title: mouse circRNA Brain Ftsj1_DF 1647 batch 1

description:
Library name: 221000001049-DS5_22Oct1049-DL005_S5_L001_R1_001
circRNA-seq of whole Brain tissue from Ftsj1_DF mice. R1 = forward, R2 = reverse, L001-L004 = lane 1-4. Two batches because of low read count in batch 1. 1653, 1654, 1655, 1656 are brothers, 1646 and 1647 as well. All mice are male


title: Ranbp2 Knockout ATAC-seq Replicate 1

status: Public on Mar 17 2026

type: SRA

city: Singapore

first: Roger

last: Foo

address: 14 Medical Drive, MD6

country: Singapore

institute: National University of Singapore

description: Library name: RKO2

library_source: genomic

data_processing:
Paired-end sequencing reads were processed and aligned using DNA-mapping tool to the mus musculus (mm10) reference genome from SnakePipes 2.7.3 (https://github.com/maxplanck-ie/snakepipes) as per default parameters. Accordingly, as part of the Snakepipes wrapper, Cutadapt was used for the trimming of adaptors and Bowtie2 was used as the aligner. The aligned bam files were filtered based on read mapping quality and duplicated reads. Normalized Bigwig files were produced using deepTools bamCoverage 1X normalized by sequencing depth for visualization.  Using default snakemake parameters within the snakePipes ATAC-seq tool, the filtered bam file is then processed to retain a maxFragmentSize of 150, with a windowSize of 20, and MACS2 was used for peak calling at qval: 0.001 and fdr: 0.05. Diffbind version 2.2.12 were used for Differential open chromatin analysis between Ranbp2 KO versus WT, using the filtered bam file as the input. Differential accessibility peaks were identified using DESeq2 function in the Diffbind package normalized by Reads in Peak (RiP) and Sequencing Depth.
Assembly: mm10
Supplementary files format and content: bigwig and narrowPeak files

molecule: genomic DNA

organism: Mus musculus

growth_protocol: 10T1/2 cells (CCL-226) were purchased from ATCC (VA, USA) and maintained in DMEM (High glucose, sodium pyruvate and L-glutamine, SH3024302, Fisher Scientific, MA, USA) supplemented with 10% FBS and 1% penicillin-streptomycin. Cells were regularly tested for mycoplasma and maintained in Plasmocin prophylactic (ant-mpp, InvivoGen, CA, USA). Cells were split to Plasmocin-free medium before any experimental procedure.

extract_protocol:
The ATAC-seq was performed as per the previously published Omni-ATAC protocol. Briefly, 50,000 10T ½ cells were pelleted at 500 g for 5 minutes and subsequently resuspended in 100 µl ATAC-resuspension buffer containing 0.5% NP40, 0.5 % Tween-20 and 0.01% Digitonin. The cells were incubated on ice for 10 minutes and then 1 ml of cold ATAC-RSB containing 0.1% Tween 20 was used to wash the cells. The nuclei were pelleted at 500 g for 5 minutes, the supernatant was carefully removed, and the nuclei were resuspended in 50 µl transposition mixture containing 25 µl of 2x TD buffer, 16.5 µl of PBS, 5 µl nuclease free water, 0.5 µl of 1% digitonin, 0.5 µl of 10% Tween-20 and 2.5 µl of transposase (Illumina Tagment DNA enzyme 1, Catalogue number 20034198). Transposition was performed by incubating the mixture at 37°C for 30 minutes in a thermoshaker, after 30 minutes, the DNA was extracted using the NEB Monarch® PCR & DNA cleanup kit (Catalogue number T1030L).
Libraries were generated by performing PCR using the Illumina/Nextera primers after which Ampure XP beads were used for library cleanup, and the DNA libraries were subsequently sequenced on the Illumina NextSeq platform with 75bp Paired-End sequencing.

tag: cell line

tag: cell type

value: Mouse Embryonic Fibroblast

tag: genotype

value: Ranbp2 Knockout


title: Ranbp2 Knockout ATAC-seq Replicate 2

description: Library name: RKO3


title: Microglia cells, APOE4_3

city: Bethesda

first: Priyanka

middle: S.

last: Narayan

state: Maryland

address: 9000 Rockville Pike

department: National Institute of Diabetes and Digestive and Kidney Diseases

country: USA

institute: Natonal Institutes of Health

description:
Library name: Sample 6
Column name in featurecounts_microglia.xlsx : APOE4_3

library_source: transcriptomic

data_processing:
The raw fastq data were aligned to human hg19 assembly using STAR 2.4.0 RNA-seq aligner. Gene raw counts were generated from the mapped data using featureCounts tool.
Assembly: hg19
Supplementary files format and content: Excel file includes raw counts for each sample.

molecule: polyA RNA

organism: Homo sapiens

source_name: Microglia

growth_protocol: Prior to differentiation, all iPSC derived cells were maintained in mTeSR Plus media (StemCell) and confirmed to be karyotypically normal. iPSCs were differentiated into microglia using protocols previously described ( McQuade, et al., 2018).

extract_protocol:
1 million cells were harvested per replicate across at least two independent derivations.
Illumina library preparation was performed using the Illumina RNA Strand PolyA library kit to prepare paired end dual index libraries.

value: Microglia


title: Ranbp2 Wildtype ATAC-seq Replicate 2

description: Library name: WT3

value: Wildtype


title: Col-0, control, systemic infection, sample 2

city: Wien

first: Gautier

last: Langin

address: Muthgasse 18

country: Austria

institute: BOKU

description: Library name: Col0_syst_M2

data_processing:
FastQC
STAR
htseq-count
Assembly: TAIR10
Supplementary files format and content: txt files with raw counts

molecule: total RNA

organism: Arabidopsis thaliana

source_name: Adult leaves

extract_protocol:
NucleoZOL
RevertAid Reverse Transcriptase

tag: tissue

value: Adult leaves

tag: treatment

value: Mock

tag: batch

value: SAR


title: Peritoneal Macrophages, replicate 2, RNAseq

city: chongqing

first: zhou

last: sha

address: 55 University City South Road, Shapingba District, Chongqing, China

country: China

institute: chongqing university

description: Library name: Sample 5

data_processing:
The raw reads were further processed with a bioinformatic pipelinetool, BMKCloud(www.biocloud.net) online platform.
Assembly: GRCm38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: macrophage

extract_protocol:
RNA was extracted from macrophages using Trizol extraction and Purelink RNA kit (ThermoFisher Scientific).
A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using Hieff NGS Ultima Dual-mode mRNA Library Prep Kit for Illumina (Yeasen Biotechnology (Shanghai) Co., Ltd.) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads.First strand cDNA was synthesized and second strand cDNA synthesis was subsequently performed. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. The library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 μl USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37°C for 15 min followed by 5 min at 95°C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

value: macrophage


title: Col-0, Pma, local infection, sample 2

description: Library name: Col0_lok_P2

value: Pma

value: local


title: Microglia cells, APOE4_1

description:
Library name: Sample 4
Column name in featurecounts_microglia.xlsx : APOE4_1


title: Ranbp2 Wildtype ATAC-seq Replicate 1

description: Library name: WT1


title: Microglia cells, APOE4_2

description:
Library name: Sample 5
Column name in featurecounts_microglia.xlsx : APOE4_2


title: Col-0, Pma, local infection, sample 1

description: Library name: Col0_lok_P1


title: Microglia cells, APOE3_3

description:
Library name: Sample 3
Column name in featurecounts_microglia.xlsx : APOE3_3


title: Peritoneal Macrophages, replicate 1, RNAseq

description: Library name: Sample 4


title: Peritoneal Macrophages, replicate 3, RNAseq

description: Library name: Sample 6


title: Ranbp2 H3K27me3 KO Replicate 3

description: Library name: Ranbp2 KO3

data_processing:
Single-end sequencing reads were aligned to mus musculus (mm10) genome using BWA mem version 0.7.5. Duplicated reads were filtered out using Samtools2 1.19 markdup function and sorted into aligned BAM files. SICER2 was used as the broad peak caller for H3K27me3 peak calling to identify significant peaks for Ranbp2 WT and KO, respectively, using the following setting: sicer -t k27me3.bed -c input.bed -s mm10 -w 200 -rt 1 -f 150 -egf 0.74 -fdr 0.01 -g 600 -e 1000. For differential peak calling, the union of peak calls for WT and KO samples was used to apply the sicer_df function at FDR<0.01.
Assembly: mm10
Supplementary files format and content: bigwig and peak bed files

extract_protocol:
H3K27me3 ChIP experiments were performed on 10T ½ cells as described previously. Briefly, the cells were cross-linked with 1% formaldehyde at room temperature for 10 minutes and the crosslinking was quenched with glycine (0.125 mol/L final concentration). Ice cold 1X PBS was used to wash the cells twice and the cells were subsequently pelleted and lysed in ChIP lysis buffer (10 mmol/L Tris-HCl, pH 8.0, 0.25% Triton X-100, 10 mmol/L EDTA, 0.1 mol/L NaCl). After lysis, the nuclei were pelleted by centrifugation and resuspended in a sonication buffer containing 1% SDS, and the chromatin was fragmented to an average size of 150-500 bp using Bioruptor Plus, from Diagenode at 10s on, 20 s off cycles. Chromatin was immunoprecipitated against H3K27me3 (Cell Signaling Technologies, #9733S) overnight, and the antibody-chromatin complexes were pulled down with Protein G Dynabeads (Invitrogen, catalogue No. 10003D). The immunoprecipitated complex was washed serially with low salt, high salt, and lithium chloride wash buffers, and crosslink reversal was performed by incubating the complex in elution buffer (1% SDS, 10 mmol/L EDTA, 50 mmol/L Tris-HCl, pH 8) overnight at 65 deg.
The immunoprecipitated DNA was extracted, and library preparation was performed with the New England Biolabs Ultra II Kit according to the manufacturer’s specifications.  Following size selection with AMPure XP beads to collect 200-600bp fragments, the ChIP DNA libraries were sequenced on the Illumina NextSeq platform with 75bp single-end sequencing.

tag: chip antibody

value: H3K27me3 (#9733S, Cell Signaling Technology)


title: Col-0, control, systemic infection, sample 1

description: Library name: Col0_syst_M1


title: Peripheral Blood, replicate 3, RNAseq

description: Library name: Sample 3


title: Col-0, control, local infection, sample 3

description: Library name: Col0_lok_M3


title: Microglia cells, APOE3_2

description:
Library name: Sample 2
Column name in featurecounts_microglia.xlsx : APOE3_2


title: Col-0, control, local infection, sample 2

description: Library name: Col0_lok_M2


title: Microglia cells, APOE3_1

description:
Library name: Sample 1
Column name in featurecounts_microglia.xlsx : APOE3_1


title: Ranbp2 H3K27me3 KO Replicate 2

description: Library name: Ranbp2 KO2


title: Col-0, control, local infection, sample 1

description: Library name: Col0_lok_M1


title: Peripheral Blood, replicate 1, RNAseq

description: Library name: Sample 1


title: Human primary NK cells, Dexamethasone treated, rep 2

city: Seoul

first: Mihue

last: Jang

address: 5, Hwarang-ro 14-gil, Seongbuk-gu

department: Medicinal Materials Research Center, Biomedical Research Division

country: South Korea

institute: Korea Institute of Science and Technology

description: Library name: Dex 2

data_processing:
ATAC-seq reads were preprocessed with Trommomatic v0.39 and aligned to GRCh38 reference genome with BWA v0.7.18.
Alignment sorting and indexing were done by Samtools v1.21.
Genomewide read depth signals were computed by bamCoverage v3.5.6.
MACS2 v2.2.9.1 was used to filter duplicate reads and call ATAC peaks.
Assembly: GRCh38
Supplementary files format and content: bigWig files for ATAC read depths
Supplementary files format and content: BED files for ATAC-seq peak

source_name: Human promary NK cells

extract_protocol:
The construction of library was performed using ATAC-Seq Library Prep Kit for Illumina (Active Motif, USA)
The construction of library was performed using ATAC-Seq Library Prep Kit for Illumina (Active Motif, USA)

value: Human primary NK cells

value: NK cell

value: WT

value: Dexamethasone


title: Ranbp2 H3K27me3 WT Replicate 3

description: Library name: Ranbp2 WT3


title: Spleen, CD23+ B cell, F1, 12h stimulated, IgG

city: Philadelphia

first: Montserrat

last: Anguera

state: PA

address: 3800 Spruce Street, Rosenthal Room 390EB

department: Biomedical Sciences

institute: University of Pennsylvania School of Veterinary Medicine

data_processing:
Adaptors were removed using Trimmomatic v0.32
N-masked mm10 genome was created using SNPsplit v0.5.0 (C57Bl/6j N-masked Castaneus) and used to generate Bowtie2 indexes
Reads were aligned to N-masked genome using Bowtie2 v2.3.4.1 with parameters [-q --local --very-sensitive-local --soft-clipped-unmapped-tlen --dovetail --no-mixed --no-discordant --phred33 -I 10 -X 1000]
Duplicates were removed using Picard MarkDuplicates v1.141
Reads mapped to regions from the ENCODE blacklist were removed
Allele-specific BAM files were then generated using SNPsplit v0.5.0 with option [--paired]
CPM normalized bigwig files were generated using deepTools v3.5.1 bamCoverage with options [--effectiveGenomeSize 2652783500 --normalizeUsing CPM --ignoreForNormalization chrX]
mean CPM normalized bigwig files were generated using the WiggleTools v1.0 mean function for each group of biological replicates followed by bedGraphToBigWig v4.0
Assembly: mm10
Supplementary files format and content: CPM normalized bigwig files for each sample
Supplementary files format and content: mean CPM normalized bigwig files for each group of biological replicates
Library strategy: CUT&RUN

