were cut using a microtome. Deparaffin Protocol - Xylene 5min x3, 100% EtOH 5min x2, 95% EtOH 5min x1. 99°C ER2 (Ph9) 15mins. 37°C 1μg/mL Proteinase K 15mins. 10%NBF 5min, NBF Stop buffer 5min x2. 37°C. Label Protocol - WTA probe mix 1:10 16hr. 37°C 50%Formamide-2xSSC mix 25mins x2. Hybridisation Protocol - Syto13, CD45  TxRed, CD4 647 60mins. Scan Protocol - FITC - SYTO1350ms, TxRed - CD45 200ms, Cy5 - CD4 200ms
Spatial transcriptome sequencing libraries were prepped with Nanostring Reagent kits according to manufacturer's suggestions.

value: coronary artery

tag: roi

tag: subset

tag: grade

tag: localisation

value: Negative control


title: sgZBTB11 #1 DMSO, 1 day, Rep2

city: La Jolla

first: Eric

middle: S.

last: Wang

state: CA

address: 10901 North Torrey Pines Road

department: Cancer Metabolism and Microenvironment Program

country: USA

institute: Sanford Burnham Prebys Medical Discovery Institute

description: Library name: D1_sg5_dmso_2

data_processing:
Data was processed using nf-core rnaseq pipeline version 3.17.0 (star_rsem) using human genome version GRCh38.p14 and Gencode annotations versions 47.
Assembly: GRCh38
Supplementary files format and content: Tab-delimited table of counts and transcripts-per-million (TPM)

source_name: MIA PaCa-2

extract_protocol:
Total RNA was extracted from cells using the Direct-zol RNA Miniprep Plus kit (Zymo Research #2072)
PolyA RNA isolation and library preparation was performed with the Watchmaker mRNA Library Prep Kit (Watchmaker Genomics: 7BK0001 ) with xGEN Stubby adaptors (IDT, Cat: 336338420) and xGEN 10nt UDIs (IDT, Cat: 336338436). Libraries were sequenced with the Element Biosciences AVITI Sequencing platform using the AVITI 2x75 High Output Cloudbreak Freestyle Kit (Element Biosciences, Cat: 860-00015).

tag: cell line

value: MIA PaCa-2

tag: cell type

value: PDAC

tag: treatment

value: sgZBTB11 #1 DMSO, 1 day


title: S461591_WTA_022

value: Severe

value: Plaque


title: Healthy donor 2 P6516 DPCD3-

description: Total RNA from Double Positive CD3- stage (DPCD3-, CD4+ CD8+ CD3- TCRαβ-) isolated from human postnatal thymus. Healthy donor 2 of 3.


title: S461591_WTA_021


title: No Template Control

organism: blank sample


title: sgZBTB11 #1 DMSO, 1 day, Rep1

description: Library name: D1_sg5_dmso_1


title: NSCs, L1

city: Changsha

first: Chaoyong

last: He

address: Tianma road

country: China

institute: Hunan university

data_processing:
Reads mapping and gene expression quantification: cDNA library samples were sequenced as described above. After removing the reads with adapters, any reads containing ‘n’ (> 10%) and low-quality reads (sQ ≤ 5), the remaining clean reads were checked by FastQC (v.0.11.5). Clean reads were aligned to the Rattus norvegicus Rnor 6.0.98 using STAR (v.2.5.3a) and the raw counts matrix were obtained by featureCounts. The expression level of genes was calculated using CPM (count per millon) as a metric, and filtered using the sum of relative abundance to eliminate the effects of sequencing depths.
PCA analysis, DEG obtain and clustering: Normalized gene expression values used to calculate the correlation coefficient among biological replicates for PCA and hierarchical clustering. The PCA was calculated with the prcomp function in R with default settings. Hierarchical clustering was performed using the pheatmap package with default settings using Pearson’s correlation. The DEGs in pairwise comparisons were identified by the R package edgeR, which performs data normalization using the trimmed mean of M-values (TMM) method. Genes with at least a two-fold change in expression and P value < 0.05 were considered to be expressed differentially. A k-means approach was used (R package pheatmap) to cluster all the DEGs identified through pairwise comparisons.
Assembly: rn6
Supplementary files format and content: tab-delimited text files include CPM values for each Sample

organism: Rattus norvegicus

source_name: brain tissue from SD rats at 1 day

growth_protocol: NSCs were isolated from cerebral cortices of 1–day-old neonatal Sprague-Dawley rats.

extract_protocol:
NSCs were expanded as neutrospheres at 37°C, 5% CO2 for 3-4 days in proliferation culture medium, which contained DMEM/F12 supplemented with 1% glutamine (Gibco), 1% sodium pyruvate (Gibco), 1% NEAA (Gibco), 2% B27 (Gibco), 0.02 ng/mL EGF, 0.02 ng/mL bFGF, 1.83 ng/mL heparin and 1% streptomycin penicillin (Gibco). The proliferation medium was replaced every 2 days. Thereafter, the NSCs neutrospheres were gathered through centrifugation (300×g, 5min), and digested with 0.25% trypsin-EDTA (Gibco) at 37℃ for 18 min. After terminating digestion mixture using 10% FBS, the cells were collected by countrification and filtered through 70 μm and 40 μm mech of cell strainer successively to obtain the NSCs of single-cell suspension. 0.2% (W/V) of Col solution mixed with equal volume of NSCs single-cell suspension to obtain final 0.75, 1.5, 3 million/mL of cell packing density system.
RNA-seq library preparation. Total RNA was isolated from each sample using the RNAmini kit (Qiagen, Germany). RNA quality was examined by gel electrophoresis and with Qubit (Thermo, Waltham, MA, USA). Strand-specific libraries were constructed using the TruSeq RNA sample preparation kit (Illumina, San Diego, CA, USA), through reverse transcription using S1000TM Touch Thermal Cycler (Bio Rad) at 53°C (45 min) - 85°C (5 min) - 4°C cycle. The generated cDNA was amplified, and quality estimated using Agilent 4200 (performed by CapitalBio Technology, Beijing). The sequences of libraries were finally obtained using the Illumina Novaseq6000 sequencer with pair-end 150 bp (PE150).

treatment_protocol: After tissue pieces of dissociation, the mixed cortical cells were first passed through a 100 μm mesh of nylon cell strainer, then plated into tissue culture flasks.

tag: strain

value: Sprague-Dawley

value: brain tissue

value: Neural Stem Cells

tag: genotype

value: wild type

tag: age

value: 1 day-old

value: Low cell packing density


title: Toxoplasma and HFF, total RNA, replicate 1

city: Cambridge

first: Sebastian

last: Lourido

state: MA

address: 455 Main Street

institute: Whitehead Institute

description: Library name: total_RNA_rep1

organism:
Toxoplasma gondii
Homo sapiens

source_name: T gondii: ME49, H sapiens: human foreskin fibroblast

growth_protocol: T. gondii were grown in human foreskin fibroblasts (HFFs) at 37°C and 5% CO2 and maintained in DMEM supplemented with 3% heat-inactivated fetal bovine serum and 10 ug/mL gentamicin.

extract_protocol:
Dishes of HFFs with intracellular tachyzoites were placed on ice, and washed with ice-cold PBS with 100 ug/mL cycloheximide twice. 1 mL lysis buffer (20 mM HEPES pH 7.5, 100 mM KCl, 5 mM MgCl2, 1% Triton X-100, 2 mM DTT, 100 ug mL-1 cycloheximide, 500 U mL-1 RNaseIn Plus (Promega), and cOmplete Protease Inhibitor Cocktail (1 tablet per 10 mL buffer, Roche)) was added, and a cell lifter was used to dissociate HFFs with intracellular parasites from the dish, combining both dishes into the 1 mL sample. Lysates were passed through a 27-gauge needle 3 times, then 30-gauge needle 3 times, before incubating on ice for 5-10 minutes. Debris was pelleted by centrifugation at 4°C 1300xg for 10 minutes, and supernatant was transferred to fresh tubes. Samples were flash-frozen in liquid nitrogen and stored at -80°C.
For ribosome profiling, RNase I (Thermo Fisher) concentration was empirically tested, after which 40 U per 1 OD260 was used. Sucrose gradient preparation, fractionation, collection of 80S ribosomes, and RNA fragment purification were performed as described in Xiang and Bartel 2021. For matched RNA-seq, probes for depletion of Toxoplasma rRNAs from total RNA samples were designed through NEB, and an equal ratio of human and Toxoplasma probes (2 uL each per reaction) were used for rRNA depletion with the NEBNext rRNA Depletion Kit (Human/Mouse/Rat, NEB, E6310L). Spike-in of GFP, Renilla luciferase, and Firefly luciferase mRNAs were added to the total RNA samples. Total RNA was fragmented with RNA Fragmentation Buffer (2 mM EDTA, 12 mM Na2CO3, 88 mM NaHCO3) by incubating at 95°C for 20 minutes followed by ethanol precipitation. Ribosome footprint and total RNA libraries were processed in parallel according to an established protocol (Subtelny et. al 2014).

value: T gondii:ME49, H sapiens:human foreskin fibroblast

value: T gondii:ME49/dKu80/dHXGPRT/TIR1


title: sgNS DOX, 5 hr, Rep3

description: Library name: 5h_sgNS_dox_3

value: sgNS DOX, 5 hr


title: JL with drought treatment (3)

city: 太原市

first: Chunlei

last: Zou

state: 山西省

address: 山西省晋中市太谷区铭贤南路1号

institute: 山西农业大学

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by trimming reads containing adapter, ploy-N or with low quality from raw data.
At the same time, Q20, Q30 and GC content of the clean data were calculated. All the downstream analyses were performed based on the clean data with high quality.
Index of the reference genome was built using hisat2-2.0.4 and paired-end clean reads were mapped to the reference genome. STAR used the method of Maximal Mappable Prefix (MMP) which can generate a precise mapping result for junction reads.
Stringtie-1.3.3b ）was used to count the read numbers mapped to each gene. And then FPKM was calculated, which expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced.
Assembly: ftp://ftp.ensemblgenomes.org/pub/release-42/plants/fasta/sorghum_bicolor/dna
Supplementary files format and content: "gene_km.xls" contains the FPKMs of each gene
Supplementary files format and content: "genes_count.xls" contains the readcount of each gene

organism: Sorghum bicolor

source_name: Leaves

extract_protocol:
Total RNA was extracted from samples using TRIzol reagent. RNA Nano 6000 Assay Kit and Bioanalyzer 2100 system (Agilent Technologies, CA, USA) were used to measure RNA concentration and detect RNA integrity.
The cDNA library was sequenced on the Illumina NovaSeq 6000 by Novogene Co., Ltd.
Strand-specific libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

value: Leaves

value: Jinliang 5

value: Drought


title: Healthy donor 2 P6515 DPPRETCR

description: Total RNA from Double Positive PRE-TCR stage (DPPRETCR, CD4+ CD8+ CD3lo TCRαβ-) isolated from human postnatal thymus. Healthy donor 2 of 3.

value: thymus


title: S461591_WTA_020

value: coronary artery


title: JL with drought treatment (2)

address: 山西省晋中市太谷区铭贤南路1号


title: S461591_WTA_019

value: Adventitia


title: Healthy donor 2 P6513 PRET

description: Total RNA from Pre T stage (PRET, CD34+ CD1a+ CD4- CD8- CD3- TCRαβ-) isolated from human postnatal thymus. Healthy donor 2 of 3.


