title: Sample_65

city: Blacksburg

first: Fernando

middle: H

last: Biase

state: VA

address: 175 West Campus Drive

department: School of Animal Sciences

institute: Virginia Tech

description: Library name: Sample_65

data_processing:
First, using trimmomatic (v 0.39), we removed adapters from the sequences, retaining only sequences that had > 100 nucleotides in length and an average quality> 30. We aligned the reads to the chicken genome (galgal1) using Hisat2 . Next, we used Samtools (v 1.10) to retain the reads with one match to the genome, followed with removing duplicates using bammarkduplicates from biobambam2 (v 2.0.95). Samples with or more than 90% of correct alignment were used for counting.
Assembly: galgal1
Supplementary files format and content: read counts in a tab delimited text file

organism: Gallus gallus

source_name: nCPa

growth_protocol: Fertilized Hubbard x Cobb-500 eggs (Gallus gallus) were obtained from a nearby commercial hatchery (same source and flock breeder age as our previous studies. Upon arrival, eggs were kept at 26.6ºC for 12 hours and then were randomly divided into a control and embryonic heat conditioning (EHC) group. These groups were separated into two incubators (Rite Farm Products Pro-1056) and labeled control and EHC, respectively. Both groups from embryonic day (ED) 0-7 were incubated at 37.5ºC and 80% relative humidity. The eggs in the control group continued to be incubated at 37.5ºC until hatch at ED 21. The EHC group was separated from the control group at ED 7 and introduced to an increase in temperature to 39.5ºC and 80% relative humidity for 12 hours per day (07:30–19:30), and 37.5ºC for the remainder of the 24 hours until ED 16. The EHC group then spent the remaining 5 days at 37.5ºC until hatch. After ED 18.5, all eggs were subjected to candling. Infertile eggs and dead embryos were removed from the study. Eggs with viable embryos were transferred to a common hatching incubator (Rite Farm Products Pro-264) and maintained within their separate groups (separate enclosed trays to prevent mixing of treatments) at 36.9ºC and 50% relative humidity for 18 hours. The temperature was gradually decreased to 35ºC until the hatch was collected. Hatched chicks were arbitrarily divided into group cages based on treatment in preparation for the acute day 4 post-hatch heat challenge. The holding room temperature was set at 30ºC, with ad libitum access to food and water, and 24 hr continuous light exposure, similar to our previous studies

extract_protocol:
Total RNA was isolated using the Total RNA purification Micro Kit (Norgen Biotek, Thorold, ON, Canada) according to the manufacturer’s instructions. Samples were thawed to room temperature (3 minutes) and vortexed for 30 seconds. 100 µl of 70% molecular-biology grade ethanol was added to the lysate and then steps were performed according to the kit’s instructions
Illumina’s Stranded Total RNA Prep, Ligation with Ribo Zero Plus Sample Prep Kit

treatment_protocol: On day 4 post-hatch, Control and EHC groups were subjected to an acute heat challenge at 36ºC. Samples were collected at three timepoints: 0 (before heat challenge; baseline), 2 hours, and 12 hours from the start of the increased temperature. Within these three time points, 10 birds were collected and euthanized from control and EHC groups, with 20 birds total for each time point. Chicks were weighed individually, euthanized by decapitation, and sexed via gonad identification.

value: nCPa

tag: biological replicate

value: Male

value: C


title: Inoculum_biorep_4

status: Public on Jun 04 2025

type: SRA

city: Dublin

first: Carsten

last: Kroeger

address: Moyne Institute of Preventive Medicine

department: Microbiology

country: Ireland

institute: Trinity College Dublin

description:
Library name: ABC141_4
The human data is in Human_RNA_seq.txt.The bacterial data is in Bacterial_RNA_seq_ABC141.txt. Column names labelled "raw" are raw readcounts, column names labelled as "normalised" are normalised read counts and column names labelled with TPM are TPM values for each entry and sample. Biological replicates are indicated after the underscore (e.g., ABC141_1 is experiment 1, ABC141_2 is experiment 2 etc.). Columns labelled ABC141 are data from the inoculum, S-inf are data from infected cells sorted, Inf are data from infected cells unsorted, Neg are data from uninfected and unsorted cells and S-Neg are data from uninfected and sorted cells.

library_source: transcriptomic

data_processing:
Bacterial RNA-seq: For calculation of bacterial gene expression, reads were mapped with bowtie2 v. 2.4.2 with the parameters -very-sensitive-local to align sequencing reads to the A. baumannii ABC141 reference genome (Lanmead & Salzberg, 2012). Only reads with the highest mapping quality (MAPQ = 44) were kept and aggregated strand-specifically with featureCounts v2.0.3 on features annotated with the types of CDS, sRNA or ncRNA (Liao et al., 2014). To filter for low expression only genes were kept that showed expression of TPM ≥10 in the majority of replicates in one or more of the sample groups resulting in a set of 3299 genes. Differential gene expression (log2 fold-changes and adjusted p-values) was calculated using DESeq2 v1.46 (Love et al., 2014).
Human RNA-seq: Data files were processed through FastQC for quality control (Andrews, 2010). Short reads were mapped to the human reference genome (hg38) using STAR v2.7.3a (Dobin et al., 2013). Uniquely mapped reads were assigned to genes with featureCounts v2.0.3 using the latest Ensembl annotation (v114) (Dyer et al., 2025). To filter for low expression, only those genes were kept that had an expression value of one or more TPM (transcripts per million) in at least half of their replicates. Differentially expressed genes were determined by DESeq2 v1.46.
Assembly: GRCh38 (human reference sequence), GCF_050269755.1 (Acinetobacter baumannii ABC141 reference sequence)
Supplementary files format and content: Human_RNA_seq.txt is a tab-delimited text file which inlcludes raw counts, TPM, normalised read counts and DESeq2 analysis for each sample (human RNA-seq)
Supplementary files format and content: Bacterial_RNA_seq_ABC141.txt is a tab-delimited text file which inlcludes raw counts, TPM, normalised read counts and DESeq2 analysis for each sample (bacterial RNA-seq)

molecule: total RNA

organism: Acinetobacter baumannii

extract_protocol:
Total RNA from infected cells, non-infected cells and ABC141 inocula was extracted following a previously described method (Kröger et al., 2018). For cultures, bacteria were lysed with 2/5 volume of ice-cold 5% (v/v) phenol, 95% (v/v) ethanol ultra-pure solution for 1 h on ice. The same lysis process was applied to the total of infected cells and mock-infected cells sorted by FACS. A centrifugation at 3220 x g for 10 min at 4°C pelleted the sample, which was resuspended with 1 mL ice-cold TRIzol and transferred into a Phase-Lock-Tube (VWR, #2302830). 400 µL of chloroform was added and the solution was shaken (without vortexing) for 10 s, followed by a 3 min incubation at RT. The tubes were centrifuged at 12000 x g at 4 °C for 15 min. Then, the aqueous phase was transferred to a new 1.5 mL tube. 450 µL of isopropanol was added and mixed before a 30 min incubation at RT. A new centrifugation at full speed for 30 min preceded three washes of the pellet with 350 µL of ethanol 75%, a 10 min incubation at RT and a 10 min centrifugation at full speed. The last supernatant was discarded and the pellet air dried before resuspension with 25 µL of RNAse-free water, followed by a 5 min incubation at 65 °C at 900 rpm. The RNA extraction quality was verified with a 1/10 dilution using the 4200 TapeStation (Agilent Technologies).
Total RNA was sent to Core Unit Systems Medicine (SysMed) sequencing facility for RNA-seq (University of Würzburg, Germany), where DNase I digestion and rRNA depletion (RiboCop) was performed. Library for the sequencing was prepared using the NEBNext Multiplex Small RNA Library Prep kit. Sequencing was performed on the Illumina NextSeq-500 Mid Output KT v2.5 (150 cycles).

tag: cell line

tag: cell type

value: somatic cell hybrid, endothelial


title: 3mo440, Pancreas, PARP2 KO

city: Barcelona

first: Neus

last: Martínez

address: Dr.Aiguader 88

department: Cancer

country: Spain

institute: Hospital del Mar Medical Research Institute

data_processing:
The quality of the raw data was checked using FastQC (version 0.11.5) [1], and the reads were trimmed for low quality and adapter using skewer (version 0.2.2)
The percentage of reads mapping to ribosomal RNA was assessed using riboPicker (version 0.4.3)
Raw reads were mapped to the Mus. musculus reference genome (Gencode M21 release corresponding to the Ensembl release 96; files GRCm38.primary_assembly.genome.fa.gz and gencode.vM21.annotation.gtf) and counted at the gene level using STAR (version 2.5.3a) and parameters '--outSAMunmapped None --outSAMtype BAM SortedByCoordinate --quantMode GeneCounts'.
Qualimap (version 2.2.1) was used to check the quality of the aligned reads. Differential expression analysis was performed in the R / Bioconductor environment, using the DESeq2 package version 1.28.1
As the library preparation protocol was reverse stranded, the 4th column of the STAR gene counts output of each sample was taken as input for DESeq2. Genes that had less than 2 read count across all samples in each analysis group were filtered out before processing the data
Assembly: mm10
Supplementary files format and content: tab-delimited text file incluces raw counts for each sample
Supplementary files format and content: tab-delimited text file incluces normalized log2 counts for each sample

organism: Mus musculus

source_name: Pancreas

extract_protocol:
Tumor samples were collected in RNA later and digested in a tissue homogeniser (Fastprep FP120 cell disruption system). RNA was harvested using Rneasy mini plus kit (Qiagen). 500ng of total RNA was used for the construction of sequencing libraries.
RNA librarier for RNA-seq were prepared using TrueSeq stranded mRNA library Prep according to manufacturer's protocol (Illumina).

tag: tissue

value: Pancreas

tag: genotype

value: PARP2 KO


title: WFS1 KO, scRNA-seq_GEX

city: Shanghai

first: Xiangyi

last: Chen

address: No. 1239, Siping Road, Shanghai, China

country: China

institute: Weida Li

description: DNBelab C4

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the DNBelab_C4_scRNA_v2.3
Assembly: GRCH38
Supplementary files format and content: Tap-separated values files and matrix files

organism: Homo sapiens

source_name: hES-derived islet organoid

extract_protocol:
SC-islets were dissociated into single cells with TrypLE and resuspended with DPBS with 0.5% fat-acid -free BSA. Added DNase I to eliminate the DNA released form the dead cells to prevent cell caking and placed the tubes containing cells on ice for preservation.
DNBelab C Series High-throughput Single-Cell RNA Library (MGI, #940-000047-00) was utilized for scRNA-seq library preparation. In brief, the single-cell suspensions were converted to barcoded scRNA-seq libraries through steps including droplet encapsulation, emulsion breakage, mRNA captured beads collection, reverse transcription, cDNA amplification and purification. cDNA production was sheared to short fragments with 250-400 bp, and indexed sequencing libraries were constructed according to the manufacturer’s protocol. Qualification was performed using Qubit ssDNA Assay Kit (Thermo Fisher Scientific) and Agilent Bioanalyzer 2100. All libraries were further sequenced by the MGISEQ-2000RS with pair-end sequencing. The sequencing reads contained 30-bp read 1 (including the 10-bp cell barcode 1, 10-bp cell barcode 2 and 10-bp unique molecular identifiers (UMI)), 100-bp read 2 for gene sequences and 10-bp barcodes read for sample index.

value: hES-derived islet organoid

tag: treatment

value: DMSO treated for 48h


title: CTRL3

first: Yu

last: Sun

address: 320 Yueyang Rd, Life Sciences Building A #1508

department: Shanghai Institute of Nutrition and Health

institute: Chinese Academy of Sciences

description: PE150 high throughout data

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to human whole genome (UCSC GRCh38/hg38) using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: GRCh38/hg38
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample ...
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample.

source_name: Human prostate

growth_protocol: Primary normal human prostate stromal cell line (PSC27) was routinely cultured in PSCC media supplemented with 10% FBS, until a total number of approximately 1,000,000 was reached in each flask and subject to treatment by the chemotherapeutic agent bleomycin (BLEO) at 50 μg/ml and/or apigenin at 10 μM, individually.

