title: WT_H3K4me3

first: James

middle: A.

last: Cain

address: Guy's Hospital, Great Maze Pond

department: Infectious Diseases

institute: King's College London

description: Library name: WT, H3K4me3, Control

data_processing:
CUT&RUN fastq files were processed using the pipeline summarised in Figure 2.2. Adapters were trimmed from fastq reads using trim-galore. Fastq files were aligned using bowtie2 (Langmead and Salzberg, 2012) to a N-Masked mouse genome (mm39). The N-Masked genome file was generated using SNPSplit (Krueger and Andrews, 2016) that required B6/CAST SNP information (.vcf) and the mm39 fasta genome sequence file. Once aligned, the aligned reads are then split into B6 (maternal) and CAST (paternal) read files for processing into .bigWigs using deeptools (Ramírez et al., 2014). Reads upstream and downstream of Mcts2 were counted using featureCounts with a custom .saf file from the aligned and split .bam file. RPKM normalisation was performed on aligned reads mapping to chr2 to alleviate normalisation artefacts derived from other chromosomes.
Assembly: mm39
Supplementary files format and content: .bigWig files showing RPKM normalisation. bigWig files also provided for split alleles post-SNPsplit processing, either RPKM normalised to the whole genome or specificallly at chromosome 2.
Library strategy: CUT&Run

growth_protocol: Hybrid C57BL/6 / CAST/EiJ mouse NSCs were extracted from the subventricular zone and expanded as previously described (Ferrón et al., 2007). NSCs were cultured in N2B27 media + Fgf2 + Egf : DMEM/F12 [Gibco, 11320033]: Neurobasal [Gibco, 21103049] at a 1:1 ratio, N2 1X final [Millipore, SCM012], B27 0.5x final [Gibco, 17504- 044], L-Glutamine 1x final [Gibco, 25030-024] and 2-mercaptoethanol 0.1mM [Gibco, 31350-010]. FGF2 [Peprotech, 100-18B] and EGF [Peprotech, 315-09] were reconstituted at in PBS + 0.1% BSA and 1µl of each growth factor was added per 10ml of N2B27 media to a final concentration of 10ng/ml. Cell culture plates were coated with 1/100th diluted GeltrexTM LDEV-Free Reduced Growth Factor Basement Membrane Matrix [Gibco, A1413201] in DMEM-F12 media prior to NSC plating. Cells were detached using Accutase [Millipore, SCR005] and passaged every 2-3 days when reaching 80% confluency. Cells being recovered from liquid nitrogen storage were cultured for one day in N2B27 + Fgf2 + Egf + RevitaCellTM Supplement 1X [ThermoFisher, A2644501].

extract_protocol:
CUT&RUN was performed on freshly detached NSCs following the protocol detailed in(Janssens and Henikoff, 2019) with some modifications detailed here. Activation buffer and Concanavalin A beads were purchased from Cell Signalling Technologies [#93569]. Digitonin concentration utilised was at 5% across all buffers and MNase digestion time was at 30mins on ice unless otherwise stated. Recovery of DNA fragments using each method was confirmed using Qubit dsDNA HS Assay [Invitrogen, Q32851]. 10ng of this DNA was utilised for generation of CUT&RUN libraries.
Libraries were generated using NEBNext® UltraTM II DNA Library Prep Kit for Illumina® [E7645S] and index using NEBNext® Mtiplex Oligos for Illumina® (Index Primers Set 1) [E7335S]. 1µl of 3µM of NEBNext Adaptor was utilised to reduce adaptor dimers. Sera-Mag select beads [Cytiva, 29343052] were used for DNA clean-up and size selection. DNA Library size was measured using Agilent High Sensitivity D1000 ScreenTape [Agilent, 5067- 5585].

value: Brain

value: Neural Stem Cells


title: UMUC3_Control_sh_Smoke_4

status: Public on Jun 11 2026

type: SRA

city: Houston

first: Karthik Reddy

last: Kami Reddy

email: karthikr@bcm.edu, amara@bcm.edu, putluri@bcm.edu, piyarath@bcm.edu

state: Texas

address: 1 Baylor Plaza

department: Molecular and Cellular Biology

country: USA

institute: Baylor College of Medicine

description: Library name: Sample 10

library_source: transcriptomic

data_processing:
Fastq files were run through fastqc for primary qc
Sequence reads were trimmed for adaptor sequence/low-quality sequence using cutadapt (parameter- Default settings)
Trimmed sequence reads were mapped to GRCh38 using Salmon
with ‘libType A’ and ‘validateMapping’ options
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include Feature counts

molecule: total RNA

organism: Homo sapiens

source_name: Xenograft Tissue

growth_protocol: UMUC3 control and FASN KD cells were grown in regular media and CSM media before engraftment.

extract_protocol:
For transcriptomics analysis from mouse xenografts, RNA was isolated from frozen tissues using the QIAGEN RNAeasy microkit.
Libraries were created from the cDNA by attaching an adenosine to the 3’ end and ligating adapters to the ends

treatment_protocol: Cells are pre-exposed to 10%CSM before engraftment

tag: tissue

value: Xenograft Tissue

tag: cell line

tag: cell type

value: Human

tag: genotype

value: Control+Smoke


title: Degos_3_CSF_Rep2

city: Bethesda

first: Stephen

middle: R

last: Brooks

state: MD

address: 50 SOUTH DR, RM 1140

department: Biodata Mining and Discovery Section

institute: NIAMS/NIH

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 v6.0.0 or v6.0.2
Assembly: GRCh38-2020-A
Supplementary files format and content: Tab-separated values files and matrix files

source_name: CSF

extract_protocol:
Skin biopsy from Degos disease patients and healthy volunteers were washed with PBS and digested enzymatically using whole skin dissociation kit (Miltenyi Biotec).  Following mechanical dissociation and filteration, cells were resuspended in 500 μL of complete RPMI-1640 with 10% FBS before sorting. Skin live cells were enriched by fluorescence-activated cell sorting (FACS) using Sytox green. PBMCs from blood were isolated according to desity centrifugation method. PBMCs and CSF samples were subjected to ACK lysis treatment to remove RBCs. Finally, single cell suspensions prepared from skin, PBMCs and CSF were counted and and cell concentration was adjusted in the range of 700-1200 cells/ul with the viability of > 70% before being used for single-cell RNA-sequencing.
Library construction was performed in accordance with 10X Genomics protocol (10X Chromium 5' v2 or 5'-HT kit).

value: CSF


title: perR mutant S. aureus, iron-replete, biol rep 1

city: London

first: Alexander

last: Sheikh

state: Ontario

address: 1400 Western Road

department: Microbiology and Immunology

country: Canada

institute: Western University

description:
Library name: Sample 4
Processed data file contains TPM values from all samples and differential expression calculations along with confidence and p-value. Each tab is named after the comparison being made and the corresponding figure utilizing this data.

data_processing:
Sequencing reads were mapped to the reference S. aureus USA300 FPR3757 genome in Geneious Prime 2025.1 (https://www.geneious.com)
Demultiplexing, quality control, and adapter trimming was performed by the Microbial Genome Sequencing Center in Pittsburgh, PA \with bcl-convert (v4.2.4)
Assembly: Staphylococcus aureus USA300_FPR3757
Supplementary files format and content: xlsx file format, contains TPM values and calculated differential expression and p-values for every transcript

organism: Staphylococcus aureus

growth_protocol: Overnight precultures grown in tryptic soy broth (TSB) with 100µM EDDHA were subcultured in technical duplicate at a starting OD600 of 0.1 in fresh TSB + EDDHA and left to grow for 3 hours at 37 °C with shaking to an OD600 of ~1.0.

extract_protocol:
Cells were normalized to an OD600 equivalent of 3.0, pelleted, lysed, and RNA extraction performed with Trizol (Invitrogen) according to manufacturer’s instructions. Extracted RNA was then subject to rigorous DNAse treatment (Invitrogen) and phenol chloroform extraction to inactivate and remove DNAse.
RNA samples were processed by the Microbial Genome Sequencing Center in Pittsburgh, PA. Library preparation was performed using Illumina’s Stranded Total RNA Prep Ligation with Ribo-Zero Plus kit and 10bp unique dual indices (UDI). Sequencing was done on a NovaSeq X Plus, producing paired end 150bp reads.

treatment_protocol: One of each technical duplicate in above protocol was spiked with 50µM ferric chloride following 3 hours of growth and then all tubes were left to grow for another hour at 37 °C with shaking.

tag: treatment

value: 100 µM EDDHA, 50 µM ferric chloride


title: KP_sgBACH1_siCTRL_3

city: Marseille

first: Luca

last: Lignitto

address: 27 Boulevard Leï Roure

country: France

institute: CNRS

description: Library name: SAMPLE_6

data_processing:
RNA-seq reads were aligned to the reference genome using Subread-align (v1.6.4) with default parameters.
Mapped reads were filtered using samtools (v1.9) with --exclude-flags 4.
Gene counts were obtained with featureCounts (v1.6.4).
Differential expression analysis was performed using DESeq2 (v1.26.0).
Assembly: mm10
Supplementary files format and content: tab-delimited raw counts for each sample

organism: Mus musculus

source_name: lung

growth_protocol: KP cells were maintained in DMEM supplemented with 10% FBS and antibiotics in humidified atmosphere with 5% CO2 at 37 C

extract_protocol:
RNA extraction kit qiagen
TruSeq Stranded mRNA Sample Preparation Guide, Part # 15031047 Rev. E

treatment_protocol: knockout by CRISPR/Cas9 and knockdown by siRNA

value: lung

value: KP

value: lung adenocarcinoma

value: KrasLSL-G12D/+; Trp53flox/flox


title: UMUC3_Control_sh_Smoke_3

description: Library name: Sample 9


title: Degos_3_CSF_Rep1

description: 10x Genomics


title: KP_sgBACH1_siCTRL_2

description: Library name: SAMPLE_5


title: perR mutant S. aureus, iron-deplete, biol rep 1

description:
Library name: Sample 3
Processed data file contains TPM values from all samples and differential expression calculations along with confidence and p-value. Each tab is named after the comparison being made and the corresponding figure utilizing this data.