title: S461588_WTA_001

value: Moderate


title: sgNS DOX, 5 hr, Rep1

description: Library name: 5h_sgNS_dox_1

value: MIA PaCa-2

value: PDAC


title: S461591_WTA_018

value: Severe


title: JL with drought treatment (1)

address: 山西省晋中市太谷区铭贤南路1号


title: Healthy donor 2 P6517 DPTCRAB+

description: Total RNA from Double Positive TCRαβ+ stage (DPTCRAB+, CD4+ CD8+ CD3+ TCRαβ+) isolated from human postnatal thymus. Healthy donor 2 of 3.


title: Healthy donor 2 P6511 ETP

description: Total RNA from Early Thymic Progenitors (ETP, CD34hi CD1a- CD4- CD8- CD3- TCRαβ-) isolated from human postnatal thymus. Healthy donor 2 of 3.


title: sgNS DMSO, 5 hr, Rep2

description: Library name: 5h_sgNS_dmso_2

value: sgNS DMSO, 5 hr


title: JL with normal water supply (2)

address: 山西省晋中市太谷区铭贤南路1号

value: Control


title: sgNS DMSO, 5 hr, Rep3

description: Library name: 5h_sgNS_dmso_3


title: JL with normal water supply (3)

address: 山西省晋中市太谷区铭贤南路1号


title: JL with normal water supply (1)

address: 山西省晋中市太谷区铭贤南路1号


title: S461591_WTA_017

value: Plaque


title: S461591_WTA_014

value: Negative control


title: SCS with drought treatment (3)

address: 山西省晋中市太谷区铭贤南路1号

value: Sanchisan


title: Healthy donor 1 P6507 DPTCRAB+

description: Total RNA from Double Positive TCRαβ+ stage (DPTCRAB+, CD4+ CD8+ CD3+ TCRαβ+) isolated from human postnatal thymus. Healthy donor 1 of 3.


title: Healthy donor 1 P6510 CD8SP

description: Total RNA from CD8 Single Positive stage (CD8SP, CD4- CD8+ CD3+ TCRαβ+) isolated from human postnatal thymus. Healthy donor 1 of 3.


title: S461591_WTA_016


title: sgNS DMSO, 5 hr, Rep1

description: Library name: 5h_sgNS_dmso_1


title: S461591_WTA_015


title: sgNS DOX, 5 hr, Rep2

description: Library name: 5h_sgNS_dox_2


title: Healthy donor 1 P6506 DPCD3-

description: Total RNA from Double Positive CD3- stage (DPCD3-, CD4+ CD8+ CD3- TCRαβ-) isolated from human postnatal thymus. Healthy donor 1 of 3.


title: Healthy donor 2 P6514 CD4ISP

description: Total RNA from CD4 Immature single positive stage (CD4ISP, CD4+ CD1a+ CD8- CD3- TCRαβ-) isolated from human postnatal thymus. Healthy donor 2 of 3.


title: SCS with drought treatment (2)

address: 山西省晋中市太谷区铭贤南路1号


title: Healthy donor 1 P6509 CD4SP

description: Total RNA from CD4 Single Positive stage (CD4SP, CD4+ CD8- CD3+ TCRαβ+) isolated from human postnatal thymus. Healthy donor 1 of 3.


title: sgZBTB11 #2 DOX, 5 hr, Rep2

description: Library name: 5h_sg6_dox_2

value: sgZBTB11 #2 DOX, 5 hr


title: sgZBTB11 #2 DOX, 5 hr, Rep1

description: Library name: 5h_sg6_dox_1


title: Healthy donor 1 P6505 DPPRETCR

description: Total RNA from Double Positive PRE-TCR stage (DPPRETCR, CD4+ CD8+ CD3lo TCRαβ-) isolated from human postnatal thymus. Healthy donor 1 of 3.


title: sgZBTB11 #2 DMSO, 5 hr, Rep3

description: Library name: 5h_sg6_dmso_3

value: sgZBTB11 #2 DMSO, 5 hr


title: S461591_WTA_013


title: SCS with normal water supply (3)

address: 山西省晋中市太谷区铭贤南路1号

value: Leaves


title: SCS with drought treatment (1)

address: 山西省晋中市太谷区铭贤南路1号


title: Healthy donor 1 P6504 CD4ISP

description: Total RNA from CD4 Immature single positive stage (CD4ISP, CD4+ CD1a+ CD8- CD3- TCRαβ-) isolated from human postnatal thymus. Healthy donor 1 of 3.


title: S461591_WTA_012


title: sgZBTB11 #2 DOX, 5 hr, Rep3

description: Library name: 5h_sg6_dox_3


title: sgZBTB11 #2 DMSO, 5 hr, Rep2

description: Library name: 5h_sg6_dmso_2


title: Healthy donor 1 P6503 PRET

description: Total RNA from Pre T stage (PRET, CD34+ CD1a+ CD4- CD8- CD3- TCRαβ-) isolated from human postnatal thymus. Healthy donor 1 of 3.


title: SCS with normal water supply (2)

address: 山西省晋中市太谷区铭贤南路1号


title: sgZBTB11 #2 DMSO, 5 hr, Rep1

description: Library name: 5h_sg6_dmso_1


title: S461591_WTA_010


title: SCS with normal water supply (1)

address: 山西省晋中市太谷区铭贤南路1号


title: Healthy donor 1 P6501 ETP

description: Total RNA from Early Thymic Progenitor stage (ETP, CD34hi CD1a- CD4- CD8- CD3- TCRαβ-) isolated from human postnatal thymus. Healthy donor 1 of 3.


title: sgZBTB11 #1 DOX, 5 hr, Rep3

description: Library name: 5h_sg5_dox_3

value: sgZBTB11 #1 DOX, 5 hr


title: S0, DKO, rep4

city: West Haven

first: Francesc

last: Lopez

state: CT

department: Department of Genetics

institute: Yale University

description: Library name: S0-K6

data_processing:
The libraries underwent 150-bp paired-end sequencing using an Illumina Novaseq X at the Yale Center for Genome Analysis (YCGA).
Adapter sequences, empty reads, and low-quality sequences were removed. Reads were trimmed using fastp v0.21.0 using default parameters.
Trimmed reads were mapped to the mouse reference genome (mm10) with HISAT2 v2.2.1. Alignments with a quality score below 20 were excluded from further analysis
Gene counts were produced with StringTie v1.3.3b [58] and the Python script “prepDE.py” provided in the package. StringTie was limited to reads matching the reference annotation GENCODE V15
Assembly: mm10
Supplementary files format and content: csv file with the raw fragment counts for each sample and gene.

molecule: polyA RNA

organism: Mus musculus

source_name: S0 cells from the E12.5 fetal liver

extract_protocol:
Total RNA was purified using the RNAqueous™-Micro Total RNA Isolation Kit (Thermo Fisher Scientific).
RNA quality was determined by estimating the A260/A280 and A260/A230 ratios by nanodrop. RNA integrity was determined by running an Agilent Bioanalyzer gel, which measures the ratio of the ribosomal peaks.  Samples with RIN values of 7 or greater were used for library preparation. Using the NEBNext Single Cell/Low Input RNA Library Prep Kit from Illumina (E6420L), a normalized RNA input between 200pg-50ng was used to generate cDNAs with the template switching method. The NEB Ultra II FS workflow was used for fragmentation, end repair, dA-tailing, adapter ligation and PCR. Indexed libraries that met appropriate cut-offs for both quantity and quality were quantified by qRT-PCR using a commercially available kit (KAPA Biosystems) and insert size distribution was determined with the LabChip GX or Agilent Bioanalyzer. Samples with a yield of ≥0.5 ng/ul were used for sequencing.

value: S0 cells from the E12.5 fetal liver

value: erythoid precursor

value: DKO


title: S461591_WTA_009

value: coronary artery

value: Adventitia


title: arsenic group_testis_5

city: Tsukuba

first: Takehiro

last: Suzuki

state: Ibaraki

address: 16-2 Onogawa

country: Japan

institute: National Institute for Environmental Studies

library_source: genomic

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trim Galore (ver. 0.6.5)
Adapter-and quality-trimmed sequencing reads were mapped to the mouse reference genomes (mm10) using the Bismark (ver. 0.22.3)
The methylation level of each CpG was calculated using a methylKit package (ver. 1.22.0)
Assembly: mm10
Supplementary files format and content: txt

molecule: genomic DNA

source_name: Testis

extract_protocol:
Testis DNA was extracted with a phenol-chloroform mixture, precipitated with ethanol, dried and dissolved in TE buffer. Testis DNA was purified using Allprep DNA/RNA mini kit (Qiagen) and was used for the construction of RRBS libraries.
RRBS libraries were prepared using NEBNext Ultra II DNA Library Prep Kit for Illumina following manufacturer's protocols.

value: Testis

value: arsenic-treated


title: S0, DKO, rep3

description: Library name: S0-K5


title: arsenic group_testis_4


title: S461591_WTA_008

value: Severe


title: S461591_WTA_007


title: S0, DKO, rep2

description: Library name: S0-K3


title: arsenic group_testis_3


title: S0, DKO, rep1

description: Library name: S0-K1


title: sgZBTB11 #1 DMSO, 5 hr, Rep3

description: Library name: 5h_sg5_dmso_3

value: MIA PaCa-2

value: PDAC

value: sgZBTB11 #1 DMSO, 5 hr


title: S461591_WTA_005

value: Plaque


title: arsenic group_testis_1


title: sgZBTB11 #1 DMSO, 5 hr, Rep2

description: Library name: 5h_sg5_dmso_2


title: S461591_WTA_006


title: S0, wild-type, rep4

description: Library name: S0-W4

value: wild type


title: S461591_WTA_011


title: S461591_WTA_004


title: S0, wild-type, rep3

description: Library name: S0-W3


title: arsenic group_testis_2


title: control group_testis_5

value: control


title: S0, wild-type, rep2

description: Library name: S0-W2


title: SPARC Overexpressed, rep3

city: Escobar

first: Antonella

last: Lombardi

state: Buenos Aires

address: Ruta 9 Km 54

country: Argentina

institute: FLENI

description: Library name: Sn3

data_processing:
Gene-level quantification was performed using HTSeq-count.
Differential expression analysis was performed using DESeq2 in R (v4.1.2).
Genes with |log2FC| > 0.585 and FDR-adjusted p-value < 0.05 were considered differentially expressed.
Hierarchical clustering and heatmaps were generated using Seaborn in Python (v3.10).
GRCh38 / hg38
Assembly: Gene-level raw counts table generated with HTSeq-count; CSV format, rows as genes and columns as samples.
Supplementary files format and content: Differential expression results from DESeq2 (log2 fold changes and adjusted p-values); CSV format.

source_name: mesenchymal stem cell

growth_protocol: Wharton’s jelly mesenchymal stem cells (WJ-MSCs) were isolated from human umbilical cords, cultured in MEM-α with 10% FBS at 37 °C and 5% CO₂, and passaged until P2–P3.