source_name: Spleen

growth_protocol: Splenic CD23+ B cells were isolated using biotin anti-mouse CD23 Antibody (Cat #101604, Biolegend) then subjected to CUT&RUN, or stimulated with 1uM CpG for 12 or 24 hours followed by CUT&RUN

extract_protocol:
Cells were collected at respective timepoint and immobilized on concanavalin A-coated beads in Wash Buffer (20mM HEPES, 150mM NaCl, 0.5mM Spermidine, 1x Protease Inhibitor Cocktail). 3ug (H3K27me3, H3K27ac, H3K9me3, IgG), 1.5ug  (H2AK119Ub), or 3:50 dilution (Suz12, Ring1B) of antibody was incubated with immobilized cells at 4°C for 5 hours with rotation in Antibody Buffer (20mM HEPES, 150mM NaCl, 0.5mM Spermidine, 1x PIC, 0.05% Digitonin, 2mM EDTA). Cells were washed then incubated with pA-MNase fusion protein at 4°C for 1 hour with rotation in Digitonin Wash Buffer (20mM HEPES, 150mM NaCl, 0.5mM Spermidine, 1x PIC, 0.05% Digitonin). Digestion was performed in Digitonin Wash Buffer at 0°C for 30 minutes by adding CaCl2 to 2mM. The digestion was stopped by adding one volume of 2X STOP Buffer (340mM NaCl, 20mM EDTA, 4mM EGTA, 0.02% Digitonin, 50ug/mL RNase A, 50ug/mL Linear Acrylamide, 2pg/mL Yeast Spike-In DNA). Chromatin was released from cells by shaking beads at 300rpm at 37°C for 10 minutes. The supernatant was incubated at 70°C for 10 min with SDS to 0.1% and 50ug of Proteinase K. DNA was then isolated with phenol:chloroform:isoamyl alcohol followed by precipitation with ammonium acetate.
Libraries were constructed with 1.5ng (H3K27me3, H3K27ac, H2AK119Ub, IgG) or 5ng (H3K9me3) of CUT&RUN DNA using NEBNext Ultra II DNA Library Prep Kit for Illumina following the manufacturor's protocol

value: Spleen

tag: Sex

value: Female

value: CD23+ B cell

value: F1 mus x cast

tag: antibody

value: IgG

value: stimulated with CpG for 12 hours


title: Spleen, CD23+ B cell, F1, 0h naïve, IgG

value: unstimulated


title: Ranbp2 H3K27me3 WT Replicate 2

description: Library name: Ranbp2 WT2

value: Mouse Embryonic Fibroblast

value: Wildtype


title: shA3B 01 CIN 612 DRIP 2

city: Chicago

first: Conor

last: Templeton

address: 300 E Superior Street

institute: Northwestern University

description: Library name: shA3B 01 CIN 612 DRIP 2

data_processing:
Initial data analysis and processing were performed by Admera Biosciences. Briefly, FastQC (v0.11.8) was used to check the quality of raw and trimmed reads. Trimmomatic (v0.38) was used to cut adapters and trim low-quality bases with a default setting. BWA (v0.7.10-r789) was used to map the trimmed reads to the reference genome* using the Burrows-Wheeler Alignment algorithm (BWA-MEM). Mapped reads that have low-quality MAPQ score (MAPQ < 10), not-properly-paired, or duplicated (assessed with Picard tools (v 2.20.4)) were removed. BAM was used to generate BW format (normalized by RPKM) for visualization. MACS (v2.2.4) was chosen to call peaks.
Agreement between biological replicates was assessed using multiBAMSummary (Galaxy Version 3.5.4+galaxy0). Principal component analyses were then plotted using plotPCA (Galaxy Version 3.5.4+galaxy0), and Pearson coefficients were plotted as a heatmap using plotCorrelation (Galaxy Version 3.5.4+galaxy0). From the BAM files, BAM Compare (Galaxy Version 3.5.4+galaxy0) was used to normalize log2 IP to input ratios for both biological replicates from Scrm and shA3B CIN 612 cells.  ComputeMatrix was used to prepare files for visualization via plotProfile and plotHeatmap. CHIPseeker (Galaxy Version 1.28.3+galaxy0) was used on the BED files generated by Admera Biosciences. MACS (v2.2.4) was used to call peaks. HOMER (Galaxy Version 4.11+galaxy0) was used to annotate the genomic location of peaks (intron, exon, etc.) and the corresponding gene name.
Assembly: Hg38
Supplementary files format and content: The FastQ files remain in GZ format.
Supplementary files format and content: The BigWig files are in bw format. Resultant peak calling datasets are in Excel Spreadsheet.

source_name: Cervix

growth_protocol: Scrm and shA3B CIN 612 cells were maintained in E-media containing 10% FBS DMEM

extract_protocol:
1 × 107 cells were harvested and collected in Southern lysis buffer before being treated with RNase A (5 ng/mL) and Proteinase K (7.5 ng/mL) at 37 °C overnight. DNA was purified from these samples using phenol-chloroform extractions, and 25 to 50 mg of DNA was used for each sample. DNA was sheared using a Bioruptor (Diagenode) on high power, 30 s on/90 s off cycles for 20 min. Input DNA was removed before loading the samples into preblocked magnetic beads in IP buffer containing 2 ug of the S9.6 antibody. Immunoprecipitations were allowed to incubate overnight at 4 °C while rotating. The next day, samples were washed 8 times with RIPA buffer for 5 min while rotating. One wash in TE buffer was performed before samples were eluted for 10 min at 65 °C in 10% sodium dodecyl sulfate (SDS), 10 mM Tris pH 7.4, 50 mM ethylenediaminetetraacetic acid (EDTA). DNA was purified from these elutions using a PCR purification kit (Qiagen) and stored at −20 °C.
Samples were stored at -80° C until being shipped to Admera Biosciences (NJ), who performed the sequencing experiments. Briefly, the library was prepared using a KAPA HyperPrep Kit (Kapa Biosystems) following the manufacturer’s recommendation. Input DNA was end-repaired and 3’-dA tailed. Adapter was then ligated to the DNA, and the ligated product was PCR amplified and cleaned up using the SPRIselect Reagent (Beckman Coulter). Quality control was then performed for the final library, followed by sequencing.

value: Cervix

value: CIN 612

value: Keratinocytes

value: HPV 31 positive


title: Ranbp2 H3K27me3 WT Replicate 1

description: Library name: Ranbp2 WT1

value: H3K27me3 (#9733S, Cell Signaling Technology)


title: Human primary NK cells, rep 2

description: Library name: WT 2

value: Human primary NK cells

value: NK cell

value: control


title: Human primary NK cells, Dexamethasone treated, rep 1

description: Library name: Dex 1

value: WT

value: Dexamethasone


title: Spleen, CD23+ B cell, F1, 24h stimulated, H3K27ac, biol rep 2

value: Spleen

value: Female

value: CD23+ B cell

value: stimulated with CpG for 24 hours


title: shA3B 01 CIN 612 Input 1

description: Library name: shA3B 01 CIN 612 Input 1


title: H3K27me3 Input

description: Library name: Input


title: S8_DOC_LAV

city: Basel

first: DBM Bioinformatics

last: Core Facility

state: BS

address: Hebelstrasse 20

department: Departement of Biomedicine

country: Switzerland

institute: University of Basel

description: Library name: 31959

data_processing:
Data analysis was performed by the Bioinformatics Core Facility, Department of Biomedicine, University of Basel. Read quality was assessed with the FastQC tool (version 0.11.9). Reads were mapped to the mouse genome mm39 with STAR (version 2.7.10a) with default parameters, except filtering out multimapping reads with more than 10 alignment locations (outFilterMultimapNmax=10) and filtering reads without evidence in the spliced junction table (outFilterType=“BySJout”).
The featureCounts function from the Rsubread package (version 2.0.6) was used to count the number of reads (5' ends) overlapping with the exons of each gene (Ensembl release 110 genes) assuming an exon union model
All subsequent analyses were performed using the R software (version 4.3.1) and Bioconductor 3.18 packages
Assembly: mm39
Supplementary files format and content: gene_counts.tsv.gz: Tab-separated file with read counts on each Ensembl gene model (version 110) for each sample

source_name: Germinal center LCMV-specific KL25  B cells

extract_protocol:
After two weeks, germinal center B cells were isolated from recipient mice by FACS sorting of live, CD45.1+ GFP+B220+ germinal center KL25 B cells in TAKARA lysis buffer, following the vendor's instructions, and frozen at -80°C until sequencing.
RNA-seq library preparation was performed at the Genomics Facility Basel using a SMART-Seq stranded kit (Takara), and controlled on an Agilent Fragment Analyzer instrument. Sequencing was performed on four lanes of an Illumina NextSeq 500 instrument to produce paired-end 38nt reads.

treatment_protocol: CD45.2 Mice were infected with either DOCILE or DOCILE-N119S chronic LCMV infection, N119S as the low-affinity variant of DOCILE. After one week, the animals received small numbers of B cells from GFP+CD45.1 KL25 mice, specific for the glycoprotein of the LCMV virus.

value: Infection with DOCILE-N119S LCMV


title: Scrm CIN 612 DRIP 2

description: Library name: Scrm CIN 612 DRIP 2


title: Spleen, CD23+ B cell, F1, 24h stimulated, H3K27ac, biol rep 1

value: F1 mus x cast


title: RNA-seq of 8505C cells: siPOLR1F3

city: Hangzhou

first: Minghua

last: Ge

address: Shangtang

institute: Zhejiang provincial people's hospital

description: Library name: B_3,si POLR1F3,8505C,24h

data_processing:
Sequence quality control was performed using fastp software(adaptor contamination, low quality bases and undetermined bases with default parameter)
Reads were mapped to the reference genome of Homo sapiens GRCh38 using HISAT2 and then assembled and calculated using StringTie
StringTie was used to perform expression level for mRNAs by calculating FPKM (FPKM = [total_exon_fragments / mapped_reads(millions) × exon_length(kB)]).
The differentially expressed genes were screened with fold change > 2 or < 0.5 and with parametric F-test comparing nested linear models (P < 0.05).
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: thyroid cancer

growth_protocol: 8505C cells were cultivated in RPMI-1640 supplied with 10% fetal bovine serum (FBS) in 37 °C humidified atmosphere containing 5% CO2.

extract_protocol:
Total RNA was isolated and purified using TRIzol reagent (Invitrogen) following the manufacturer's procedure.  1μg of total RNA was used for the construcion of sequencing library.
Poly (A) RNA was purified and fragmented into small pieces which be synthesized into cDNA using Invitrogen SuperScript™ II Reverse Transcriptase (Thermo Fisher). Then, the ligated products were amplified with PCR. Finally, the 2×150 bp paired-end sequencing was carried out on illumina Novaseq™ 6000 (LC-Bio Technology).