extract_protocol:
Cells from both culture conditions were lysed for RNA preparation using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 μg of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: To induce senescence, bleomycin (BLEO) was added to the media at 50 μg/ml, and cells were treated for 12 h before media change. Cells were allowed to stay in culture with appropriate media change until 7-10 days later when they were exposed to apigenin at 10 μM for 2-3 days, then lysed or immediately collected for lysis.

value: Human prostate

value: Human PSC27 prostate stromal cell

value: Stromal

value: Wild type


title: 3mo401, Pancreas, PARP2 KO


title: Sample_172

country: USA

description: Library name: Sample_172

source_name: POAH

value: POAH

tag: time point

tag: Sex


title: BLEO1

description: PE150 high throughout data

value: Bleomycin


title: CTRL2

description: PE150 high throughout data


title: CTRL1

description: PE150 high throughout data


title: N2, DMSO, rep4

city: Changsha

first: Guolin

last: Li

state: Hunan

address: 177 Lushan Road

department: College of Life Sciences

institute: Hunan Normal University

data_processing:
A cDNA library was sequenced run with Illumina Novaseq 6000 sequence platform.
Cutadapt(https://cutadapt.readthedocs.io/en/stable/, version:cutadapt-1.9)was used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases. Then sequence quality was verified using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). including the Q20, Q30 and GC-content of the clean data.
HISAT2(https://daehwankimlab.github.io/hisat2/, version:hisat2-2.2.1) package was used to align reads of all samples to the reference genome
StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Assembly: GCF_000002985.6
Supplementary files format and content: xlsx file includes FPKM and count values for each Sample

organism: Caenorhabditis elegans

source_name: whole animal

extract_protocol:
Total RNA was extracted using Trizol reagent (thermofisher, 15596018) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA, 5067-1511) , high-quality RNA samples with RIN number > 7.0 were used to construct sequencinglibrary. After total RNA was extracted, mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT)(Thermo Fisher, CA, USA) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module(NEB, cat.e6150, USA) under 94℃ 5-7min).
The cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used tosynthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H(NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA). An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR.

value: whole animal

tag: Stage

value: DMSO


title: Inoculum_biorep_2

description:
Library name: ABC141_2
The human data is in Human_RNA_seq.txt.The bacterial data is in Bacterial_RNA_seq_ABC141.txt. Column names labelled "raw" are raw readcounts, column names labelled as "normalised" are normalised read counts and column names labelled with TPM are TPM values for each entry and sample. Biological replicates are indicated after the underscore (e.g., ABC141_1 is experiment 1, ABC141_2 is experiment 2 etc.). Columns labelled ABC141 are data from the inoculum, S-inf are data from infected cells sorted, Inf are data from infected cells unsorted, Neg are data from uninfected and unsorted cells and S-Neg are data from uninfected and sorted cells.


title: Sample_175

description: Library name: Sample_175

value: EHC


title: LnCaP cells, pBabe-GNA13, biol rep 2

city: Singapore

first: Patrick

middle: J

last: Casey

address: 8 College Road

department: Cancer and Stem Cell Biology

country: Singapore

institute: Duke NUS Medical School

data_processing:
Sequencing read quality was assessed via FastQC software (version 0.11.7)
Reads were mapped to the human reference transcriptome (Gencode version 38), via the STAR aligner
Reads were aggregated into gene counts via the featureCounts function in the Rsubread R package 9 (version 1.30.9)
Differences in library sizes among the samples were adjusted via TMM normalization and potential sample outliers were evaluated via Principal Component Analysis (PCA) through the princomp function in R.
Assembly: Gencode version 38
Supplementary files format and content: Tab-delimited text file include CPM values in the log2 scale for each Sample

source_name: LnCaP

growth_protocol: LnCaP cells were maintained in RPMI supplemented with 10% FBS and 1% Pen/Strep in humidified incubator with 5% CO2 at 37 deg Celcius

extract_protocol:
Total RNA was extracted (RNeasy mini kit, Qiagen)
RNA libraries for RNA-seq were prepared by Novogene, Singapore

treatment_protocol: 3 million cells were seeded in 10-cm plates in 3 biological replicates and cultured for 48 h until the cells reached 80% confluency

value: LnCaP

value: prostate cancer cells

value: GNA13 overexpression


title: 3mo398, Pancreas, PARP2 KO


title: Sample_144

description: Library name: Sample_144

source_name: PVN

value: PVN

value: Female

value: C


title: sgZbtb20-2_T2(4w)_ATO_Thy_FB_R3

city: Ithaca

first: Andrew

last: Grimson

state: NY

address: 445 Biotechnology Bldg

department: Molecular Biology and Genetics

institute: Cornell University

description:
Library name: 12
Thymocytes from thymic organoids

data_processing:
Fastq files were generated with cellranger mkfastq (10x Genomics) by NovoSeq X. Raw count tables were generated with cellranger count v7.2.0 (10x Genomics) [cellranger count --id = ID --transcriptome = /path/to/ refdata-gex-mm10-2020-A/--fastqs = /path/to/directories --sample = list --feature-ref= /path/to/control-feature-ref-file-all-conditions/ --localcores=16 -check-library-compatibility= false]. The feature reference files used an untethered approach [pattern =(BC) sequence = GCTCACCTATTAG/capture sequence]. To create aggregate files, cell ranger aggr was utilized [cell ranger aggr --id = ID –csv=/path/to/molecule.h5 files/]. The aggregated file of control and Zbtb20 loss conditions were utilized for downstream analysis (is provided).
Assembly: mouse mm10 assembly
Supplementary files format and content: Aggregate Cell Ranger software output files (barcodes.tsv, features.tsv, matrix.mtx) are provided,Feature_reference for sgZbtb20 condition is provided as .csv file

molecule: polyA RNA

source_name: Aritificial Thymic Organoids

growth_protocol: 1) GFP-Cas9 HSCs extraction and culture HSCs were extracted from GFP-Cas9 mice following cervical dislocation. Femur and tibia bones were isolated and flushed with 10ml RP-10 using a 27-gauge needle. Bone marrow extracts were processed into a single-cell suspension and cells from a single mouse were pooled. After pelleting at 500g for 5 minutes, cells were resuspended in ice-cold MACS buffer through a 70µM filter. This wash step was repeated twice and cells were pelleted at 500g for 5 minutes. Biotin cocktail (1ml) containing CD5, CD19, CD11b, GR-1 (Ly6G), B220 (CD45R) and Ter119 was added to each pellet and incubated at 4°C for 20 minutes. Following incubation, 9ml MACS was added and spun at 500g for 5 mins. The supernatant was aspirated and the pellet was resuspended in 750µl streptavidin mix, which contained 75µl streptavidin beads and 675µl MACS. This mixture was further incubated for 15 minutes at 4°C. After the incubation, 9ml of MACs was added and spun at 500g for 5 mins. After a further spin with 9ml MACS, cells were passed through an LS column (Invitrogen) following a buffer wash. Finally, cells were resuspended in transplant media comprising RP-10 and cytokines (mSCF, 50ng/ml; IL-6, 10ng/ml; IL-3, 10ng/ml; and, Flt3l, 10ng/ml) with 1x penicillin/streptomycin and cultured overnight in non-tissue culture treated 6 well-plates.  2) Murine artificial thymic organoid (M-ATO) cultures M-ATOs were generated with modifications as described below48. MS5-mDLL4 cells were harvested by trypsinization and resuspended in a serum-free M-ATO RPMI-B27 culture medium. RPMI-B27 media contains RPMI 1640, 4% B27 supplement (ThermoFisher Scientific, #17504-044), 30 uM L-ascorbic acid 2-phosphate sesquimagnesium salt hydrate (Sigma-Aldrich, #A8960-5G; reconstituted in PBS), 1% penicillin/streptomycin, 1% Glutamax, 5 ng/ml rmFLT3L (Peprotech, #250-31L), 5 ng/ml rmIL-7 (Peprotech, #217-17), 10 ng/ml rmSCF (SCF was added only for the first week of culture; Peprotech, #250-03) and bmercaptoethanol (0.05mM; Sigma-Aldrich, #M7522). RPMI-B27 was made fresh weekly. 1.5x105 MS5-mDLL4 cells were combined with purified transduced Lin-Sca+Kit+ HSCs (1,000 cells per ATO; extracted as described above) and centrifuged at 300g for 5 min at 4°C in a swinging bucket centrifuge. Supernatants were carefully removed, and the cell pellet was resuspended in 5 ul RPMI-B27 per M-ATO and mixed by brief vortexing. M-ATOs were plated on a 0.4 um Millicell transwell insert (EMD Millipore, #PICM0RG50) and placed in a 6-well plate containing 1 mL RPMI-B27 per well. Medium was changed every 3-4 days by aspiration from around the transwell insert, followed by replacement with 1 mL with fresh RPMI-B27/cytokines. M-ATO cells were harvested by adding FACS buffer (PBS/0.5% bovine serum album/2mM EDTA) to each well and briefly disaggregating the M-ATO by pipetting with a 1 mL pipet, followed by passage through a 50 um nylon strainer. For M-ATO phenotyping, M-ATO thymocytes were isolated after staining (described above) and FACS-sorting at different timepoints (week1, week 2, week 3 to 4). They were then characterized by the cell-surface antibody phenotyping as follows:  DN1-4 (Live+CD45.2+CD3+/TCRb+CD44hi/loCD25hi/lo or CD45+ Live+ Lin- CD4- CD8- CD44hi/loCD25hi/lo) and DP (CD3+TCRb+CD4+CD8+ or CD45+ Live+ Lin- CD3+TCRb+CD4+CD8+). For single-cell RNA sequencing using 3' Direct capture perturb-seq approach, M-ATO thymocytes were isolated by FACS-sorting at different time points (Week 2: day 12, Week 3 to 4: day 27) and different gating strategies and different gRNAs were employed to generate the scRNAseq profiles. To generate scRNAseq profiles of week 2 thymocytes in Figure 7 and Figure S9 either CD45+ Live+ Lin- CD4- CD8- CD44hi/loCD25hi/lo or Live+CD45.2+CD3+TCRb+ CD4-/CD8- populations were used respectively. To generate scRNAseq profiles of week 4 thymocytes in Figure 7 and Figure S9 either CD45+ Live+ Lin- CD3+TCRb+ CD4+/CD8+ or Live+CD45.2+CD3+TCRb+ CD4+/CD8+ populations were used respectively.

extract_protocol:
To generate scRNAseq profiles of week 2 thymocytes either CD45+ Live+ Lin- CD4- CD8- CD44hi/loCD25hi/lo was used respectively. To generate scRNAseq profiles of week 4 thymocytes (Figure 7)  CD45+ Live+ Lin- CD3+TCRb+ CD4+/CD8+ population was used.
Single cell suspensions were run on a Chromium X instrument and libraries prepared following the Chromium Next GEM Single Cell 3' RNA-Seq Assay v3.1 Dual Index with Feature Barcode technology for CRISPR Screening user guide (10x Genomics, CG000316, RevD)128. We targeted 6,000 cells and used 12 cycles of cDNA amplification. Sample quality was confirmed using a Qubit (RNA HS kit; Thermo Fisher) to determine concentration and a Fragment Analyzer (Agilent) to determine RNA integrity. Every sample had an associated feature barcode except the control libraries.

treatment_protocol: 20 mg of retroviral plasmid DNA (sgGFP-Cr2 or sgZbtb20-Cr3-cs2) with 6 mg pCL-Eco plasmid DNA were transfected using 60 ml Lipofectamine 2000 in 3 ml OptiMEM (Invitrogen) for 8 h in antibiotic-free media into Platinum-E ecotropic packaging cells (Cell Biolabs). These cells were plated at a concentration of 2 million cells per 10-cm plate (Becton Dickinson) two days prior to transfection. Media in platinum-E ecotropic packaging cells were replaced 7 h after transfection and these cells were further incubated for 72 h. Following 72h, filtered retroviral supernatants were harvested and applied to HSCs  in plates coated with Retronectin (20 mg/ml; Takara Bio).The transduction process involved spinning at 2,000g for 2 h at 32°C. Transduced cells were harvested after 48 hours, and Lin-Sca+Kit+ cells were isolated by FACS sorting, characterized by the following cell-surface antibody phenotyping: Lin- (Ter119-, B220-, Gr1-, NK1.1-, CD5-, CD3-), Sca+ and Kit+.