extract_protocol:
Total RNA was extracted using TRIzol reagent following the manufacturer’s instructions. RNA was DNase-treated and precipitated using sodium acetate and ethanol. RNA integrity was assessed by electrophoresis.
Libraries were prepared using the Illumina TruSeq Stranded Total RNA Library Prep Gold Kit with Ribo-Zero, following protocol 1000000040499 v00 (Macrogen).  Raw FASTQ files were aligned to the human reference genome (GRCh38/hg38) using STAR v2.7.

treatment_protocol: WJ-MSCs were genetically modified via lentiviral transduction to overexpress or knock down SPARC. Post-transduction, cells were selected with puromycin (2 µg/mL) for 48–72 h and maintained in MEM-α + 10% FBS.

value: mesenchymal stem cell

value: S

value: SPARC Overexpressed


title: sgZBTB11 #1 DOX, 5 hr, Rep2

description: Library name: 5h_sg5_dox_2

value: sgZBTB11 #1 DOX, 5 hr


title: S0, wild-type, rep1

description: Library name: S0-W1

value: S0 cells from the E12.5 fetal liver

value: erythoid precursor


title: S461591_WTA_003

value: coronary artery


title: control group_testis_4


title: S461591_WTA_002

value: Adventitia


title: control group_testis_3

value: Testis


title: S461591_WTA_001


title: control group_testis_2


title: sgZBTB11 #1 DOX, 5 hr, Rep1

description: Library name: 5h_sg5_dox_1


title: SPARC Overexpressed, rep1

description: Library name: Sn1


title: SPARC Overexpressed, rep2

description: Library name: Sn2


title: Kidney organoids generated from 250K cells

city: Pamplona

first: Asier

last: Ullate-Agote

state: Navarra

address: Av. de Pío XII, 55

department: Hemato-Oncology

institute: CIMA

library_source: transcriptomic single cell

data_processing:
Demultiplexing, alignment to the Homo sapiens (hg38) genome and quantification using the annotation from Ensembl v93 was performed using 10X Genomics Cell Ranger (v3.0.1)
Downstream analysis steps (quality control filtering, normalization, integration, clustering and differential expression) were performed using the R package Seurat (v4.0.5)
Assembly: hg38
Supplementary files format and content: HDF5 Feature Barcode Matrix containing a Gene x Cells UMI count matrix

source_name: kidney organoid

extract_protocol:
After the indicated time point kidney organoids were collected and washed twice with PBS, and further dissociated into a single cell suspension by treating them with Accumax (07921, Stem Cell Technologies) for 15 min at 37ºC followed by Trypsin-EDTA 0.25% (wt/vol) trypsin (25300-054, Life Technologies) for additional 15 min at 37ºC. The reaction was deactivated by adding 10% FBS. The cell suspension was then passed through a 40μm cell strainer. After centrifugation at 1,000 RPM for 5 minutes cell numbers and viability were analyzed using Countess Automated Cell Counter (Invitrogen). This method generated single cell suspension with greater than 90% viability. Cell suspensions were frozen until further use. For library construction cells were thawed and centrifuged at 1,000 RPM for 5 minutes. Cell numbers and viability were analyzed using Countess Automated Cell Counter (Invitrogen) and cell suspensions were loaded onto a well of a 10X Chromium Single Cell instrument. Barcoding and cDNA synthesis were performed according to the manufacturer´s instructions. The cDNA libraries were constructed using the 10X Chromium Single cell 3' Library Kit v3 according to the manufacturer's original protocol and sequenced with a NextSeq 500 (R1:28, R2:55, i7:8) instrument.
scRNA libraries were prepared for sequencing using standard Illumina protocols

value: kidney organoid

value: human embryonic stem cell

value: XY

value: Kidney organoid protocol

tag: sample type

value: 250K Organoid


title: WT PQ 50 replicate 4

city: Paris

first: Monot

last: Marc

address: 25, rue du docteur roux

department: Genomes and Genetics

country: France

institute: Institut Pasteur

data_processing:
The RNA‐seq analysis was performed with the Sequana framework (Cokelaer et al, 2017 doi:10.21105/joss.00352)
Version used: RNA‐seq pipeline (v0.13.0)
FeatureCounts 2.0.1 with the multimapper option was used to produce the count matrix, assigning reads to features using corresponding primary annotation with strand-specificity information.
Differential expression testing was conducted using DESeq2 (PMID: 25516281)
Assembly: Leptospira interrogans serovar manilae, NZ_CP011931.1
Supplementary files format and content: Files in CSV that contains Gene_ID, log2FoldChange, pvalue

organism: Leptospira interrogans

source_name: Manilae strain L495

extract_protocol:
Total RNA was extracted from biofilm or planktonic cells. Cells were collected by centrifugation for 15 min at 3000xg at 4°C and resuspended in 1mL TRIzol
RNA libraries for RNA-seq were prepared using Illumina Stranded Total RNA Prep Ligation with Ribo-Zero Plus prep kit following manufacturer's protocol

value: bacterial cells

value: Manilae strain L495

value: serovar Manilae strain L495


title: SPARC Knockdown, rep3

description: Library name: KDn3

value: mesenchymal stem cell

value: Kd

value: SPARC Knockdown


title: control group_testis_1

value: control


title: WT PQ 10 replicate 4


title: Kidney organoids generated from 0.5K cells

value: kidney organoid protocol

value: 0.5K Organoid


title: SPARC Knockdown, rep2

description: Library name: KDn2


title: sgZBTB11 #1 DMSO, 5 hr, Rep1

description: Library name: 5h_sg5_dmso_1

value: MIA PaCa-2

value: PDAC

value: sgZBTB11 #1 DMSO, 5 hr


title: 2_AA_3

city: Singpore

first: danxia

last: he

address: Jurong West St 61

country: Singapore

institute: School of biological sciences, Nanyang techolo

data_processing:
Trimmomatic (version 0.36) software was used for raw data cleanning
clean data were mapped to Tair10 by using Hisat2 with default parameters
DEG lists were identified by using edgeR with cut-offs of log fold-change ≥ log2 and false discovery rate < 0.05
Assembly: tair 10
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

organism: Arabidopsis thaliana

growth_protocol: Seedlings were firstly grown on 1/2 MS solid medium. 5-day old seedlings were transferred into liquid 1/2 MS for extra 5 days.

extract_protocol:
Whole plants were frozen in liquid nitrogen, and RNA was harvested using RNA extraction kit from QIAGEN. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: 100 nM flg22 and 200 uM 2'-AA water solution were used for treatment

value: seedlings

value: 2_AA treatment

tag: ecotype

value: wild type


title: arsenic group 4

source_name: Sperm

extract_protocol:
Sperm DNA was extracted with a phenol-chloroform mixture, precipitated with ethanol, dried and dissolved in TE buffer. Sperm DNA was purified using Allprep DNA/RNA mini kit (Qiagen) and was used for the construction of RRBS libraries.
RRBS libraries were prepared using NEBNext Ultra II DNA Library Prep Kit for Illumina following manufacturer's protocols.

value: Sperm

value: arsenic-treated


title: WT PQ 50 replicate 3

value: bacterial cells


title: 2_AA_2


title: WT PQ 10 replicate 3

value: Manilae strain L495


title: SPARC Knockdown, rep1

description: Library name: KDn1


title: Wild Type, rep3

description: Library name: WTn3

value: WT


title: 2_AA_1


title: arsenic group 3


title: WT PQ 50 replicate 2

value: serovar Manilae strain L495


title: A collection of FOVs in a severe atherosclerotic artery taken on the NanoString CosMx platform

hyb_protocol: 970 RNA probes (950 core probes from NanoString's Human Universal Cell Characterization panel and 20 custom probes) were hybridised onto the samples overnight at 37°C for 16 hours. Hybridisation is followed by 2x 25min stringent washes and 2x 2min SSC washes.

scan_protocol: Stained samples were scanned in the CosMx SMI platform with the following setting: DAPI at 24ms; B2M/CD298 at 100ms; PanCK at 33ms: and CD45 at 50ms.

data_processing: Data analysis was performed using AtoMx Spatial Informatics Platform (v1.2) following the User Manual instructions. Cells were subsequently re-segmented using AtoMx version 1.3 and underwent quality control according the the User Manual. Subsequent data analysis was performed in R (version 4.4.1).

label_protocol: Samples were stained with fluorescent antibodies against CD298, B2M, PanCK and CD45. Samples were also stained with DAPI as a nuclear marker. All antibodies are part of NanoString's CosMx segmentation marker panel.

extract_protocol: 5µm FFPE sections on glass slides were baked overnight at 60°C. Deparaffinisation and Antigen Retrieval were performed using the Leica Bond Rx autostainer.

tag: lesion severity

value: Severe


title: Wild Type, rep2

description: Library name: WTn2

value: mesenchymal stem cell


title: arsenic group 1


title: control group 5

value: control


title: flg22_2

value: flg22 treatment


title: WT untreated replicate 3


title: arsenic group 2


title: WT PQ 10 replicate 2


title: Wild Type, rep1

description: Library name: WTn1


title: WT untreated replicate 4


title: WT untreated replicate 2


title: control group 4


title: A collection of FOVs in a moderate atherosclerotic artery taken on the NanoString CosMx platform

value: Moderate


title: A collection of FOVs in a mild atherosclerotic artery taken on the NanoString CosMx platform

value: Mild


title: arsenic group 5


title: WT PQ 50 replicate 1


title: control group 3


title: WT PQ 10 replicate 1


title: mock_2

value: no-treatment


title: control root 14d-2

city: Champenoux

first: Annegret

last: Kohler

address: Centre Grand Est Nancy

institute: INRAE

description:
Library name: C-Rtips2-2
This sample is from control roots at 14d. It is thesecond of two biological replicates used in this experiment.

data_processing:
Illumina software was used by the Genotoul sequencing facilities (Toulouse, France) to generate fastq raw data files
Raw reads were trimmed for low quality (quality score 0.05), Illumina adapters and sequences shorter than 15 nucleotides and aligned to the Populus trichocarpa v4.1 primary transcripts available at Phytozome (https://phytozome-next.jgi.doe.gov/info/Ptrichocarpa_v4_1l) using CLC Genomics Workbench v24.. For read mapping the CLC genomic workbench parameters were the following: minimum length fraction 0.9, minimum similarity frac-tion 0.9, Mismatch cost = 2, insertion cost = 3, Deletion cost = 3 and the maximum number of hits for a read was set to 10. The unique mapped reads number for each transcript were determined and then normalized to RPKM (Reads Per Kilobase of exon model per Million mapped reads) and TPM.
We calculated differential expression of genes with DESeq2
Assembly: reference genome sequence of Populus trichocarpa v4.1 (at Phytozome (https://phytozome-next.jgi.doe.gov/info/Ptrichocarpa_v4_1l)
Supplementary files format and content: tab-delimited text file including Phytozome v4.1 ID,  normalised expression values  RPKM and TPM, as well as unique mapped reads

organism: Populus tremula x Populus alba

source_name: Control roots

growth_protocol: Laccaria bicolor S238N and Populus tremula x alba 717-1B4 in vitro co-cultures were made according to the sandwich system , with small modifications. In brief, L. bicolor was pre-cultured in dark at 25°C for one week on sugar-reduced Pachlewski agar medium P20. P. tremula x alba micro-cuttings were stimulated to root for 1 week on solid Murashige and Skoog  (MS) medium supplemented with 2 mg/L IBA (Indol-3-butyric acid) and subsequently transferred to cellophane covered MS plates. After three weeks of incubation at 25°C with a 16h photoperiod, poplar explants were  transferred to cellophane covered P20 medium supplemented with 0.1% MES. To allow plant-fungal interaction,  the cellophane covered with L. bicolor pre-cultures was placed in an inverted position on the roots.  Control plates, containing control plants  were prepared and handled the  same way as co-cultures. All plates were incubated at 20°C with a 16h photoperiod. Samples (100 mg fresh weight) for RNA extraction were taken after  14  days of (co-)culture from control roots and EcM (i.e. all fungal and mixed plant-fungal material within 0.5 cm distance of a root), snap frozen in liquid nitrogen and stored at -80°C.