value: 100 µM EDDHA


title: UMUC3_Control_sh_Smoke_2

description: Library name: Sample 8


title: Degos_13_CSF

description: 10x Genomics


title: Wild-type S. aureus, iron-replete, biol rep 1

description:
Library name: Sample 2
Processed data file contains TPM values from all samples and differential expression calculations along with confidence and p-value. Each tab is named after the comparison being made and the corresponding figure utilizing this data.

value: wild-type


title: KP_sgBACH1_siCTRL_1

description: Library name: SAMPLE_4


title: KP_sgCTRL_siCTRL_3

description: Library name: SAMPLE_3


title: Wild-type S. aureus, iron-deplete, biol rep 1

description:
Library name: Sample 1
Processed data file contains TPM values from all samples and differential expression calculations along with confidence and p-value. Each tab is named after the comparison being made and the corresponding figure utilizing this data.


title: Degos_5_CSF_Rep1

description: 10x Genomics


title: ChIP_UMUC3_Input_Smoke_FASNKD_rep1

first: H. Courtney

last: Hodges

state: TX

address: 1 Baylor Plaza, BCM 229

department: Department of Molecular & Cellular Biology

description:
Library name: ChIP_UMUC3_Input_Smoke_FASNKD_rep1
Input

library_source: genomic

data_processing:
ChIP-seq reads were aligned to the hg38 genome assembly using Bowtie v2.4.1.
Fragments with read qualities greater than 10 were considered for further analysis.
All bigWig files are unscaled counts and require scaling before comparison across samples.
Assembly: hg38
Supplementary files format and content: Unscaled bigWig files of genome-wide coverage

molecule: genomic DNA

growth_protocol: UMUC3 Control sh and FASN KD cells were cultured in MEM (Sigma) supplemented with 1% penicillin/streptomycin (PS) and 10% FBS

extract_protocol:
Lysates were obtained from sonicated nuclei crosslinked with either 1% formaldehyde, followed by 125mM glycine to stop cross-linking. Protein-DNA complexes were isolated by immunoprecipitation.
All libraries were barcoded and prepared for sequencing using standard Illumina protocols.

treatment_protocol: Cells were treated with 10% cigarette smoke media (10%CSM) prepared in MEM supplemented with 1% penicillin/streptomycin (PS) and 10% FBS. Control cells are cultured in regular media conditions.

value: FASN KD

value: 10% CSM media


title: UMUC3_FASN_KD_2

description: Library name: Sample 5

value: KD


title: KP_sgCTRL_siCTRL_2

description: Library name: SAMPLE_2


title: Degos_3_PBMC_PostRuxo_Wk_1

description: 10x Genomics

source_name: PBMC

value: PBMC


title: KP_sgCTRL_siCTRL_1

description: Library name: SAMPLE_1


title: UMUC3_FASN_KD_1

description: Library name: Sample 4


title: PM_rep3

first: Hye Kyung

last: Lee

address: 8 CENTER DR RM 107

department: National Institute of Diabetes and Digestive and Kidney (NIDDK)

institute: National Institutes of Health (NIH)

description: Library name: Sample 6

data_processing:
The fastq files were subjected to QC analyses using the FastQC tool (version 0.11.9). Quality filtering and alignment of the raw reads was done using Trimmomatic (version 0.36) and subsequently aligned to the reference genome mm10 and hg19 applying STAR RNA-seq aligner (version 2.7.11b), Samtools (version 1.9) and Picard (version 2.9.2). Htseq (version 0.9.1) was applied to calculate raw read counts.
Assembly: mm10
Supplementary files format and content: raw read counts from RNA-seq samples

molecule: polyA RNA

source_name: Hippocampus

growth_protocol: Pregnant mice were randomly divided and intranasally administered the PM on days 9, 12, and 15 of pregnancy. The mice delivered pups on day 21 of pregnancy. Hippocampal tissues were collected from the pups at 14–18 weeks of age.

extract_protocol:
Total RNA was extracted from frozen hippocampus tissue of mice using the PureLink RNA Mini kit according to the manufacturer’s instructions (Thermo Fisher Scientific). The concentration and quality of RNA were assessed by an Agilent Bioanalyzer 2100 (Agilent Technologies, CA). Ribosomal RNA was removed from 1 ug of total RNAs with more than RIN value 8.0 and cDNA was synthesized using SuperScript III (Invitrogen). Libraries for sequencing were prepared according to the manufacturer’s instructions with NEBNext Ultra II RNA Library Prep Kit (New England Biolabs, NEB#E7775) and 100bp paired-end sequencing was done with a NovaSeq 6000 instrument (Illumina).
Libraries for sequencing were prepared using standard New England Biolabs's protocols.

value: Hippocampus

value: particulate matter (PM) (200ug/kg)


title: UMUC3_Control_sh_3

description: Library name: Sample 3

value: Xenograft Tissue

value: Control


title: ChIP_UMUC3_Input_Nosmoke_Control_rep1

description:
Library name: ChIP_UMUC3_Input_Nosmoke_Control_rep1
Input

value: Control sh

value: Regular media


title: PM_rep2

description: Library name: Sample 5


title: ChIP_UMUC3_Input_Smoke_Control_rep1

description:
Library name: ChIP_UMUC3_Input_Smoke_Control_rep1
Input


title: UMUC3_Control_sh_2

description: Library name: Sample 2

value: Human


title: ChIP_UMUC3_H3K18ac_Smoke_FASNKD_rep2

description:
Library name: ChIP_UMUC3_H3K18ac_Smoke_FASNKD_rep2
H3K18Ac CHIP-seq in UMUC3 FASN KD cells treated under 10%CSM  (Cigarette smoke media) conditions


title: PM_rep1

description: Library name: Sample 4


title: UMUC3_Control_sh_1

description: Library name: Sample 1


title: Degos_13_PBMC

description: 10x Genomics


title: ChIP_UMUC3_H3K18ac_Smoke_FASNKD_rep1

description:
Library name: ChIP_UMUC3_H3K18ac_Smoke_FASNKD_rep1
H3K18Ac CHIP-seq in UMUC3 FASN KD cells treated under 10%CSM  (Cigarette smoke media) conditions


title: Degos_12_PBMC

description: 10x Genomics


title: CHIR induced Zone3 hepatocyte

city: Toronto

first: Jeff

last: Liu

address: 101 College Street, RM 4-601

department: Princess Margaret Cancer Center

institute: University Health Network

description:
Library name: CHIR
10X Genomics

data_processing:
Sequencing library generation, data filtering to exclude cells a high mitovhondria ration (>4 SD above means) and low library size (<1500), and normalization using scran R packages wirh default settings was performed. Cell clustering using Seurat with standard procedures, and differential expression analysis as previously described (Innes and Bader, 2018; MacParland et al., 2018)
Assembly: GRCh38
Supplementary files format and content: Tab-separated values and mtx count matrix

source_name: Liver

extract_protocol:
Single-RN-seq was performed on both XAV and CHIR treated mature hPSC-hep 3D aggregate at day 53 following 18 days maturation periods from hepatic progenitor cells.
Samples processing was performed as outlined by the 10X Genomics single cell 3’ v2 Reagent user guide and previously described in details (MaParland nature comm, 2018).

value: Liver

value: hPSC

value: Hepatocyte


title: ChIP_UMUC3_H3K18ac_Smoke_Control_rep2

description:
Library name: ChIP_UMUC3_H3K18ac_Smoke_Control_rep2
H3K18Ac CHIP-seq in UMUC3 Control sh cells treated under 10%CSM  (Cigarette smoke media) conditions


title: XAV induced Zone1 hepatocyte

description:
Library name: XAV
10X Genomics


title: UMUC3_FASN_KD_3

description: Library name: Sample 6


title: Degos_11_PBMC

description: 10x Genomics


title: ChIP_UMUC3_H3K18ac_Smoke_Control_rep1

description:
Library name: ChIP_UMUC3_H3K18ac_Smoke_Control_rep1
H3K18Ac CHIP-seq in UMUC3 Control sh cells treated under 10%CSM  (Cigarette smoke media) conditions


title: Vehicle_rep1

description: Library name: Sample 1

value: normal saline (Veh)


title: PAG178_Inf_E2

city: Abu dhabi

first: Youssef

last: Idaghdour

state: Abu dhabi

address: Saadiyat Marina District

department: Biology

country: United Arab Emirates

institute: NYUAD

data_processing:
raw reads were processed using Trimmomatic v0.36 to remove adapter sequences and low-quality bases (Phred quality score < 20).
 Filtered reads were then mapped to the human reference genome (Ensembl GRCh38 release-84) using STAR v2.5.0c.
Transcripts abundances were estimated as transcripts per million
Only genes with a minimum of 1 TPM in 10 samples per experimental condition were retained for downstream analysis
Genome_build: hg38
Supplementary_files_format_and_content: TPM

source_name: PAG178 Inf E2 Malaria Symptomatic stage mRNA Year2 Sample

extract_protocol:
globin-mRNA depletion using the GlobinClear kit (Thermo Fisher)
KAPA Stranded RNA-Seq kit with RiboErase (Kapa Biosystems) and 100 bp paired-end sequencing using the TruSeq SBS Kit v3 - HS (Illumina)

value: Blood

tag: visit

value: Malaria Symptomatic stage


title: Degos_10_PBMC

description: 10x Genomics


title: WT 3 monocytes, 3 dpi

city: Irvine

first: Hannah

last: Debray

state: CA

address: 3342 McGaugh Hall

department: MBB

institute: University of California Irvine

description:
Library name: Sample 7
Column name in counts_monocytes.txt: WT3_Aligned.out.bam

data_processing:
Trimmomatc 0.39 was used for quality control and adaptor trimming
Trimmed sequence reads were mapped to mouse GRCm39 primary assembly (Gencode release 27) using STAR aligner (Version 2.5.4b)
Reads were counted using FeatureCounts, part of the Subread package.
Assembly: mm39
Supplementary files format and content: tab-delimited text file with raw counts for each sample
Supplementary files format and content: tab-delimited excel file with differential gene expression data for each sample

source_name: Peritoneal exudate cells

growth_protocol: C57Bl/6J "WT" and "TREM2 KO" age-matched mice were kept in standard housing conditions until age 6-10 weeks

extract_protocol:
RNA was harvested using RNeasy mini kit (Qiagen), then used for sequencing library construction.
NEBNext Ultra II Library Prep Kit for Illumina (New England Biolabs) was used to create RNA libraries.