value: Aritificial Thymic Organoids

value: 4 week (3 to 4 week)

value: Thymocytes (CD45+ Live+ Lin- CD3+TCRb+ CD4+/CD8+ )

value: Retroviral transduction


title: LnCaP cells, pBabe-GNA13, biol rep 3


title: Inoculum_biorep_3

description:
Library name: ABC141_3
The human data is in Human_RNA_seq.txt.The bacterial data is in Bacterial_RNA_seq_ABC141.txt. Column names labelled "raw" are raw readcounts, column names labelled as "normalised" are normalised read counts and column names labelled with TPM are TPM values for each entry and sample. Biological replicates are indicated after the underscore (e.g., ABC141_1 is experiment 1, ABC141_2 is experiment 2 etc.). Columns labelled ABC141 are data from the inoculum, S-inf are data from infected cells sorted, Inf are data from infected cells unsorted, Neg are data from uninfected and unsorted cells and S-Neg are data from uninfected and sorted cells.

value: somatic cell hybrid, endothelial


title: Sample_80

description: Library name: Sample_80

value: nCPa


title: 3mo308, Pancreas, WT

value: Pancreas

value: WT


title: LnCaP cells, pBabe-GNA13, biol rep 1


title: Sample_14

description: Library name: Sample_14

value: Male


title: postPBS_F3_RNAseq

city: Minneapolis

first: Natalia

last: Tretyakova

state: Minnesota

address: 2231 6th St SE Room 2-147

department: Medicinal Chemistry

institute: University of Minnesota

data_processing:
Trimmomatic for adapter and low-quality base removal
HISAT2 for read mapping
Samtools for alignment sorting and filtering
featureCounts for gene expression quantification
edgeR for gene expression analyses
Assembly: mm10
Supplementary files format and content: CSV with Ensembl identifier, base mean expression, log2(fold change), nominal P-value, and FDR value
Supplementary files format and content: Tab-delimited text matrix with raw fragment counts of gene expression
Supplementary files format and content: BED with extra column for methylation fraction

source_name: Lung

extract_protocol:
Alveolar type II epithelial cells (Type II pneumocytes) were isolated according to published procedures. Briefly, the lungs were perfused with 10 mL cold phosphate buffered saline (PBS) before enzymatic digestion with 2 mL of dispase infused into the lung, after which they were removed and incubated in an additional 2 mL of dispase for one hour. The lungs were then manually disintegrated and the resulting cell suspension labeled with antibodies specific for CD11c, CD11b, F4/80, CD19, CD45 and CD16/CD32 (Thermo Fisher Scientific). Samples  were pooled to include three sets of lungs per sample for a total of three samples for FACS separation. Type II pneumocytes were isolated by negative selection and thus identified as the unlabeled cell population. Type II pneumocytes were also gated as sideward scatter high (SSChigh) cell population which minimizes contamination with lymphoid cells by selecting cells with a higher granularity. The cells were separated by fluorescence activated cell sorting (FACS)  using a BD FACS Aria II P07800142 (BSL2) (BD Biosciences, San Jose, CA). Following isolation via FACS, Type II pneumocytes were pelleted by centrifugation. The samples were first centrifuged for 12 min at 200 x g and 4°C and the supernatant was removed, except for the bottom 1 mL, which was transferred to a 1.7 mL Eppendorf tube. To this tube, 500 µL of PBS was added, and the tube was centrifuged for 12 min at 200 x g at 4°C. The supernatant was removed while the bottom 100 μL was saved. One mL of PBS was added to the tube, and the sample was centrifuged for 12 min at 800 x g and 4°C. After this final centrifugation, all supernatant is removed, and the cell pellet was used to isolate DNA and RNA using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Hilden Germany) according to the man-ufacturer’s instructions.
Total RNA samples were converted to Illumina sequencing libraries using SMARTer Stranded Total RNA-Seq Kit – Pico Mammalian Input (Takara Bio USA, Mountain View CA).
Alveolar type II epithelial cells (Type II pneumocytes) were isolated according to published procedures. Briefly, the lungs were perfused with 10 mL cold phosphate buffered saline (PBS) before enzymatic digestion with 2 mL of dispase infused into the lung, after which they were removed and incubated in an additional 2 mL of dispase for one hour. The lungs were then manually disintegrated and the resulting cell suspension labeled with antibodies specific for CD11c, CD11b, F4/80, CD19, CD45 and CD16/CD32 (Thermo Fisher Scientific). Samples  were pooled to include three sets of lungs per sample for a total of three samples for FACS separation. Type II pneumocytes were isolated by negative selection and thus identified as the unlabeled cell population. Type II pneumocytes were also gated as sideward scatter high (SSChigh) cell population which minimizes contamination with lymphoid cells by selecting cells with a higher granularity. The cells were separated by fluorescence activated cell sorting (FACS)  using a BD FACS Aria II P07800142 (BSL2) (BD Biosciences, San Jose, CA). Following isolation via FACS, Type II pneumocytes were pelleted by centrifugation. The samples were first centrifuged for 12 min at 200 x g and 4°C and the supernatant was removed, except for the bottom 1 mL, which was transferred to a 1.7 mL Eppendorf tube. To this tube, 500 µL of PBS was added, and the tube was centrifuged for 12 min at 200 x g at 4°C. The supernatant was removed while the bottom 100 μL was saved. One mL of PBS was added to the tube, and the sample was centrifuged for 12 min at 800 x g and 4°C. After this final centrifugation, all supernatant is removed, and the cell pellet was used to isolate DNA and RNA using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Hilden Germany) according to the man-ufacturer’s instructions.

value: Lung

tag: gender

value: female

value: Alveolar type II epithelial cells

value: 7 weeks intranasal PBS


title: bladder_cancer_TURBT_2

type: RNA

city: San Diego

first: Elai

last: Davicioni

state: California

address: 9725 Lusk Blvd

institute: Veracyte, Inc

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials and protocols

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
Data was normalized uisng SCAN (SCAN.UPC package from Bioconductor)
probe group file: HuEx-1_0-st-v2.r2.pgf
meta-probeset file: HuEx-1_0-st-v2.r2.dt1.hg38.core.mps

label: biotin

source_name: FFPE bladder cancer

label_protocol: RNA was amplified, fragmented and biotinylated using the WT-Ovation FFPE system (NuGen, San Carlos, CA) according to the manufacturer’s recommendations with minor modifications

extract_protocol: After histopathologic review of formalin-fixed, paraffin-embedded (FFPE) tumor blocks from each case by an expert pathologist, the tumor block with the index lesion was selected for specimen processing. The index lesion was identified as the FFPE block with the biopsy core containing the highest pathologic Gleason grade and the greatest linear length of tumor. At least 0.5 mm of linear tumor was required. Tissue sections were macrodissected to enrich for tumor used for RNA extraction.

value: male

tag: age at randomization

tag: clinical stage


title: sgZbtb20-2_T1(2w)_ATO_Thy_FB_R3

description:
Library name: 11
Thymocytes from thymic organoids

value: 2 week

value: Thymocytes (CD45+ Live+ Lin- CD4- and CD8- )


title: LnCaP cells, pBabe-vector, biol rep 3

value: LnCaP

value: prostate cancer cells


title: sgZbtb20-2_T2(4w)_ATO_Thy_GEX_R3

description:
Library name: 10
Thymocytes from thymic organoids

value: Aritificial Thymic Organoids

value: 4 week (3 to 4 week)


title: N2, DMSO, rep1

value: whole animal

value: DMSO


title: Sample_44

description: Library name: Sample_44

value: nCPa

value: EHC


title: postPBS_F2_RNAseq


title: 3mo313, Pancreas, WT

value: Pancreas

value: WT


title: Sample_45

description: Library name: Sample_45

value: PVN

value: Male


title: LnCaP cells, pBabe-vector, biol rep 2


title: LnCaP cells, pBabe-vector, biol rep 1


title: sgZbtb20-2_T1(2w)_ATO_Thy_GEX_R3

description:
Library name: 9
Thymocytes from thymic organoids

value: Retroviral transduction


title: postLPS_F3_RNAseq

value: Lung

value: female

value: Alveolar type II epithelial cells

value: 3 weeks intranasal LPS, followed by 4 weeks intranasal PBS


title: 3mo309, Pancreas, WT


title: sgGFP_T2(4w)_ATO_Thy_GEX_R3

description:
Library name: 8
Thymocytes from thymic organoids

value: Thymocytes (CD45+ Live+ Lin- CD3+TCRb+ CD4+/CD8+ )

value: sgGFP


title: Sample_146

description: Library name: Sample_146

value: Female

value: C


title: postLPS_F1_RNAseq


title: sgZbtb20-2_T2(4w)_ATO_Thy_FB_R2

description:
Library name: 6
Thymocytes from thymic organoids

value: Aritificial Thymic Organoids

value: 4 week (3 to 4 week)


title: Control_day4

city: Adelaide

first: Naiara

middle: G

last: Bediaga

state: South Australia

address: 4 North Terrace

department: Adelaide Centre for Epigenetics and the South Australian Immunogenomics Cancer Institute, Faculty of Health and Medical Sciences

country: Australia

institute: The University of Adelaide

description: Control (4 day)

data_processing:
Cellranger (v7.2.0) to map reads against human compbined reference (m/h38)
Assembly: hg38
Supplementary files format and content: tab separated files value fiiles and matrix files

source_name: PBMC

extract_protocol:
PBMCs were cultured in NK cell media (RPMI 1640 medium containing GlutaMAX, 10% FBS, 1% P-S, 1% MEM Non-Essential Amino Acids Solution and 1% Sodium Pyruvate) without cytokines or with a combination of IL-15 (10ng/mL) and TGF-β (1-10 ng/mL) for 4 days.
4 single cell RNA libraries were constructed using a Chromium controller (10X Genomics Chromium Single Cell 3' V3.1 chemistry).
A total of 12 cDNA amplification cycles and 14 cycles of library amplification were used.

value: PBMC


title: Sample_125

description: Library name: Sample_125

value: nCPa


title: sgGFP_T1(2w)_ATO_Thy_GEX_R3

description:
Library name: 7
Thymocytes from thymic organoids

value: 2 week

value: Thymocytes (CD45+ Live+ Lin- CD4- and CD8- )


title: Inoculum_biorep_1

description:
Library name: ABC141_1
Biological replicates are indicated after the underscore (e.g., ABC141_1 is experiment 1, ABC141_2 is experiment 2 etc.). Columns labelled ABC141 are data from the inoculum, S-inf are data from infected cells sorted, Inf are data from infected cells unsorted, Neg are data from uninfected and unsorted cells and S-Neg are data from uninfected and sorted cells.

value: somatic cell hybrid, endothelial


title: WFS1 KO, scRNA-seq_bead_merging_files

description:
DNBelab C4
This sample includes raw files that only serve the auxiliary role of merging beads,they only provide information about the combination of two different types of beads.Due to previous research findings, the use of microfluidic technology inevitably results in the phenomenon of multiple beads entering the same oil droplet, leading to a situation where one cell corresponds to multiple cell barcodes. Therefore, MGISEQ-2000RS employ the technology to identify the presence of multiple beads in a single oil droplet (based on the extremely low probability of repetition of the combination of two types of beads in each droplet)

value: hES-derived islet organoid

value: DMSO treated for 48h


title: Treated_day1

description: Treated for 1 day

value: IL-15 and TGF-β (1 day)


title: Sample_173

description: Library name: Sample_173

value: Male


title: Sample_143

description: Library name: Sample_143


title: Control_day1

description: Control (1 day)


title: Treated_day4

description: Treated for 4 days

value: IL-15 and TGF-β (4 days)


title: postPBS_M3_RNAseq

value: Lung

value: male

value: Alveolar type II epithelial cells

value: 7 weeks intranasal PBS


title: Sample_145

description: Library name: Sample_145

value: POAH

value: Female

value: C


title: postPBS_F1_RNAseq

value: female


title: postLPS_F2_RNAseq

value: 3 weeks intranasal LPS, followed by 4 weeks intranasal PBS


title: MOLM13 cells, shRUNX1, 59

city: Beijing

first: Qian

address: Qinghuayuan Stress

institute: Tsinghua University

data_processing:
Adapters and low quality reads were trimmed with fastp v0.20.1 with parameter "-q 20".
Trimmed sequence reads were mapped to hg19 using Hisat2 v2.2.0 with default parameters.
Aligned reads stored in SAM format were manipulated to generate bam files using SAMtools v1.7 with parameter "-Sb -q 20".
FeatureCounts v2.0.1 was applied to calculate the counts per gene under default parameters.
Differentially expressed genes were identified using R package DESeq2 v1.26.0. Please note that the 'Kasumi1_shRUNX1_count.txt' was generated comparing control and shRUNX1 treated RNA abundance using previously published control data (GSE207233; GSM6282809, GSM6282810 and GSM6282811).
Assembly: hg19
Supplementary files format and content: tab-delimited text files include counts per gene for each Sample

growth_protocol: Cells were cultured in RPMI 1640 medium with 10% fetal bovine serum and 1% penicillin/streptomycin at 37°C and 5% CO2.