value: thyroid cancer

value: anaplastic thyroid cancer cells

value: POLR1F silenced


title: Scrm CIN 612 DRIP 1

description: Library name: Scrm CIN 612 DRIP 1

value: Cervix

value: CIN 612

value: Keratinocytes


title: Ranbp2 H3K27me3 KO Replicate 1

description: Library name: Ranbp2 KO1

value: Mouse Embryonic Fibroblast

value: Ranbp2 Knockout

value: H3K27me3 (#9733S, Cell Signaling Technology)


title: S7_DOC_LAV

description: Library name: 31958

value: Germinal center LCMV-specific KL25  B cells


title: Spleen, CD23+ B cell, F1, 12h stimulated, H3K27ac, biol rep 2

value: stimulated with CpG for 12 hours


title: Peripheral Blood, replicate 2, RNAseq

description: Library name: Sample 2

value: macrophage


title: Scrm CIN 612 Input 1

description: Library name: Scrm CIN 612 Input 1

value: HPV 31 positive


title: Human primary NK cells, rep 1

description: Library name: WT 1

value: Human primary NK cells

value: NK cell

value: WT

value: control


title: S6_DOC_LAV

description: Library name: 31957

value: Infection with DOCILE-N119S LCMV


title: RNA-seq of 8505C cells: siPOLR1F2

description: Library name: B_2,si POLR1F2,8505C,24h

value: thyroid cancer

value: anaplastic thyroid cancer cells


title: DEAF1 (ChIP-Seq)

city: NEW HAVEN

first: Museog

last: Choe

state: CT

address: 10 Amistad Street, Ste 214J

department: Genetics

institute: Yale University

description:
Library name: ChIP-seq sample2
iDeal ChIP-seq kit
ChIP_annotated_peaks.csv

data_processing:
For RNA-seq, Sequencing reads were first quality-trimmed using fastp (v0.20.1) with adapter detection enabled and a minimum length cutoff of 25 bp. The quality of the trimmed reads was evaluated with FastQC (v0.11.9). Trimmed paired-end reads were aligned to the human reference genome (GRCh38) using STAR (v2.7.9a), with the primary assembly FASTA file and GTF annotations obtained from Ensembl (release 112). The alignment included both transcriptome and gene count quantification modes. Parameters allowed for a maximum of 20 multimapping reads and required a minimum overhang of 8 bp for splice junctions. Aligned reads were sorted and indexed using samtools (v1.10), and transcript quantification was performed with Salmon (v1.5.2) in alignment-based mode using the sorted BAM files, accounting for sequence and GC biases.  For ATAC-seq, Nextera adapters with Trimmomatic, aligned reads using BWA mem, discarded mitochondrial reads and sorted/indexed with Samtools, marked duplicates using Picard MarkDuplicates, called peaks with MACS2, identified differential accessibility with DiffBind, performed motif analysis using HOMER , annotated peaks with ChIPseeker, and generated coverage tracks using deepTools. For, ChIP-seq, The quality of reads was checked using “FastQC”. The data processing were conducted with nfcore chip seq pipeline v2.0.0 (https://nf-co.re/chipseq/2.0.0/docs/usage) with default settings (GRCh38). Peak files were generated by nfcore pipeline with macs2, and those peak files were intersected with NPC’s ABC model output enhancer–promoter interaction bedpe files to produce DEAF1 bound enhancer–promoter pairs in bedpe format. The target genes of DEAF1 bound enhancers were utilized to proceed DAVID ontology analysis.
Assembly: GRCh38
Supplementary files format and content: TPM.csv, ATAC_annotatedPeaks.csv, H1_annotated_peaks.csv, ChIP_annotated_peaks.csv

source_name: hESC

extract_protocol:
for RNAseq, RNA was extracted using RNeasy plus universal mini prep kit (Quiagen). 1 ug total RNA was used for construction of sequencing libraries. For ATAC-seq hESC with or without mutation were lysed in cold liysis buffer(10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl₂, 0.1% IGEPAL CA-630). And Nuclei were pelleted by centrifugation at 500 × g for 5 min at 4°C and subsequently treated with Tn5 transposase for library construction. for ChIPseq, H1 hESCs were cross-linked with 1% formaldehyde for 10 min at RT, quenched with 125 mM glycine for 5 min at RT, and collected. ChIP-seq of DEAF1 was performed using rabbit anti-DEAF1 antibody (Bethyl Laboratories, A303-187A)
for RNA-seq, Truseq stranded mRNA library prep kit (Illumina) was used following manufacture's protocol. For ATAC-seq, Library prep was performed following Nextera® DNA Library Prep Kit (Illumina). For ChIP-seq, Library prep was performed following iDeal ChIP-seq kit.

value: hESC


title: shA3B 01 CIN 612 DRIP 1

description: Library name: shA3B 01 CIN 612 DRIP 1

value: Cervix

value: CIN 612


title: Spleen, CD23+ B cell, F1, 12h stimulated, H3K27ac, biol rep 1

value: Spleen

value: Female

value: CD23+ B cell

value: F1 mus x cast


title: RNA-seq of 8505C cells: NC2

description: Library name: A_2,si NC2,8505C,24h

value: NC


title: S5_DOC_LAV

description: Library name: 31956

value: Germinal center LCMV-specific KL25  B cells


title: RNA-seq of 8505C cells: NC3

description: Library name: A_3,si NC3,8505C,24h


title: S4_DOC

description: Library name: 31955

value: Infection with DOCILE LCMV


title: Input (ChIP-Seq)

description:
Library name: ChIP-seq sample1
iDeal ChIP-seq kit
ChIP_annotated_peaks.csv

value: Input


title: Spleen, CD23+ B cell, F1, 0h naïve, H3K27ac, biol rep 3

value: unstimulated


title: RNA-seq of 8505C cells: siPOLR1F1

description: Library name: B_1,si POLR1F1,8505C,24h

value: POLR1F silenced


title: MUT (ATAC-seq)

description:
Library name: ATAC-seq sample3
the Nextera® DNA Library Prep Kit
ATAC_annotatedPeaks.csv

value: mutation


title: Spleen, CD23+ B cell, F1, 12h stimulated, H3K27ac, biol rep 3

value: stimulated with CpG for 12 hours


title: RNA-seq of 8505C cells: NC1

description: Library name: A_1,si NC1,8505C,24h

value: thyroid cancer


title: S3_DOC

description: Library name: 31954


title: Spleen, CD23+ B cell, F1, 0h naïve, H3K27ac, biol rep 1


title: KAS-Seq CR2M Input

city: Manchester

first: Aamena

middle: Y

last: Patel

address: Dover Street

country: United Kingdom

institute: University of Manchester

description: Library name: SN42

data_processing:
The reads were mapped on hg38 using bowtie2 and MACS2 (v2.2.7.1) broadpeaks option was used for peak calling.
deeptools (v3.5.1) was used to construct bigwig files with rpkm settings (bamCoverage), average density plots (computeMatrix and plotProfile) and heatmaps (computeMatrix and plotHeatmap).
Assembly: hg38
Supplementary files format and content: bigwigs

growth_protocol: MCF7 cells (n=2) were cultured with DMEM with 10% Fetal Bovine Serum, Penicillin, Streptomycin and 2 mM Glutamine in a 12 well plate.

extract_protocol:
After labelling, 10,000 labelled cells were collected for further reactions. For tagmentation, 50 ng of biotinylated DNA and 7.5 ul of the enzyme from Illumina Tagment DNA TDE1 enzyme and buffer kit were used.
The transpositioned and amplified DNA samples were sequenced using NovaSeq 6000 with 1% PhiX spike-in generating paired-end reads.

treatment_protocol: Cells were labelled with 5 mM N3-kethoxal for 10 minutes.

tag: disease state

value: ER+ breast cancer

value: human breast cancer


title: S2_DOC

description: Library name: 31953


title: H1 (ATAC-seq)

description:
Library name: ATAC-seq sample1
the Nextera® DNA Library Prep Kit
H1_annotated_peaks.csv

value: hESC

value: wild type


title: Spleen, CD23+ B cell, F1, 24h stimulated, H3K27me3, biol rep 1

value: Spleen

value: stimulated with CpG for 24 hours


title: CNTL (ATAC-seq)

description:
Library name: ATAC-seq sample2
the Nextera® DNA Library Prep Kit
ATAC_annotatedPeaks.csv

value: CNTL


title: Spleen, CD23+ B cell, F1, 12h stimulated, H3K27me3, biol rep 3

value: Female

value: CD23+ B cell

value: F1 mus x cast


title: KAS-Seq CR1M Input

description: Library name: SN41


title: MUT-3, D70 (RNA-Seq)

description:
Library name: RNA-seq sample6
truseq stranded mrna library
TPM.csv

source_name: Brain organoid

value: Brain organoid


title: S1_DOC

description: Library name: 31952

value: Germinal center LCMV-specific KL25  B cells

value: Infection with DOCILE LCMV


title: Spleen, CD23+ B cell, F1, 0h naïve, H3K27ac, biol rep 2

value: unstimulated


title: KAS-Seq CR1M

description: Library name: SN35


title: MUT-2, D70 (RNA-Seq)

description:
Library name: RNA-seq sample5
truseq stranded mrna library
TPM.csv

value: mutation


title: KAS-Seq CR2M

description: Library name: SN36


title: Spleen, CD23+ B cell, F1, 12h stimulated, H3K27me3, biol rep 1

value: stimulated with CpG for 12 hours


title: shNSUN2#2-3

city: suzhou

first: Wenjuan

last: Ma

state: Jiang su

address: 199 Ren'ai Rd

department: Hematology Center Cyrus Tang medical institute

institute: Soochow University

data_processing:
Paired-end reads were harvested from Illumina NovaSeq 6000 sequencer, and were quality controlled by Q30.
After 3’ adaptor-trimming and low quality reads removing by cutadapt software (v1.9.3), the high quality clean reads were aligned to the reference genome with hisat2 software (v2.0.4)
Then, HTSeq software (v0.9.1) was used to get the raw count, and edgeR was used to perform normalization, then differentially expressed mRNAs were identified by p-value and fold change.
GO and Pathway enrichment analysis were performed based on the differentially expressed mRNAs.
Assembly: HG19
Supplementary files format and content: Gene Expression Profiling.xlsx includes raw counts/Normalized counts for each sample

source_name: Peripheral Blood

growth_protocol: jurkat cells were cultured in 1640 medium in a 37° incubator containing 5% CO2

extract_protocol:
RNA was harvested using Rneasy mini kit(tian gen).500ng of total RNA was used for the consyruction of sequencing libraries
RNA libaary for RNA-seq were prepared use Illumina NovaSeq 6000 platform

treatment_protocol: Scrambled and shNSUN2 sequence were delivered with lentiviral vectors into Jurkat cells.

value: Peripheral Blood

value: Jurkat

value: T-ALL leukemia  cell


title: MUT-1, D70 (RNA-Seq)

description:
Library name: RNA-seq sample4
truseq stranded mrna library
TPM.csv


title: shNSUN2#2-2


title: CNTL-2, D70 (RNA-Seq)

description:
Library name: RNA-seq sample2
truseq stranded mrna library
TPM.csv


title: Spleen, CD23+ B cell, F1, 0h naïve, H3K27me3, biol rep 3


title: CNTL-3, D70 (RNA-Seq)

description:
Library name: RNA-seq sample3
truseq stranded mrna library
TPM.csv


title: shNSUN2#2-1


title: In_vivo_DN3_rep1

city: Pasadena

first: Brendan

middle: W

last: MacNabb

state: CA

address: 1200 E California Blvd

institute: California Institute of Technology

description:
Library name: In_vivo_DN3_rep1
genomic accessibility

data_processing:
Sequences reads were mapped to the GRCm38/mm10 mouse reference genome using Bowtie 2 following adapter trimming by SeqPurge. PCR duplicates were removed using Picard and low-quality (Q <30) reads were filtered out using Samtools.  Peak calling was conducted by employing Genrich for ATAC-seq, and mitochondrial and blacklisted regions were excluded for peak calling. Bigwig files were generated using deepTools (v 3.5.1) with binSize 20bp and counts per million (CPM) normalization.
Assembly: GRCm38/mm10
Supplementary files format and content: Bigwig files showing normalized counts per genomic region
Supplementary files format and content: Peak files  in narrowPeak format

source_name: thymus

extract_protocol:
Nuclei were isolated from the cells by incubating the cells for two minutes on ice in nuclei buffer (130 mM NaCl, 5 mM MgCl2, 5 mM KCl, 0.05 mM EDTA, 10% v/v glycerol, and 25 mM HEPES) containing 0.1% NP40 and 0.01% Tween-20 at a concentration of 1,000 cells per uL, followed by a wash with 500 uL nuclei buffer and centrifugation for 5 min at 500 xg, 4C.
Bulk ATAC-seq library was constructed after transposition reaction using Tn5 transposases (Illumina #15027916) by following previously published protocol (Corces et al., 2017 Nat Methods, PMID: 28846090). Sub-nucleosomal and 1-nucleosome bound DNA fragments were selected using Ampure XP beads, first by depleting large genomic DNA fragments (0.6X Ampure XP) then by selecting all DNA fragments except primer dimers (1.8X Ampure XP).

treatment_protocol: Primary lineage depletion was performed by PNA panning for 70 minutes at 4C with occasional swirling. Secondary depletion was performed using magnetic separation. The cells were stained with a cocktail of biotinylated antibodies against CD3, CD4, CD8, TCRb, TCRgd, CD11b, CD11c, Gr-1, Ter-119, NK1.1, CD49b, CD122, and CD19, followed by incubation with streptavidin microbeads and negative selection on a magnetic column. These lineage-depleted cells were then stained with flourescent-conjugated antibodies recognizing Kit, CD44, CD25, and CD45, as well as floursecent-labelled streptavidin. The cells were stained with a viability dye immediately prior to sorting. The populations were defined as follows for the puroposes of cell sorting: ETP: Live, Lin-neg CD45+ CD44+ Kit+ CD25-neg; ETP_trans: Live, Lin-neg CD45+ CD44+ Kit+ CD25-lo; DN2a: Live, Lin-neg CD45+ CD44+ Kit-hi CD25+; DN2b: Live, Lin-neg CD45+ CD44+ Kit-int CD25+; DN3: Live, Lin-neg CD45+ CD44-neg Kit-neg CD25+; DN4: Live, Lin-neg CD45+ CD44-neg Kit-neg CD25-neg. 30,000-50,000 cells were used as input per replicate based on the yields from the sorts.