treatment_protocol: Mice were infected with 200 GFP-fluorescent Toxoplasma gondii parasites. Mice were humanely euthanized on day 3 post infection. 1x10^5 monocytes were sorted from peritoneal exudate cells on a BD FACS Aria Fusion.

value: Peritoneal exudate cells

value: Monocytes

value: WT

value: Toxoplasma gondii infection

tag: time

value: Day 3


title: ChIP_UMUC3_H3K18ac_Nosmoke_FASNKD_rep2

description:
Library name: ChIP_UMUC3_H3K18ac_Nosmoke_FASNKD_rep2
H3K18Ac CHIP-seq in UMUC3 FASN KD cells treated with  regular culture media

value: FASN KD


title: ChIP_UMUC3_H3K18ac_Nosmoke_FASNKD_rep1

description:
Library name: ChIP_UMUC3_H3K18ac_Nosmoke_FASNKD_rep1
H3K18Ac CHIP-seq in UMUC3 FASN KD cells treated with  regular culture media


title: WT 2 monocytes, 3 dpi

description:
Library name: Sample 6
Column name in counts_monocytes.txt: WT2_Aligned.out.bam


title: PAG174_Inf_E2

source_name: PAG174 Inf E2 Malaria Symptomatic stage mRNA Year2 Sample


title: Degos_8_PBMC

description: 10x Genomics

value: PBMC


title: ChIP_UMUC3_H3K18ac_Nosmoke_Control_rep2

description:
Library name: ChIP_UMUC3_H3K18ac_Nosmoke_Control_rep2
H3K18Ac CHIP-seq in UMUC3 Control sh cells treated with  regular culture media


title: WT 1 monocytes, 3 dpi

description:
Library name: Sample 5
Column name in counts_monocytes.txt: WT1_Aligned.out.bam


title: PAG172_Inf_E2

source_name: PAG172 Inf E2 Malaria Symptomatic stage mRNA Year2 Sample


title: Degos_7_PBMC

description: 10x Genomics


title: ChIP_UMUC3_H3K18ac_Nosmoke_Control_rep1

description:
Library name: ChIP_UMUC3_H3K18ac_Nosmoke_Control_rep1
H3K18Ac CHIP-seq in UMUC3 Control sh cells treated with  regular culture media


title: TREM2 KO 4 monocytes, 3 dpi

description:
Library name: Sample 4
Column name in counts_monocytes.txt: KO4_Aligned.out.bam

value: TREM2 KO


title: PAG171_Inf_E2

source_name: PAG171 Inf E2 Malaria Symptomatic stage mRNA Year2 Sample


title: Degos_6_PBMC

description: 10x Genomics


title: HSD4

city: Barcelon

first: Lidia

last: Mateo

address: C/ Baldiri Reixac 10

country: Spain

institute: Institute for Research in Biomedicine (IRB Barcelona)

description:
Library name: HSD4
Third instar larvae fed with HSD diet.

data_processing:
Adapters from reads were removed using trim galore (v.0.6.7) (https://github.com/FelixKrueger/TrimGalore) with default parameters. Resulting reads were aligned to the dm6 D. melanogaster genome version using STAR (v.2.7.10a) (Dobin et al. 2013). The count matrix was generated in R (https://www.R-project.org/) through the function “featureCounts” of the Rsubread package (Liao, Smyth, and Shi 2019).
Assembly: Drosophila melanogaster Genome Reference 6.18
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

organism: Drosophila melanogaster

source_name: third instar larvae macrophages

growth_protocol: Prior to the hemocyte extraction, larvae were maintained in vials in climate controlled growth chambers with a 12:12 hours light:dark cycle at 25℃

extract_protocol:
mRNA was isolated from total RNA using the kit NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs).
NGS libraries were prepared from the purified mRNA using the NEBNext Ultra II RNA Library Prep Kit for Illumina (New England Biolabs). 18 cycles of PCR amplification were applied to all libraries. The final libraries were quantified using the Qubit dsDNA HS assay (Invitrogen) and quality controlled with the Bioanalyzer 2100 DNA HS assay (Agilent). An equimolar pool was prepared with the twenty libraries and submitted for sequencing at the Centro Nacional de Análisis Genómico (CNAG).

treatment_protocol: Larvae were fed with standard sucrose-yeast medium (CD) or fed with standard sucrose-yesat medium suplemented with 10x sucrose (HSD).

value: third instar larvae macrophages

value: macrophages

value: Wild-type

value: HSD

tag: batch


title: TREM2 KO 3 monocytes, 3 dpi

description:
Library name: Sample 3
Column name in counts_monocytes.txt: KO3_Aligned.out.bam


title: PAG170_Inf_E2

source_name: PAG170 Inf E2 Malaria Symptomatic stage mRNA Year2 Sample


title: Degos_5_PBMC

description: 10x Genomics


title: HSD3

description:
Library name: HSD3
Third instar larvae fed with HSD diet.


title: PAG166_Inf_E2

source_name: PAG166 Inf E2 Malaria Symptomatic stage mRNA Year2 Sample


title: TREM2 KO 2 monocytes, 3 dpi

description:
Library name: Sample 2
Column name in counts_monocytes.txt: KO2_Aligned.out.bam


title: Degos_4_PBMC

description: 10x Genomics


title: HSD2

description:
Library name: HSD2
Third instar larvae fed with HSD diet.


title: TREM2 KO 1 monocytes, 3 dpi

description:
Library name: Sample 1
Column name in counts_monocytes.txt: KO1_Aligned.out.bam


title: PAG165_Inf_E2

source_name: PAG165 Inf E2 Malaria Symptomatic stage mRNA Year2 Sample


title: Degos_3_PBMC

description: 10x Genomics


title: HSD1

description:
Library name: HSD1
Third instar larvae fed with HSD diet.


title: 2888, Female

city: Palo Alto

first: Xiao

last: Han

state: California

address: 265 Campus Drive

institute: Stanford University

data_processing:
RNAs isolated from three biological replicates of the four brain regions were sequenced on Illumina NovaSeq 6000 platform with paired-end 100 bp read length and average sequencing depth of 22.02 million reads (11.01 million paired). Raw reads were stripped of adaptor sequences and removed low quality bases using Trimmomatic  (version 0.33). The processed reads with lengths greater than 35 nt were defined as clean reads. Then the filtered reads were aligned to the mm10 genome with TopHat  (version 2.1.1, default parameters). The number of reads mapped to each Ensemble gene was counted using the HTSeq  (version 2.0.1).
Assembly: mm10
Supplementary files format and content: Tab-delimited text file includes raw counts for each sample

source_name: CA1 hippocampal region

extract_protocol:
Total RNA was extracted using PureLink RNA Mini Kit
Total RNA samples were converted to a library using Illumina TruSeq stranded mRNA kit

treatment_protocol: Cas9 mice were stereotaxically injected by SIK3 sgRNA AAV (2 female and 2 male) or control sgRNA AAV (2 female and 2 male).

value: CA1 hippocampal region

value: KO


title: CD5

description:
Library name: CD5
Third instar larvae fed with CD diet.

value: CD


title: Degos_2_PBMC

description: 10x Genomics


title: Degos_9_PBMC

description: 10x Genomics


title: 2883, Female


title: PAG161_Inf_E2

source_name: PAG161 Inf E2 Malaria Symptomatic stage mRNA Year2 Sample

value: Blood


title: Degos_1_PBMC

description: 10x Genomics


title: CD4

description:
Library name: CD4
Third instar larvae fed with CD diet.


title: 2882, Male


title: PAG159_Inf_E2

source_name: PAG159 Inf E2 Malaria Symptomatic stage mRNA Year2 Sample

value: Malaria Symptomatic stage


title: CD3

description:
Library name: CD3
Third instar larvae fed with CD diet.


title: HV_8_PBMC

description: 10x Genomics


title: 2881, Male


title: PAG158_Inf_E2

source_name: PAG158 Inf E2 Malaria Symptomatic stage mRNA Year2 Sample


title: Degos_14_Skin_Scar_Lesion_2

description: 10x Genomics

source_name: Skin

value: Skin


title: CD1

description:
Library name: CD1
Third instar larvae fed with CD diet.


title: 2892, Female

value: Control


title: PAG157_Inf_E2

source_name: PAG157 Inf E2 Malaria Symptomatic stage mRNA Year2 Sample


title: Degos_14_Skin_Scar_Lesion_1_Rep2

description: 10x Genomics


title: ELF-CLAMP sequencing, batch 3.

city: Edinburgh

first: Fernando

last: Bellido Molias

address: Crewe Rd S,

country: United Kingdom

institute: University of Edinburgh

description:
Library name: ELF-CLAMP-Batch3
Count of identified reads originating for every viewpoint in Chip 3 for Batch 3

data_processing:
Selection of reads starting from the corresponding viewpoints (cutadapt)
Filter out reads that do not originate from specific ELF-CLAMP guide-RNA bindings, keeping only those that continue with the downstream gene sequence after the viewpoint (using Cutadapt).
Align reads to the reference mouse genome
Characterize the presence of genomic modifications
Visualize the alingments on IGV and evaluate the DNA editing events.
Assembly: Mus musculus (house mouse) genome assembly GRCm39 (mm39) from Genome Reference Consortium
Supplementary files format and content: txt files indicating the number of reads identified for every viewpoint (per Chip).
Supplementary files format and content: bam files with the alignments (mouse genome) for every group of reads coming from the same viewpoint can be generated using the code in the supplementary file "code_for_analysis.sh". https://github.com/fbm48/Tillotson

source_name: tail tissue

extract_protocol:
To characterize potential genomic rearrangement events, we adapted ELF-CLAMP (Enrichment of Long DNA Fragments using Capture and Linear Amplification) where regions of interest (up to 2 kb) are amplified from viewpoints using in vitro transcription followed by Nanopore long read RNA sequencing.
RNA molecules generated through the ELF-CLAMP protocol were sequenced using Nanopore RNA-seq technology on MinION chips (R9.4.1). The RNA library was prepared using Direct RNA Sequencing Kit SQK-RNA002.