extract_protocol:
Total RNA was extracted with RNeasy plus kit (Qiagen) for Kasumi-1 cells and TRIZOL reagent (Invitrogen) for MOLM13 cells.
RNA libraries for RNA-seq were prepared using standard Illumina protocols.

treatment_protocol: Kasumi-1 and MOLM13 cells were infected with lentiviruses expressing shRNAs. After 48 h of transduction, puromycin (1 μg/mL) was added into medium for another 48 h to select shRNA expressing cells.

value: Human acute myeloblastic leukemia

value: RUNX1 shRNA


title: sgZbtb20-2_T1(2w)_ATO_Thy_GEX_R2

description:
Library name: 3
Thymocytes from thymic organoids

value: Aritificial Thymic Organoids

value: 2 week

value: Thymocytes (CD45+ Live+ Lin- CD4- and CD8- )

value: Retroviral transduction


title: Sample_142

description: Library name: Sample_142


title: MOLM13 cells, shRUNX1, 28


title: sgGFP_T2(4w)_ATO_Thy_GEX_R2

description:
Library name: 2
Thymocytes from thymic organoids

value: 4 week (3 to 4 week)

value: Thymocytes (CD45+ Live+ Lin- CD3+TCRb+ CD4+/CD8+ )

value: sgGFP


title: postPBS_M2_RNAseq

value: Lung

value: male


title: postLPS_M3_RNAseq

value: Alveolar type II epithelial cells


title: MOLM13 cells, shJMJD1C, 63

value: JMJD1C shRNA


title: Sample_124

description: Library name: Sample_124

value: POAH

value: Male


title: sgGFP_T1(2w)_ATO_Thy_GEX_R2

description:
Library name: 1
Thymocytes from thymic organoids


title: postLPS_M2_RNAseq


title: Sample_147

description: Library name: Sample_147

value: PVN

value: Female

value: C


title: Sample_126

description: Library name: Sample_126


title: postLPS_M1_RNAseq

value: 3 weeks intranasal LPS, followed by 4 weeks intranasal PBS


title: MOLM13 cells, shControl, 2

description:
MOLM13_shJMJD1C_count.txt
MOLM13_shRUNX1_count.txt

value: Human acute myeloblastic leukemia

value: control shRNA


title: 3wPBS_F3_RNAseq

value: female

value: 3 weeks intranasal PBS


title: MOLM13 cells, shJMJD1C, 61


title: sgZbtb20_T2(4w)_ATO_Thy_FB

description: Thymocytes from thymic organoids

data_processing:
Fastq files were generated with cellranger mkfastq (10x Genomics) by NovoSeq X. Raw count tables were generated with cellranger count v7.2.0 (10x Genomics) [cellranger count --id= ID --transcriptome= /path/to/ refdata-gex-mm10-2020-A/--fastqs= /path/to/directories --sample= list --feature-ref= /path/to/feature-ref-file/ --localcores=16 -check-library-compatibility= false]. The feature reference files used an untethered approach [pattern =(BC) sequence = GCTCACCTATTAG/capture sequence]. To create aggregate files, cell ranger aggr was utilized [cell ranger aggr --id= ID –csv=/path/to/molecule.h5 files/]. The aggregated file of control and Zbtb20 loss conditions were utilized for downstream analysis (is provided).
Assembly: mouse mm10 assembly
Supplementary files format and content: Aggregate Cell Ranger software output files (barcodes.tsv, features.tsv, matrix.mtx) are provided,Feature_reference for sgZbtb20 is provided as .csv file

growth_protocol: 1) GFP-Cas9 HSCs extraction and culture HSCs were extracted from GFP-Cas9 mice following cervical dislocation. Femur and tibia bones were isolated and flushed with 10ml RP-10 using a 27-gauge needle. Bone marrow extracts were processed into a single-cell suspension and cells from a single mouse were pooled. After pelleting at 500g for 5 minutes, cells were resuspended in ice-cold MACS buffer through a 70µM filter. This wash step was repeated twice and cells were pelleted at 500g for 5 minutes. Biotin cocktail (1ml) containing CD5, CD19, CD11b, GR-1 (Ly6G), B220 (CD45R) and Ter119 was added to each pellet and incubated at 4°C for 20 minutes. Following incubation, 9ml MACS was added and spun at 500g for 5 mins. The supernatant was aspirated and the pellet was resuspended in 750µl streptavidin mix, which contained 75µl streptavidin beads and 675µl MACS. This mixture was further incubated for 15 minutes at 4°C. After the incubation, 9ml of MACs was added and spun at 500g for 5 mins. After a further spin with 9ml MACS, cells were passed through an LS column (Invitrogen) following a buffer wash. Finally, cells were resuspended in transplant media comprising RP-10 and cytokines (mSCF, 50ng/ml; IL-6, 10ng/ml; IL-3, 10ng/ml; and, Flt3l, 10ng/ml) with 1x penicillin/streptomycin and cultured overnight in non-tissue culture treated 6 well-plates.  2) Murine artificial thymic organoid (M-ATO) cultures M-ATOs were generated with modifications as described below. MS5-mDLL4 cells were harvested bytrypsinizationand resuspended in serum free M-ATO culture medium ((RPMI 1640), 4% B27 supplement, 30μM L-ascorbic acid 2-phosphate sesquimagnesium salt hydrate reconstituted in PBS, 1% penicillin/streptomycin, 1% Glutamax, 5ng/ml rmFLT3L, 5ng/ml rmIL-7, 10ng/ml rmSCF (SCF was added only for the first week of culture) and beta mercaptoethanol (bME; 0.05mM)). RPMI-B27 was made fresh weekly. 1.5x105MS5-mDLL4 cells were combined with purified transduced Lin-Sca+Kit HSC cells (1000 cells / ATO) and centrifuged at 300gfor 5min at 4°C in a swinging bucket centrifuge. Supernatants were carefully removed, and the cell pellet was resuspended in 5μl RPMI-B27 per M-ATO and mixed by brief vortexing. M-ATOs were plated on a 0.4μm Millicell transwell insert placed in a 6-well plate containing 1mL RPMI-B27 per well. Medium was changed every 3-4days by aspiration from around the transwell insert followed by replacement with 1mL with fresh RPMI-B27/cytokines. M-ATO cells were harvested by adding FACS buffer (PBS/0.5% bovine serum album/2mM EDTA) to each well and briefly disaggregating the M-ATO by pipetting with a 1mL pipet, followed by passage through a 50μm nylon strainer.

extract_protocol:
For single-cell RNA sequencing using, M-ATO thymocytes were isolated by FACS sorting at different timepoints (Week 2: day 12, Week 3 to 4: day 27), isolating with Live+CD45.2+CD3+TCRb+.
Single cell suspensions were run on a Chromium X instrument and libraries prepared following the Chromium Next GEM Single Cell 3' RNA-Seq Assay v3.1 Dual Index with Feature Barcode technology for CRISPR Screening user guide (10x Genomics, CG000316, RevD)128. We targeted 6,000 cells and used 12 cycles of cDNA amplification. Sample quality was confirmed using a Qubit (RNA HS kit; Thermo Fisher) to determine concentration and a Fragment Analyzer (Agilent) to determine RNA integrity. Every sample had an associated feature barcode except the control libraries.

value: Aritificial Thymic Organoids

value: 4 week (3 to 4 week)

value: Thymocytes (CD3+ TCRb+)

value: Retroviral transduction


title: totalRNA_siCTRL_NT_REP1

city: Orsay

first: Céline

middle: M.

last: Labbé

address: Rue Henri Becquerel

country: France

institute: Institut Curie

data_processing:
RNA-seq data have been analyzed with the Institut Curie RNA-seq Nextflow pipeline (v3.1.4, https://doi.org/10.5281/zenodo.7443721). Briefly, raw reads were first trimmed with Trimgalor. Reads were aligned on the human reference genome (hg19) using STAR (STAR_2.6.1a_08-27). Genes abundance has been then estimated using STAR (STAR_2.6.1a_08-27). .
Assembly: Hg19
Supplementary files format and content: coma delimited text file includes raw counts for each sample

extract_protocol:
RNA was isolated using the TRIzol-chloroform method and treated with DNase I (TURBO DNA-free; Invitrogen™, #AM1907) according to the manufacturer’s instructions. After DNase treatment, RNA was quantified using a Nanodrop 2000 spectrophotometer (Thermo Scientific™), and 1 μg total RNA was used to synthesize cDNA using SuperScript III Reverse Transcriptase (200 U/μL; Invitrogen™, #18080044) and random hexamer primers (Invitrogen™, #SO142), according to the manufacturer’s instructions.
RNA sequencing libraries were prepared from 500ng to 1µg of total RNA or mRNA-enriched from heavy polysome fractions using the Illumina TruSeq Stranded mRNA Library preparation kit which allows to perform a strand specific sequencing. Nanodrop spectrophotometer was used to assess purity of RNA based on absorbance ratios (260/280 and 260/230) and BioAnalyzer for RNA integrity (RIN>9). A first step of polyA+ selection using magnetic beads is done to focus sequencing on polyadenylated transcripts. After fragmentation, cDNA synthesis was performed and resulting fragments were used for dA-tailing followed by ligation of TruSeq indexed adapters. PCR amplification was finally achieved to generate the final barcoded cDNA libraries. The libraries were equimolarly pooled and subjected to qPCR quantification using the KAPA library quantification kit (Roche).

value: melanoma

value: siCTRL

value: NT


title: Sample_174

description: Library name: Sample_174


title: HEK-293T

city: qingdao

first: chengwen

last: gao

state: shandong

address: Huangdao Qingdao Shandong

institute: Affiliated Hospital of Qingdao University

description: Library name: HEK-293T

data_processing:
*library strategy: modified STARR-seq
Expression data for the SNP fragments were processed by converting raw counts to Transcripts Per Million (TPM) and filtering out low-expressed fragments. Residual log expression normalization and hierarchical clustering were performed to assess sample quality, with outliers identified based on D-statistics and removed from the dataset. Pairwise global alignments compared relevant sequences, summarizing results with alignment scores. The filtered expression data and sequence alignment outputs were saved for further analysis.Enhancer activity analysis followed the method described by Tippens et al.66 Raw sequencing reads were processed using the "voom" function from the R limma package (v3.40.6). Input and output samples were treated as separate experimental conditions, and eSNPs were identified based on significantly higher expression in the output compared to the input. A false discovery rate (FDR)-adjusted p-value less than 0.05 and a fold change greater than 1.5 (log₂FC > 0.585) defined eSNPs (Table S2). SNPs showing significantly reduced expression were classified as candidate silencer SNPs.To identify baaSNPs among the eSNPs, differential allelic regulatory activity was calculated using the mpra package (v1.14.0)43. The analysis employed the `mpralm()` function, which uses a linear model to measure differential regulatory activity between two alleles. This provided summary statistics for each variant, including t-statistics, p-values, log fold changes, B-statistics, and average expression .
Supplementary files format and content: csv files include counts for each cell lines

extract_protocol:
Neuro-2a, SH-SY5Y, HEK-293T, and PC-12 cells were cultured to logarithmic growth phase, reaching a density of 2×107 cells on the day of transfection. Transfections were performed using Xfect™ Transfection Reagent (Takara, Cat. No. 631317, China) under optimized conditions established from preliminary experiments. The purified plasmid DNA from the constructed library was transfected into the cells, and each experiment was conducted in triplicate to ensure reproducibility.
Before cell transfection, the plasmid library was used to construct the input sequencing library. For the initial PCR, 100 ng of the plasmid library underwent a one-step PCR. The purified products were then subjected to two additional rounds of PCR with sample index primers. High-fidelity KAPA HiFi HotStart ReadyMix (Roche, Cat. No. KK2601, USA) was used in all PCR steps to ensure accurate amplification. The final products were prepared for paired-end sequencing on the Illumina NovaSeq 6000 platform. After transfection, total RNA was extracted using the E.Z.N.A.® Total RNA Midiprep Kit (Omega Bio-Tek, Cat. No. R6664, USA). Polyadenylated RNA was isolated using VAHTS mRNA Capture Beads (Vazyme, Cat. No. N401, China) and reverse-transcribed with the HiScript III 1st Strand cDNA Synthesis Kit (Vazyme, Cat. No. R312-02, China). The resulting cDNA was treated with RNase A and purified using AMPure XP beads. Two rounds of PCR amplification were performed, with products purified using Agencourt SPRIselect Reagent (Beckman Coulter, Cat. No. B23318, USA). Three biological replicates were prepared for both input and output sequencing libraries, which were then sequenced using paired-end 150 bp reads on the Illumina NovaSeq 6000 platform.