extract_protocol:
Total RNA was extracted from control root and mixed plant-fungal biomass (100 mg) using the RNeasy Plant Mini Kit (Qiagen). Biomass was ground in liquid nitrogen prior to extraction and an on column DNAse I treatment was included in the protocol. For samples containing poplar roots (EcM), extraction buffer RLC was supplemented with 2% PEG (polyethylene glycol) 8000.
Preparation of libraries from total RNA (TruSeq Stranded mRNA Kit Illumina) and 2 x 150 bp Illumina HiSeq3000 sequencing was performed at the GET platform (Gé-nopole Toulouse Midi-Pyrénées, Auzeville, France) following their standard protocol.

value: Control roots

tag: time

value: 14 days

tag: batch

value: TimecourseJR


title: mock_1

tag: tissue

value: seedlings

value: wild type


title: control group 2

value: Sperm


title: control group 1


title: WT untreated replicate 1

value: bacterial cells


title: PT06, HSPCs, cell:48

status: Public on Jul 14 2025

city: Beijing

first: Menghan

last: Liu

address: Yiheyuan Road

institute: Peking University

description: Library name: PT06_48

data_processing:
For in silico isolation of RNA from DNA reads, we used Cutadapt (version 3.5) to identify and extract RNA reads that contained a specific sequence (GGTTGAGGTAGTATTGCGCAATG) within the GAT5-RT primer from the 5-prime end of Read 2. The RNA reads and DNA reads were then processed separately as two files. For Hi-C data, reads were mapped to the hg38 reference genome with BWA-mem2 in “5SP” mode. Contacts and 3D genome structures were generated with Hickit software using default parameters. To remove potential contamination from RNA reads, we cleaned contacts between two exons from the same transcript, which accounted for ~0.04% of all contacts. For RNA data, we first removed reads containing no poly-A sequence following GAT5-RT primer sequence. We then aligned Read 1 to the hg38 reference genome using STAR. Duplicates were removed based on UMIs with UMI-tools. RNA count matrix was generated by FeatureCounts with parameters “-O -M --fraction”. We used RNAsnpSplit for phasing of allele- specific RNA counts.
Assembly: hg38
Supplementary files format and content: Hi-C pairs files

source_name: HSPCs from the bone marrow of AML patients

extract_protocol:
The mononuclear cells were isolated from each patient’s whole blood sample by using the Ficoll product. After density gradient centrifugation performed at 2000 × g for 20 minutes at 9:0 (brake off), cells were resuspended with 1xPBS. Then, we use red blood cell lysis solution (Solarbio) to remove red blood cells for 6 to 8 mins on ice. The cells were resuspended and stained with flow cytometry antibodies CD34, CD117, CD45, 7-AAD, CD38 (Biolegend). After 20 minutes, cells were sorted by BD FACS Aria SORP to get CD34⁺CD117⁺CD38⁻ hematopoietic stem and progenitor cells (HSPCs).
Library was performed according to the HiRES protocol published at bio-protocol before. Briefly, sorted single cells were fixed with final 1.75% paraformaldehyde (PFA), followed by quenching with 2% BSA at a 10:1 volume ratio. Then, cells were resuspended in ice-cold wash buffer (10 mM Tris pH 8.0, 10 mM NaCl, 0.1 mg/mL BSA ) supplemented with protease inhibitor and Recombinant RNase Inhibitor. The resuspended cells were processed strictly by reverse transcription, in situ Hi-C, flowing sorting, amplification and library preparation. Each barcoded single-cell libraries were pooled and purified with 0.6× and 0.15× AMPure XP beads. The final libraries were sequenced with paired-end 150-bp reads on a NovaSeq X Plus (Illumina) platform.

value: HSPCs


title: flg22_3


title: PT06, HSPCs, cell:47

description: Library name: PT06_47

value: HSPCs from the bone marrow of AML patients


title: flg22_1


title: PT06, HSPCs, cell:46

description: Library name: PT06_46


title: PT06, HSPCs, cell:44

description: Library name: PT06_44


title: PT06, HSPCs, cell:42

description: Library name: PT06_42


title: PT06, HSPCs, cell:40

description: Library name: PT06_40


title: PT06, HSPCs, cell:45

description: Library name: PT06_45


title: NSCs, H3

value: Sprague-Dawley

value: brain tissue

value: Neural Stem Cells

value: 1 day-old

value: High cell packing density


title: PT06, HSPCs, cell:43

description: Library name: PT06_43


title: control root 14d-1

description:
Library name: C-Rtips2-1
This sample is from control roots at 14d. It is the first of two biological replicates used in this experiment.