value: thymus

value: Live Lin-neg CD45+ CD44-neg Kit-neg CD25+

value: wild-type C57BL/6J


title: Spleen, CD23+ B cell, F1, 0h naïve, H3K27me3, biol rep 1

value: Spleen


title: In_vivo_DN3_rep2

description:
Library name: In_vivo_DN3_rep2
genomic accessibility


title: In_vivo_DN4_rep2

description:
Library name: In_vivo_DN4_rep2
genomic accessibility

value: Live Lin-neg CD45+ CD44-neg Kit-neg CD25-neg


title: In_vivo_DN4_rep1

description:
Library name: In_vivo_DN4_rep1
genomic accessibility


title: In_vivo_DN3_rep3

description:
Library name: In_vivo_DN3_rep3
genomic accessibility


title: Scrambled-3


title: Hollow-3

city: Jinhua

first: QI

last: TU

address: 365 Renmin East Road, Wucheng District

institute: Zhejiang University School of Medicine

description: Library name: Sample9

data_processing:
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (llumia) according to the manufacturer's instructions.After cluster generation, the library preparations were sequenced on an lllumina platform and 150 bp paired-end reads were generated.
Assembly: ENSRNOG
Supplementary files format and content: .xlsx

organism: Rattus norvegicus

source_name: nerve

extract_protocol:
Total RNA was extracted from regenerated sciatic nerve tissues using TRIzol reagent according to the manufacturer’s instructions.
RNA libraries were prepared using a strand-specific mRNA library preparation protocol, following these steps:
mRNAs containing poly(A) tails were enriched using Oligo(dT) magnetic beads.
Purified mRNAs were fragmented into short fragments using a fragmentation buffer.
First-strand cDNA was synthesized using random hexamer primers.
Second-strand cDNA synthesis was performed using dUTP instead of dTTP, enabling strand specificity because uracil-containing templates cannot be amplified during PCR. During this step, end repair and dA-tailing were also performed.
Sequencing adapters were ligated to the cDNA fragments. DNA magnetic beads were used for purification and fragment selection to obtain libraries with insert sizes of 250–350 bp.
Adapter-ligated fragments were PCR amplified and purified again using DNA magnetic beads.
The constructed libraries were quantified using a Qubit fluorometer, fragment size distribution was assessed using a Qsep400 high-throughput biofragment analyzer, and the effective library concentration was further quantified by qPCR.
The libraries were sequenced on an Illumina NovaSeq 6000 platform using a paired-end 150 bp (PE150) sequencing strategy.

value: nerve


title: Scrambled-2


title: Neuroinvasion, replicate 3, RNAseq

source_name: Liver

extract_protocol:
RNA was extracted from mouse liver tissues using Trizol extraction and Purelink RNA kit (ThermoFisher Scientific).
A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using Hieff NGS Ultima Dual-mode mRNA Library Prep Kit for Illumina (Yeasen Biotechnology (Shanghai) Co., Ltd.) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads.First strand cDNA was synthesized and second strand cDNA synthesis was subsequently performed. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. The library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 μl USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37°C for 15 min followed by 5 min at 95°C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

value: Liver


title: In_vivo_DN2b_rep3

description:
Library name: In_vivo_DN2b_rep3
genomic accessibility

value: Live Lin-neg CD45+ CD44+ Kit-int CD25+


title: Spleen, CD23+ B cell, F1, 12h stimulated, H3K27me3, biol rep 2

value: Female

value: CD23+ B cell

value: F1 mus x cast


title: Neuroinvasion, replicate 2, RNAseq


title: Spleen, CD23+ B cell, F1, 0h naïve, H3K27me3, biol rep 2

value: unstimulated


title: In_vivo_DN2b_rep2

description:
Library name: In_vivo_DN2b_rep2
genomic accessibility


title: Hollow-2

description: Library name: Sample8


title: Scrambled-1


title: Neuroinvasion, replicate 1, RNAseq


title: In_vivo_DN2b_rep1

description:
Library name: In_vivo_DN2b_rep1
genomic accessibility


title: M51-4LM

city: Ariake

first: Ryoji

last: Yao

state: Tokyo

country: Japan

institute: Cancer Institute, JFCR

description:
M51-4LM
row_count_DTC.csv

data_processing:
Quantification were carried out using Salmon.
Transcript-level abundance estimation was perfomed using Tximport with the argument, countFromAbundance .
Assembly: gencode.v30.transcripts
Supplementary files format and content: column separated value file includes row counts for each Sample

source_name: colorectal cancer

extract_protocol:
Organoids were colected and signle cells were prepared in TrypLE.
RNA libraries for RNA-seq were prepared using TruSeq Stranded mRNA LT Sample Prep Kit following manufacturer's protocols.

value: colorectal cancer

value: organoid


title: Hollow-1

description: Library name: Sample7


title: In_vivo_DN2a_rep3

description:
Library name: In_vivo_DN2a_rep3
genomic accessibility

value: Live Lin-neg CD45+ CD44+ Kit-hi CD25+


title: AFMC-AA-SP-3

description: Library name: Sample6


title: CNTL-1, D70 (RNA-Seq)

description:
Library name: RNA-seq sample1
truseq stranded mrna library
TPM.csv

value: Brain organoid

value: wild type


title: Baseline, replicate 3, RNAseq


title: Baseline, replicate 2, RNAseq


title: In_vivo_DN2a_rep2

description:
Library name: In_vivo_DN2a_rep2
genomic accessibility

value: thymus


title: M51-3LM

description:
M51-3LM_R
row_count_DTC.csv


title: AFMC-AA-SP-2

description: Library name: Sample5


title: In_vivo_DN2a_rep1

description:
Library name: In_vivo_DN2a_rep1
genomic accessibility


title: M51-2T

description:
M51-2T_R
row_count_DTC.csv


title: AFMC-AA-SP-1

description: Library name: Sample4


title: M51-1T

description:
M51-1T
row_count_DTC.csv


title: Mild infection, replicate 3, RNAseq


title: In_vivo_ETP_trans_rep3

description:
Library name: In_vivo_ETP_trans_rep3
genomic accessibility

value: Live Lin-neg CD45+ CD44+ Kit+ CD25-lo


title: AFMC-3

description: Library name: Sample3


title: M214-3LM

description:
M214-3LM
row_count_DTC.csv


title: M214-1T

description:
M214-1T
row_count_DTC.csv


title: AFMC-2

description: Library name: Sample2


title: Mild infection, replicate 2, RNAseq


title: In_vivo_ETP_trans_rep2

description:
Library name: In_vivo_ETP_trans_rep2
genomic accessibility

value: wild-type C57BL/6J


title: AFMC-1

description: Library name: Sample1


title: M145-3LuM

description:
M145-3LuM
row_count_DTC.csv


title: In_vivo_ETP_trans_rep1

description:
Library name: In_vivo_ETP_trans_rep1
genomic accessibility


title: In_vivo_ETP_rep3

description:
Library name: In_vivo_ETP_rep3
genomic accessibility

value: Live Lin-neg CD45+ CD44+ Kit+ CD25-neg


title: Baseline, replicate 1, RNAseq


title: PC-3 LCN2-KO#1

city: Aachen

first: Ralf

last: Weiskirchen

address: Pauwelsstr. 30

department: IFMPEGKC

country: Germany

institute: RWTH University Hospital Aachen

description: Library name: Sample 2

data_processing:
The resulting sequencing runs were demultiplexed and converted to FASTQ format using Illumina bcl2fastq conversion software (version 2.20), and these FASTQ files were utilized for subsequent downstream analyses. Raw sequencing reads were assessed for quality using FastQC (v0.11.8) (Babraham). Following the evaluation, adapters and bases with Phred scores below 20 were eliminated. Any reads shorter than 35 bp were discarded using cutadapt (v1.9.1) (Martin 2011), and reads were aligned to the reference genome using STAR (v2.7.11a) (Dobin et al., 2013). Gene abundances were then estimated using featureCounts (v2.0.6) and the pseudoalignment-based methods kallisto (v0.48.0) (Bray et al., 2016) and salmon (v.1.10.2) (Patro et al., 2017), followed by median-of-ratios normalization (Love and Huber, 2014). For annotation purposes, the Human GRCh38.p14 reference transcriptome (Ensembl) was employed. To generate a candidate list of genes with potentially changed expression upon LCN2 depletion, which was later verified by RT-qPCR, we filtered out lowly expressed genes and only retained genes with log2 fold-changes ≥ 2 as estimated by featureCounts, kallisto, and salmon
Assembly: Human GRCh38.p14
Supplementary files format and content: Tab-delimited txt file represents estimated_counts, TPM

source_name: PC-3 LCN2-KO#1

growth_protocol: PC-3 cells (CRL-1435; RRID:CVCL_0035) were obtained from the German branch (LGC Standards GmbH, Wesel, Germany) of the American Type Culture Collection (ATCC). Both, the parental PC-3 cells and the previously established clone #1 of PC-3 lacking LCN2 (referred to as PC-3 LCN2-KO#1) (Schröder et al., 2022) were cultured in Dulbecco’s Modified Eagle Medium (DMEM, #D6171, Sigma-Aldrich, Merck, Taufkirchen, Germany) supplemented with 10% (v/v) fetal bovine serum (FBS, #F7524, Sigma-Aldrich), 2 mM L-glutamine (#G7513, Sigma-Aldrich), and 1× penicillin/streptomycin (DE17-602E, Lonza, Cologne, Germany). The cultures were maintained at 37 °C in a humidified atmosphere with 5% CO₂ and split when they reached 70-80% confluency. For subculturing, the cells were rinsed with phosphate-buffered saline (PBS) and detached using Accutase solution (#A6964-100ML, Sigma-Aldrich).

extract_protocol:
Total RNA from both parental PC-3 cells and clone #1 cells, isolated from cells grown to 70% confluence, underwent next-generation sequencing (NGS) to identify differentially expressed genes influenced by LCN2 deficiency. The RNA samples were initially assessed for concentration, purity, and integrity using UV spectrophotometry and an Agilent 4200 TapeStation (Agilent Technologies Inc., Waldbronn, Germany).
After removal of ribosomal RNA, the remaining mRNA fraction was converted into a sequencing library using the NEBNext® Multiplex Oligos for Illumina® Index Primers Set 1 (#E7335S, New England Biolabs, Frankfurt am Main, Germany). These libraries were then sequenced on an Illumina instrument using 300-cycle MiSeq Reagent kit V2 cartridges (Illumina Inc., San Diego, CA, USA). All cDNA library preparations and sequencing procedures were conducted at the IZKF Genomic Facility, University Hospital Aachen

treatment_protocol: no treatement, cell were cultured under standard conditions

value: PC-3 LCN2-KO#1

value: prostate cancer cell

value: no treatment

tag: time

value: Day 0


title: Neuroinvasion

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1.
Assembly: GRCm38
Supplementary files format and content: Tar archives include tab-separated values files and matrix files (barcodes.tsv, features.tsv, matrix.mtx).

extract_protocol:
Isolated PBMCs from the mice were transported in sterile culture dish with 10 ml Dulbecco's Phosphate-Buffered Saline (DPBS, Thermo Fisher Scientific) on ice to remove the residual tissue storage solution, then minced on ice. We used dissociation enzyme 0.25% Trypsin (Thermo Fisher Scientific) and 10 ug/mL DNase I (Sigma) dissolved in PBS with 5% Fetal Bovine Serum (FBS, GIBCO) to digest the tissues.
10× beads that were then subject to second-strand cDNA synthesis, adaptor ligation, and universal amplification. Sequencing libraries were prepared using randomly interrupted whole-transcriptome amplification products to enrich the 3’ end of the transcripts linked with the cell barcode and UMI. All the remaining procedures including the library construction were performed according to the standard manufacturer's protocol (Chromium Single Cell 3ʹ v3).

value: Peripheral Blood

value: PBMC

tag: condition

value: Neuroinvasion


title: PC-3 cells, parental

description: Library name: Sample 1

value: WT


title: M145-2LuM

description:
M145-2LuM
row_count_DTC.csv

value: colorectal cancer


title: M145-1T

description:
M145-1T
row_count_DTC.csv

value: organoid


title: In_vivo_ETP_rep1

description:
Library name: In_vivo_ETP_rep1
genomic accessibility


title: cy0973, M6/M6, control

status: Public on Mar 16 2026

city: Madison

first: David

middle: H

last: O'Connor

state: WI

address: 585 Science Drive

department: Pathology and Laboratory Medicine

institute: University of Wisconsin-Madison

description:
Library name: M006327_cy0973_PBMC
10X Genomics

data_processing:
Reference genomes were created for each sample from the FASTA and GTF files for the given genotype (available as supplementary files on the sample records) using the Cell Ranger mkref command. The demultiplexing, barcode processing, gene counting and aggregation were done using Cell Ranger software v2.1.1 (https://support.10Xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: Mmul_10
Supplementary files format and content: Tab-separated values files and matrix files. GTF and FASTA files of the reference genome used to process samples with Cell Ranger

organism: Macaca fascicularis

source_name: peripheral blood mononuclear

extract_protocol:
PBMC from Mauritian-origin cynomolgus and Indian-origin rhesus macaques were isolated from fresh whole blood by Ficoll-Plaque centrifugation and transported immediately to the University of Wisconsin Biotech Center for 5' RNAseq analysis
Chromium GEX libraries were generated according to the manufacter's instructions for 5' single cell RNAseq (v2 NextGEM User Guide Rev.E). Briefly, PBMC were resuspended in master mix and loaded together with partioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was reverse transcripted to full-length cDNA, which contains an Illumina R1 primer sequence, a 16 nt 10X Barcode, a 10 nt unique molecular identifier and a 13 nt template switch oligo. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR, enzymatically fragmented and appropriately sized fragments were selected with SPRIselect reagent for subsequent library construction. During library construction An Illumina R2 primer sequence, paired-end constructs with P5 and P7 sequences plus i5 and i7 sample index sequences were added during library construction. The resulting templates from two animals were sequenced on a NovaSeq X+ instrument with a 1.5B flow cell. A modified sequencing protocol was used with 29 cycles for R1 to collect 10X barcode/UMI sequences, followed by 289 cycles for R2. This protocol maximized the amount of sequence data from the highly polymorphic 5' end of each cDNA molecule so that transcripts from closely related MHC alleles could be resolved.