title: sgZbtb20_T2(4w)_ATO_Thy_GEX

description: Thymocytes from thymic organoids


title: sgZbtb20_T1(2w)_ATO_Thy_FB

description: Thymocytes from thymic organoids

value: 2 week


title: 3wPBS_F2_RNAseq

value: Lung

value: Alveolar type II epithelial cells


title: sgZbtb20_T1(2w)_ATO_Thy_GEX

description: Thymocytes from thymic organoids


title: 3wPBS_F1_RNAseq


title: postPBS_M1_RNAseq

value: male

value: 7 weeks intranasal PBS


title: MOLM13, shRNA, input

library_source: genomic

data_processing:
Adapters and low-quality bases were trimmed with trim_galore v0.6.4 with parameter "-q 20 --length 20 --stringency 2”.
Trimmed reads were aligned to the hg19 genome with Bowtie2 v2.3.5.1 with default parameters.
Aligned reads stored in SAM format were manipulated to generate bam files using SAMtools v1.7.
Peaks were called using MACS2 v2.1.1.
RPKM normalized bigwig files were generated using bamCoverage of deepTools v3.3.0.
Assembly: hg19
Supplementary files format and content: bigWig

molecule: genomic DNA

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes at room temperature. After quenching and cell lysis, chromatin was sonicated and inbubated with antibody/beads. DNA/protein complexes were then eluted and reverse crosslinked at 65 °C for 6 h. DNA was next purified using phenol/chloroform extraction and ethanol precipitation.
ChIP-seq libraries were prepared using End-It DNA End-Repair Kit, Klenow Fragment (3´→ 5´ exo-) and Quick Ligation kit. Libraries were amplified using 16 cycles on the thermocycler and then subjected for size selection using AMPure XP beads.

treatment_protocol: For RUNX1 KD ChIP-seq, MOLM13 and Kasumi-1 cells were infected with lentiviruses expressing shRNAs. After 48 h of transduction, puromycin (1 μg/mL) was added into medium for another 48 h to select shRNA expressing cells.


title: sgZbtb20-2_T2(4w)_ATO_Thy_GEX_R2

description:
Library name: 4
Thymocytes from thymic organoids

value: Thymocytes (CD45+ Live+ Lin- CD3+TCRb+ CD4+/CD8+ )


title: MOLM13, shRUNX1, 92, JMJD1C

tag: antibody

value: Human acute myeloblastic leukemia


title: MOLM13 cells, shControl, 1

value: control shRNA


title: Sample_176_

description: Library name: Sample_176_

value: nCPa

value: Male

value: EHC


title: sgGFP_T2(4w)_ATO_Thy_GEX

description: Thymocytes from thymic organoids

value: Aritificial Thymic Organoids

value: 4 week (3 to 4 week)

value: sgGFP


title: 3wLPS_F3_RNAseq

value: female

value: 3 weeks intranasal LPS


title: MOLM13, shRUNX1, 59, JMJD1C


title: sgGFP_T1(2w)_ATO_Thy_GEX

description: Thymocytes from thymic organoids

value: Thymocytes (CD3+ TCRb+)

value: Retroviral transduction


title: MOLM13, shNC, 2, JMJD1C


title: Novirus_T2(4w)_ATO_Thy_GEX

description: Thymocytes from thymic organoids

value: No gRNA


title: Sample_160

description: Library name: Sample_160

value: POAH

value: Female


title: 3wPBS_M3_RNAseq

value: Lung

value: male

value: Alveolar type II epithelial cells

value: 3 weeks intranasal PBS


title: Sample_157

description: Library name: Sample_157


title: Sample_161

description: Library name: Sample_161

value: nCPa


title: Utx-cKO

city: Philadelphia

first: Brian

middle: C.

last: Capell

state: PA

address: 421 Curie Boulevard Biomedical Research Building 1020 Biomedical Research Building 1020

department: Dermatology

institute: University of Pennsylvania

hyb_protocol: Probe hybridization was performed overnight (16-24h) at 50°C. The following day, excess unbound probes were washed with PBST and a post-hybridization wash buffer incubated at 37°C for 30min. The probes were ligated at 37°C for 2hrs followed by rolling cycle amplification at 30°C for 2hrs with PBST washes in between steps. A post-amplification wash was performed with TE buffer followed by incubation with reducing agent for 10min. An autofluorescence quenching step was performed for 10min to limit background noise followed by 100% ethanol washes.

scan_protocol: Slides were loaded onto the Xenium Analyzer image and ROIs (regions of interest) specified for imaging. Xenium instrument imaging processing, decoding, quality score generation, and DAPI-based cell segmentation was automatically performed by the Xenium Analyzer system.

data_processing: Output files for downstream analysis included the cell-feature matrix (HDF5 format), transcripts file, and cell boundaries csv file. Sections used were previously harvested and paraffin embedded dorsal skin sections processed as described in above methods (n = 3 <9-week-old females for all groups and n = 1 >52-week-old females for all groups: WT females, Utx-cKO females). Both age groups were averaged to get a total of n = 4 biological replicates for all groups and all analysis was done on this mixed cohort.

source_name: Whole skin

label_protocol: Probes were designed to contain two regions that hybridize to the target RNA along with a gene-specific barcode sequence to generate a circular DNA probe once probe ends are ligated (thus ensuring high specificity). Lyophilized custom probes were resuspended in TE buffer and then preheated by incubating for 2min at 95°C followed by 1min on ice.

growth_protocol: Normal murine development

extract_protocol: FFPE blocks from skin tissues of interest were sectioned at 5μm thickness onto provided Xenium slides and stored in a dessicator at room temperature until use. The Xenium workflow was performed according to the 10X Xenium protocol (Protocol #: CG000580, CG000582, CG000584). Xenium slides were baked for 2hrs at 60°C followed by deparaffinization in xylene (2x, 10min each) and rehydration with an ethanol gradient as follows: 100% ethanol (2x, 3min each), 96% (2x, 3min each), 70% (1x, 3min), nuclease-free H2O. Slides were then de-crosslinked with the following thermocycler conditions: 80°C for 30min, 22°C for 10min and then washed with PBST. Next, the mRNAs were targeted with a custom 480 gene panel combined with negative control probes.

tag: strain/gender

value: B6/129 females


title: Novirus_T1(2w)_ATO_Thy_GEX

description: Thymocytes from thymic organoids

value: 2 week


title: Kasumi1, shRNA, input

value: Human acute myeloblastic leukemia


title: Kasumi1, shRUNX1, 92, JMJD1C


title: Sample_149

description: Library name: Sample_149

data_processing:
First, using trimmomatic (v 0.39), we removed adapters from the sequences, retaining only sequences that had > 100 nucleotides in length and an average quality> 30. We aligned the reads to the chicken genome (galgal1) using Hisat2 . Next, we used Samtools (v 1.10) to retain the reads with one match to the genome, followed with removing duplicates using bammarkduplicates from biobambam2 (v 2.0.95). Samples with or more than 90% of correct alignment were used for counting.
Assembly: galgal1
Supplementary files format and content: read counts in a tab delimited text file

extract_protocol:
Total RNA was isolated using the Total RNA purification Micro Kit (Norgen Biotek, Thorold, ON, Canada) according to the manufacturer’s instructions. Samples were thawed to room temperature (3 minutes) and vortexed for 30 seconds. 100 µl of 70% molecular-biology grade ethanol was added to the lysate and then steps were performed according to the kit’s instructions
Illumina’s Stranded Total RNA Prep, Ligation with Ribo Zero Plus Sample Prep Kit

value: EHC


title: WT control


title: Kasumi1, shRUNX1, 28, JMJD1C


title: Sample_150

description: Library name: Sample_150

value: PVN


title: Sample_148

description: Library name: Sample_148


title: 3wPBS_M1_RNAseq


title: Sample_158

description: Library name: Sample_158

value: Male


title: 4411_MGI

city: Anderlecht

first: Valerie

last: Vandenbempt

state: Vlaams-Brabant

address: Lenniksebaan 808

country: Belgium

institute: Université Libre de Bruxelles

description: 10X genomics

data_processing:
Assembly: ChGr38
Cellranger
Supplementary files format and content: filtered feature bc matrix

source_name: Breast cancer tissue

extract_protocol:
Tissue extraction and dispersion
Chromium Next GEM Single Cell 3ʹ

value: Breast cancer tissue


title: Sample_177

description: Library name: Sample_177


title: 3wLPS_M2_RNAseq

value: 3 weeks intranasal LPS


title: 4066_MGI

description: 10X genomics


title: Kasumi1, shNC, 2, JMJD1C


title: 3wLPS_M3_RNAseq


title: MOLM13, shNC, 1, JMJD1C


title: 3wLPS_F1_RNAseq

value: female


title: Kasumi1, shNC, 1, JMJD1C


title: 4399_MGI

description: 10X genomics


title: 3wPBS_M2_RNAseq


title: 3wLPS_M1_RNAseq


title: 3wLPS_F2_RNAseq


title: Uninfected_sorted_biorep_4

description:
Library name: SNeg_4
The human data is in Human_RNA_seq.txt.The bacterial data is in Bacterial_RNA_seq_ABC141.txt. Column names labelled "raw" are raw readcounts, column names labelled as "normalised" are normalised read counts and column names labelled with TPM are TPM values for each entry and sample. Biological replicates are indicated after the underscore (e.g., ABC141_1 is experiment 1, ABC141_2 is experiment 2 etc.). Columns labelled ABC141 are data from the inoculum, S-inf are data from infected cells sorted, Inf are data from infected cells unsorted, Neg are data from uninfected and unsorted cells and S-Neg are data from uninfected and sorted cells.