treatment_protocol: To produce null alleles (with Cas9 RNA-guided nuclease mediated mutations), single guide RNAs (sgRNAs) were designed to target exons of interest

value: tail tissue


title: PAG156_Inf_E2

source_name: PAG156 Inf E2 Malaria Symptomatic stage mRNA Year2 Sample


title: 2891, Male


title: Degos_14_Skin_Scar_Lesion_1_Rep1

description: 10x Genomics


title: ELF-CLAMP sequencing, batch 2.

description:
Library name: ELF-CLAMP-Batch2
Count of identified reads originating for every viewpoint in Chip 2 for Batch 2


title: 2890, Female


title: Degos_5_Skin_Scar

description: 10x Genomics


title: PAG155_Inf_E2

source_name: PAG155 Inf E2 Malaria Symptomatic stage mRNA Year2 Sample


title: Degos_2_Skin_L1_TCR

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.0.0 or v6.0.2
Assembly: GRCh38-2020-A
Supplementary files format and content: Tab-separated values files and matrix files
Library strategy: scTCR-seq

extract_protocol:
Skin biopsy from Degos disease patients and healthy volunteers were washed with PBS and digested enzymatically using whole skin dissociation kit (Miltenyi Biotec).  Following mechanical dissociation and filteration, cells were resuspended in 500 μL of complete RPMI-1640 with 10% FBS before sorting. Skin live cells were enriched by fluorescence-activated cell sorting (FACS) using Sytox green. Peripheral blood mononuclear cells (PBMCs) from blood were isolated according to desity centrifugation method. PBMCs and CSF samples were subjected to ACK lysis treatment to remove RBCs. Finally, single cell suspensions prepared from skin, PBMCs and CSF were counted and and cell concentration was adjusted in the range of 700-1200 cells/ul with the viability of > 70% before being used for single-cell capturing. cDNA was generated using 5' 10X kit and subsequenctly used for gene expression library and single cell TCR library preparation.
Single cell TCR library construction was performed in accordance with 10X Genomics protocol (10X Chromium 5' v2 or 5'-HT kit).


title: ELF-CLAMP sequencing, batch 1.

description:
Library name: ELF-CLAMP-Batch1
Count of identified reads originating for every viewpoint in Chip 1 for Batch 1


title: 2889, Male


title: PAG153_Inf_E2

source_name: PAG153 Inf E2 Malaria Symptomatic stage mRNA Year2 Sample


title: Degos_4_Skin_Scar

description: 10x Genomics


title: PAG162_Inf_E2

source_name: PAG162 Inf E2 Malaria Symptomatic stage mRNA Year2 Sample


title: KP_sgCTRL_siFEM1B_2

description: Library name: SAMPLE_8

source_name: lung

value: lung

value: KP

value: lung adenocarcinoma

value: KrasLSL-G12D/+; Trp53flox/flox


title: Degos_3_PBMC_PostRuxo_Wk_0_TCR

description: 10x Genomics

source_name: PBMC

value: PBMC


title: PAG151_Inf_E2

source_name: PAG151 Inf E2 Malaria Symptomatic stage mRNA Year2 Sample


title: MDA-MB-231 cells, Sch A 2

city: Wuhan

first: Yu

last: Zhou

address: No. 16, West Huangjiahu Road, Hongshan District

country: China

institute: Hubei University of Chinese Medicine

description: Library name: B4

data_processing:
CLC Genomics Workbench
Assembly: GRCh38
Supplementary files format and content: csv files includes FPKM values for all samples

source_name: breast

extract_protocol:
Total RNA was isolated from tissue and cell samples with TRIzol reagent (Sangon Biotech) according to the manufacturer's protocol, and library preparation was conducted following RNA concentration quantification using a Nanodrop 2000.
The paired-end (PE) library was constructed following the manufacturer's protocol of the ABclonal mRNA-seq Library Preparation Kit (ABclonal, China).

value: breast

value: breast cancer cells


title: Degos_3_Skin_Scar_Rep2

description: 10x Genomics


title: MDA-MB-231 cells, Sch A 1

description: Library name: B3


title: PAG148_Inf_E2

source_name: PAG148 Inf E2 Malaria Symptomatic stage mRNA Year2 Sample


title: Degos_14_PBMC_TCR

description: 10x Genomics


title: Degos_3_Skin_Scar_Rep1

description: 10x Genomics


title: Degos_13_PBMC_TCR

description: 10x Genomics


title: MDA-MB-231 cells, control 2

description: Library name: A4


title: PAG147_Inf_E2

source_name: PAG147 Inf E2 Malaria Symptomatic stage mRNA Year2 Sample


title: Degos_1_Skin_Scar_Rep2

description: 10x Genomics


title: Degos_5_PBMC_TCR

description: 10x Genomics


title: UMUC3_Control_sh_Smoke_1

description: Library name: Sample 7

source_name: Xenograft Tissue

value: Xenograft Tissue

value: Human

value: Control+Smoke


title: MDA-MB-231 cells, control 1

description: Library name: A3


title: Degos_5_CSF_Rep2

description: 10x Genomics

source_name: CSF

value: CSF


title: PAG146_Inf_E2

source_name: PAG146 Inf E2 Malaria Symptomatic stage mRNA Year2 Sample


title: Degos_1_Skin_Scar_Rep1

description: 10x Genomics


title: Degos_14_Skin_L3_TCR

description: 10x Genomics


title: PAG145_Inf_E2

source_name: PAG145 Inf E2 Malaria Symptomatic stage mRNA Year2 Sample


title: ChIP_UMUC3_Input_Nosmoke_FASNKD_rep1

description:
Library name: ChIP_UMUC3_Input_Nosmoke_FASNKD_rep1
Input

value: FASN KD

value: Regular media


title: Degos_3_PBMC_PostRuxo_Wk_0

description: 10x Genomics


title: Degos_3_Skin_TCR

description: 10x Genomics

source_name: Skin


title: Degos_4_Skin_Inflam

description: 10x Genomics


title: 3T3-L1 adipocytes Treated replicate 3

type: RNA

city: Cape Town

first: Anelisiwe

last: Hyera

state: Western Cape

address: Robert Sobukwe Rd, Bellville,

department: Biotechnology

country: South Africa

institute: University of the Western Cape

description:
Test
SAMPLE 6
Treatment 3

data_processing:
Ct values were exported and normalized to four housekeeping genes (ACTβ, GAPDH, GUSβ, HSP90AB1). Stability of reference genes was evaluated using RefFinder (geNorm, Normfinder, BestKeeper, comparative ΔCt). Fold change was calculated using the 2^-ΔΔCt method. Ct values >35 were excluded. Genes with fold regulation ≥1.5 and p ≤ 0.05 were considered differentially expressed.
[functional enrichment] DEGs were analyzed using ShinyGO v8.0 for GO terms (BP, CC, MF) and KEGG pathways. FDR-adjusted p-values <0.05 were considered significant.
[protein interaction]  STRING module in Cytoscape (v3.10.2) was used to construct PPI networks for up- (n=18) and downregulated (n=17) DEGs. Hub genes were identified using CytoHubba with the degree method.

label: SYBR Green

source_name: 3T3-L1 differentiated adipocytes

label_protocol: cDNA synthesis was performed using the RT² First Strand Kit (Qiagen). PCR was performed on the Mouse Adipogenesis RT² Profiler PCR Array (PAMM-049ZA) with RT² SYBR® Green qPCR Mastermix (Qiagen) on the QuantStudio™ 3 Real-Time PCR System (Applied Biosystems).

extract_protocol: Total RNA was extracted using the RNeasy Mini Kit (Qiagen, Maryland, USA) according to manufacturer’s instructions. RNA concentration and purity were measured using NanoDrop One and Qubit™ RNA HS and BR assays.

value: 3T3-L1 mature adipocyte

tag: activation agent

value: 12.5 nM cAuNPs


title: PAG144_Inf_E2

source_name: PAG144 Inf E2 Malaria Symptomatic stage mRNA Year2 Sample

value: Blood

value: Malaria Symptomatic stage


title: 3T3-L1 adipocytes Treated replicate 2

description:
Test
SAMPLE 5
Treatment 2


title: Degos_3_Skin_Inflam_PostRuxo_Wk_0_Rep2

description: 10x Genomics

value: Skin


title: Degos_3_PBMC_PostEculi

description: 10x Genomics


title: Degos_3_PBMC_PostRuxo_Wk_12

description: 10x Genomics


title: PAG143_Inf_E2

source_name: PAG143 Inf E2 Malaria Symptomatic stage mRNA Year2 Sample


title: term_female_high3

city: Durham

first: Integrative

last: Bioinformatics

state: NC

address: 111 TW Alexander Drive

department: BCBB

institute: NIEHS

description: Library name: Terminal.1316

data_processing:
Reads were aligned to the rn7 reference genome with STAR version 2.6
Read counts for annotated genes were obtained with Rsubread version 2.14
Normalized counts were obtained with DESq2 version 1.42
Assembly: rn7
Supplementary files format and content: DESeq2 normalized counts in tab delimited file

organism: Rattus norvegicus

source_name: heart

extract_protocol:
RNAeasy Kit (Qiagen)
Illumina TruSeq Stranded mRNA

value: heart

value: cART

tag: Sex

value: female


title: 3T3-L1 adipocytes Treated replicate 1

description:
Test
SAMPLE 4
Treatment 1


title: term_male_high5

description: Library name: Terminal.1309

value: male


title: Old-GFP-rep3

city: Cambridge

first: Yuancheng Ryan

last: Lu

state: MA

address: 455 Main St

institute: Whitehead Institute for Biomedical Research

description: Library name: Old-GFP-4

data_processing:
Paired-end human and mouse reads were mapped to the canonical chromosomes of the GRCh38/hg38 or GRCm38/mm10 genome genomes, respectively, with STAR (v 2.7.1a) using a genome index created using Ensembl 96 gene models (with sjdbOverhang=100). Gene counts were obtained for all genes using featureCounts (v1.6.2) and the same GTF file as for STAR and options "-p -s 1".
Assembly: mm10
Supplementary files format and content: csv; gene feature counts table

source_name: RPE

extract_protocol:
Total RNA was extracted following the TRIzol Reagent User Guide (Thermo Fisher Scientific). Glycogen (1 μl of 10 mg ml−1 solution) was added to the supernatant to increase RNA recovery. RNA was quantified using a Qubit 2.0 Fluorometer (Life Technologies), and RNA integrity was determined using TapeStation (Agilent Technologies).
RNA library preparations, sequencing reactions were conducted at Genewiz. A SMART-Seq v4 Ultra Low Input Kit for Sequencing was used for full-length cDNA synthesis and amplification (Clontech), and Illumina Nextera XT library was used for sequencing library preparation. In brief, cDNA was fragmented and adaptors were added using Transposase, followed by limited-cycle PCR to enrich and add an index to the cDNA fragments. The final library was assessed by a Qubit 2.0 Fluorometer and an Agilent TapeStation.