title: PT06, HSPCs, cell:38

description: Library name: PT06_38


title: PT06, HSPCs, cell:37

description: Library name: PT06_37


title: PT06, HSPCs, cell:36

description: Library name: PT06_36


title: mock_3


title: PT06, HSPCs, cell:33

description: Library name: PT06_33


title: PT06, HSPCs, cell:34

description: Library name: PT06_34


title: PT06, HSPCs, cell:32

description: Library name: PT06_32


title: PT06, HSPCs, cell:31

description: Library name: PT06_31


title: PT06, HSPCs, cell:27

description: Library name: PT06_27


title: PT06, HSPCs, cell:28

description: Library name: PT06_28


title: PT06, HSPCs, cell:29

description: Library name: PT06_29


title: PT06, HSPCs, cell:26

description: Library name: PT06_26


title: PT06, HSPCs, cell:25

description: Library name: PT06_25


title: PT06, HSPCs, cell:24

description: Library name: PT06_24


title: PT06, HSPCs, cell:41

description: Library name: PT06_41


title: PT06, HSPCs, cell:23

description: Library name: PT06_23


title: PT06, HSPCs, cell:20

description: Library name: PT06_20


title: PT06, HSPCs, cell:22

description: Library name: PT06_22


title: PT06, HSPCs, cell:21

description: Library name: PT06_21


title: PT06, HSPCs, cell:14

description: Library name: PT06_14


title: PT06, HSPCs, cell:15

description: Library name: PT06_15


title: PT06, HSPCs, cell:18

description: Library name: PT06_18


title: PT06, HSPCs, cell:39

description: Library name: PT06_39


title: PT06, HSPCs, cell:13

description: Library name: PT06_13


title: PT06, HSPCs, cell:19

description: Library name: PT06_19


title: PT06, HSPCs, cell:17

description: Library name: PT06_17


title: PT06, HSPCs, cell:35

description: Library name: PT06_35


title: PT06, HSPCs, cell:12

description: Library name: PT06_12


title: PT06, HSPCs, cell:16

description: Library name: PT06_16


title: PT06, HSPCs, cell:11

description: Library name: PT06_11


title: PT06, HSPCs, cell:10

description: Library name: PT06_10


title: PT06, HSPCs, cell:09

description: Library name: PT06_09


title: PT06, HSPCs, cell:07

description: Library name: PT06_07


title: PT06, HSPCs, cell:08

description: Library name: PT06_08


title: PT06, HSPCs, cell:04

description: Library name: PT06_04


title: PT06, HSPCs, cell:05

description: Library name: PT06_05


title: PT06, HSPCs, cell:30

description: Library name: PT06_30


title: PT06, HSPCs, cell:03

description: Library name: PT06_03


title: PT06, HSPCs, cell:02

description: Library name: PT06_02


title: PT05, HSPCs, cell:96

description: Library name: PT05_96


title: PT06, HSPCs, cell:01

description: Library name: PT06_01


title: PT05, HSPCs, cell:94

description: Library name: PT05_94


title: PT05, HSPCs, cell:95

description: Library name: PT05_95


title: PT05, HSPCs, cell:93

description: Library name: PT05_93


title: PT05, HSPCs, cell:89

description: Library name: PT05_89


title: PT05, HSPCs, cell:91

description: Library name: PT05_91


title: PT05, HSPCs, cell:90

description: Library name: PT05_90


title: PT05, HSPCs, cell:92

description: Library name: PT05_92


title: PT05, HSPCs, cell:88

description: Library name: PT05_88


title: PT05, HSPCs, cell:82

description: Library name: PT05_82


title: PT05, HSPCs, cell:87

description: Library name: PT05_87


title: PT05, HSPCs, cell:86

description: Library name: PT05_86


title: PT05, HSPCs, cell:83

description: Library name: PT05_83


title: PT05, HSPCs, cell:84

description: Library name: PT05_84


title: PT05, HSPCs, cell:78

description: Library name: PT05_78


title: PT05, HSPCs, cell:81

description: Library name: PT05_81


title: PT05, HSPCs, cell:85

description: Library name: PT05_85


title: PT05, HSPCs, cell:76

description: Library name: PT05_76


title: PT05, HSPCs, cell:80

description: Library name: PT05_80


title: PT05, HSPCs, cell:75

description: Library name: PT05_75


title: PT06, HSPCs, cell:06

description: Library name: PT06_06


title: PT05, HSPCs, cell:77

description: Library name: PT05_77


title: PT05, HSPCs, cell:71

description: Library name: PT05_71


title: PT05, HSPCs, cell:72

description: Library name: PT05_72


title: PT05, HSPCs, cell:73

description: Library name: PT05_73


title: PT05, HSPCs, cell:74

description: Library name: PT05_74


title: PT05, HSPCs, cell:70

description: Library name: PT05_70


title: PT05, HSPCs, cell:68

description: Library name: PT05_68


title: PT05, HSPCs, cell:67

description: Library name: PT05_67


title: PT05, HSPCs, cell:64

description: Library name: PT05_64


title: PT05, HSPCs, cell:65

description: Library name: PT05_65


title: PT05, HSPCs, cell:63

description: Library name: PT05_63


title: PT05, HSPCs, cell:62

description: Library name: PT05_62


title: PT05, HSPCs, cell:61

description: Library name: PT05_61


title: PT05, HSPCs, cell:60

description: Library name: PT05_60


title: PT05, HSPCs, cell:59

description: Library name: PT05_59


title: PT05, HSPCs, cell:79

description: Library name: PT05_79


title: PT05, HSPCs, cell:58

description: Library name: PT05_58


title: PT05, HSPCs, cell:56

description: Library name: PT05_56


title: PT05, HSPCs, cell:53

description: Library name: PT05_53


title: PT05, HSPCs, cell:55

description: Library name: PT05_55


title: PT05, HSPCs, cell:57

description: Library name: PT05_57


title: PT05, HSPCs, cell:51

description: Library name: PT05_51


title: PT05, HSPCs, cell:52

description: Library name: PT05_52


title: PT05, HSPCs, cell:54

description: Library name: PT05_54


title: PT05, HSPCs, cell:50

description: Library name: PT05_50


title: PT05, HSPCs, cell:48

description: Library name: PT05_48


title: PT05, HSPCs, cell:45

description: Library name: PT05_45


title: PT05, HSPCs, cell:47

description: Library name: PT05_47


title: PT05, HSPCs, cell:46

description: Library name: PT05_46


title: PT05, HSPCs, cell:42

description: Library name: PT05_42


title: PT05, HSPCs, cell:44

description: Library name: PT05_44


title: PT05, HSPCs, cell:43

description: Library name: PT05_43


title: PT05, HSPCs, cell:41

description: Library name: PT05_41


title: PT05, HSPCs, cell:40

description: Library name: PT05_40


title: PT05, HSPCs, cell:66

description: Library name: PT05_66


title: PT05, HSPCs, cell:39

description: Library name: PT05_39


title: PT05, HSPCs, cell:33

description: Library name: PT05_33


title: PT05, HSPCs, cell:34

description: Library name: PT05_34


title: PT05, HSPCs, cell:36

description: Library name: PT05_36


title: PT05, HSPCs, cell:30

description: Library name: PT05_30


title: PT05, HSPCs, cell:31

description: Library name: PT05_31


title: PT05, HSPCs, cell:32

description: Library name: PT05_32


title: PT05, HSPCs, cell:28

description: Library name: PT05_28


title: PT05, HSPCs, cell:29

description: Library name: PT05_29


title: PT05, HSPCs, cell:49

description: Library name: PT05_49


title: PT05, HSPCs, cell:21

description: Library name: PT05_21


title: PT05, HSPCs, cell:26

description: Library name: PT05_26


title: PT05, HSPCs, cell:24

description: Library name: PT05_24


title: PT05, HSPCs, cell:25

description: Library name: PT05_25


title: PT05, HSPCs, cell:27

description: Library name: PT05_27


title: PT05, HSPCs, cell:23

description: Library name: PT05_23


title: PT05, HSPCs, cell:20

description: Library name: PT05_20


title: PT05, HSPCs, cell:22

description: Library name: PT05_22


title: PT05, HSPCs, cell:18

description: Library name: PT05_18


title: PT05, HSPCs, cell:13

description: Library name: PT05_13


title: PT05, HSPCs, cell:14

description: Library name: PT05_14


title: PT05, HSPCs, cell:12

description: Library name: PT05_12


title: PT05, HSPCs, cell:38

description: Library name: PT05_38


title: PT05, HSPCs, cell:11

description: Library name: PT05_11


title: PT05, HSPCs, cell:16

description: Library name: PT05_16


title: PT05, HSPCs, cell:10

description: Library name: PT05_10


title: PT05, HSPCs, cell:09

description: Library name: PT05_09


title: PT05, HSPCs, cell:37

description: Library name: PT05_37


title: PT05, HSPCs, cell:17

description: Library name: PT05_17


title: PT05, HSPCs, cell:15

description: Library name: PT05_15


title: PT05, HSPCs, cell:07

description: Library name: PT05_07


title: PT05, HSPCs, cell:04

description: Library name: PT05_04


title: PT05, HSPCs, cell:06

description: Library name: PT05_06


title: PT05, HSPCs, cell:05

description: Library name: PT05_05


title: PT05, HSPCs, cell:03

description: Library name: PT05_03


title: PT05, HSPCs, cell:02

description: Library name: PT05_02


title: PT05, HSPCs, cell:01

description: Library name: PT05_01


title: PT05, HSPCs, cell:19

description: Library name: PT05_19


title: PT04, HSPCs, cell:96

description: Library name: PT04_96


title: PT04, HSPCs, cell:94

description: Library name: PT04_94


title: PT04, HSPCs, cell:95

description: Library name: PT04_95


title: PT04, HSPCs, cell:90

description: Library name: PT04_90


title: PT04, HSPCs, cell:91

description: Library name: PT04_91


title: PT04, HSPCs, cell:89

description: Library name: PT04_89


title: PT04, HSPCs, cell:88

description: Library name: PT04_88


title: PT04, HSPCs, cell:87

description: Library name: PT04_87


title: PT04, HSPCs, cell:85

description: Library name: PT04_85


title: PT04, HSPCs, cell:86

description: Library name: PT04_86


title: PT04, HSPCs, cell:84

description: Library name: PT04_84


title: PT04, HSPCs, cell:83

description: Library name: PT04_83


title: PT04, HSPCs, cell:81

description: Library name: PT04_81


title: PT04, HSPCs, cell:82

description: Library name: PT04_82


title: PT04, HSPCs, cell:77

description: Library name: PT04_77


title: PT04, HSPCs, cell:78

description: Library name: PT04_78


title: PT04, HSPCs, cell:79

description: Library name: PT04_79


title: PT04, HSPCs, cell:80

description: Library name: PT04_80


title: PT04, HSPCs, cell:76

description: Library name: PT04_76


title: PT05, HSPCs, cell:08

description: Library name: PT05_08


title: PT04, HSPCs, cell:75

description: Library name: PT04_75


title: PT04, HSPCs, cell:73

description: Library name: PT04_73


title: PT04, HSPCs, cell:71

description: Library name: PT04_71


title: PT04, HSPCs, cell:69

description: Library name: PT04_69


title: PT04, HSPCs, cell:72

description: Library name: PT04_72


title: PT04, HSPCs, cell:70

description: Library name: PT04_70


title: PT04, HSPCs, cell:74

description: Library name: PT04_74


title: PT04, HSPCs, cell:93

description: Library name: PT04_93


title: PT04, HSPCs, cell:92

description: Library name: PT04_92


title: PT04, HSPCs, cell:68

description: Library name: PT04_68


title: PT04, HSPCs, cell:67

description: Library name: PT04_67


title: PT04, HSPCs, cell:64

description: Library name: PT04_64


title: PT04, HSPCs, cell:66

description: Library name: PT04_66


title: PT04, HSPCs, cell:63

description: Library name: PT04_63


title: PT04, HSPCs, cell:61

description: Library name: PT04_61


title: PT04, HSPCs, cell:62

description: Library name: PT04_62


title: PT04, HSPCs, cell:58

description: Library name: PT04_58


title: PT04, HSPCs, cell:59

description: Library name: PT04_59


title: PT04, HSPCs, cell:57

description: Library name: PT04_57


title: PT04, HSPCs, cell:56

description: Library name: PT04_56


title: PT04, HSPCs, cell:54

description: Library name: PT04_54


title: PT04, HSPCs, cell:52

description: Library name: PT04_52


title: PT04, HSPCs, cell:51

description: Library name: PT04_51


title: PT04, HSPCs, cell:53

description: Library name: PT04_53


title: PT04, HSPCs, cell:47

description: Library name: PT04_47


title: PT04, HSPCs, cell:46

description: Library name: PT04_46


title: PT04, HSPCs, cell:48

description: Library name: PT04_48


title: PT04, HSPCs, cell:45

description: Library name: PT04_45


title: PT04, HSPCs, cell:55

description: Library name: PT04_55


title: PT04, HSPCs, cell:50

description: Library name: PT04_50


title: PT04, HSPCs, cell:44

description: Library name: PT04_44


title: PT04, HSPCs, cell:65

description: Library name: PT04_65


title: PT04, HSPCs, cell:40

description: Library name: PT04_40


title: PT04, HSPCs, cell:39

description: Library name: PT04_39


title: PT04, HSPCs, cell:42

description: Library name: PT04_42


title: PT04, HSPCs, cell:37

description: Library name: PT04_37


title: PT04, HSPCs, cell:36

description: Library name: PT04_36


title: PT04, HSPCs, cell:60

description: Library name: PT04_60


title: PT04, HSPCs, cell:34

description: Library name: PT04_34


title: PT04, HSPCs, cell:32

description: Library name: PT04_32


title: PT04, HSPCs, cell:31

description: Library name: PT04_31


title: PT04, HSPCs, cell:35

description: Library name: PT04_35


title: PT04, HSPCs, cell:30

description: Library name: PT04_30


title: PT04, HSPCs, cell:41

description: Library name: PT04_41


title: PT04, HSPCs, cell:29

description: Library name: PT04_29


title: PT04, HSPCs, cell:28

description: Library name: PT04_28


title: PT04, HSPCs, cell:27

description: Library name: PT04_27


title: PT04, HSPCs, cell:26

description: Library name: PT04_26


title: PT04, HSPCs, cell:25

description: Library name: PT04_25


title: PT04, HSPCs, cell:49

description: Library name: PT04_49


title: PT04, HSPCs, cell:23

description: Library name: PT04_23


title: PT04, HSPCs, cell:43

description: Library name: PT04_43


title: PT04, HSPCs, cell:19

description: Library name: PT04_19


title: PT04, HSPCs, cell:22

description: Library name: PT04_22