data_processing:
Bacterial RNA-seq: For calculation of bacterial gene expression, reads were mapped with bowtie2 v. 2.4.2 with the parameters -very-sensitive-local to align sequencing reads to the A. baumannii ABC141 reference genome (Lanmead & Salzberg, 2012). Only reads with the highest mapping quality (MAPQ = 44) were kept and aggregated strand-specifically with featureCounts v2.0.3 on features annotated with the types of CDS, sRNA or ncRNA (Liao et al., 2014). To filter for low expression only genes were kept that showed expression of TPM ≥10 in the majority of replicates in one or more of the sample groups resulting in a set of 3299 genes. Differential gene expression (log2 fold-changes and adjusted p-values) was calculated using DESeq2 v1.46 (Love et al., 2014).
Human RNA-seq: Data files were processed through FastQC for quality control (Andrews, 2010). Short reads were mapped to the human reference genome (hg38) using STAR v2.7.3a (Dobin et al., 2013). Uniquely mapped reads were assigned to genes with featureCounts v2.0.3 using the latest Ensembl annotation (v114) (Dyer et al., 2025). To filter for low expression, only those genes were kept that had an expression value of one or more TPM (transcripts per million) in at least half of their replicates. Differentially expressed genes were determined by DESeq2 v1.46.
Assembly: GRCh38 (human reference sequence), GCF_050269755.1 (Acinetobacter baumannii ABC141 reference sequence)
Supplementary files format and content: Human_RNA_seq.txt is a tab-delimited text file which inlcludes raw counts, TPM, normalised read counts and DESeq2 analysis for each sample (human RNA-seq)
Supplementary files format and content: Bacterial_RNA_seq_ABC141.txt is a tab-delimited text file which inlcludes raw counts, TPM, normalised read counts and DESeq2 analysis for each sample (bacterial RNA-seq)

extract_protocol:
Total RNA from infected cells, non-infected cells and ABC141 inocula was extracted following a previously described method (Kröger et al., 2018). For cultures, bacteria were lysed with 2/5 volume of ice-cold 5% (v/v) phenol, 95% (v/v) ethanol ultra-pure solution for 1 h on ice. The same lysis process was applied to the total of infected cells and mock-infected cells sorted by FACS. A centrifugation at 3220 x g for 10 min at 4°C pelleted the sample, which was resuspended with 1 mL ice-cold TRIzol and transferred into a Phase-Lock-Tube (VWR, #2302830). 400 µL of chloroform was added and the solution was shaken (without vortexing) for 10 s, followed by a 3 min incubation at RT. The tubes were centrifuged at 12000 x g at 4 °C for 15 min. Then, the aqueous phase was transferred to a new 1.5 mL tube. 450 µL of isopropanol was added and mixed before a 30 min incubation at RT. A new centrifugation at full speed for 30 min preceded three washes of the pellet with 350 µL of ethanol 75%, a 10 min incubation at RT and a 10 min centrifugation at full speed. The last supernatant was discarded and the pellet air dried before resuspension with 25 µL of RNAse-free water, followed by a 5 min incubation at 65 °C at 900 rpm. The RNA extraction quality was verified with a 1/10 dilution using the 4200 TapeStation (Agilent Technologies).
Total RNA was sent to Core Unit Systems Medicine (SysMed) sequencing facility for RNA-seq (University of Würzburg, Germany), where DNase I digestion and rRNA depletion (RiboCop) was performed. Library for the sequencing was prepared using the NEBNext Multiplex Small RNA Library Prep kit. Sequencing was performed on the Illumina NextSeq-500 Mid Output KT v2.5 (150 cycles).

value: somatic cell hybrid, endothelial


title: Sample_71

description: Library name: Sample_71

value: C


title: MOLM13, EGR1, 4C

data_processing:
Adapters and low quality reads were trimmed with trim_galore v0.6.4.
4C mapping pipeline 4Cker was used to filter, analysis, and visualize the 4C-seq data.
Assembly: hg19
Supplementary files format and content: tab-delimited text files contain normalized counts near bait.
Library strategy: 4C-seq

extract_protocol:
Cells were fixed with 2% formaldehyde for 10 minutes at room temperature. After quenching and cell lysis, the nuclei were then treated with SDS followed by the treatment of Triton X-100 solution to sequester the SDS. Next, the nuclei were taken up for digestion with DpnII and ligation. After the first ligation, DNA were reverse crosslinked, purified and subjected for the second digestion with NlaIII and the second ligation. DNA was then purified using phenol–chloroform–IAA solution extraction and ethanol precipitation. Dissolved DNA was further purified with QIAquick PCR Purification Kit (QIAGEN, 28104).
Extracted DNA were served as template to perform PCR reactions. PCR products were purified using QIAquick PCR Purification Kit (QIAGEN, 28104) and KAPA DNA beads. The libraries were then sequenced on Illumina platform.


title: M9 control 28 days

city: Magdalenka

first: Grzegorz

middle: Roman

last: juszczak

address: Jastrzebiec, ul Postepu 36A

country: Poland

institute: Institute of Genetics and Animal Biotechnology

description:
enrichment of polyadenylated RNA
stranded library

data_processing:
Initial data analysis included quality validation of raw and trimmed data in fastq format using MultiQC and FastQC tools, trimming of adapters using Trim Galore, alignment of reads to mouse GRCm39 genome assembly using hisat2, quality validation of the aligned data using MultiQC / BamQC and feature counting with featureCounts. The count files were analyzed with edgeR package. The data derived from all 48 samples were filtered by filterByExpr function. The data were normalized with the normLibSizes function using default TMM method. Differences between groups were tested with the edgeR exactTest while Bonferroni-Hochberg method was used to calculate adjusted p-values.
Assembly: mouse GRCm39 genome assembly
Supplementary files format and content: Excel file containing CPM values for each sample and results of statistical comparisons between groups.

source_name: hippocampus

extract_protocol:
RNA was extracted from the individual hippocampal samples using the GeneMATRIX Universal RNA Purification Kit (Eurx) according to the manufacturer-supplied protocol. Obtained RNA samples were additionally purified with the DNase Max kit (Qiagen) to remove remnants of DNA.
Library construction protocol included mRNA enrichment with Oligo dT, RNA fragmentation and reverse transcription (second-strand cDNA synthesis with dUTP instead of dTTP for preparation of stranded specific mRNA libraries), end repair, A-tailing, adaptor ligation, PCR amplification, single strand separation and cyclization and DNA nanoball synthesis preceinding  sequencing on DNBseq platform.

treatment_protocol: The mice were assigned to three corticosterone-treated groups that received the glucocorticoid dissolved in drinking water (100 g/mL) for 5, 14 or 28 nights and to three control groups that were euthanized at the same time as corticosterone treated animals. Bottles with drinking water were changed every evening at the end of the light phase. Sample collection was performed during the first hour of the light phase following the last night of treatment.

value: hippocampus

tag: developmental stage

value: adult

tag: strain

value: Swiss-Webster

value: vehicle

tag: time

value: 28 days


title: MOLM13, RUNX1


title: Sample_74

first: Fernando

address: 175 West Campus Drive

institute: Virginia Tech

description: Library name: Sample_74

value: nCPa

tag: biological replicate


title: Sample_118

description: Library name: Sample_118

value: POAH

value: Female


title: M59 control 28 days

value: male


title: LNCaP_OE_3

city: San Antonio

first: Yidong

state: Texas

address: 8403 Floyd Curl Drive, MSC 7784

department: Population Health Sciences

institute: UT Health Science Center at San Antonio

data_processing:
Illumina bcl2fastq software used for base-calling
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using TopHat2 aligner.
gene count measurements were obtained using HTSeq using refseq annotation. LNCaP_KO_1 was not used in the differential expression analysis.
Assembly: hg19
Supplementary files format and content: The processed data files are in tabular format.  The first column contains the gene symbols and the second column contain the read counts of the gene using htseq-count

source_name: LNCaP  with RPS6KB1 OE, rep 3

growth_protocol: LNCaP, LNCaP RPS6KB1 KO and LNCaP RPS6KB1 OE cells were cultured using RPMI 1640 medium supplemented with 10% FBS, antibiotic/anti-mycotic agent (Corning and is cat# 30-004-CI). Media for LNCaP OE cells was also supplemented with 20 microg/ml puromycin.

extract_protocol:
Total RNA was extracted using TRIzol reagent and Zymo Research Total RNA extraction kit  and quantified using nanodrop and Agilent bioanalyzer.
Total RNA samples were used for sequencing library preparation with KAPA RNA HyperPrep kit with RiboErase (HMR) following KAPA RNA library preparation protocol. Each library was bar-coded and then pooled for sequencing run paired-end sequencing protocol.

treatment_protocol: Cells were treated with Berberine prepared as 10mg/ml stock (Sigma B3251) in 100% methanol (Sigma 179337) and filtered using a 0.20μm filter (Corning 431222). For RPS6KB1 KO and OE cells: freshly procured LNCaP cells were used to generate stable RPS6KB1 knockout (KO) cells using CRISPR/Cas9 system by Applied StemCell Inc (Milpitas, CA). Two gRNAs targeting exon 4 of RPS6KB1 locus produced double strand breaks, generating a 56 base pair deletion.  RPS6KB1 KO cells were maintained in complete RPMI medium.

tag: cell lines

value: LNCaP Prostate cancer cell line

tag: rps6kb1 status

value: LNCaP OE


title: M7 control 28 days

tag: tissue


title: LNCaP_OE_2

source_name: LNCaP  with RPS6KB1 OE, rep 2


title: Uninfected_sorted_biorep_3

first: Carsten

address: Moyne Institute of Preventive Medicine

institute: Trinity College Dublin

description:
Library name: SNeg_3
The human data is in Human_RNA_seq.txt.The bacterial data is in Bacterial_RNA_seq_ABC141.txt. Column names labelled "raw" are raw readcounts, column names labelled as "normalised" are normalised read counts and column names labelled with TPM are TPM values for each entry and sample. Biological replicates are indicated after the underscore (e.g., ABC141_1 is experiment 1, ABC141_2 is experiment 2 etc.). Columns labelled ABC141 are data from the inoculum, S-inf are data from infected cells sorted, Inf are data from infected cells unsorted, Neg are data from uninfected and unsorted cells and S-Neg are data from uninfected and sorted cells.

tag: cell line

tag: cell type


title: Sample_159

city: Blacksburg

description: Library name: Sample_159

value: PVN

tag: time point

value: Male

tag: treatment

value: EHC


title: M57 control 28 days

tag: Sex


title: Sample_119

description: Library name: Sample_119

source_name: nCPa


title: M30 control 28 days


title: Sample 6, CTCF, ChIP

city: Oklahoma City

middle: M

last: Gaffney

state: OK

address: 825 NE 13th Street

department: Genes and Human Disease

institute: Oklahoma Medical Research Foundation

data_processing:
Adapters were removed from sequenced fastq files by fastp (options: detect_adapter_for_pe -l 50 -x –g). Samples 3 and 6 were downsampled to 200M reads using seqtk for downstream processing.
Reads were aligned to the human genome using Bowtie2’s H. sapiens GRCh38 no alt analysis set with a mapQ > 10 and the following options: for global alignment: --very-sensitive -L 30 --score-min L,-0.6,-0.2 --end-to-end –reorder, and for local alignment: --very-sensitive -L 20 --score-min L,-0.6,-0.2 --end-to-end –reorder
Reads were processed using a MboI hg38 restriction fragment bed file and the HiC-Pro analysis pipeline
HiChIP peak sets were called within each sample separately using MACS2 with defaults, a genome size = 2913022398, and FDR q = 0.01. A consensus peak set was generated from individual peak profiles using DiffBind for reproducible peaks observed in all four samples.
CTCF loops were called within the pediatric samples using HiChipper
Assembly: hg38
Supplementary files format and content: bigWig, narrowPeak and mango

source_name: Primary B cells

extract_protocol:
B cells (~2x106 each sample) were fixed in 1% formaldehyde at room temperature for 10 min. After quenching and cell lysis, chromatin was fragmented with the Covaris E220 system
DNA was purified by Zymo DNA Clean & Concentrator kit (Zymo, D4003). Streptavidin C1 beads were used to capture biotin-labeled DNA fragments. The sequencing libraries were generated on the streptavidin C1 beads using Illumina Tagment DNA Enzyme and Buffer kit (Illumina, 20034198)

value: Primary B cells

tag: chip antibody

value: CTCF, Cell Signaling, 3418S


title: Sample_64

last: Biase

description: Library name: Sample_64

value: C


title: LNCaP_OE_1

source_name: LNCaP  with RPS6KB1 OE, rep 1


title: Uninfected_sorted_biorep_1

city: Dublin

last: Kroeger

description:
Library name: SNeg_1
The human data is in Human_RNA_seq.txt.The bacterial data is in Bacterial_RNA_seq_ABC141.txt. Column names labelled "raw" are raw readcounts, column names labelled as "normalised" are normalised read counts and column names labelled with TPM are TPM values for each entry and sample. Biological replicates are indicated after the underscore (e.g., ABC141_1 is experiment 1, ABC141_2 is experiment 2 etc.). Columns labelled ABC141 are data from the inoculum, S-inf are data from infected cells sorted, Inf are data from infected cells unsorted, Neg are data from uninfected and unsorted cells and S-Neg are data from uninfected and sorted cells.