value: RPE


title: E-CM1

city: Matsumoto

first: Shin

last: Kadota

address: 3-1-1 Asahi

department: Regenerative Science and Medicine

country: Japan

institute: Shinshu University

description: Library name: Sample 4

data_processing:
RNA-seq reads were trimmed using Trimmomatic (v0.39).
All samples were mapped to the hg38 human genome using STAR (v2.7.11b), and a gene count matrix was generated using featureCounts (v2.0.6).
Raw counts were normalized with transcripts per million (TPM) normalization.
Assembly: hg38
Supplementary files format and content: Tab-delimited text files containing raw gene-level read counts
Supplementary files format and content: csv file includes TPM values for each Sample

source_name: Cardiomyocytes

growth_protocol: Undifferentiated hiPSCs were cultured as a monolayer in Essential 8 medium (Thermo Fisher Scientific, Waltham, MA, USA) on Matrigel (Corning, NY, USA) -coated plates. For differentiation, 1 μM CHIR99021 was added to the culture. On the following day (Day 0), the medium was replaced with a cardiac differentiation medium consisting of RPMI 1640 supplemented with B27 minus insulin (Thermo Fisher Scientific). Activin A (100 ng/mL; R&D Systems, Minneapolis, MN, USA) was added to the medium on Day 0, followed by 5 ng/mL BMP4 (R&D Systems) and 1 μM CHIR99021 (Sigma-Aldrich, St. Louis, MO, USA) on Day 1, and 1 μM XAV939 (Sigma-Aldrich) on Day 3. On Day 5, the medium was changed to cardiac differentiation medium without any additional supplements. On Day 7, the medium was switched to RPMI 1640 with B27 supplement (Thermo Fisher Scientific). From Day 9 to Day 11, cardiomyocyte purification was conducted using glucose- and glutamine-free DMEM medium (Gibco, A14430-01) supplemented with 4 mM lactate. On Day 11, the media was changed to RPMI 1640 with B27 supplement. The medium was changed every 2-3 days until Day 19. On Day 19, both non-expanded and expanded CMs, with or without additional treatment with BCH001, were subjected to heat shock at 43 °C for 30 min. After the heat shock, the medium was replaced with RPMI 1640 supplemented with B27, 100 ng/mL insulin-like growth factor 1 (IGF-1), 200 nM cyclosporin A, and 5 μM Y-27632. On Day 20, the cells were dissociated using Trypsin-EDTA at 37 °C for 15 min, resuspended in CELLBANKER 1 Plus reagent (Takara Bio, Shiga, Japan, CB023), and transferred into cryovials. The cryovials were placed in a controlled-rate freezing container (CoolCell, Corning) and stored at -80 °C. On the following day, they were transferred to a -150 °C freezer for long-term storage.

extract_protocol:
RNA was extracted from frozen cells using the NucleoSpin RNA Kit (Takara Bio).
Library preparation was carried out using the Nextera DNA Library Preparation Kit, followed by sequencing on the NovaSeq 6000 platform (Illumina, San Diego, CA, USA).

treatment_protocol: On Day 12 of differentiation, cells were dissociated with Trypsin-EDTA at 37 °C for 15 min and then replated onto Matrigel-coated dishes at a density of 8 × 104 cells/cm2 in RPMI 1640 medium supplemented with B27, 2 μM CHIR99021, 5 μM Y-27632 and 10% KnockOut Serum Replacement (Thermo Fisher Scientific). From Day 13 onward, the medium was replaced with RPMI 1640 supplemented with B27 and containing 2 μM CHIR99021 and was refreshed every two days. On Day 18, CHIR99021 was replaced with 2 μM Wnt-C59 (S7037, Selleck chemicals, Houston, TX, USA). For generating E-CM-B or E-CM-R, cells were treated with either 10 μM BCH001 (S8977, Selleck chemicals) or 1 μM RG7834 (T12719, TargetMol Chemicals, Boston, MA, USA), respectively, from Day 12 to Day 20.

value: Cardiomyocytes

value: human induced pluripotent stem cell-derived cardiomyocytes

value: Venus-Akaluc Knocked-in

value: expanded


title: Degos_14_PBMC

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.0.0 or v6.0.2
Assembly: GRCh38-2020-A
Supplementary files format and content: Tab-separated values files and matrix files

extract_protocol:
Skin biopsy from Degos disease patients and healthy volunteers were washed with PBS and digested enzymatically using whole skin dissociation kit (Miltenyi Biotec).  Following mechanical dissociation and filteration, cells were resuspended in 500 μL of complete RPMI-1640 with 10% FBS before sorting. Skin live cells were enriched by fluorescence-activated cell sorting (FACS) using Sytox green. PBMCs from blood were isolated according to desity centrifugation method. PBMCs and CSF samples were subjected to ACK lysis treatment to remove RBCs. Finally, single cell suspensions prepared from skin, PBMCs and CSF were counted and and cell concentration was adjusted in the range of 700-1200 cells/ul with the viability of > 70% before being used for single-cell RNA-sequencing.
Library construction was performed in accordance with 10X Genomics protocol (10X Chromium 5' v2 or 5'-HT kit).

value: PBMC


title: interim_male_ctrl2

description: Library name: Interim.1405


title: Degos_3_Skin_Inflam_PostRuxo_Wk_0_Rep1

description: 10x Genomics


title: E-CM-R2

description: Library name: Sample 11

value: expanded with RG7834


title: PAG137_Inf_E2

source_name: PAG137 Inf E2 Malaria Symptomatic stage mRNA Year2 Sample


title: Degos_3_PBMC_PostRuxo_Wk_4_Rep2

description: 10x Genomics

source_name: PBMC


title: Degos_2_Skin_Inflam_Lesion_2

description: 10x Genomics


title: 3T3-L1 adipocytes Control replicate 3

description:
Control
SAMPLE 3
Control 3

value: Control


title: Degos_3_PBMC_PostRuxo_Wk_4_Rep1

description: 10x Genomics


title: Degos_2_Skin_Inflam_Lesion_1

description: 10x Genomics


title: PAG136_Inf_E2

source_name: PAG136 Inf E2 Malaria Symptomatic stage mRNA Year2 Sample


title: 3T3-L1 adipocytes Control replicate 2

description:
Control
SAMPLE 2
Control 2

value: 3T3-L1 mature adipocyte


title: PAG124_Inf_E2

source_name: PAG124 Inf E2 Malaria Symptomatic stage mRNA Year2 Sample


title: Degos_1_Skin_Inflam_Rep2

description: 10x Genomics


title: E11.5_F0_9

city: Otsu

first: Shoma

last: Matsumoto

state: Shiga

address: Setatsukinowa-cho

department: Research Center for Animal Life Science

institute: Shiga University of Medical Science

description: Library name: E11.5_F0_9

data_processing:
DNA barcode sequences were extracted from fastq files using the plasmid sequence for transgenic mouse generation (pNM1419_iSeq_Reference.fa; supplementary file).
Read count and integration of similar barcode sequences were performed by starcode v1.4 (Zorita et al., 2015).
Assembly: pNM1419_iSeq_Reference.fa

source_name: E11.5 embryo

extract_protocol:
E11.5 mouse embryos with DNA barcode-linked EGFP were minced and enzymatically into single cell. Genomic DNA was extracted and purified using phenol/chloroform.
Genomic DNA was amplified using transgene-specific primers with Illumina index sequences. PCR was performed using KOD One PCR Master Mix -Blue- (Takara). The amplicons were purified by FastGene Gel/PCR Extraction Kit (Nippon Genetics).

value: E11.5 embryo

value: DNA barcode-linked GFP Tg


title: Degos_1_Skin_Inflam_Rep1

first: Stephen

last: Brooks

address: 50 SOUTH DR, RM 1140

description: 10x Genomics


title: PAG123_Inf_E2

source_name: PAG123 Inf E2 Malaria Symptomatic stage mRNA Year2 Sample

value: Blood

value: Malaria Symptomatic stage


title: 05idSERSECLIPINPUT2

city: La Jolla

first: Gene

last: Yeo

address: 2880 Torrey Pines Scenic Dr. Room 3805/Yeo Lab

institute: UCSD

description: biol rep 2 size-matched input

data_processing:
Data was processed using the eCLIP pipeline and available at: http://github.com/yeolab/eclip
Unique Molecular Identifiers (UMIs) were extracted from raw sequencing reads with umi_tools extract
Post-umi-extracted reads were trimmed for adapter sequences and barcode sequences (eCLIP samples) using cutadapt.
Trimmed reads were mapped against RepBase with STAR to remove reads mapping to repetitive sequences (--outFilterMultimapNmax 30 --alignEndsType EndToEnd --outFilterMultimapScoreRange 1 --outSAMmode Full --outFilterType BySJout --outSAMtype BAM Unsorted --outFilterScoreMin 10 --outReadsUnmapped Fastx --outSAMattributes All)
Remaining reads were mapped to the appropriate genome build (hg19) using STAR aligner (--outFilterMultimapNmax 1 --alignEndsType EndToEnd --outFilterMultimapScoreRange 1 --outSAMmode Full --outFilterType BySJout --outSAMtype BAM Unsorted --outFilterScoreMin 10 --outReadsUnmapped Fastx --outSAMattributes All)
Uniquely mapped reads were removed of PCR duplicates with umi_tools
Peak clusters were identified with CLIPper, available at: https://github.com/YeoLab/clipper
Clusters enriched over corresponding size-matched input (SMInput) were identified using a custom Perl script, available in the main eCLIP repository as: overlap_peakfi_with_bam.pl
Overlapping enriched clusters (peaks) were merged with a custom perl script, available in the main eCLIP repository as: compress_l2foldenrpeakfi_for_replicate_overlapping_bedformat.pl
Peaks that overlapped common exclusion/non-specific binding regions (available at: https://www.encodeproject.org/references/ENCSR922QVQ/) were removed with BEDtools
Assembly: hg19
Supplementary files format and content: bigwigs contain RPM-normalized read densities of uniquely-mapped reads
Supplementary files format and content: BED files contain CLIPper peak clusters. Columns 4 and 5 describe the -log10(p-value) and log2(fold) enrichment IP over corresponding SMInput.