value: peripheral blood mononuclear

value: control

tag: age

value: 12.1 years

value: female


title: L. monocytogenes NCTC 10887, 22 °C, on polystyrene, biol rep 1

city: Hamburg

first: Tim

last: Hoffmann

state: Hamburg

address: Ohnhorststraße 18

institute: Universität Hamburg

description:
Library name: Sample 5
Lm22PS1

data_processing:
Raw data in FASTQ format were first cleaned using fastp (Chen, 2023), removing adapter sequences, poly-N-containing reads and low-quality reads (Phred score < 20).
Gene-specific read counts were determined using FeatureCounts (2.0.6) (Liao et al., 2014).
To quantify gene expression, the FPKM value (fragments per kilobase of transcript per million mapped reads) was calculated for each gene to ensure comparability between genes and samples.
Differential expression analysis was performed using the DESeq2 R package (1.42.0) (Love et al., 2014)
The p-values were adjusted using the Benjamini-Hochberg correction for multiple testing.
Assembly: The cleaned reads were aligned using Bowtie2 (2.5.4) (Langmead et al., 2009) to the reference genome of L. monocytogenes NCTC 10887 (PRJNA1358932).
Supplementary files format and content: .txt file include differential gene expression data as well as fpkm values

organism: Listeria monocytogenes

source_name: L. monocytogenes NCTC 10887

growth_protocol: L. monocytogenes NCTC 10887 was grown in BHI broth at 37 °C on a shaker for 16 h. After incubation, a 200 mL suspension of BHI broth containing 5.0 × 10e7 cfu/mL was created in a flask and incubated at 37 °C, 130 rpm, for 16 h. After incubation, the 200 mL suspension was pelleted by centrifugation (Eppendorf, Centrifuge 5804 R) in sterile 50 mL tubes (Cat. No. 227 261, Greiner Bio-one, Munich, Germany) at 3,230 × g at RT for 10 min. The supernatant was discarded and the pellet was resuspended in sterile PBS (Cat. No. 0780-10L, VWR Chemicals, Solon, Ohio, USA) buffer and centrifuged again under the same conditions to wash away any remaining BHI broth. Finally, the pellet was resuspended in sterile PBS buffer, the viable count was adjusted to 2.0 × 10e10 cfu/mL and the suspension was transferred into a sterile Erlenmeyer flask. The concentrated cell suspension was used to moisten 25 g of commercially available corn salad (Contrada scorziello anc., Eboli, Italy), which was performed by immersing each corn salad leaf individually into the cell suspension using sterile tweezers. Immersed leaves were incubated for 24 h at 4 °C and 22 °C under sterile conditions. After incubation, the leaves were placed in a sterile plastic bag (T256.2, Carl Roth, Karlsruhe, Germany) containing 50 mL sterile PBS buffer. The following protocol for pulsifying corn salad to harvest cells was derived from Giese & Weiss (2025). Briefly, the bag was placed in a Pulsifier® (Microgen Bioproducts Ltd., Eastleigh, Great Britain) and the corn salad was washed by high frequency pulses for 30 s, resulting in the bacteria being suspended in the PBS buffer. The cell suspension was transferred in a sterile plastic bag containing a lateral fleece insert (EP17.1, Carl Roth, Karlsruhe, Germany) to filter any major debris. The filtered cell suspension was transferred into a sterile 50 mL tube and pelleted by centrifugation at 3,230 × g at 4 °C for 10 min. For incubation of L. monocytogenes NCTC 10887 on polystyrene, cells were prepared as described in for the corn salad until the step of fully washing away the BHI broth with PBS buffer. For final resuspension in PBS, the cell count was adjusted to 1.0 × 10e9 cfu/mL. 10 mL of this cell suspension together with 10 mL sterile PBS buffer were then transferred into sterile polystyrene petri dishes (Cat. No. 633180, Greiner Bio-One International GmbH, Frickenhausen, Germany), which served as the polystyrene surface investigated in this study. This was performed 20 times, accounting for one biological replicate. After incubation at 4 °C and 22 °C, the supernatant was discarded and a cell scraper (Cat. No. C5981, Merck KGaA, Darmstadt, Germany) was used to scrape the attached cells off the petri dish and transfer them into a 50 mL tube. Cells were then pelleted by centrifugation at 3234 × g at 4 °C for 10 min and the supernatants were discarded. For each condition tested, two biological replicates were created, each consisting of 20 petri dishes.

extract_protocol:
The L. monocytogenes NCTC 10887 cell pellets acquired were resuspended in 1 mL Trizol®. Resuspended cells were transferred into ZR BashingBead Lysis Tubes (0.1 & 0.5 mm beads) (Cat. No. S6012-50, Zymo Research, Freiburg, Germany) and shook over 10 min at 2,700 rpm. Afterwards, RNA extraction was performed as described in Direct-zol RNA Miniprep (w/Trizol) Kit (Cat. No. R2051, Zymo Research, Freiburg, Germany). RNA was eluted with 50 µL ultrapure water and stored at -80 °C.
Library preparation, sequencing, and data analysis were performed by Novogene GmbH (Munich, Germany), ribosomal RNA was eliminated from the total RNA, accompanied by ethanol precipitation. For quantification of the library, Qubit and real-time PCR were used, and the Agilent 2100 Bioanalyzer for size distribution detection. The libraries were pooled according to their effective concentration and the required data volume and sequenced on an Illumina NovaSeq 6000 platform.

value: L. monocytogenes NCTC 10887

value: bacteria

value: 22 °C

tag: attachment surface

value: polystyrene


title: L. monocytogenes NCTC 10887, 22 °C, on corn salad, biol rep 1

description:
Library name: Sample 7
Lm22Vl1

value: corn salad


title: cy0975, M1/M1, control

description:
Library name: M006146_cy0975_PBMC
10X Genomics

value: 7.3 years

value: male


title: L. monocytogenes NCTC 10887, 22 °C, on polystyrene, biol rep 2

description:
Library name: Sample 6
Lm22PS2


title: c20006, M3/M3, control

description:
Library name: M006146_c20006_PBMC
10X Genomics

value: 3.8 years


title: In_vivo_ETP_rep2

description:
Library name: In_vivo_ETP_rep2
genomic accessibility

value: thymus

value: Live Lin-neg CD45+ CD44+ Kit+ CD25-neg

value: wild-type C57BL/6J


title: L. monocytogenes NCTC 10887, 4 °C, on corn salad, biol rep 1

description:
Library name: Sample 3
Lm04Vl1

value: 4 °C


title: Control

description: 10x Genomics

value: Peripheral Blood

value: PBMC

value: Baseline


title: L. monocytogenes NCTC 10887, 4 °C, on corn salad, biol rep 2

description:
Library name: Sample 4
Lm04Vl2


title: L. monocytogenes NCTC 10887, 4 °C, on polystyrene, biol rep 2

description:
Library name: Sample 2
Lm04PS2


title: cy0692, M2/M4, control

description:
Library name: M006327_cy0692_PBMC
10X Genomics

value: peripheral blood mononuclear

value: control

value: 11.5 years


title: MG1655 OxyRc_RecA730 double mutant rep. 1

city: Warsaw

first: Damian

last: Gawel

address: Marymoncka 99/103

department: Cell Biology and Immunology

country: Poland

institute: Centre of Postgraduate Medical Education

description: Library name: MG1655.OR1

data_processing:
Bowtie2 v2.5.2 - Genomic Indexing and alignment
SamTools v1.18 - bam file sorting
FeatureCounts v1.5.0 - Gene counting
EdgeR v4.2.2 - Differential Gene Expression Analysis
Assembly: GCF_000005845.2_ASM584v2
Supplementary files format and content: txt files, aligned gene counts for each sample

organism: Escherichia coli

source_name: Bacteria

growth_protocol: Luria-Bertani (LB) broth and minimal (MM) solid and liquid media were standard recipes. Solid media contained 1.5% agar (Difco). MM media were supplemented with Vogel-Bonner salts and 0.4% glucose, 750 μg/mL phenyl-β-D-galactopyranoside (P-gal), or 0.2% lactose (Lac), as the sole carbon source. When required, antibiotics or selection agents were added at the following final concentrations: chloramphenicol (cam), 20 μg/mL; kanamycin (kan), 50 μg/mL; rifampicin (rif), 100 µg/ml; tetracycline (tet), 15 μg/mL; ampicillin (amp), 50 μg/mL; and 6-azauracil (6-aza), 40 µg/mL. All media and chemicals were purchased from Sigma-Aldrich (Merck; USA).

extract_protocol:
Three separate cultures each for the MG1655-based strains NR13438 (control), NR13446 (oxyR2c), NR13479 (recA730), and NR13480 (oxyR2c_recA730), were grown o/n in LB at 37 °C. The next day, these cultures were used to inoculate 20 mL of fresh LB medium at a 1:100 dilution and grown until the OD600 of 0.5. The cultures (2 mL) were cooled on ice and harvested for total RNA isolation by centrifugation. The pellets were resuspended in 0.2 mL of lysozyme solution (15 mg/mL in 10 mM Tris-HCl pH 8, 1 mL EDTA) and incubated at RT for 15 min. Total RNA was isolated using the RNeasy Mini Kit (Qiagen; Germany) according to the manufacturer recommended protocol, including the on-column DNAse treatment step.
Illumina Truseq Stranded mRNA library kit

treatment_protocol: Overnight cultures were diluted in fresh LB broth, grown to 2-3 x 108 cells/mL, spun down, and resuspended in half of volume ice-cold 0.9% NaCl. A 10-mL aliquot was then irradiated in a Petri dish with 254-nm UV light at 1.2 J/m2s. Appropriate dilutions of samples were plated before and after irradiation on LB plates to determine cell survival. All procedures were performed in subdued light conditions. For mutant frequency determination, 0.5 mL of the irradiated samples were added to 5 mL of LB broth and incubated overnight at 37 °C. The next day, 100 μL of the cultures were plated on LB/Rif, LB/Nal, and MM/P-gal to score mutant colonies, and 100 μL of 106 diluted cultures were plated on LB or MM plates to determine total cell counts. The plates were incubated 20 h (LB, LB/Rif and LB/Nal) or 40 h (MM, MMP-gal) at 37 °C.

tag: strain

value: Bacteria


title: MG1655 OxyRc_RecA730 double mutant rep. 2

description: Library name: MG1655.OR2


title: MG1655 OxyRc single mutant rep. 3

description: Library name: MG1655 O3

value: OxyRc


title: L. monocytogenes NCTC 10887, 22 °C, on corn salad, biol rep 2

description:
Library name: Sample 8
Lm22Vl2

value: L. monocytogenes NCTC 10887

value: bacteria

value: 22 °C


title: MG1655 OxyRc_RecA730 double mutant rep. 3

description: Library name: MG1655.OR3


title: L. monocytogenes NCTC 10887, 4 °C, on polystyrene, biol rep 1

description:
Library name: Sample 1
Lm04PS1

value: polystyrene


title: MG1655 OxyRc single mutant rep. 1

description: Library name: MG1655.O1


title: MG1655 RecA730 single mutant rep. 2

description: Library name: MG1655.R2


title: MG1655 RecA730 single mutant rep. 1

description: Library name: MG1655.R1


title: MG1655 RecA730 single mutant rep. 3

description: Library name: MG1655.R3


title: MG1655 Control rep. 3

description: Library name: MG1655.K3

value: WT


title: MG1655 Control rep. 1

description: Library name: MG1655.K1


title: Sample 51_Photoreceptor Nuclei, LongGMR-Gal4 > UAS-Gnmt, H3K4me3, Replicate 4

city: West Lafayette

first: Seth

last: Lammert

state: IN

address: 175 South University Street

department: Biochemistry

institute: Purdue University

description: Library name: Sample 51

data_processing:
Adaptors trimmed using Trimmomatic
Alignment using bowtie2, dovetail mates considered concordant
Indexing, generation of BAM files using Samtools
BAM files deduplicated using Samtools
BigWigs generated using deepTools, CPM-normalized
Assembly: BDGP6.46
Supplementary files format and content: Deduplicated, CPM-normalized BigWigs
Library strategy: CUT&Run

organism: Drosophila melanogaster

source_name: Outer photoreceptors

growth_protocol: Drosophila were maintained in population cages in a 25°C incubator with a 12:12 hour light:dark cycle.