value: somatic cell hybrid, endothelial


title: Uninfected_not_sorted_biorep_5

description:
Library name: Neg_5
The human data is in Human_RNA_seq.txt.The bacterial data is in Bacterial_RNA_seq_ABC141.txt. Column names labelled "raw" are raw readcounts, column names labelled as "normalised" are normalised read counts and column names labelled with TPM are TPM values for each entry and sample. Biological replicates are indicated after the underscore (e.g., ABC141_1 is experiment 1, ABC141_2 is experiment 2 etc.). Columns labelled ABC141 are data from the inoculum, S-inf are data from infected cells sorted, Inf are data from infected cells unsorted, Neg are data from uninfected and unsorted cells and S-Neg are data from uninfected and sorted cells.


title: Sample_73

description: Library name: Sample_73


title: M32 control 28 days

value: hippocampus

value: adult


title: Uninfected_not_sorted_biorep_4

description:
Library name: Neg_4
The human data is in Human_RNA_seq.txt.The bacterial data is in Bacterial_RNA_seq_ABC141.txt. Column names labelled "raw" are raw readcounts, column names labelled as "normalised" are normalised read counts and column names labelled with TPM are TPM values for each entry and sample. Biological replicates are indicated after the underscore (e.g., ABC141_1 is experiment 1, ABC141_2 is experiment 2 etc.). Columns labelled ABC141 are data from the inoculum, S-inf are data from infected cells sorted, Inf are data from infected cells unsorted, Neg are data from uninfected and unsorted cells and S-Neg are data from uninfected and sorted cells.


title: Sample 5, CTCF, ChIP


title: Sample 3, CTCF, ChIP


title: Uninfected_not_sorted_biorep_3

description:
Library name: Neg_3
The human data is in Human_RNA_seq.txt.The bacterial data is in Bacterial_RNA_seq_ABC141.txt. Column names labelled "raw" are raw readcounts, column names labelled as "normalised" are normalised read counts and column names labelled with TPM are TPM values for each entry and sample. Biological replicates are indicated after the underscore (e.g., ABC141_1 is experiment 1, ABC141_2 is experiment 2 etc.). Columns labelled ABC141 are data from the inoculum, S-inf are data from infected cells sorted, Inf are data from infected cells unsorted, Neg are data from uninfected and unsorted cells and S-Neg are data from uninfected and sorted cells.


title: Sample_120

description: Library name: Sample_120


title: Sample_72

description: Library name: Sample_72


title: Uninfected_sorted_biorep_2

description:
Library name: SNeg_2
The human data is in Human_RNA_seq.txt.The bacterial data is in Bacterial_RNA_seq_ABC141.txt. Column names labelled "raw" are raw readcounts, column names labelled as "normalised" are normalised read counts and column names labelled with TPM are TPM values for each entry and sample. Biological replicates are indicated after the underscore (e.g., ABC141_1 is experiment 1, ABC141_2 is experiment 2 etc.). Columns labelled ABC141 are data from the inoculum, S-inf are data from infected cells sorted, Inf are data from infected cells unsorted, Neg are data from uninfected and unsorted cells and S-Neg are data from uninfected and sorted cells.


title: M28 control 28 days

value: Swiss-Webster

value: vehicle


title: Sample_75

description: Library name: Sample_75


title: Uninfected_not_sorted_biorep_2

description:
Library name: Neg_2
The human data is in Human_RNA_seq.txt.The bacterial data is in Bacterial_RNA_seq_ABC141.txt. Column names labelled "raw" are raw readcounts, column names labelled as "normalised" are normalised read counts and column names labelled with TPM are TPM values for each entry and sample. Biological replicates are indicated after the underscore (e.g., ABC141_1 is experiment 1, ABC141_2 is experiment 2 etc.). Columns labelled ABC141 are data from the inoculum, S-inf are data from infected cells sorted, Inf are data from infected cells unsorted, Neg are data from uninfected and unsorted cells and S-Neg are data from uninfected and sorted cells.


title: M8 corticosterone 28 days

value: corticosterone

value: 28 days


title: HEK293T, RNA, wt, rep 2

first: Zonggui

state: Beijing

address: No.5 Yiheyuan Road Haidian District

department: Academy for Advanced Interdisciplinary Studies

institute: Peking University

data_processing:
Trimmed adapter by using cutadapt (v3.5)
Removed rRNA reads by using bowtie2 (v2.4.4)
Mapped to hg38 by using STAR (v2.7.9a)
Quantify circRNA by using CIRCExplorer3
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

extract_protocol:
Total RNA was isolated using TRIzol reagent (Invitrogen, 15596018) or FastPure Cell/Tissue Total RNA Isolation Kit V2  (Vazyme Biotech Co., Ltd). Total RNA was treated with TURBO DNase (Invitrogen, AM2238) to remove Genomic DNA. The RNA was purified by RNA Clean& Concentrator Kits (Zymo Research, R1013) and then mRNA was isolated using oligo d(T)25 Magnetic Beads (NEB, S1419S). The supernatant polyA minus (polyA-) RNA was collected and purified by RNA Clean& Concentrator Kits (Zymo Research, R1013)
After the digestion of linear RNAs with RNase R (Epicentre Technologies, USA) and removal of ribosomal RNAs using NEBNext® rRNA Depletion Kit v2 (Human/Mouse/Rat), the resultant RNAs were regarded as circRNAs and subjected to generating sequencing library. Sequencing libraries were prepared with NEBNext® Ultra™ II Directional RNA Library Prep Kit (E7765).

value: human embryonic kidney 293 cells

tag: genotype

value: WT


title: M58 corticosterone 28 days

value: male


title: Sample_66

description: Library name: Sample_66


title: Sample 2, CTCF, ChIP


title: Uninfected_not_sorted_biorep_1

description:
Library name: Neg_1
The human data is in Human_RNA_seq.txt.The bacterial data is in Bacterial_RNA_seq_ABC141.txt. Column names labelled "raw" are raw readcounts, column names labelled as "normalised" are normalised read counts and column names labelled with TPM are TPM values for each entry and sample. Biological replicates are indicated after the underscore (e.g., ABC141_1 is experiment 1, ABC141_2 is experiment 2 etc.). Columns labelled ABC141 are data from the inoculum, S-inf are data from infected cells sorted, Inf are data from infected cells unsorted, Neg are data from uninfected and unsorted cells and S-Neg are data from uninfected and sorted cells.


title: Sample_70

description: Library name: Sample_70

value: POAH

value: Female


title: M56 corticosterone 28 days


title: Sample_116

description: Library name: Sample_116

value: nCPa


title: RNA from IRF3 KD epthelium, replicate 3

city: SHREVEPORT

first: Jason

last: Bodily

state: LA

address: 1501 Kings Highway

institute: LSU Health - Shreveport

description: Library name: Sample 30

data_processing:
Sample reads from fastq files were consolidated. Base calling and quality scoring were performed with Illumina Real Time Analysis software (RTA, version 2.4.11) .  Transcripts were quantified with RSEM 1.3.0.
Assembly: Reads were aligned to a concatenated human genome (ChrGRCh38p12v30) and HPV 16 genome (HPV16-NC_0015263) with STAR 2.5.31.
Supplementary files format and content: fastq.gz

source_name: Organotypic culture

growth_protocol: HFFs were cultured and maintained in Dulbecco’s modified Eagle’s medium (DMEM), supplemented with 10% bovine growth serum (BGS). HFK-derived were cultivated in E medium and supplemented with 5% fetal bovine serum (FBS) in the presence of mitomycin-treated HFFs. To generate organotypic rafts, low passage-numberr HFKs harboring HPV16 (with confirmed episomal status) were used, with HFFs embedded in collagen in the dermal equivalent. At least three different human foreskin fibroblast (HFF) lines and three human foreskin keratinocyte (HFK) donor backgrounds were used for all the raft experiments. Constructs wre lifted to the air-liquid interface and fed with E medion + 5% FBS from below. Following 14 days, stromal and epithelial compartments were mechanically separated.

extract_protocol:
Total RNAs were isolated using a Qiagen Qiacube
Libraries were prepared using Illumina’s TruSeq Stranded mRNA LS kit

value: Organotypic culture

value: Human foreskin keratinocyte immortalized with HPV16 episomal genomes

value: Wild type

value: Grown in organotypic culture 14 days in the presence of IRF3 KD fibroblasts


title: HEK293T, RNA, wt, rep 1

last: Chen


title: HEK293T, circRNA, wt, rep 2


title: M54 corticosterone 28 days


title: HEK293T, circRNA, wt, rep 1


title: RNA from IRF3 KD epthelium, replicate 2

description: Library name: Sample 29


title: M31 corticosterone 28 days


title: M26 control 28 days


title: Uninfected_not_sorted_biorep_6

description:
Library name: Neg_6
The human data is in Human_RNA_seq.txt.The bacterial data is in Bacterial_RNA_seq_ABC141.txt. Column names labelled "raw" are raw readcounts, column names labelled as "normalised" are normalised read counts and column names labelled with TPM are TPM values for each entry and sample. Biological replicates are indicated after the underscore (e.g., ABC141_1 is experiment 1, ABC141_2 is experiment 2 etc.). Columns labelled ABC141 are data from the inoculum, S-inf are data from infected cells sorted, Inf are data from infected cells unsorted, Neg are data from uninfected and unsorted cells and S-Neg are data from uninfected and sorted cells.

value: somatic cell hybrid, endothelial


title: Sample_92

description: Library name: Sample_92

value: Male

value: EHC


title: HEK293T, RNA, oe-hnRNPK, rep 2

value: hnRNPK over-expression


title: RNA from IRF3 KD epthelium, replicate 1

description: Library name: Sample 28


title: M27 corticosterone 28 days

value: hippocampus

value: adult

value: Swiss-Webster


title: HEK293T, RNA, oe-hnRNPK, rep 1

value: human embryonic kidney 293 cells


title: M12 corticosterone 28 days

value: corticosterone

value: 28 days


title: Sample_115

description: Library name: Sample_115

source_name: POAH

value: POAH


title: RNA from NTC epthelium, replicate 2

description: Library name: Sample 23

value: Grown in organotypic culture 14 days in the presence of NTC fibroblasts


title: M10 corticosterone 28 days

value: male


title: Sample_91

description: Library name: Sample_91


title: RNA from NTC epthelium, replicate 1

description: Library name: Sample 22

value: Organotypic culture


title: HEK293T, circRNA, oe-hnRNPK, rep 1


title: M52 control 14 days

value: vehicle

value: 14 days


title: Sample_67

description: Library name: Sample_67


title: RNA from IRF3 KD fibroblasts replicate 3

description: Library name: Sample 15

value: Human foreskin fibroblast

value: IRF3 KD shRNA

value: Grown in organotypic culture 14 days


title: Caenorhabditis elegans, fed on Δfur,24h

city: WuHan

first: Donghao

last: Gao

state: Hubei

address: College of Life Sciences, Wuhan University, 299 Bayi Road, Wuchang District, Wuhan, Hubei Province, China.

institute: WuHan University

description: Library name: Sample3

data_processing:
Raw sequencing data were first quality-controlled using FASTX_TOOLKIT (Version 0.0.14), evaluated with FASTAQ (0.19.5), and ribosomal RNA contamination assessed via Rfam database (Version14.8). Sequence alignment was performed using STAR (Version 2.7.1a). Gene annotation utilized NR database (Version 2022.10), Pfam database (Version 35.0), KEGG database (Version 2022.10), eggNOG database (Version 2020.06), Swiss-prot database (Version 2022.10), and GO database (Version 2022.0915). Expression analysis was conducted using Salmon (Version 1.3.0) and differential expression statistics with DEseq2 (Version 1.24.0). Gene enrichment analysis was performed using KEGG, GO, and COG databases.
Assembly: Pseudomonas donghuensis HYS  AJJP00000000.1;  Caenorhabditis elegans GCA_000002985.3.
Supplementary files format and content: csv files include TPM values for each sample

source_name: Complete Caenorhabditis elegans

growth_protocol: Escherichia coli OP50 cultured in LB medium at 37℃ . HYS and the fur-deletion strain were cultured in LB medium at 30℃. Wild-type N2 Bristol strain Caenorhabditis elegans were fed with E. coli OP50 on NGM plates at 22 ℃.