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

extract_protocol:
Extraction was performed using the RBP-eCLIP Kit (#ECK001, Eclipse Bioinnovations, San Diego, CA). 2x10^7 MDA-MB-231 cells were used for each replicate. Cell culture medium was replaced with ice-cold PBS and cross-linking was performed at 254 nM UV with a setting of 400 mJoules/cm^2. After cross-linking, cells were scraped, washed, counted, centrifuged, and snap-frozen. Cells were lysed, sonicated using a Bioruptor Pico (Diagenode, Denville, NJ), and digested with DNase and Ambion RNase-I Cloned (#AM2294, ThermoFisher Scientific). Immunoprecipitation was performed with mouse monoclonal anti-SerRS antibody (#sc-271032, Santa Cruz Biotechnology) bound to goat anti-mouse IgG magnetic beads (#S1430, New England Biolabs). Size-matched input (SMInput) samples were taken before antibody enrichment. Samples were washed, adapters were added, protein-RNA complexes were separated by SDS-PAGE electrophoresis and transferred to nitrocellulose membranes by wet transfer. The membrane section containing the complexes was cut out and digested with Proteinase mix supplied by the manufacturer. Resulting RNAs were purified and reverse transcribed. Resulting cDNA was purified and adapters were ligated on the ends.
cDNA was quantified by qRT-PCR, and libraries were amplified by PCR according to manufacturer instructions. Libraries were gel-purified from a 3% low-melting temperature agarose gel, pooled, analyzed by Agilent TapeStation, and sequenced on a NextSeq 2000 (Illumina).

value: triple-negative breast cancer

value: WT

tag: eclip antibody

value: input


title: 04idSERSECLIPINPUT1

description: biol rep 1 size-matched input


title: E11.5_F0_8

description: Library name: E11.5_F0_8


title: PAG122_Inf_E2

source_name: PAG122 Inf E2 Malaria Symptomatic stage mRNA Year2 Sample


title: 03idSERSECLIP3

description: biol rep 3

value: SerRS (SCBT, #sc-271032)


title: 316-34Eto3, etoposide, day 2

city: Niigata

first: Hideaki

last: Matsui

state: Niigata

address: 1  Bancho-757 Asahimachidori, Chuo Ward

department: Brain Research Institute

institute: Niigata University

data_processing:
TruSeq stranded mRNA LT Sample Prep Kit
Trimmed reads are mapped to reference genome with HISAT2
After the read mapping, Stringtie was used for transcript assembly. Expression profile was calculated for each sample and transcript/gene as read count, FPKM (Fragment per Kilobase of transcript per Million mapped reads) and TPM (Transcripts Per Kilobase Million).
Assembly: Homo sapiens GRCh38 (NCBI_109.20200522)
Supplementary files format and content: tab-delimited raw file include raw count values for each sample

source_name: HeLa

growth_protocol: HeLa cells were cultured in DMEM (Nacalai Tesque, Kyoto, Japan) supplemented with 10% FBS (BioWest, Nuaillé, France) and 1% penicillin‒streptomycin solution (Wako, Osaka, Japan) at 37°C under 5% CO2

extract_protocol:
Total cellular RNA was isolated using TRIzol reagent (Thermo Fisher Scientific) and a Direct-zol RNA kit (Zymo Research, Irvine, CA, USA) according to the manufacturer’s instructions.
Libraries were prepared using the TruSeq RNA Sample Prep Kit v2 (Illumina, San Diego, CA, USA) according to the manufacturer’s guidelines.

treatment_protocol:
APP-deficient or mutant HeLa cells were generated using the CRISPR-Cas9 system. The APP gRNA sequence was cloned and inserted into pSpCas9 (BB)-2A-Puro (PX495) v.2.0 (plasmid #62988; Addgene, Cambridge, MA, USA)
After treatment with 2 μg/ml puromycin for 48 hr, the cells were grown and passaged in medium without puromycin for 7 days and then spread in four 96-well plates at 0.75 cells/100 μl.
HeLa and APP mutant cells (316,15 and 316-34) were treated with etoposide (20 μM, 2 days).

value: HeLa

value: APP mutant

value: Etoposide 20 µM, 2 days


title: 316-34Eto2, etoposide, day 2


title: E11.5_F1_3

description: Library name: E11.5_F1_3


title: E11.5_F1_2

description: Library name: E11.5_F1_2


title: 01idSERSECLIP1

description: biol rep 1


title: PAG118_Inf_E2

source_name: PAG118 Inf E2 Malaria Symptomatic stage mRNA Year2 Sample


title: 316-34Eto1, etoposide, day 2


title: E11.5_F1_1

description: Library name: E11.5_F1_1


title: PAG116_Inf_E2

source_name: PAG116 Inf E2 Malaria Symptomatic stage mRNA Year2 Sample


title: SLE_7_PBMC

city: Bethesda

institute: NIAMS/NIH

description:
Library name: SLE_7_PBMC
10x Genomics

extract_protocol:
Skin biopsy from Degos disease patients and healthy volunteers were washed with PBS and digested enzymatically using whole skin dissociation kit (Miltenyi Biotec).  Following mechanical dissociation and filteration, cells were resuspended in 500 μL of complete RPMI-1640 with 10% FBS before sorting. Skin live cells were enriched by fluorescence-activated cell sorting (FACS) using Sytox green. PBMCs from blood were isolated according to desity centrifugation method. PBMCs and CSF samples were subjected to ACK lysis treatment to remove RBCs. Finally, single cell suspensions prepared from skin, PBMCs and CSF were counted and and cell concentration was adjusted in the range of 700-1200 cells/ul with the viability of > 70% before being used for single-cell RNA-sequencing.
Library construction was performed in accordance with 10X Genomics protocol (10X Chromium 5' v2 or 5'-HT kit). Single-cell RNA-sequencing


title: SLE_8_PBMC

description:
Library name: SLE_8_PBMC
10x Genomics


title: 316-34-3, APP mutant, day0


title: PKW-B6_9

description: Library name: PKW-B6_9


title: PKW-B6_8

description: Library name: PKW-B6_8


title: PAG115_Inf_E2

source_name: PAG115 Inf E2 Malaria Symptomatic stage mRNA Year2 Sample


title: 316-34-1, APP mutant, day0


title: PKW-B6_7

description: Library name: PKW-B6_7


title: SLE_6_PBMC

description:
Library name: SLE_6_PBMC
10x Genomics


title: PAG111_Inf_E2

source_name: PAG111 Inf E2 Malaria Symptomatic stage mRNA Year2 Sample


title: 316-15Eto3, etoposide, day 2


title: SLE_5_PBMC

description:
Library name: SLE_5_PBMC
10x Genomics


title: PAG110_Inf_E2

source_name: PAG110 Inf E2 Malaria Symptomatic stage mRNA Year2 Sample


title: PKW-B6_5

description: Library name: PKW-B6_5


title: PAG107_Inf_E2

source_name: PAG107 Inf E2 Malaria Symptomatic stage mRNA Year2 Sample


title: 316-15Eto2, etoposide, day 2


title: SLE_3_PBMC

description:
Library name: SLE_3_PBMC
10x Genomics


title: PKW-B6_4

description: Library name: PKW-B6_4


title: PAG102_Inf_E2

source_name: PAG102 Inf E2 Malaria Symptomatic stage mRNA Year2 Sample


title: PKW-B6_3

description: Library name: PKW-B6_3


title: SLE_2_PBMC

description:
Library name: SLE_2_PBMC
10x Genomics


title: PAG100_Inf_E2

source_name: PAG100 Inf E2 Malaria Symptomatic stage mRNA Year2 Sample


title: 316-15-2, APP mutant, day0


title: SLE_1_PBMC

description:
Library name: SLE_1_PBMC
10x Genomics


title: PKW-B6_2

description: Library name: PKW-B6_2


title: PAG099_Inf_E2

source_name: PAG099 Inf E2 Malaria Symptomatic stage mRNA Year2 Sample


title: 316-15-1, APP mutant, day0


title: PKW-B6_1

description: Library name: PKW-B6_1


title: HelaEto3, etoposide, day 2

value: APP WT


title: Deogs14_BCR

description:
Library name: Deogs14_BCR
10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.0.0 or v6.0.2
Assembly: GRCh38-2020-A
Supplementary files format and content: Tab-separated values files and matrix files
Library strategy: BCR-Seq

extract_protocol:
Skin biopsy from Degos disease patients and healthy volunteers were washed with PBS and digested enzymatically using whole skin dissociation kit (Miltenyi Biotec).  Following mechanical dissociation and filteration, cells were resuspended in 500 μL of complete RPMI-1640 with 10% FBS before sorting. Skin live cells were enriched by fluorescence-activated cell sorting (FACS) using Sytox green. Peripheral blood mononuclear cells (PBMCs) from blood were isolated according to desity centrifugation method. PBMCs and CSF samples were subjected to ACK lysis treatment to remove RBCs. Finally, single cell suspensions prepared from skin, PBMCs and CSF were counted and and cell concentration was adjusted in the range of 700-1200 cells/ul with the viability of > 70% before being used for single-cell capturing. cDNA was generated using 5' 10X kit and subsequenctly used for gene expression library and single cell TCR library preparation.
Single cell TCR library construction was performed in accordance with 10X Genomics protocol (10X Chromium 5' v2 or 5'-HT kit). Single-cell TCR-sequencing

tag: disease

value: Degos disease


title: mES_BC_mix_1-7

description: Library name: mES_BC_mix_1-7

source_name: mouse embryonic stem cell

value: mouse embryonic stem cell


title: HBMVEC, Oligomeric amyloid beta, 12hr, 2

city: Daegu

first: Do-Geun

last: Kim

address: Cheomdan-ro 61

department: Dementia Research Group

country: South Korea

institute: Korea Brain Research Institute

description:
Library name: Ab_12h_2
HBMVEC treated with oligomeric Abeta (1 uM) for 12 hours

data_processing:
Raw reads were quality-checked and adapter-trimmed using Trimmomatic v0.38.
Reads were aligned to the human reference genome (GRCh38, Ensembl release 102) using HISAT2 v2.1.0.
Gene-level counts were obtained using StringTie v2.1.3b.
Assembly: Human genome GRCh38 (Ensembl release 102).
Supplementary files format and content: Tab-delimited text file including gene-level read counts, FPKM, and TPM values for each sample.