title: PT04, HSPCs, cell:16

description: Library name: PT04_16


title: PT04, HSPCs, cell:18

description: Library name: PT04_18


title: PT04, HSPCs, cell:21

description: Library name: PT04_21


title: PT04, HSPCs, cell:17

description: Library name: PT04_17


title: PT04, HSPCs, cell:15

description: Library name: PT04_15


title: PT04, HSPCs, cell:11

description: Library name: PT04_11


title: PT04, HSPCs, cell:13

description: Library name: PT04_13


title: PT04, HSPCs, cell:14

description: Library name: PT04_14


title: PT04, HSPCs, cell:33

description: Library name: PT04_33


title: PT04, HSPCs, cell:09

description: Library name: PT04_09


title: PT04, HSPCs, cell:10

description: Library name: PT04_10


title: PT04, HSPCs, cell:07

description: Library name: PT04_07


title: PT04, HSPCs, cell:08

description: Library name: PT04_08


title: PT04, HSPCs, cell:12

description: Library name: PT04_12


title: PT04, HSPCs, cell:06

description: Library name: PT04_06


title: PT04, HSPCs, cell:03

description: Library name: PT04_03


title: PT04, HSPCs, cell:04

description: Library name: PT04_04


title: PT04, HSPCs, cell:05

description: Library name: PT04_05


title: PT04, HSPCs, cell:02

description: Library name: PT04_02


title: PT04, HSPCs, cell:01

description: Library name: PT04_01


title: PT03, HSPCs, cell:48

description: Library name: PT03_48


title: PT04, HSPCs, cell:24

description: Library name: PT04_24


title: PT03, HSPCs, cell:46

description: Library name: PT03_46


title: PT03, HSPCs, cell:45

description: Library name: PT03_45


title: PT03, HSPCs, cell:43

description: Library name: PT03_43


title: PT03, HSPCs, cell:42

description: Library name: PT03_42


title: PT03, HSPCs, cell:44

description: Library name: PT03_44


title: PT03, HSPCs, cell:39

description: Library name: PT03_39


title: PT03, HSPCs, cell:41

description: Library name: PT03_41


title: PT03, HSPCs, cell:37

description: Library name: PT03_37


title: PT03, HSPCs, cell:36

description: Library name: PT03_36


title: PT03, HSPCs, cell:40

description: Library name: PT03_40


title: PT03, HSPCs, cell:34

description: Library name: PT03_34


title: PT03, HSPCs, cell:35

description: Library name: PT03_35


title: PT03, HSPCs, cell:32

description: Library name: PT03_32


title: PT03, HSPCs, cell:31

description: Library name: PT03_31


title: PT03, HSPCs, cell:30

description: Library name: PT03_30


title: PT03, HSPCs, cell:29

description: Library name: PT03_29


title: PT03, HSPCs, cell:33

description: Library name: PT03_33


title: PT03, HSPCs, cell:26

description: Library name: PT03_26


title: PT03, HSPCs, cell:25

description: Library name: PT03_25


title: PT03, HSPCs, cell:22

description: Library name: PT03_22


title: PT03, HSPCs, cell:21

description: Library name: PT03_21


title: PT03, HSPCs, cell:47

description: Library name: PT03_47


title: PT03, HSPCs, cell:20

description: Library name: PT03_20


title: PT03, HSPCs, cell:19

description: Library name: PT03_19


title: PT03, HSPCs, cell:23

description: Library name: PT03_23


title: PT03, HSPCs, cell:17

description: Library name: PT03_17


title: PT03, HSPCs, cell:18

description: Library name: PT03_18


title: PT03, HSPCs, cell:38

description: Library name: PT03_38


title: PT03, HSPCs, cell:16

description: Library name: PT03_16


title: PT03, HSPCs, cell:15

description: Library name: PT03_15


title: PT03, HSPCs, cell:14

description: Library name: PT03_14


title: PT03, HSPCs, cell:13

description: Library name: PT03_13


title: PT03, HSPCs, cell:12

description: Library name: PT03_12


title: PT03, HSPCs, cell:11

description: Library name: PT03_11


title: PT03, HSPCs, cell:10

description: Library name: PT03_10


title: PT03, HSPCs, cell:08

description: Library name: PT03_08


title: PT03, HSPCs, cell:07

description: Library name: PT03_07


title: PT03, HSPCs, cell:27

description: Library name: PT03_27


title: PT03, HSPCs, cell:28

description: Library name: PT03_28


title: PT03, HSPCs, cell:04

description: Library name: PT03_04


title: PT03, HSPCs, cell:02

description: Library name: PT03_02


title: PT03, HSPCs, cell:06

description: Library name: PT03_06


title: PT03, HSPCs, cell:24

description: Library name: PT03_24


title: PT02, HSPCs, cell:48

description: Library name: PT02_48


title: PT03, HSPCs, cell:05

description: Library name: PT03_05


title: PT03, HSPCs, cell:01

description: Library name: PT03_01


title: PT02, HSPCs, cell:45

description: Library name: PT02_45


title: PT02, HSPCs, cell:46

description: Library name: PT02_46


title: PT02, HSPCs, cell:47

description: Library name: PT02_47


title: PT02, HSPCs, cell:43

description: Library name: PT02_43


title: PT02, HSPCs, cell:44

description: Library name: PT02_44


title: PT02, HSPCs, cell:41

description: Library name: PT02_41


title: PT02, HSPCs, cell:42

description: Library name: PT02_42


title: PT02, HSPCs, cell:40

description: Library name: PT02_40


title: PT02, HSPCs, cell:34

description: Library name: PT02_34


title: PT02, HSPCs, cell:35

description: Library name: PT02_35


title: PT02, HSPCs, cell:32

description: Library name: PT02_32


title: PT02, HSPCs, cell:31

description: Library name: PT02_31


title: PT02, HSPCs, cell:38

description: Library name: PT02_38


title: PT03, HSPCs, cell:03

description: Library name: PT03_03


title: PT02, HSPCs, cell:29

description: Library name: PT02_29


title: PT02, HSPCs, cell:33

description: Library name: PT02_33


title: PT02, HSPCs, cell:28

description: Library name: PT02_28


title: PT02, HSPCs, cell:25

description: Library name: PT02_25


title: PT02, HSPCs, cell:39

description: Library name: PT02_39


title: PT02, HSPCs, cell:30

description: Library name: PT02_30


title: PT02, HSPCs, cell:26

description: Library name: PT02_26


title: PT02, HSPCs, cell:24

description: Library name: PT02_24


title: PT02, HSPCs, cell:27

description: Library name: PT02_27


title: PT02, HSPCs, cell:20

description: Library name: PT02_20


title: PT02, HSPCs, cell:22

description: Library name: PT02_22


title: PT02, HSPCs, cell:17

description: Library name: PT02_17


title: PT02, HSPCs, cell:16

description: Library name: PT02_16


title: PT02, HSPCs, cell:21

description: Library name: PT02_21


title: PT02, HSPCs, cell:18

description: Library name: PT02_18


title: PT02, HSPCs, cell:15

description: Library name: PT02_15


title: PT02, HSPCs, cell:14

description: Library name: PT02_14


title: PT02, HSPCs, cell:36

description: Library name: PT02_36


title: PT02, HSPCs, cell:37

description: Library name: PT02_37


title: PT02, HSPCs, cell:13

description: Library name: PT02_13


title: PT02, HSPCs, cell:11

description: Library name: PT02_11


title: PT02, HSPCs, cell:10

description: Library name: PT02_10


title: PT02, HSPCs, cell:09

description: Library name: PT02_09


title: PT02, HSPCs, cell:08

description: Library name: PT02_08


title: PT02, HSPCs, cell:05

description: Library name: PT02_05


title: PT02, HSPCs, cell:07

description: Library name: PT02_07


title: PT02, HSPCs, cell:04

description: Library name: PT02_04


title: PT02, HSPCs, cell:06

description: Library name: PT02_06


title: PT02, HSPCs, cell:03

description: Library name: PT02_03


title: PT02, HSPCs, cell:23

description: Library name: PT02_23


title: PT04, HSPCs, cell:20

description: Library name: PT04_20


title: PT01, HSPCs, cell:47

description: Library name: PT01_47


title: PT02, HSPCs, cell:02

description: Library name: PT02_02


title: PT01, HSPCs, cell:46

description: Library name: PT01_46


title: PT02, HSPCs, cell:01

description: Library name: PT02_01


title: PT01, HSPCs, cell:48

description: Library name: PT01_48


title: PT02, HSPCs, cell:19

description: Library name: PT02_19


title: PT01, HSPCs, cell:45

description: Library name: PT01_45


title: PT01, HSPCs, cell:44

description: Library name: PT01_44


title: PT01, HSPCs, cell:42

description: Library name: PT01_42


title: PT01, HSPCs, cell:37

description: Library name: PT01_37


title: PT01, HSPCs, cell:43

description: Library name: PT01_43


title: PT01, HSPCs, cell:36

description: Library name: PT01_36


title: PT01, HSPCs, cell:35

description: Library name: PT01_35


title: PT02, HSPCs, cell:12

description: Library name: PT02_12


title: PT01, HSPCs, cell:32

description: Library name: PT01_32


title: PT01, HSPCs, cell:34

description: Library name: PT01_34


title: PT01, HSPCs, cell:33

description: Library name: PT01_33


title: PT01, HSPCs, cell:27

description: Library name: PT01_27


title: PT01, HSPCs, cell:29

description: Library name: PT01_29


title: PT01, HSPCs, cell:26

description: Library name: PT01_26


title: PT01, HSPCs, cell:31

description: Library name: PT01_31


title: PT01, HSPCs, cell:30

description: Library name: PT01_30


title: PT01, HSPCs, cell:24

description: Library name: PT01_24


title: PT01, HSPCs, cell:28

description: Library name: PT01_28


title: PT01, HSPCs, cell:23

description: Library name: PT01_23


title: PT01, HSPCs, cell:25

description: Library name: PT01_25


title: PT01, HSPCs, cell:40

description: Library name: PT01_40


title: PT01, HSPCs, cell:18

description: Library name: PT01_18


title: PT01, HSPCs, cell:17

description: Library name: PT01_17


title: PT01, HSPCs, cell:22

description: Library name: PT01_22


title: PT01, HSPCs, cell:21

description: Library name: PT01_21


title: PT01, HSPCs, cell:20

description: Library name: PT01_20


title: PT01, HSPCs, cell:16

description: Library name: PT01_16


title: PT01, HSPCs, cell:15

description: Library name: PT01_15


title: PT01, HSPCs, cell:39

description: Library name: PT01_39


title: PT01, HSPCs, cell:41

description: Library name: PT01_41


title: PT01, HSPCs, cell:19

description: Library name: PT01_19


title: PT01, HSPCs, cell:14

description: Library name: PT01_14


title: PT01, HSPCs, cell:13

description: Library name: PT01_13


title: PT01, HSPCs, cell:38

description: Library name: PT01_38


title: PT01, HSPCs, cell:10

description: Library name: PT01_10


title: PT01, HSPCs, cell:11

description: Library name: PT01_11


title: PT01, HSPCs, cell:12

description: Library name: PT01_12


title: PT01, HSPCs, cell:09

description: Library name: PT01_09


title: PT01, HSPCs, cell:06

description: Library name: PT01_06


title: PT01, HSPCs, cell:05

description: Library name: PT01_05


title: PT01, HSPCs, cell:04

description: Library name: PT01_04


title: PT01, HSPCs, cell:07

description: Library name: PT01_07


title: PT01, HSPCs, cell:03

description: Library name: PT01_03


title: PT01, HSPCs, cell:01

description: Library name: PT01_01


title: PT01, HSPCs, cell:02

description: Library name: PT01_02


title: Mb436_nrf2

city: Cardiff

first: Darius

last: McPhail

address: University Hospital of Wales

institute: Cardiff University

description: Library name: 14

data_processing:
Base calling was performed using CASAVA base recognition on the Illumina NovaSeq X Plus platform.  1. Quality Control and Read Preprocessing Raw sequencing reads in FASTQ format were processed using fastp to obtain high-quality clean reads. During this step, adapter sequences, reads containing poly-N stretches, and low-quality reads were removed. Quality metrics including Q20, Q30, and GC content were calculated to assess read quality. All downstream analyses were based on these filtered, high-quality reads.  2. Read Alignment to Reference Genome The reference genome and corresponding gene annotation files were obtained from a public genome repository. Clean reads were aligned to the reference genome using HISAT2 (v2.2.1). Reference genome indexing was performed with HISAT2, and splice-aware alignment was enabled using gene annotation files to improve mapping accuracy.  3. Transcript Assembly and Novel Transcript Detection Aligned reads were assembled into transcripts using StringTie (v2.2.3) in a reference-guided mode. StringTie reconstructs full-length transcripts, including potential novel isoforms, using a network flow algorithm and an optional de novo assembly step. This approach facilitates the identification and quantification of splice variants for each gene locus.  4. Gene Expression Quantification Gene-level read counts were obtained using featureCounts (v2.0.6). Expression levels were normalized and expressed as FPKM (Fragments Per Kilobase of transcript per Million mapped reads), which accounts for both sequencing depth and gene length.  5. Differential Expression Analysis Differential gene expression analysis was conducted using DESeq2 (v1.42.0). DESeq2 models count data using a negative binomial distribution, and p-values were adjusted using the Benjamini–Hochberg method to control the false discovery rate (FDR). Genes were considered significantly differentially expressed if they met the following thresholds: adjusted p-value (padj) ≤ 0.05 and |log₂(fold change)| ≥ 1.
Assembly: ensembl_109_homo_sapiens_grch38_primary
Supplementary files format and content: Bam and Bam.bai

source_name: Breast Tumour

growth_protocol: MDA-MB-436 cells were purchased from ATCC. MDA-MB-436 cells were cultured in DMEM (Merck D6429), supplemented with 15% Foetal Bovine Serum (FBS), 2mM L-Glutamine (Sigma Aldrich), 0.01 mg/mL insulin (Lonza, BE02-033E20), 100 U/mL Penicillin/streptomycin (Merck P4333). Cells were grown in humidified incubators at 37°C, 5% (v/v) CO2. Medium was replenished every 48 h, and cells were passaged with Trypsin-EDTA (Gibco 25200056) when cells reached 80-90 % confluency. Passage number was maintained below 30.