extract_protocol:
200 male flies in triplicate or quadruplicate were collected at 10 days post eclosion and at Zeitgeber time 12 (ZT 12). GFP-positive photoreceptor nuclei were immunoprecipitated using the nuclei immunoenrichment protocol (dx.doi.org/10.17504/protocols.io.buiqnudw), followed by CUT&RUN (dx.doi.org/10.17504/protocols.io.zcpf2vn) with indicated antibodies (IgG - EpiCypher CUTANA IgG Negative Control Antibody, H3K9me3 - abcam # ab176916 (1 ug) , H3K27me3 - EpiCypher # 13-0055 (1 ug), H3K4me - abcam # ab8895 (.5 ug) ,H3K4me3 -EpiCypher # 13-0060 (1 ug)). IgG control samples use equivalent amounts of antibody with respective experimental samples. Samples were digested with MNase for 20 minutes.
(0.4 ng - samples 1-19, or .65ng - samples 20-51) of DNA from each CUT&RUN reaction was used to prepare libraries using the NEBNext® Ultra™ II DNA Library Prep Kit for Illumina® from New England Biolabs.  Modifications to the library preparation were made to preserve short DNA fragments (dx.doi.org/10.17504/protocols.io.bagaibse)

value: Outer photoreceptors

value: male

value: adult, day 10

tag: cut&run antibody

tag: matching igg_control_sample

value: Sample 49


title: Sample 50_Photoreceptor Nuclei, LongGMR-Gal4 > UAS-Gnmt, H3K4me, Replicate 4

description: Library name: Sample 50

value: Sample 48


title: Sample 49_Photoreceptor Nuclei, LongGMR-Gal4 > UAS-Gnmt, IgG 2, Replicate 4

description: Library name: Sample 49

value: IgG


title: Sample 47_Photoreceptor Nuclei, w1118 control, H3K4me3, Replicate 4

description: Library name: Sample 47

value: Sample 45


title: Sample 48_Photoreceptor Nuclei, LongGMR-Gal4 > UAS-Gnmt, IgG 1, Replicate 4

description: Library name: Sample 48


title: Sample 43_Photoreceptor Nuclei, LongGMR-Gal4 > UAS-Gnmt, H3K4me3, Replicate 3

description: Library name: Sample 43

value: Sample 41


title: Sample 46_Photoreceptor Nuclei, w1118 control, H3K4me, Replicate 4

description: Library name: Sample 46

value: Sample 44


title: Sample 44_Photoreceptor Nuclei, w1118 control, IgG 1, Replicate 4

description: Library name: Sample 44


title: MG1655 Control rep. 2

description: Library name: MG1655.K2


title: Sample 45_Photoreceptor Nuclei, w1118 control, IgG 2, Replicate 4

description: Library name: Sample 45


title: Sample 37_Photoreceptor Nuclei, w1118 control, IgG 2, Replicate 3

description: Library name: Sample 37


title: Sample 40_Photoreceptor Nuclei, LongGMR-Gal4 > UAS-Gnmt, IgG 1, Replicate 3

description: Library name: Sample 40


title: Sample 32_Photoreceptor Nuclei, LongGMR-Gal4 > UAS-Gnmt, IgG 1, Replicate 2

description: Library name: Sample 32


title: Sample 33_Photoreceptor Nuclei, LongGMR-Gal4 > UAS-Gnmt, IgG 2, Replicate 2

description: Library name: Sample 33


title: Sample 34_Photoreceptor Nuclei, LongGMR-Gal4 > UAS-Gnmt, H3K4me, Replicate 2

description: Library name: Sample 34

value: Sample 32


title: Sample 35_Photoreceptor Nuclei, LongGMR-Gal4 > UAS-Gnmt, H3K4me3, Replicate 2

description: Library name: Sample 35

value: Sample 33


title: Sample 36_Photoreceptor Nuclei, w1118 control, IgG 1, Replicate 3

description: Library name: Sample 36


title: Sample 39_Photoreceptor Nuclei, w1118 control, H3K4me3, Replicate 3

description: Library name: Sample 39

value: Sample 37


title: Sample 31_Photoreceptor Nuclei, w1118 control, H3K4me3, Replicate 2

description: Library name: Sample 31

value: Sample 29


title: Sample 41_Photoreceptor Nuclei, LongGMR-Gal4 > UAS-Gnmt, IgG 2, Replicate 3

description: Library name: Sample 41


title: Sample 38_Photoreceptor Nuclei, w1118 control, H3K4me, Replicate 3

description: Library name: Sample 38

value: Sample 36


title: Sample 29_Photoreceptor Nuclei, w1118 control, IgG 2, Replicate 2

description: Library name: Sample 29


title: Sample 26_Photoreceptor Nuclei, LongGMR-Gal4 > UAS-Gnmt, H3K4me, Replicate 1

description: Library name: Sample 26

value: Sample 24


title: Sample 28_Photoreceptor Nuclei, w1118 control, IgG 1, Replicate 2

description: Library name: Sample 28


title: Sample 27_Photoreceptor Nuclei, LongGMR-Gal4 > UAS-Gnmt, H3K4me3, Replicate 1

description: Library name: Sample 27

value: Sample 25


title: Sample 30_Photoreceptor Nuclei, w1118 control, H3K4me, Replicate 2

description: Library name: Sample 30

value: Sample 28


title: Sample 25_Photoreceptor Nuclei, LongGMR-Gal4 > UAS-Gnmt, IgG 2, Replicate 1

description: Library name: Sample 25

value: Outer photoreceptors


title: Sample 23_Photoreceptor Nuclei, w1118 control, H3K4me3, Replicate 1

description: Library name: Sample 23

value: male

value: Sample 21


title: Sample 19_Photoreceptor Nuclei, LongGMR-Gal4 > UAS-Gnmt, H3K27me3, Replicate 3

description: Library name: Sample 19

value: adult, day 10

value: Sample 17


title: Sample 22_Photoreceptor Nuclei, w1118 control, H3K4me, Replicate 1

description: Library name: Sample 22

value: Sample 20


title: Sample 42_Photoreceptor Nuclei, LongGMR-Gal4 > UAS-Gnmt, H3K4me, Replicate 3

description: Library name: Sample 42

value: Sample 40


title: Sample 21_Photoreceptor Nuclei, w1118 control, IgG 2, Replicate 1

description: Library name: Sample 21

value: IgG


title: Sample 20_Photoreceptor Nuclei, w1118 control, IgG 1, Replicate 1

description: Library name: Sample 20


title: Sample 17_Photoreceptor Nuclei, LongGMR-Gal4 > UAS-Gnmt, IgG, Replicate 3

description: Library name: Sample 17


title: Sample 14_Photoreceptor Nuclei, LongGMR-Gal4 > UAS-Gnmt, IgG, Replicate 2

description: Library name: Sample 14


title: Sample 24_Photoreceptor Nuclei, LongGMR-Gal4 > UAS-Gnmt, IgG 1, Replicate 1

description: Library name: Sample 24


title: Sample 13_Photoreceptor Nuclei, LongGMR-Gal4 > UAS-Gnmt, H3K27me3, Replicate 1

description: Library name: Sample 13

value: Sample 11


title: Sample 18_Photoreceptor Nuclei, LongGMR-Gal4 > UAS-Gnmt, H3K9me3, Replicate 3

description: Library name: Sample 18


title: Sample 10_Photoreceptor Nuclei, w1118 control, H3K27me3, Replicate 3

description: Library name: Sample 10

value: Sample 9


title: Sample 12_Photoreceptor Nuclei, LongGMR-Gal4 > UAS-Gnmt, H3K9me3, Replicate 1

description: Library name: Sample 12


title: Sample 9_Photoreceptor Nuclei, w1118 control, H3K9me3, Replicate 3

description: Library name: Sample 9


title: MG1655 OxyRc single mutant rep. 2

description: Library name: MG1655.O2

value: Bacteria

value: OxyRc


title: Sample 11_Photoreceptor Nuclei, LongGMR-Gal4 > UAS-Gnmt, IgG, Replicate 1

description: Library name: Sample 11


title: Sample 7_Photoreceptor Nuclei, w1118 control, H3K9me3, Replicate 2

description: Library name: Sample 7

value: Sample 6


title: Sample 16_Photoreceptor Nuclei, LongGMR-Gal4 > UAS-Gnmt, H3K27me3, Replicate 2

description: Library name: Sample 16

value: Sample 14


title: Sample 4_Photoreceptor Nuclei, w1118 control, IgG, Replicate 2

description: Library name: Sample 4


title: Sample 15_Photoreceptor Nuclei, LongGMR-Gal4 > UAS-Gnmt, H3K9me3, Replicate 2

description: Library name: Sample 15


title: Sample 1_Photoreceptor Nuclei, w1118 control, IgG, Replicate 1

description: Library name: Sample 1


title: Sample 6_Photoreceptor Nuclei, w1118 control, IgG, Replicate 3

description: Library name: Sample 6


title: Sample 2_Photoreceptor Nuclei, w1118 control, H3K9me3, Replicate 1

description: Library name: Sample 2

value: Sample 1


title: Photoreceptor Nuclei, LongGMR-Gal4 > UAS-Gnmt, Zeitgeber Time 16, Replicate 1

data_processing:
Adaptors trimmed using Trimmomatic. Removed leading 5 bases from forward reads as per Ovation® SoLo® RNA-Seq library preparation kit specifications
Alignment using HISAT2
SAM file processing using SAMtools
BigWigs generated using deepTools, CPM-normalized
Assembly: BDGP6.46 (GCA_000001215.4)
Supplementary files format and content: CPM-normalized BigWigs

molecule: nuclear RNA

extract_protocol:
100 male flies in triplicate were collected at 10 days post eclosion and at the indicated Zeitgeber times (ZT0, ZT4, ZT8, ZT12, ZT16, ZT20). GFP-positive photoreceptor nuclei were immunoprecipitated using the nuclei immunoenrichment protocol (dx.doi.org/10.17504/protocols.io.buiqnudw), followed by RNA isolation and purification.
10 ng of nuclear RNA was used to prepare libraries using the Ovation® SoLo® RNA-Seq library preparation kit from Tecan with Drosophila AnyDeplete probes.

value: Day 10

tag: zeitgeber time


title: Photoreceptor Nuclei, LongGMR-Gal4 > UAS-Gnmt, Zeitgeber Time 16, Replicate 3

tag: cell type


title: Photoreceptor Nuclei, LongGMR-Gal4 > UAS-Gnmt, Zeitgeber Time 20, Replicate 3

tag: genotype


title: Photoreceptor Nuclei, LongGMR-Gal4 > UAS-Gnmt, Zeitgeber Time 20, Replicate 1


title: Photoreceptor Nuclei, LongGMR-Gal4 > UAS-Gnmt, Zeitgeber Time 20, Replicate 2


title: Photoreceptor Nuclei, LongGMR-Gal4 > UAS-Gnmt, Zeitgeber Time 16, Replicate 2


title: Sample 5_Photoreceptor Nuclei, w1118 control, H3K27me3, Replicate 2

description: Library name: Sample 5

tag: tissue

value: Sample 4


title: Photoreceptor Nuclei, LongGMR-Gal4 > UAS-Gnmt, Zeitgeber Time 12, Replicate 3

value: Outer photoreceptors


title: Sample 8_Photoreceptor Nuclei, w1118 control, IgG, Replicate 4

description: Library name: Sample 8

value: male


title: Photoreceptor Nuclei, LongGMR-Gal4 > UAS-Gnmt, Zeitgeber Time 8, Replicate 3


title: Photoreceptor Nuclei, LongGMR-Gal4 > UAS-Gnmt, Zeitgeber Time 12, Replicate 2


title: Photoreceptor Nuclei, LongGMR-Gal4 > UAS-Gnmt, Zeitgeber Time 8, Replicate 1


title: Photoreceptor Nuclei, LongGMR-Gal4 > UAS-Gnmt, Zeitgeber Time 4, Replicate 3


title: Sample 3_Photoreceptor Nuclei, w1118 control, H3K27me3, Replicate 1

description: Library name: Sample 3


title: Photoreceptor Nuclei, LongGMR-Gal4 > UAS-Gnmt, Zeitgeber Time 12, Replicate 1


title: Photoreceptor Nuclei, LongGMR-Gal4 > UAS-Gnmt, Zeitgeber Time 8, Replicate 2


title: Photoreceptor Nuclei, LongGMR-Gal4 > UAS-Gnmt, Zeitgeber Time 4, Replicate 2


title: Sample 30, lesional scalp

city: New York

first: Emma

last: Guttman-Yassky

state: New York

address: 5 E 98th St

department: Dermatology

institute: Icahn School of Medicine at Mount Sinai

description:
Library name: Sample 30
10x Genomics

data_processing:
The demultiplexing, barcode processing, and gene counting + aggregation were conducted using the Cell Ranger software v8.0. Briefly, raw 5′ scRNA-seq data were processed with Cell Ranger v8.0 using the gene expression pipeline to generate gene-by-cell count matrices from Illumina FASTQ files derived from Chromium 5′ libraries. Reads were aligned to the appropriate reference transcriptome, cell barcodes were corrected and filtered to distinguish high-quality cells from background, and unique molecular identifiers (UMIs) were collapsed to obtain per-gene UMI counts per cell, followed by generation of unfiltered and filtered count matrices and summary QC metrics for downstream analysis.
Assembly: GRCh38
Supplementary files format and content: Tab-separated value files and matrix files

source_name: Skin

extract_protocol:
Frozen tissues were rapidly thawed, minced, and subjected to two sequential enzymatic digestions in Liberase TL (2 mg/ml stock diluted in PBS) at 37 °C with gentle rotation to obtain a single-cell suspension, with an optional brief secondary digestion in 0.05% Trypsin for highly cohesive samples. Following digestion, released cells were filtered through FBS-prewetted 40–70 µm strainers into RPMI containing 20% FBS, washed with cold PBS, and pelleted by low-speed centrifugation at 4 °C before final resuspension in RPMI with 2% BSA and RNase inhibitor for 10x Genomics GEM generation. Cell concentration and viability were assessed using a LUNA automated cell counter with Acridine Orange/Propidium Iodide staining prior to loading.
Library preparation was performed using the Chromium NextGEM Single Cell 5' Kit v2 (Dual Index) to generate 5′ gene expression libraries from amplified full-length cDNA produced after GEM-RT and cDNA amplification according to manufacturer's protocol. The amplified cDNA was first enzymatically fragmented, followed by combined end repair and A-tailing reactions, with reaction products subjected to a double-sided SPRIselect cleanup to enrich for appropriately sized inserts. Size-selected fragments then underwent adaptor ligation to add truncated Illumina sequencing adaptors, another SPRIselect cleanup to remove excess adaptors and small fragments, and a final sample index PCR that incorporated P5, P7, i5, and i7 sequences to yield dual-indexed, Illumina-ready 5′ gene expression libraries.