extract_protocol:
For the Caenorhabditis elegans  samples, collected nematodes were ground rapidly from liquid nitrogen and processed using an RNA extraction kit (Nanjing, Vazyme, RC112). Ground nematodes were resuspended in lysis buffer, added to a genomic DNA removal column, centrifuged at 12,000 rpm for 1 minute, filtrate collected, and RNA adsorbed, washed twice, and eluted using RNase-free water. For bacteria samples, mRNA was extracted using the Trizol method. Following the lysis of bacterial cells, guanidine isothiocyanate in Trizol was employed to denature proteins and inhibit RNase activity. RNA was then separated from the aqueous phase through chloroform partitioning, and total RNA (including mRNA) was precipitated with isopropanol. Subsequently, impurities were removed by ethanol washing, and the final product was dissolved in nuclease-free water.
For the Caenorhabditis elegans samples, including the Dual-RNA seq samples, the enriched mRNA consisted of complete RNA sequences, which were randomly fragmented by adding fragmentation buffer to generate small fragments of approximately 300 bp. Under the action of reverse transcriptase, random primers were utilized to synthesize a single strand of cDNA using mRNA as the template, followed by the synthesis of the second strand to form a stable double-stranded structure. The double-stranded cDNA structure featured sticky ends, which were converted to blunt ends by adding End Repair Mix. Subsequently, an A base was added to the 3' end, and the products were purified and size-selected after adapter ligation, followed by PCR amplification of the selected products to obtain the final library. For the bacterial samples, the TruSeq™ Stranded Total RNA Library Prep Kit was employed to construct the library. In the synthesis of the second strand of cDNA, dUTP was used in place of dTTP in the dNTP reagent, resulting in the incorporation of A/U/C/G bases in the second strand of cDNA. Prior to PCR amplification, UNG enzyme was utilized to digest the second strand of cDNA, ensuring that the library contained only the first strand of cDNA.

treatment_protocol: 1000 adult nematodes were transferred to NGM plates smeared with pathogenic bacteria(HYS，and fur mutant)and OP50, incubated at 22 ℃ for 24 hours

value: Complete Caenorhabditis elegans

value: Caenorhabditis elegans cell

value: WT

value: fed on fur mutant


title: Sample_68

description: Library name: Sample_68

value: nCPa

value: Male

value: EHC


title: RNA from IRF3 KD fibroblasts replicate 2

description: Library name: Sample 14


title: Sample_81

description: Library name: Sample_81

value: PVN

value: Female


title: Sample_79

description: Library name: Sample_79

value: POAH


title: M50 control 14 days

value: hippocampus

value: adult

value: male

value: Swiss-Webster


title: RNA from IRF3 KD fibroblasts replicate 1

description: Library name: Sample 13

value: Organotypic culture

value: Human foreskin fibroblast


title: RNA from NTC epthelium, replicate 3

description: Library name: Sample 24

value: Human foreskin keratinocyte immortalized with HPV16 episomal genomes

value: Wild type

value: Grown in organotypic culture 14 days in the presence of NTC fibroblasts


title: Caenorhabditis elegans, fed on HYS, 24h, dual-RNA seq with colonized HYS

description:
Library name: Sample1
The sample represents the interaction between HYS and C. elegans, from which total RNA was extracted for high-throughput sequencing, involving both C. elegans and the HYS colonizing its intestinal tract, with each respective genome matched. Consequently, the raw data includes sequencing results for C. elegans fed with HYS as well as sequencing results for the HYS samples colonizing the nematode's gut.

value: Complete Caenorhabditis elegans

value: Caenorhabditis elegans cell

value: WT

value: fed on HYS


title: M3 control 14 days

value: vehicle

value: 14 days


title: Sample_93

description: Library name: Sample_93

value: PVN

value: Male

value: EHC


title: M25 control 14 days

value: hippocampus

value: adult


title: RNA from NTC fibroblasts, replicate 3

description: Library name: Sample 9

value: NTC shRNA

value: Grown in organotypic culture 14 days


title: replicate 5 oxycodone therapeutic exposed (0-24hpf) total RNA at 48 hpf

city: Bozeman

first: Christa

last: Merzdorf

state: Montana

address: 109 Lewis Hall

department: MCB

institute: Montana State University

description: Library name: R7OT

data_processing:
Sequenced by NovaGene via Novaseq X Plus Platform paired end reads
Raw reads are available as the fq.gz files
Trimmed via trimmomatic, and ran through rCorrector, then mapped to GRCz11 (ensemble) constructed reference library via Salmon. The aggregated count matrixes for each condition are availible as the txt files
Assembly: These are raw reads from Novaseq X plus seqeuncing and count matrixes as txt files
Supplementary files format and content: txt files of aggregated count matrixes, see above
Supplementary files format and content: the counts derived from Salmon

organism: Danio rerio

source_name: Total embryo (50 embryo homogenate)

growth_protocol: zebrafish embryos were maintained in 0.3x Danieau solution at 28.5C

extract_protocol:
Trizol Chloroform extraction of total RNA followed by Dnase I treatment, and Monarch RNA cleanup kit (T2030L). All samples were confirmed to have A260/A280 ratios between 1.8 and 2.0 on Nanodrop spectrophotometer. All samples were confirmed to have RNA integrity numbers of above 7 via Agilent Bioanalyzer 2100
Zymo-Seq RiboFree Total RNA library Kit (R30003)

treatment_protocol: one of the following conditions: fentanyl effluent (FE; 0.629 pg/mL), fentanyl therapeutic (FT; 3.14 ng/mL), oxycodone effluent (OE; 10.6 pg/mL), oxycodone therapeutic (OT; 35.14 ng/mL), Control. Opioid exposed embryos were exposed from 0 to 24 hpf. At 24 hpf embryos were washed to remove opioids and allowed to develop normally until 48 hpf.

value: Total embryo (50 embryo homogenate)

value: 35.14ng/mL oxycodone

tag: batch


title: HEK293T, circRNA, oe-hnRNPK, rep 2

value: human embryonic kidney 293 cells

value: hnRNPK over-expression


title: Sample_117

description: Library name: Sample_117

source_name: PVN

value: Female


title: Sample_69

description: Library name: Sample_69


title: Sample_41

description: Library name: Sample_41

value: nCPa

value: C


title: RNA from NTC fibroblasts, replicate 1

description: Library name: Sample 7

value: Organotypic culture

value: Human foreskin fibroblast


title: RNA from NTC fibroblasts, replicate 2

description: Library name: Sample 8


title: sgZbtb20-2_T1(2w)_ATO_Thy_FB_R2

city: Ithaca

first: Andrew

address: 445 Biotechnology Bldg

institute: Cornell University

description:
Library name: 5
Thymocytes from thymic organoids

data_processing:
Fastq files were generated with cellranger mkfastq (10x Genomics) by NovoSeq X. Raw count tables were generated with cellranger count v7.2.0 (10x Genomics) [cellranger count --id = ID --transcriptome = /path/to/ refdata-gex-mm10-2020-A/--fastqs = /path/to/directories --sample = list --feature-ref= /path/to/control-feature-ref-file-all-conditions/ --localcores=16 -check-library-compatibility= false]. The feature reference files used an untethered approach [pattern =(BC) sequence = GCTCACCTATTAG/capture sequence]. To create aggregate files, cell ranger aggr was utilized [cell ranger aggr --id = ID –csv=/path/to/molecule.h5 files/]. The aggregated file of control and Zbtb20 loss conditions were utilized for downstream analysis (is provided).
Assembly: mouse mm10 assembly
Supplementary files format and content: Aggregate Cell Ranger software output files (barcodes.tsv, features.tsv, matrix.mtx) are provided,Feature_reference for sgZbtb20 condition is provided as .csv file

source_name: Aritificial Thymic Organoids

extract_protocol:
To generate scRNAseq profiles of week 2 thymocytes either CD45+ Live+ Lin- CD4- CD8- CD44hi/loCD25hi/lo was used respectively. To generate scRNAseq profiles of week 4 thymocytes (Figure 7)  CD45+ Live+ Lin- CD3+TCRb+ CD4+/CD8+ population was used.
Single cell suspensions were run on a Chromium X instrument and libraries prepared following the Chromium Next GEM Single Cell 3' RNA-Seq Assay v3.1 Dual Index with Feature Barcode technology for CRISPR Screening user guide (10x Genomics, CG000316, RevD)128. We targeted 6,000 cells and used 12 cycles of cDNA amplification. Sample quality was confirmed using a Qubit (RNA HS kit; Thermo Fisher) to determine concentration and a Fragment Analyzer (Agilent) to determine RNA integrity. Every sample had an associated feature barcode except the control libraries.

value: Aritificial Thymic Organoids

value: 2 week

value: Thymocytes (CD45+ Live+ Lin- CD4- and CD8- )

value: Retroviral transduction


title: replicate 4 oxycodone therapeutic exposed (0-24hpf) total RNA at 48 hpf

description: Library name: R5OT

value: WT


title: Sample_23

description: Library name: Sample_23


title: replicate 3 oxycodone therapeutic exposed (0-24hpf) total RNA at 48 hpf

description: Library name: R4OT


title: replicate 2 oxycodone therapeutic exposed (0-24hpf) total RNA at 48 hpf

description: Library name: R2OT


title: M19 control 14 days

value: hippocampus

value: adult

value: male

value: Swiss-Webster

value: vehicle

value: 14 days


title: Caenorhabditis elegans, fed on OP50(control), 24h

description: Library name: Sample2

value: Complete Caenorhabditis elegans

value: Caenorhabditis elegans cell

value: fed on OP50


title: M48 control 14 days


title: Sample_17

description: Library name: Sample_17

value: nCPa

value: Male

value: C


title: Sample_22

description: Library name: Sample_22

value: POAH

value: Female


title: M49 corticosterone 14 days

value: corticosterone


title: replicate 4 oxycodone effluent exposed (0-24hpf) total RNA at 48hpf

description: Library name: R4OE

value: Total embryo (50 embryo homogenate)

value: 10.6pg/mL oxycodone


title: LNWT_TRT_3

source_name: LNCaP  with radiation treatment, rep 3

value: LNCaP Prostate cancer cell line

value: LNCaP WT

value: Radiation (2Gy)


title: replicate 5 oxycodone effluent exposed (0-24hpf) total RNA at 48hpf

description: Library name: R6OE

value: WT


title: replicate 2 oxycodone effluent exposed (0-24hpf) total RNA at 48hpf

description: Library name: R2OE


title: M51 corticosterone 14 days

value: hippocampus

value: adult

value: male

value: Swiss-Webster


title: M47 corticosterone 14 days

value: 14 days


title: LNWT_TRT_1

source_name: LNCaP  with radiation treatment, rep 1


title: M4 corticosterone 14 days


title: LNWT_TRTBER_1

source_name: LNCaP with Berberine and radiation traetment, rep 1

value: Berberine+Radiation


title: Sample_13

description: Library name: Sample_13

value: Male


title: Sample_42

description: Library name: Sample_42

value: PVN

value: C


title: Sample_16

description: Library name: Sample_16

value: POAH


title: LNWT_CON_3

source_name: LNCaP treated with DMSO, rep 3

value: Vehicle


title: M1 control 14 days

value: vehicle


title: M2 corticosterone 14 days

value: corticosterone


title: replicate 1 oxycodone effluent exposed (0-24hpf) total RNA at 48hpf

description: Library name: R1OE

value: Total embryo (50 embryo homogenate)

value: 10.6pg/mL oxycodone


title: Sample_24

description: Library name: Sample_24

value: Female


title: LNWT_CON_2

source_name: LNCaP treated with DMSO, rep 2

value: LNCaP Prostate cancer cell line

value: LNCaP WT


title: LNWT_TRTBER_3

source_name: LNCaP with Berberine and radiation traetment, rep 3


title: replicate 3 oxycodone effluent exposed (0-24hpf) total RNA at 48hpf

description: Library name: R3OE

value: WT


title: M23 control 14 days

source_name: hippocampus

value: hippocampus

value: adult

value: male


title: M6 corticosterone 14 days

value: Swiss-Webster

value: 14 days