source_name: primary HBMVEC

growth_protocol: Primary human brain microvascular endothelial cells (HBMVECs) were cultured in complete classic media with 2% culture boost and 1% penicillin-streptomycin on attachment factor-coated plates at 37°C and 5% CO2 for 2–3 days.

extract_protocol:
After treatment, cells were washed with PBS and total RNA was extracted using TRIzol reagent according to the manufacturer’s instructions. RNA concentration and integrity were assessed using Quant-IT RiboGreen and TapeStation RNA ScreenTape. Only samples with RIN > 7.0 were used.
0.5 μg of total RNA per sample was used to construct libraries with the TruSeq Stranded Total RNA Library Prep Gold Kit (Illumina). rRNA was removed using the Ribo-Zero kit, mRNA was fragmented, and cDNA was synthesized with SuperScript II and random primers. Libraries were PCR-enriched, quantified, and quality-checked before sequencing.

treatment_protocol: HBMVECs were treated with Amyloid beta oligomer for 1, 4 or 12 hours.

value: primary HBMVEC

value: brain microvascular endothelial cells

value: Oligomeric amyloid beta (1 uM)


title: mES_BC_mix_1-3

description: Library name: mES_BC_mix_1-3


title: PAG082_Inf_E2

data_processing:
raw reads were processed using Trimmomatic v0.36 to remove adapter sequences and low-quality bases (Phred quality score < 20).
 Filtered reads were then mapped to the human reference genome (Ensembl GRCh38 release-84) using STAR v2.5.0c.
Transcripts abundances were estimated as transcripts per million
Only genes with a minimum of 1 TPM in 10 samples per experimental condition were retained for downstream analysis
Genome_build: hg38
Supplementary_files_format_and_content: TPM

source_name: PAG082 Inf E2 Malaria Symptomatic stage mRNA Year2 Sample

extract_protocol:
globin-mRNA depletion using the GlobinClear kit (Thermo Fisher)
KAPA Stranded RNA-Seq kit with RiboErase (Kapa Biosystems) and 100 bp paired-end sequencing using the TruSeq SBS Kit v3 - HS (Illumina)


title: Degos10_BCR

description:
Library name: Degos10_BCR
10x Genomics

source_name: PBMC

value: PBMC


title: mES_BC_mix_1-1

description: Library name: mES_BC_mix_1-1

value: DNA barcode-linked GFP Tg


title: HelaEto1, etoposide, day 2


title: Hela3, control, day0


title: mES_BC_13-25

description: Library name: mES_BC_13-25


title: Deogs8_BCR

description:
Library name: Deogs8_BCR
10x Genomics


title: PAG076_Inf_E2

source_name: PAG076 Inf E2 Malaria Symptomatic stage mRNA Year2 Sample

value: Blood


title: Hela2, control, day0


title: mES_BC_6-10

description: Library name: mES_BC_6-10


title: Hela1, control, day0


title: Degos3_BCR

description:
Library name: Degos3_BCR
10x Genomics


title: In-vitro CRISPR Screen of Epigenetic Regulators in the Dabrafenib/Trametinib treated WND238 Cells

city: Philadelphia

first: Yeqing

last: Chen

state: PA

address: 3601 Spruce Street

institute: The Wistar Institute

description: Library name: ND238_Epi_DT_R3

data_processing:
We utilized the MAGeCK (Model-based Analysis of Genome-wide CRISPR-Cas9 Knockout) software suite to calculate negative and positive enrichment scores and corresponding ranks. These enrichment scores were derived using the Robust Rank Aggregation (RRA) method, which evaluates whether single-guide RNAs (sgRNAs) targeting a particular gene cluster significantly at the top or bottom of the ranked list, more frequently than expected by chance. A lower RRA score indicates a stronger enrichment or depletion of a gene, suggesting a more significant impact on the observed phenotype.
Assembly: hg38
Supplementary files format and content: table
Library strategy: CRISPR Screen

source_name: In-vitro cell line

growth_protocol: WND238 cells are cultured in TU2% media consisting of 80% MCDB 153, 10% Leibovitz’s L-15, 2% FBS, 2.4 mM CaCl2, and passaged using 0.05% trypsin-EDTA.

extract_protocol:
Post-treatment WND238 cells were trypsinized, washed, and processed with Dead Cell Removal Kit (Miltenyi Biotec) following manufacturer’s instructions. Genomic DNA (gDNA) extracted from 1 million cells using Blood & Cell Culture DNA Mini Kit (Qiagen cat. no. 13323).
Genomic DNA with ≥1000× coverage (6.7 µg) was extracted, quantified, and used for indel amplification of integrated gRNAs via 26–28 cycles of PCR using NEBNext Q5 Hot Start HiFi Master Mix and CROPseq-NGS-Fwd/Rev primers. PCR products (expected size: 291–298 bp) were validated by agarose gel electrophoresis, purified using the Monarch DNA Gel Extraction Kit, pooled, and sequenced on a NextSeq 1000 (Illumina) with a P1 100-cycle kit (dual indexing, single-end; 8 bp × 8 bp × 120 bp).

treatment_protocol: WND238 cells are treated for one week with media containing 0.3 µM dabrafenib and 30 nM trametinib refreshed every two days.

value: In-vitro cell line

value: Melanoma

value: BRAF V600E

value: Dabrafenib/Trametinib


title: 316-15Eto1, etoposide, day 2


title: SLE_4_PBMC

description:
Library name: SLE_4_PBMC
10x Genomics


title: 316-15-3, APP mutant, day0


title: SODL2

city: Málaga

first: María Luisa

last: Carrégalo Ríos

state: Malaga

address: Blvr Louis Pasteur 31

institute: Universidad de Málaga

description: Library name: SODL2

data_processing:
The raw reads were pre-processed with SeqTrimNext using the specific NGS technology configuration parameters (Falgueras et al., 2010). This pre-processing removes low quality, ambiguous and low complexity stretches, linkers, adapters, vector fragments, and contaminated sequences while keeping the longest informative parts of the reads. SeqTrimNext also discarded sequences below 25 bp. Subsequently, clean reads were aligned and annotated using the Cucumis melo genome as the reference with Bowtie2 (Langmead and Salzberg, 2012) in BAM files, which were then sorted and indexed using SAMtools v1.484110 (Li et al., 2009).
Uniquely localized reads were used to calculate the read number value for each gene via Sam2counts (https://github.com/vsbuffalo/sam2counts). Differentially expressed genes (DEGs) between treatments were analyzed via DEgenes Hunter, which provides a combined p value calculated (based on Fisher’s method) using the nominal p values provided by from edgeR113 (Robinson et al., 2010) and DEseq2114 (Anders and Huber, 2010).
Assembly: DHL92 v4
Supplementary files format and content: tab-delimited files include FPKM of the samples and gene names

organism: Cucumis melo

source_name: Seeds

extract_protocol:
Total RNA was extracted from frozen tissues, harvested at different times after treatment by RNAprep Pure Tissue Kit (TIANGEN)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Seeds


title: Degos1_BCR

description:
Library name: Degos1_BCR
10x Genomics


title: PAG070_Inf_E2

city: Abu dhabi

first: Youssef

last: Idaghdour

address: Saadiyat Marina District

institute: NYUAD

source_name: PAG070 Inf E2 Malaria Symptomatic stage mRNA Year2 Sample

value: Malaria Symptomatic stage


title: SLE8_BCR

description:
Library name: SLE8_BCR
10x Genomics

value: SLE


title: PAG084_Inf_E2

source_name: PAG084 Inf E2 Malaria Symptomatic stage mRNA Year2 Sample


title: Degos13_BCR

description:
Library name: Degos13_BCR
10x Genomics


title: HelaEto2, etoposide, day 2

source_name: HeLa

value: HeLa

value: Etoposide 20 µM, 2 days


title: PAG083_Inf_E2

source_name: PAG083 Inf E2 Malaria Symptomatic stage mRNA Year2 Sample


title: SODH2

description: Library name: SODH2


title: Degos11_BCR

description:
Library name: Degos11_BCR
10x Genomics

value: Degos disease


title: 96502

city: Ann Arbor

first: Lam

last: Tsoi

state: MI

address: Medical Sciences 1 Bldg. 1301 E. Catherine

institute: University of Michigan

description: Library name: 96502

data_processing:
STAR for alignment
HTSeq for gene quantification
Assembly: hg19
Supplementary files format and content: gene by sample count matrix

source_name: firbroblast

growth_protocol: Primary dermal fibroblasts were cultured from human skin buttocks skin. Cells were grown in alpha MEM containing 10% FBS and antibiotics at 37 degrees celcius in an humidified incubator with 5% CO2.

extract_protocol:
Total RNA was prepared by using an RNAeasy mini kit (Qiagen) following the manufacture"s instructions.
The RNA-seq library was prepared by the UM Advanced Genomic Core, and sequenced by the HiSeq platform

treatment_protocol: Fibroblasts were treated with latrunculin A for 24 hours, then harvested for total RNA. In some experiments, latrunculin A was removed for four or eight hours prior to harvesting the cells to determine the recovery of gene expression to baseline before treatment.