extract_protocol:
After knockdown, the medium was removed and cells were washed once with D-PBS. RNAprotect reagent (Qiagen, 76106) was then added, and cells were incubated for 5 minutes at 37 °C before being collected into RNase-free tubes. Samples were briefly centrifuged at 1000 × g, and the RNAprotect reagent was removed.  Total RNA was extracted using the Qiagen RNeasy Mini Kit, following the manufacturer's instructions. Briefly, cell pellets were resuspended in RLT lysis buffer (supplemented with β-mercaptoethanol) and vortexed vigorously. The lysates were passed through a QIAshredder column, followed by a gDNA Eliminator column. An equal volume of 70% ethanol was added to the flow-through, which was then applied to an RNeasy spin column. The columns were washed, and RNA was eluted in RNase-free H₂O.  RNA concentration was quantified using the Invitrogen Qubit High Sensitivity RNA Assay. Samples were stored at –80 °C.
RNA samples were sent to Novogene for processing and RNA-sequencing. Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesised using random hexamer primers, followed by the second strand cDNA synthesis using either dTTP for non strand specific library or dUTP for strand specific library. These libraries were ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. The strand specific library was ready

treatment_protocol: Cells were trypsinised and collected prior to reverse transfection. Reverse transfection was carried out using siRNA SMARTpools (Dharmacon™ ON-TARGETplus siRNA) and DharmaFECT-1 transfection reagent (Dharmacon™, Horizon Discovery Ltd.). The siRNA SMARTpools targeted either AIFM2 or NFE2L2. Alternatively, non-targeting siRNA controls were used. Transfections were performed in 12-well plates according to the manufacturer's instructions.  Briefly, siRNA was diluted in unsupplemented DMEM and combined with DharmaFECT-1 transfection reagent (1.2 μL per well) and mixed gently. 200 μL of the transfection solution was added to each well, after which the siRNA/DharmaFECT-1 complexes were allowed to form for 30 minutes at room temperature. Subsequently, 800 μL of complete medium containing 80,000 cells was added to each well on top of the transfection mixture. After 24 hours, the medium was replaced. Cells were cultured for a total of 72 hours before RNA extraction.  For IONP-treated cells, treatment with 500 μM (Fe²⁺) of IONP@DLin-MC3-DMA was performed for 48 hours, with the end of treatment coinciding with the completion of the 72-hour knockdown period. IONP-treated cells were also subjected to non-targeting siRNA-mediated knockdown.

value: Breast Tumour

value: Breast cancer cell

value: NFE2L2 knockdown

value: NFE2L2 transfection


title: Mb436_nrf1

description: Library name: 13


title: Mb436_fsp4

description: Library name: 12

value: AIFM2 knockdown

value: AIFM2 siRNA transfection


title: Mb436_ionp4

description: Library name: 8

value: WT

value: Non-targeting siRNA transfection + iron oxide nanoparticle


title: Mb436_fsp2

description: Library name: 10


title: Mb436_fsp3

description: Library name: 11


title: Mb436_fsp1

description: Library name: 9


title: Mb436_nrf4

description: Library name: 16


title: Mb436_ionp3

description: Library name: 7


title: Mb436_nrf3

description: Library name: 15


title: Mb436_ionp2

description: Library name: 6


title: Mb436_nt4

description: Library name: 4

value: Non-targeting siRNA transfection


title: Mb436_ionp1

description: Library name: 5


title: Mb436_nt2

description: Library name: 2


title: Mb436_nt3

description: Library name: 3


title: NonSparkT replicate 2 scATACseq

city: PARIS

first: Joshua

last: Waterfall

state: Please select:

address: 26 rue d'Ulm

department: Department of Translational Research and Inserm U830

institute: Institut Curie

description: Library name: SCAF3219_NonSpark

library_source: genomic single cell

data_processing:
Demultiplexing was performed with CellRanger mkfastq
Demultiplexed data was processed with CellRanger count pipeline
CellRanger output was processed with the ArchR pipeline and replicates were integrated with Harmony
Assembly: mm10
Supplementary files format and content: CellRanger output file: fragments.tsv.gz

source_name: spleen

extract_protocol:
Nuclei of sorted CD5lowCD11ahigh and CD5highCD11alow T cell subpopulations from OT-1 Rag1-/- mice were isolated following the nuclei isolation protocol for Single Cell ATAC Sequencing (Low Cell Input) provided from 10x Genomics. Cell lysis was performed for 5 min on ice. Nuclei concentration was quantified using Trypan Blue and a Countess II FL Automated Cell Counter.
scATACseq libraries were performed according to 10X Genomics guidelines

value: spleen

value: T cells

value: sorted CD5highCD11alow


title: SparkT replicate 2 scATACseq

description: Library name: SCAF3218_Spark2

value: sorted CD5lowCD11ahigh


title: NonSparkT replicate 1 scATACseq

description: Library name: SCAF3176_NonSpark


title: PT01, HSPCs, cell:08

description: Library name: PT01_08

value: HSPCs from the bone marrow of AML patients

value: HSPCs


title: SparkT replicate 1 scATACseq

description: Library name: SCAF3175_Spark


title: Mb436_nt1

description: Library name: 1


title: 1_R22_SucraloseDuringExpansion

city: Pittsburgh

first: Drew

middle: Nicholas

last: Wilfahrt

state: PA

address: 5535 Kamin Street

department: Immunology

institute: University of Pittsburgh

description: OT-1 T cells, Sucralose exposure only during final 6 days of cell culture (Expansion only), Day 7, mouse 1

data_processing:
All data were analyzed using Partek Flow build version 11.0.24.0226
Unaligned reads were aligned to genome using STAR
Raw Gene count values were calculated using "Quantify to annotation model (Partek E/M)"
Features where filtered to exclude features where the maximum among all samples is <= 1.0
Gene counts were normalized to Median Ratio
Differential expression analysis determined using DESeq2 with cutoffs of 2 fold and p value<0.05
Assembly: mm10
Supplementary files format and content: csv file contains Reads per kilo base of transcript per million mapped reads (RPKM)

source_name: splenocytes

growth_protocol: To expand OT-I mouse CD8+ T cells in vitro, bulk splenocytes were plated in the presence of the T cells’ cognate peptide (250ng/mL SIINFEKL) at a concentration of 1e7 cells/mL in RPMI supplemented with 10% FBS (v/v) and 50U/mL mouse IL-2 at 37°C with 5% CO2 for 24 hours. After 24 hours, cells were washed with fresh RPMI and plated at a concentration of 1e6/mL with 50ug/mL IL-2. Cultures were fed daily and kept at this concentration for the duration of expansion.

extract_protocol:
RNeasy Plus Mini Kit
Illumina Stranded mRNA prep

treatment_protocol: Sucralose was added to the fresh culture media daily at a final concentration of 0.22g/L for indicated timepoints. For "Sucralose Whole Time", cells were grown in RPMI supplemented with sucralose for the entire 7 days of culture; for "Sucralose During Activation", cells were cultured in RPMI supplemented with sucralose for the first 24 hours of culture, and then cultured in control RPMI for the remaining 6 days; For "Sucralose during expansion", cells were cultured in control RPMI during the initial 24 hours of activation, and then cultured in RPMI supplemented with sucralose for the final 6 days of culture.

value: splenocytes

value: CD8+ T cell

value: Day 7


title: 3_R22_SucraloseDuringExpansion

description: OT-1 T cells,  Sucralose exposure only during final 6 days of cell culture (Expansion only), Day 7, mouse 3


title: 3_22R_SucraloseDuringActivation

description: OT-1 T cells, Sucralose exposure only during first 24 hours of culture (Activation Only), Day 7, mouse 3


title: 2_R22_SucraloseDuringExpansion

description: OT-1 T cells,  Sucralose exposure only during final 6 days of cell culture (Expansion only), Day 7, mouse 2


title: 2_22R_SucraloseDuringActivation

description: OT-1 T cells, Sucralose exposure only during first 24 hours of culture (Activation Only), Day 7, mouse 2


title: 1_22R_SucraloseDuringActivation

description: OT-1 T cells, Sucralose exposure only during first 24 hours of culture (Activation Only), Day 7, mouse 1


title: 3_22_SucraloseWholeTime

description: OT-1 T cells, Sucralose exposure during entire 7 days of culture (Sucralose Whole Time), Day 7, mouse 3

value: Sucralose Whole Time


title: 2_RPMI_CTRL

description: OT-1 T cells, untreated, Day 7, mouse 2

value: untreated


title: 3_RPMI_CTRL

description: OT-1 T cells, untreated, Day 7, mouse 3


title: NSD1 frameshift mutation, rep4

type: genomic

city: Irvine

first: Minji

last: Byun

address: 829 Health Science Rd, 311

department: Microbiology and Molecular Genetics

institute: University of California Irvine

description: DNA from an hESC clone carrying a heterozygous frameshift mutation in NSD1

hyb_protocol: Standard Illumina protocol

scan_protocol: Standard Illumina protocol

data_processing:
Infinium idat files were processed and mapped to human genome 38 (hg38) using preprocessQuantile in minfi (version 1.50.0). Probes for non-CpG sites, probes not mapped to hg38, and poor quality probes with detection p values greater than 0.01 were removed. Cross reactive probes were removed using maxprobes (version 0.0.2) R package. M-values were then extracted and were adjusted with ComBat (sva version 3.52.0) for individual BeadChip batch effects using the Sentrix ID. The adjusted M values were converted to beta values by taking the inverse log2.
*processed value definition: average beta (Sample_bVals_detP.txt is linked to the Series record)

label: Cy3 and Cy5

label_protocol: Standard Illumina protocol

growth_protocol: Human embryonic stem cells were maintained under feeder-free condition in StemFlex media (Thermo Fisher Scientific) on Cultrex (R&D Systems)-coated plates.

extract_protocol: Genomic DNA was extracted and purified from cells using Zymo Quick-DNA microprep kit according to standard instructions.