value: Skin

value: Lesional

value: n/a, human scalp


title: Photoreceptor Nuclei, LongGMR-Gal4 > UAS-Gnmt, Zeitgeber Time 4, Replicate 1


title: Sample 29, lesional scalp

description:
Library name: Sample 29
10x Genomics


title: Sample 28, lesional scalp

description:
Library name: Sample 28
10x Genomics


title: SC5314 UME6OE, bio rep_3

city: Athens

first: Katharina

last: Goerlich

state: GA

address: 120E Green St

department: Microbiology

institute: University of Georgia

description: Library name: KG21_3

data_processing:
Original data file from high-throughput sequencing platform (Illumina) is transformed to sequenced reads by CASAVA base recognition.
Raw data are stored in FASTQ(fq) format files, which contain sequences of reads and corresponding base quality.
Removed reads with adapter contamination. Removed reads when uncertain nucleotides constitute more than 10% of either read. Removed reads when low quality nucleotides constitute more than 50% of the read.
HISAT2 was used to align reads to provided reference genome (http://www.candidagenome.org/download/sequence/C_albicans_SC5314/Assembly22/current/C_albicans_SC5314_A22_current_chromosomes.fasta.gz).
Assembly: Assembly 22
Supplementary files format and content: txt files include FPKM values for each sample based on condition

organism: Candida albicans

source_name: Yeast and hyphae

growth_protocol: C. albicans cells were grown in RPMI for 4hrs at 37C shaking.

extract_protocol:
RNA extraction was performed by disrupting cells with Zirconia beads and isolating RNA using 25:24:1 phenol:chloroform:isoamylalcohol in combination with a Qiagen Rneasy Mini Kit
Sequencing libraries were generated by purifying messenger RNA from total RNA using poly-T oligo–attached magnetic beads. The first cDNA was synthesized using random hexamer primers, followed by sequencing of both ends of cDNA fragments using the Illumina platform

value: Yeast and hyphae

tag: treatment

value: RPMI, 4hrs


title: Sample 27, lesional scalp

description:
Library name: Sample 27
10x Genomics

tag: batch


title: Photoreceptor Nuclei, LongGMR-Gal4 > UAS-Gnmt, Zeitgeber Time 0, Replicate 3


title: Photoreceptor Nuclei, LongGMR-Gal4 > UAS-Gnmt, Zeitgeber Time 0, Replicate 2


title: SC5314 UME6OE, bio rep_2

description: Library name: KG21_2


title: Sample 25, lesional scalp

description:
Library name: Sample 25
10x Genomics


title: Photoreceptor Nuclei, LongGMR-Gal4 > UAS-Gnmt, Zeitgeber Time 0, Replicate 1


title: SC5314 UME6OE, bio rep_1

description: Library name: KG21_1


title: SC5314 ndt80△/△UME6OE, bio rep_3

description: Library name: KG16_3


title: SC5314 ndt80△/△UME6OE, bio rep_2

description: Library name: KG16_2


title: Sample 24, lesional scalp

description:
Library name: Sample 24
10x Genomics


title: SC5314 ndt80△/△, bio rep_3

description: Library name: KG11_3


title: Sample 23, lesional scalp

description:
Library name: Sample 23
10x Genomics


title: Photoreceptor Nuclei, LongGMR-Gal4 > UAS-GnmtS145A, Zeitgeber Time 20, Replicate 3


title: Sample 22, lesional scalp

description:
Library name: Sample 22
10x Genomics


title: Photoreceptor Nuclei, LongGMR-Gal4 > UAS-GnmtS145A, Zeitgeber Time 20, Replicate 2


title: SC5314 ndt80△/△, bio rep_1

description: Library name: KG11_1


title: SC5314 WT, bio rep_3

description: Library name: MC22_3

value: WT


title: Photoreceptor Nuclei, LongGMR-Gal4 > UAS-GnmtS145A, Zeitgeber Time 20, Replicate 1


title: SC5314 WT, bio rep_2

description: Library name: MC22_2


title: SC5314 WT, bio rep_1

description: Library name: MC22_1


title: Photoreceptor Nuclei, LongGMR-Gal4 > UAS-GnmtS145A, Zeitgeber Time 16, Replicate 3


title: SC5314 ndt80△/△, bio rep_2

description: Library name: KG11_2


title: SC5314 ndt80△/△UME6OE, bio rep_1

description: Library name: KG16_1


title: Acinetobacter venetianus RAG-1 biofilm grown on the electrode was subjected to a BOD shock for 2 h.

city: Tianjin

first: Yilian

last: Han

state: Tianjin

address: 38 Tongyan Road, Haihe Education Park, Jinnan District

institute: Nankai University

description:
Library name: RAG-1_DT
treatment

data_processing:
Raw reads were quality-checked and adaptor sequences were removed using standard quality control procedures.
Clean reads were mapped to the reference genome of Acinetobacter venetianus RAG-1 using a suitable aligner.
Gene-level read counts were generated and normalized to produce expression values.
Assembly: reference genome of Acinetobacter venetianus RAG-1
Supplementary files format and content: Tab-delimited text file containing gene-level expression values for all samples. The first column contains gene identifiers, followed by expression values for HR, ER, DT and AT samples.

organism: Acinetobacter venetianus RAG-1 = CIP 110063

source_name: Acinetobacter venetianus RAG-1: electrode-associated biofilm

growth_protocol: RAG-1 cells were cultured in appropriate growth medium under aerobic conditions at 30°C until reaching the required physiological stage for each experimental condition. For heterotrophic respiration (HR), cells were grown in nutrient broth to logarithmic phase. For electrotrophic conditions (ER, DT, AT), cells were grown as electrode-associated biofilms in an electrochemical system.

extract_protocol:
Total RNA was extracted using a commercial bacterial RNA extraction kit following the manufacturer's instructions. RNA quality and integrity were assessed prior to library construction.
RNA libraries were prepared using a stranded RNA library preparation kit following the manufacturer's protocol after rRNA depletion.

treatment_protocol: Four physiological states were sampled:HR: heterotrophic respiration;ER: electrotrophic respiration at baseline current stabilization;DT: biofilm collected during BOD testing at minimum current;

value: Acinetobacter venetianus RAG-1:electrode-associated biofilm

value: wild type strain RAG-1

value: BOD testing


title: Acinetobacter venetianus RAG-1， electroautotrophic biological cathode was cultivated for 3 days

description:
Library name: RAG-1_ER
treatment

value: electrotrophic respiration


title: Sample 26, lesional scalp

description:
Library name: Sample 26
10x Genomics


title: Acinetobacter venetianus RAG-1 biofilm recovered for 2 h after BOD exposure.

description:
Library name: RAG-1_AT
treatment

value: post-BOD recovery


title: Photoreceptor Nuclei, LongGMR-Gal4 > UAS-GnmtS145A, Zeitgeber Time 16, Replicate 2


title: Sample 21, lesional scalp

description:
Library name: Sample 21
10x Genomics


title: Acinetobacter venetianus RAG-1 was cultured heterotrophically in LB medium for 15 h.

description:
Library name: RAG-1_HR
control

source_name: Acinetobacter venetianus RAG-1: planktonic cells

value: Acinetobacter venetianus RAG-1:planktonic cells

value: heterotrophic respiration


title: Photoreceptor Nuclei, LongGMR-Gal4 > UAS-GnmtS145A, Zeitgeber Time 16, Replicate 1

value: Day 10


title: Photoreceptor Nuclei,LongGMR-Gal4 > UAS-GnmtS145A, Zeitgeber Time 12, Replicate 3


title: Primary pancreas tumor, survival endpoint, mouse 27124

city: Houston

first: Fredrik

middle: Ivar

last: Thege

state: Texas

address: 6565 MD Anderson Blvd

department: Translational Molecular Pathology

institute: UT MD Anderson Cancer Center

description: Library name: 22_27124-Pa13_S22_ME

data_processing:
Guide sequences from the Onco1 library were matched to FASTQ files to generate raw counts.
Supplementary files format and content: csv-file, table raw guide counts
Library strategy: CRISPR Screen

source_name: Pancreas

extract_protocol:
Flash frozen tissues or cell pellets were homogenized in ATL buffer and genomic DNA was isolated using the Qiagen DNeasy blood and tissue kit. Plasmid DNA was isolated using Qiagen EndoFree MaxiPrep kit.
A region of genomic or plasmid DNA containing the guide sequences was amplified using direct PCR (NEBNext Ultra II Q5) with dual-indexed primers. Libraries were sequenced using 75 cycle single-end sequencing.

value: Pancreas

tag: cell line

value: Whole pancreas tissue

value: PPKS


title: Primary pancreas tumor, survival endpoint, mouse 27123

description: Library name: 21_27123-Pa6_S21_ME


title: Sample 18, nonlesional scalp

description:
Library name: Sample 18
10x Genomics

value: Skin

value: Nonlesional


title: Sample 19, lesional scalp

description:
Library name: Sample 19
10x Genomics

value: Lesional

value: n/a, human scalp


title: Sample 17, nonlesional scalp

description:
Library name: Sample 17
10x Genomics


title: Primary pancreas tumor, survival endpoint, mouse 27119

description: Library name: 138_27119-Panc3_S124_ME


title: Sample 20, lesional scalp

description:
Library name: Sample 20
10x Genomics


title: Primary pancreas tumor, survival endpoint, mouse 27152

description: Library name: 20_27152-Pa7_S20_ME


title: Primary pancreas tumor, survival endpoint, mouse 26886

description: Library name: 3_26886-Pa13_S3_ME


title: Primary pancreas tumor, survival endpoint, mouse 26882

description: Library name: 1_26882-Pa5_S1_ME


title: Sample 16 nonlesional scalp

description:
Library name: Sample 16
10x Genomics


title: Primary lung tumor, survival endpoint, mouse 27146

description: Library name: 147_27146-LuT7_S133_ME

source_name: Lung

value: Lung

value: Whole lung tissue


title: Primary lung tumor, survival endpoint, mouse 27137

description: Library name: 19_27137-Lu5_S19_ME


title: Photoreceptor Nuclei, LongGMR-Gal4 > UAS-GnmtS145A, Zeitgeber Time 8, Replicate 3

tag: Sex

value: male

value: Outer photoreceptors


title: Photoreceptor Nuclei,LongGMR-Gal4 > UAS-GnmtS145A, Zeitgeber Time 12, Replicate 1


title: Sample 15, nonlesional scalp

description:
Library name: Sample 15
10x Genomics


title: Photoreceptor Nuclei, LongGMR-Gal4 > UAS-GnmtS145A, Zeitgeber Time 8, Replicate 2


title: Primary lung tumor, survival endpoint, mouse 26651

description: Library name: 16_26651-Lu6_S16_ME


title: Primary lung tumor, survival endpoint, mouse 26864

description: Library name: 17_26864-Lu6_S17_ME


title: Primary lung tumor, survival endpoint, mouse 26835

description: Library name: 18_26835-Lu2_S18_ME


title: Primary lung tumor, survival endpoint, mouse 26653

description: Library name: 15_26653-Lu4_S15_ME


title: Mild infection, replicate 1, RNAseq

city: chongqing

first: zhou

last: sha

address: 55 University City South Road, Shapingba District, Chongqing, China

institute: chongqing university

data_processing:
The raw reads were further processed with a bioinformatic pipelinetool, BMKCloud(www.biocloud.net) online platform.
Assembly: GRCm38
Supplementary files format and content: Tab-separated values files and matrix files