value: human embryonic stem cell

tag: mutation(cdna)

tag: mutation(protein)


title: 1_22_SucraloseWholeTime

description: OT-1 T cells, Sucralose exposure during entire 7 days of culture (Sucralose Whole Time), Day 7, mouse 1


title: NSD1 frameshift mutation, rep3


title: 1_RPMI_CTRL

description: OT-1 T cells, untreated, Day 7, mouse 1


title: UUATAC-seq datasets of Axolotl_VasDeferens B

city: Hangzhou

first: Guoji

last: Guo

state: Zhejiang

address: Yuhangtang street 866

department: Zhejiang University School of Medicine

institute: Center for Stem Cell and Regenerative Medicine

description:
Library name: UUATAC_Axolotl_VasDeferens 2
single-nucleus ATAC profile of Axolotl_Prostate

data_processing:
The FASTQ files generated by MGI sequencer were split by the T7 index using the software splitBarcode (version 0.1.6, https://github.com/MGI-tech-bioinformatics/splitBarcode). Reads with barcode base quality lower than 10 or more than two mismatches per index were removed. Then the cell barcode was tagged into the query name of each reads using Drop-Seq tools  (version 2.5.1, https://github.com/broadinstitute/Drop-seq). The cell barcode of each read pair consists of four components: T7 index, Hy AS barcode, Hy B barcode and Tn5 barcode (128, 768, 8 and 192 indexes, respectively). We corrected each barcode to its original sequence if only one base was mismeasured in each barcode component. Bam files with tagged barcodes were split by Tn5 barcodes and then merged by tissue information. Different samples were marked by different Tn5 barcodes. Subsequently, reads were aligned to reference genomes of axolotl (AmexG_v6.0-DD) using BWA (version 0.7.15, https://github.com/lh3/bwa) with default parameters in paired-end mode to obtain the bam file.
To deal with the Tn5 insertion bias, we performed the function alignmentSieve of deepTools (version 3.5.1, https://github.com/deeptools/deepTools) to shift each read. Next, paired-reads with mapping quality higher than 30 were converted to fragments. And then nonduplicate fragments with length range from 10bp to 1000bp were extracted. We generated one fragment file for each tissue.
Assembly: AmexG_v6.0-DD
Supplementary files format and content: BED files recording coordinates of fragments captured by UUATAC-seq

organism: Ambystoma mexicanum

source_name: Vas deferens

extract_protocol:
Whole organs were then dissected in the following order: heart, lung, gill, gall bladder, pancreas, liver, cloaca, stomach, intestine, bladder, brain, kidney, spleen, limb and gonad. The samples were quickly transferred into cold DPBS, washed and then manually pulverized using a mortar and pestle within a liquid nitrogen bath. The pulverized tissues were suspended in 1mL of Nuclear Isolation Buffer (NIB) and followed by incubation for 1.5-3 min to isolate the nuclei. The NIB's formulation and permeabilization time for each tissue were listed in Supplementary Table 2. The suspension of each tissue was transferred to 15 mL centrifuge tubes pre-filled with 5mL of WB (wash buffer, 0.2% BSA, 3 mM MgCl2 in DPBS), filtered through 40 μm strainers and centrifuged at 650 × g for 5 min at 4°C. We resuspended the nuclei in 1 mL of WB and filtered the suspension through 20 μm size strainers, pelleted at 650 × g for 5 min and resuspended in the appropriate amount of DPBS to give a final concentration of 5,000 nuclei per microlitre.
Library preparations were performed with the UUATAC-seq protocol

treatment_protocol: The axolotl was anesthetized by 0.1% ethyl 3-aminobenzoate methanesulfonate salt (Sigma-Aldrich) in water prior to heart perfusion with 0.8× PBS.

value: Vas deferens

value: d/d


title: DNMT3A gain of function mutation, rep3

description: DNA from an hESC clone carrying a heterozygous Asp333Asn mutation in DNMT3A


title: DNMT3A gain of function mutation, rep4


title: NSD1 frameshift mutation, rep2


title: NSD1 frameshift mutation, rep1


title: UUATAC-seq datasets of Axolotl_Stomach_A

description: single-nucleus ATAC profile of Axolotl_Stomach_A

source_name: Stomach

value: d/dA. mexicanumstrain

value: Stomach


title: DNMT3A gain of function mutation, rep2

description: DNA from an hESC clone carrying a heterozygous Trp330Arg mutation in DNMT3A


title: DNMT3A R882H mutation, rep2

description: DNA from an hESC clone carrying a heterozygous Arg882His mutation in DNMT3A


title: UUATAC-seq datasets of Axolotl_Stomach_B

description: single-nucleus ATAC profile of Axolotl_Stomach_B


title: UUATAC-seq datasets of Axolotl_Spleen_C

description: single-nucleus ATAC profile of Axolotl_Spleen_C

source_name: Spleen

value: Spleen


title: UUATAC-seq datasets of Axolotl_Spleen_B

description: single-nucleus ATAC profile of Axolotl_Spleen_B


title: DNMT3A R882H mutation, rep1


title: UUATAC-seq datasets of Axolotl_Spleen_A

description: single-nucleus ATAC profile of Axolotl_Spleen_A


title: UUATAC-seq datasets of Axolotl_Pancreas_C

description: single-nucleus ATAC profile of Axolotl_Pancreas_C

source_name: Pancreas

value: Pancreas


title: DNMT3A frameshift mutation, rep3

description: DNA from an hESC clone carrying a heterozygous frameshift mutation in DNMT3A


title: DNMT3A frameshift mutation, rep2


title: 2_22_SucraloseWholeTime

description: OT-1 T cells, Sucralose exposure during entire 7 days of culture (Sucralose Whole Time), Day 7, mouse 2


title: UUATAC-seq datasets of Axolotl_Stomach_C

description: single-nucleus ATAC profile of Axolotl_Stomach_C


title: DNMT3A frameshift mutation, rep1


title: UUATAC-seq datasets of Axolotl_Pancreas_B

description: single-nucleus ATAC profile of Axolotl_Pancreas_B


title: wild type hESC, rep4

description: DNA from a wild-type hESC clone

value: WT


title: UUATAC-seq datasets of Axolotl_VasDeferens C

description:
Library name: UUATAC_Axolotl_VasDeferens 3
single-nucleus ATAC profile of Axolotl_Prostate


title: UUATAC-seq datasets of Axolotl_Pancreas_A

description: single-nucleus ATAC profile of Axolotl_Pancreas_A


title: UUATAC-seq datasets of Axolotl_Liver_C

description: single-nucleus ATAC profile of Axolotl_Liver_C

source_name: Liver

value: Liver


title: wild type hESC, rep3

description: DNA from a wild-type hESC clone


title: wild type hESC, rep2

description: DNA from a wild-type hESC clone


title: UUATAC-seq datasets of Axolotl_VasDeferens A

description:
Library name: UUATAC_Axolotl_VasDeferens 1
single-nucleus ATAC profile of Axolotl_Prostate


title: wild type hESC, rep1

description: DNA from a wild-type hESC clone


title: UUATAC-seq datasets of Axolotl_Liver_B

description: single-nucleus ATAC profile of Axolotl_Liver_B


title: PT03, HSPCs, cell:09

description: Library name: PT03_09


title: UUATAC-seq datasets of Axolotl_Liver_A

description: single-nucleus ATAC profile of Axolotl_Liver_A


title: HCC1937 cells, E33 extract

city: Puebla

first: Marta

middle: Elena

last: Hernandez-Caballero

state: Puebla

address: 13 sur 2702 Colonia Volcanes, Puebla, Mexico

department: Facultad de Medicina

country: Mexico

institute: Benemerita Universidad Autonoma de Puebla

description: Library name: Sample 12

data_processing:
Raw data was quality-controlled with FastQC v0.12.1
Adapters and low-quality reads near the 3’ and 5’ ends were removed with fastp v0.23.4
Paired-end clean reads were aligned to the reference genome Homo_sapiens.GRCh38 with Salmon v1.10.3.
DESeq2 v_1.44.0, which is based on a negative binomial distribution was used to identify DEGs
Data visualization and manipulation tools were computed utilizing R version 4.4.1.
Assembly: Homo_sapiens.GRCh38
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: breast, mamary gland

growth_protocol: MDA-MB-231 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in a humidified atmosphere with 5% CO2 at  37C. HCC1937 cells were maintained in RPMI 1640 supplemented with 10% fetal bovine serum (FBS) and antibiotics in a humidified atmosphere with 5% CO2 at  37C

extract_protocol:
30 ng of RNA was utilized for the transcriptome library preparation per sample. Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads.
RNA libraries for RNAseq were  prepared using TruSeq Stranded Total RNA following manufacturer's protocols

treatment_protocol: MDA-MB-231 cells were treated with 140 µg/mL of Kalanchoe pinnata aqueous extract and HCC1937 cells with 66 µg/mL, during 72h

value: breast, mamary gland

value: Epithelial cell

value: Extract, 72h


title: DNMT3A gain of function mutation, rep1

description: DNA from an hESC clone carrying a heterozygous Trp330Arg mutation in DNMT3A


title: UUATAC-seq datasets of Axolotl_Limb_C

description: single-nucleus ATAC profile of Axolotl_Limb_C

source_name: Limb

value: Limb


title: HCC1937 cells, E32 extract

description: Library name: Sample 11


title: UUATAC-seq datasets of Axolotl_Limb_B

description: single-nucleus ATAC profile of Axolotl_Limb_B


title: HCC1937 cells, E31 extract

description: Library name: Sample 10


title: UUATAC-seq datasets of Axolotl_Limb_A

description: single-nucleus ATAC profile of Axolotl_Limb_A


title: HCC1937 cells, E27 control

description: Library name: Sample 9

value: Control, 72h


title: UUATAC-seq datasets of Axolotl_Kidney_C

description: single-nucleus ATAC profile of Axolotl_Kidney_C

source_name: Kidney

value: Kidney


title: HCC1937 cells, E26 control

description: Library name: Sample 8


title: UUATAC-seq datasets of Axolotl_Intestine_C

description: single-nucleus ATAC profile of Axolotl_Intestine_C

source_name: Intestine

value: Intestine


title: MDA-MB-231 cells, E9 extract

description: Library name: Sample 6


title: UUATAC-seq datasets of Axolotl_Kidney_A

description: single-nucleus ATAC profile of Axolotl_Kidney_A


title: MDA-MB-231 cells, E8 extract

description: Library name: Sample 5


title: HCC1937 cells, E25 control

description: Library name: Sample 7


title: MDA-MB-231 cells, E7 extract

description: Library name: Sample 4


title: UUATAC-seq datasets of Axolotl_Lung

description: single-nucleus ATAC profile of Axolotl_Lung

source_name: Lung

value: Lung


title: UUATAC-seq datasets of Axolotl_Intestine_B

description: single-nucleus ATAC profile of Axolotl_Intestine_B


title: UUATAC-seq datasets of Axolotl_Intestine_A

description: single-nucleus ATAC profile of Axolotl_Intestine_A


title: UUATAC-seq datasets of Axolotl_Heart

description: single-nucleus ATAC profile of Axolotl_Heart

source_name: Heart

value: Heart


title: MDA-MB-231 cells, E3 control

description: Library name: Sample 3


title: MDA-MB-231 cells, E2 control

description: Library name: Sample 2


title: UUATAC-seq datasets of Axolotl_Gill

description: single-nucleus ATAC profile of Axolotl_Gill

source_name: Gill

value: Gill


title: UUATAC-seq datasets of Axolotl_GallBladder_C

description: single-nucleus ATAC profile of Axolotl_GallBladder_C

source_name: GallBladder

value: GallBladder

value: d/d


title: MDA-MB-231 cells, E1 control

description: Library name: Sample 1