value: Liver


title: Photoreceptor Nuclei,LongGMR-Gal4 > UAS-GnmtS145A, Zeitgeber Time 12, Replicate 2


title: Sample 13, nonlesional scalp

description:
Library name: Sample 13
10x Genomics


title: Photoreceptor Nuclei, LongGMR-Gal4 > UAS-GnmtS145A, Zeitgeber Time 8, Replicate 1


title: Sample 14, nonlesional scalp

description:
Library name: Sample 14
10x Genomics


title: Primary lung tumor, survival endpoint, mouse 26648

description: Library name: 12_26648-Lu3_S12_ME


title: Primary lung tumor, survival endpoint, mouse 26649

description: Library name: 14_26649-Lu3_S14_ME


title: Primary lung tumor, survival endpoint, mouse 26410

description: Library name: 13_26410-Lu3_S13_ME


title: Sample 10, healthy control scalp

description:
Library name: Sample 10
10x Genomics

value: Healthy Control


title: Primary lung tumor, survival endpoint, mouse 26837

description: Library name: 10_26837-Lu3_S10_ME


title: Sample 11, healthy control scalp

description:
Library name: Sample 11
10x Genomics


title: Sample 12, nonlesional scalp

description:
Library name: Sample 12
10x Genomics


title: Primary lung tumor, survival endpoint, mouse 26647

description: Library name: 9_26647-Lu3_S9_ME


title: Sample 9, healthy control scalp

description:
Library name: Sample 9
10x Genomics


title: Photoreceptor Nuclei, LongGMR-Gal4 > UAS-GnmtS145A, Zeitgeber Time 4, Replicate 3


title: PPKS mouse pancreas, non-targeted sgRNA, survival endpoint, mouse 25468

description:
Library name: 25468NT
75 SE

data_processing:
FASTQ files from different lanes were concatenated and adaptor trimmed. FASTQ reads were then aligned to the mm39 mouse transcriptome using the STAR aligner to generate raw counts.
Assembly: GRCm39 (mm39)
Supplementary files format and content: cvs-file, table with raw counts

extract_protocol:
total RNA was extracted from flash frozen pancreas tissues using Qiagen Allprep Mini kit (including optional on-column DNase treatment)
Directional mRNA-seq libraries were generated using KAPA mRNA HyperPrep kit, libraries were single-indexed using Illumina TruSeq single index adapters. 800 ng total RNA was used to generate libraries. Libraries were sequenced on an Illumina NextSeq550 sequencer (75 cycles, single end)

treatment_protocol: PPKS mice were treated with Myc-targeting or non-targeting CMV-Cre/U6-sgRNA(MS2) lentivirus through retrograde ductal injection. Tissues were collected at survival endpoint.

value: Whole pancreas tumor


title: Photoreceptor Nuclei, LongGMR-Gal4 > UAS-GnmtS145A, Zeitgeber Time 4, Replicate 2


title: Primary lung tumor, survival endpoint, mouse 26646

description: Library name: 11_26646-Lu6_S11_ME


title: PPKS mouse pancreas, non-targeted sgRNA, survival endpoint, mouse 25003

description:
Library name: 25003NT
75 SE


title: Photoreceptor Nuclei, LongGMR-Gal4 > UAS-GnmtS145A, Zeitgeber Time 0, Replicate 3


title: Photoreceptor Nuclei, LongGMR-Gal4 > UAS-GnmtS145A, Zeitgeber Time 4, Replicate 1


title: Photoreceptor Nuclei, LongGMR-Gal4 > UAS-GnmtS145A, Zeitgeber Time 0, Replicate 2


title: PPKS mouse pancreas, non-targeted sgRNA, survival endpoint, mouse 23654

description:
Library name: 23654NT
75 SE


title: PPKS mouse pancreas, Myc-targeted sgRNA, survival endpoint, mouse 22466

description:
Library name: 22466Myc
75 SE


title: Sample 7, healthy control scalp

description:
Library name: Sample 7
10x Genomics


title: PPKS mouse pancreas, non-targeted sgRNA, survival endpoint, mouse 23830

description:
Library name: 23830NT
75 SE


title: Photoreceptor Nuclei, LongGMR-Gal4 > UAS-GnmtS145A, Zeitgeber Time 0, Replicate 1


title: PPKS mouse pancreas, Myc-targeted sgRNA, survival endpoint, mouse 24318

description:
Library name: 24318Myc
75 SE


title: Sample 6, healthy control scalp

description:
Library name: Sample 6
10x Genomics


title: Photoreceptor Nuclei, w1118 control, Zeitgeber Time 20, Replicate 3


title: PPKS mouse pancreas, Myc-targeted sgRNA, survival endpoint, mouse 23329

description:
Library name: 23329Myc
75 SE


title: PPKS mouse pancreas, Myc-targeted sgRNA, survival endpoint, mouse 22490

description:
Library name: 22490Myc
75 SE


title: Sample 5, healthy control scalp

description:
Library name: Sample 5
10x Genomics


title: Photoreceptor Nuclei, w1118 control, Zeitgeber Time 20, Replicate 1


title: Sample 8, healthy control scalp

description:
Library name: Sample 8
10x Genomics


title: Photoreceptor Nuclei, w1118 control, Zeitgeber Time 20, Replicate 2


title: Brain Organoid, DEAB, Day 60, Riboseq, biol rep 3

city: Shanghai City

first: Yali

last: Li

address: No.320, Yueyang Avenue

institute: Center for Excellence in Molecular Cell Science

description:
D60_Riboseq_matrix.tsv
D60_DEAB_Riboseq_3

library_source: other

data_processing:
library strategy: Ribo-seq
discarding low-quality reads
trimming adapter sequence
removing ribosomal RNA(rRNA)
non-rRNA sequencing reads were aligned to human genomic reference (hg38) using HISAT2
Assembly: GRCh38
Supplementary files format and content: matrix files

molecule: other

extract_protocol:
For RNA-seq, total mRNA was extracted from D60 organoids treated with DMSO, MTK or DEAB by using the RNeasy Mini kit. For Ribo-seq, cellular RNA were extracted by mild lysis buffer and Lysates oforganoids were treated with 750 U RNase I for 45 minutes at room temperature. Samples were then transferred to an ultracentrifuge tube on a sucrose cushion (~34%) and centrifuged at 70,000 rpm at 4C for 4 hr.
RNA libraries for bulk RNA-seq were prepared using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® following manufacturer's protocols. For riboseq, Ribosome-protected fragments were purified using miRNeasy RNA isolation kit (QIAGEN, cat. No. 217004). RNA was size selected by running a polyacrylamide gel, and then dephosphorylated, linker ligated, and then subjected to RT-PCR, circularization, rRNA depletion, and 10-12 cycles of PCR. The enzymes used were T4 PNK (NEB, cat. No. M0201S), T4 RNA ligase 2, truncated (NEB, cat. No. M0242S), Universal miRNA Cloning Linker (NEB, cat. No. S1315S), Superscript III (Invitrogen, cat. No 18080-044), Circ Ligase (Epicentre, cat. No. CL4111K), NEBNext® High-Fidelity 2X PCR Master Mix (cat. No. M0541L). Resulting fragments were size selected from an 8% acrylamide non-denaturing gel and purified by incubation overnight with DNA gel extraction buffer (300 mM NaCl, 10 mM Tris (pH 8) and 1 mM EDTA).

treatment_protocol: The medium with the addition of DMSO or 18.5 μM MTK or 10 μM DEAB was refreshed every day from day 20 to day 60.

value: Human embryonic stem cells

value: WT

value: cerebral differentiation with DEAB treatment

value: Day 60


title: PPKS mouse pancreas, non-targeted sgRNA, survival endpoint, mouse 24893

description:
Library name: 24893NT
75 SE

value: Pancreas


title: Brain Organoid, DEAB, Day 60, Riboseq, biol rep 1

description:
D60_Riboseq_matrix.tsv
D60_DEAB_Riboseq_1


title: Brain Organoid, MTK, Day 60, Riboseq, biol rep 3

description:
D60_Riboseq_matrix.tsv
D60_MTK_Riboseq_3

value: cerebral differentiation with MTK treatment


title: Sample 4, healthly control scalp

description:
Library name: Sample 4
10x Genomics

value: Skin


title: Photoreceptor Nuclei, w1118 control, Zeitgeber Time 16, Replicate 3

value: Day 10


title: Sample 3, healthy control scalp

description:
Library name: Sample 3
10x Genomics


title: Brain Organoid, DMSO, Day 60, Riboseq, biol rep 2

description:
D60_Riboseq_matrix.tsv
D60_DMSO_Riboseq_2

value: cerebral differentiation with DMSO treatment


title: Brain Organoid, DEAB, Day 60, Riboseq, biol rep 2

description:
D60_Riboseq_matrix.tsv
D60_DEAB_Riboseq_2


title: Brain Organoid, DMSO, Day 60, Riboseq, biol rep 3

description:
D60_Riboseq_matrix.tsv
D60_DMSO_Riboseq_3


title: Sample 1, healthy control scalp

description:
Library name: Sample 1
10x Genomics

value: n/a, human scalp


title: Photoreceptor Nuclei, w1118 control, Zeitgeber Time 16, Replicate 2


title: Brain Organoid, MTK, Day 60, Riboseq, biol rep 1

description:
D60_Riboseq_matrix.tsv
D60_MTK_Riboseq_1


title: Sample 2, healthly control scalp

description:
Library name: Sample 2
10x Genomics


title: PPKS mouse pancreas, Myc-targeted sgRNA, survival endpoint, mouse 23822

description:
Library name: 23822Myc
75 SE

value: PPKS


title: RNA-seq in HeLa Nigericin Replicate 3

city: Salt Lake City

first: Emily

middle: Rose

last: Wilson

state: UT

address: 2000 Circle of Hope

department: Oncological Sciences

institute: Huntsman Cancer Institute

description:
Library name: HeLa_Nigericin_rep3
Nigericin positive control

data_processing:
reads alignment: Bowtie2
read counts calculation: RSEM
Assembly: hg38
Supplementary files format and content: RSEM output

source_name: Cervical cancer cell line

growth_protocol: HeLa cells were cultured in complete DMEM (10% FBS, 1% Penicillin-Streptomycin; Corning) at humidified 37 degrees Celsius and 5% CO2 before and after treatment.

extract_protocol:
RNA was extracted using Quick-RNA Miniprep Kit (Zymo) at 48 hours for GeCas12a2 conditions or 5 hours for Nigericin condition and kept at -80 degrees Celsius until poly-A library preparation.
NEB Ultra II Directional RNA Library Prep with poly-A mRNA isolation

treatment_protocol: 250 pmol of GeCa12a2 in complex with either gGFP or gNT were delivered by electroporation to 5x10^5 HeLa cells. Control conditions were either treated with PBS electroporation or 5 uM Nigericin (MedChemExpress).

value: Cervical cancer cell line

value: HeLa

value: Nigericin


title: Brain Organoid, MTK, Day 60, Riboseq, biol rep 2

description:
D60_Riboseq_matrix.tsv
D60_MTK_Riboseq_2


title: Photoreceptor Nuclei, w1118 control, Zeitgeber Time 16, Replicate 1

value: male

value: Outer photoreceptors


title: RNA-seq in HeLa Nigericin Replicate 2

description:
Library name: HeLa_Nigericin_rep2
Nigericin positive control


title: Brain Organoid, DMSO, Day 60, Riboseq, biol rep 1

description:
D60_Riboseq_matrix.tsv
D60_DMSO_Riboseq_1


title: Photoreceptor Nuclei, w1118 control, Zeitgeber Time 12, Replicate 3


title: Photoreceptor Nuclei, w1118 control, Zeitgeber Time 12, Replicate 2


title: Brain Organoid, MTK, Day 60, RNAseq, biol rep 1

description:
D60_RNAseq_matrix.tsv
D60_MTK_RNAseq_1

data_processing:
discarding low-quality reads
trimming adapter sequence
removing ribosomal RNA(rRNA)
non-rRNA sequencing reads were aligned to human genomic reference (hg38) using HISAT2
Assembly: GRCh38
Supplementary files format and content: matrix files


title: Brain Organoid, DEAB, Day 60, RNAseq, biol rep 2

description:
D60_RNAseq_matrix.tsv
D60_DEAB_RNAseq_2


title: Brain Organoid, MTK, Day 60, RNAseq, biol rep 3

description:
D60_RNAseq_matrix.tsv
D60_MTK_RNAseq_3


title: Brain Organoid, DEAB, Day 60, RNAseq, biol rep 3

description:
D60_RNAseq_matrix.tsv
D60_DEAB_RNAseq_3


title: Brain Organoid, DMSO, Day 60, RNAseq, biol rep 1

description:
D60_RNAseq_matrix.tsv
D60_DMSO_RNAseq_1


title: Photoreceptor Nuclei, w1118 control, Zeitgeber Time 8, Replicate 3