value: firbroblast


title: PAG064_Inf_E2

source_name: PAG064 Inf E2 Malaria Symptomatic stage mRNA Year2 Sample


title: PAG080_Inf_E2

source_name: PAG080 Inf E2 Malaria Symptomatic stage mRNA Year2 Sample


title: SODH1

description: Library name: SODH1


title: SLE6_BCR

description:
Library name: SLE6_BCR
10x Genomics


title: 96501

description: Library name: 96501


title: PAG062_Inf_E2

source_name: PAG062 Inf E2 Malaria Symptomatic stage mRNA Year2 Sample


title: SMOCK2

description: Library name: SMOCK2


title: Degos4_BCR

description:
Library name: Degos4_BCR
10x Genomics


title: SLE5_BCR

description:
Library name: SLE5_BCR
10x Genomics


title: 96500

description: Library name: 96500

value: DMSO


title: SMOCK1

description: Library name: SMOCK1


title: PAG061_Inf_E2

source_name: PAG061 Inf E2 Malaria Symptomatic stage mRNA Year2 Sample


title: SLE4_BCR

description:
Library name: SLE4_BCR
10x Genomics


title: 96499

description: Library name: 96499


title: PAG074_Inf_E2

source_name: PAG074 Inf E2 Malaria Symptomatic stage mRNA Year2 Sample


title: RODL2

description: Library name: RODL2

source_name: 5-day-old radicle

value: 5-day-old radicle


title: SLE3_BCR

description:
Library name: SLE3_BCR
10x Genomics


title: PAG060_Inf_E2

source_name: PAG060 Inf E2 Malaria Symptomatic stage mRNA Year2 Sample


title: 96498

description: Library name: 96498


title: PAG058_Inf_E2

source_name: PAG058 Inf E2 Malaria Symptomatic stage mRNA Year2 Sample


title: PAG071_Inf_E2

source_name: PAG071 Inf E2 Malaria Symptomatic stage mRNA Year2 Sample


title: SLE2_BCR

description:
Library name: SLE2_BCR
10x Genomics

source_name: PBMC


title: RODL1

description: Library name: RODL1


title: 96497

description: Library name: 96497


title: PAG056_Inf_E2

source_name: PAG056 Inf E2 Malaria Symptomatic stage mRNA Year2 Sample


title: In-vitro CRISPR Screen of Epigenetic Regulators in the treatment naïve WND238 Cells

description: Library name: ND238_Epi_CTRL_R1

source_name: In-vitro cell line

value: Treatment naïve


title: RODH2

description: Library name: RODH2


title: SLE1_BCR

description:
Library name: SLE1_BCR
10x Genomics

value: PBMC


title: 96496

description: Library name: 96496


title: PAG055_Inf_E2

source_name: PAG055 Inf E2 Malaria Symptomatic stage mRNA Year2 Sample


title: RODH1

description: Library name: RODH1


title: SODL1

description: Library name: SODL1

source_name: Seeds


title: SLE8_TCR

description:
Library name: SLE8_TCR
10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.0.0 or v6.0.2
Assembly: GRCh38-2020-A
Supplementary files format and content: Tab-separated values files and matrix files
Library strategy: TCR-Seq


title: 96495

description: Library name: 96495


title: PAG053_Inf_E2

source_name: PAG053 Inf E2 Malaria Symptomatic stage mRNA Year2 Sample


title: 96503

description: Library name: 96503


title: RMOCK2

description: Library name: RMOCK2


title: SLE7_TCR

description:
Library name: SLE7_TCR
10x Genomics


title: PAG069_Inf_E2

source_name: PAG069 Inf E2 Malaria Symptomatic stage mRNA Year2 Sample


title: 96494

description: Library name: 96494

source_name: firbroblast


title: RMOCK1

description: Library name: RMOCK1


title: PAG049_Inf_E2

source_name: PAG049 Inf E2 Malaria Symptomatic stage mRNA Year2 Sample


title: 96493

description: Library name: 96493


title: SLE6_TCR

description:
Library name: SLE6_TCR
10x Genomics


title: PAG044_Inf_E2

source_name: PAG044 Inf E2 Malaria Symptomatic stage mRNA Year2 Sample


title: UAC treatment group

city: Shanghai

first: luxiang

last: zou

state: SHANGHAI

address: No.639, Zhizaoju Road, Shanghai

institute: shanghai ninth hospital

description:
Library name: UAC treatment group
10x Genomics

data_processing:
We performed alignment to this amended reference using 10x Cell Ranger v7.0 , which employs the STAR sequence aligner. The reference genome was the human genome GRCh38 or the mouse genome mm10. Overall, 36,000 cells passed the quality control. To remove the cells with low quality, cells with gene number over 500 and the ratio of mitochondria lower than 0.20 were maintained, and genes with at least one feature count in more than three cells were used for the following analysis. We determined gene expression counts using unique molecular identifiers (UMIs) for each cell barcode-gene combination. Following alignment, we filtered cell barcodes to identify those which contain cells using the approach implemented in Cell Ranger v7.0 , and only these barcodes were considered for downstream analysis including clustering and cell type identification, differential expression analysis by Seurat(v4.0.1).
Assembly: Rattus norvegicus
Supplementary files format and content: Excel Microsoft Office Open XML Format Spreadsheet file

source_name: cartilage and subchondral bone

growth_protocol: SD-rat in SPF environment

extract_protocol:
The criteria applied to filter low-quality cells were as follows: gene number < 200 or > 10,000, UMI > 1000, mitochondrial gene proportion > 0.3. Harmony was used to remove batch effects from all samples, a process in which cells are grouped by cell type rather than dataset-specific conditions
We prepared single cell RNA-seq libraries with Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 on the Chromium Controller(10× Genomics).We prepared single cell suspensions from cultured cell lines and single cells were suspended in PBS containing 0.04% BSA.The cell suspension was loaded onto the Chromium Next GEM Chip G and ran the Chromium Controller to generate single-cell gel beads in the emulsion(GEMs) according to the manufacturer’s recommendation.captured cells were lysed and the released RNA was barcoded through reverse transcription in individual GEMs. Barcoded, full-length cDNA was generated and libraries were constructed according to the performer’s protocol .The quality of libraries was assessed by Qubit 4.0 and the Agilent 2100. Sequencing was performed on the Illumina NovaSeq 6000 with a sequencing depth of at least 50,000 reads per cell and 150 bp (PE150) paired-end reads (performed by Biomarker Technologies Corporation, Beijing, China).

treatment_protocol: AAV articular injection into temporomandibular joint

value: cartilage and subchondral bone

value: chondrocytes, osteoclast

value: WT rat with AAV injection

value: AAV injection+model establisment

value: 16 condyles mixed into 1 sample


title: PAG038_Inf_E2

source_name: PAG038 Inf E2 Malaria Symptomatic stage mRNA Year2 Sample

value: Blood


title: 96492

description: Library name: 96492


title: SLE5_TCR

description:
Library name: SLE5_TCR
10x Genomics


title: SLE7_BCR

description:
Library name: SLE7_BCR
10x Genomics


title: SLE4_TCR

description:
Library name: SLE4_TCR
10x Genomics


title: UAC establishment group

description:
Library name: UAC establishment group
10x Genomics


title: In vivo, Uninjured brain, rep 3

city: Alcalá de Henares

first: Sergio

last: Gascón

state: Madrid

address: Avenida de León, 1

department: Department of Molecular and Cellular Neuroscience

institute: Cajal Neuroscience Center - CSIC

description:
Library name: RNA23
Intact cortical tissue (CD171-).

data_processing:
Raw paired-end reads were aligned to the reference genome using HISAT2.
Assembly: GRCm39
Supplementary files format and content: Comma-delimited csv file contains raw counts for each sample

source_name: cortex

extract_protocol:
RNA was extracted using the ReliaPrep™ RNA Miniprep System (Promega).
RNA libraries were prepared using the Novogene NGS RNA Library Prep Set (PT042).

treatment_protocol: Based on Bregma coordinates, surgical lancet injuries were performed creating a grid in the following coordinates: A/P -1.6 mm to -2.5 mm, M/L ±1.5 mm to ±2.5 mm, and D/V 0.5 mm. One day after the injury, the lesion core was dissected and dissociated with the Papain Dissociation System (Worthington), and subjected to a FACS sorting protocol (previously described). For in vitro samples, after 1 day, the core of the lesion was dissected and cultured in vitro for 6 days in DMEM/F12 medium supplemented with glucose (45%, 1:100), penicillin/streptomycin (1:100), B27 (1:200), 10% fetal bovine serum (FBS), and GlutaMax, at 37ºC in 8% CO₂ . The whole resulting cell culture was included in the analysis.

value: cortex

value: WT

value: uninjured cortex

tag: strain

tag: age

value: 2-3 months old


title: 06idSERSECLIPINPUT3

description: biol rep 3 size-matched input

value: triple-negative breast cancer

value: input


title: PAG037_Inf_E2

source_name: PAG037 Inf E2 Malaria Symptomatic stage mRNA Year2 Sample

value: Malaria Symptomatic stage


title: 3T3-L1 adipocytes Control replicate 1

description:
Control
SAMPLE 1
Control 1

data_processing:
Ct values were exported and normalized to four housekeeping genes (ACTβ, GAPDH, GUSβ, HSP90AB1). Stability of reference genes was evaluated using RefFinder (geNorm, Normfinder, BestKeeper, comparative ΔCt). Fold change was calculated using the 2^-ΔΔCt method. Ct values >35 were excluded. Genes with fold regulation ≥1.5 and p ≤ 0.05 were considered differentially expressed.
[functional enrichment] DEGs were analyzed using ShinyGO v8.0 for GO terms (BP, CC, MF) and KEGG pathways. FDR-adjusted p-values <0.05 were considered significant.
[protein interaction]  STRING module in Cytoscape (v3.10.2) was used to construct PPI networks for up- (n=18) and downregulated (n=17) DEGs. Hub genes were identified using CytoHubba with the degree method.

source_name: 3T3-L1 differentiated adipocytes

extract_protocol: Total RNA was extracted using the RNeasy Mini Kit (Qiagen, Maryland, USA) according to manufacturer’s instructions. RNA concentration and purity were measured using NanoDrop One and Qubit™ RNA HS and BR assays.

value: 3T3-L1 mature adipocyte

value: Control


title: SLE3_TCR

description:
Library name: SLE3_TCR
10x Genomics

value: SLE


title: Control group

description:
Library name: Control group
10x Genomics

value: AAV injection


title: In vivo, Uninjured brain, rep 2

description:
Library name: RNA22
Intact cortical tissue (CD171-).


title: PAG036_Inf_E2

source_name: PAG036 Inf E2 Malaria Symptomatic stage mRNA Year2 Sample


title: FKBP12KO Treg [GZ_20]

type: genomic

city: Berlin

first: Julia

middle: K

last: Polansky

address: Augustenburger Platz1

country: Germany

institute: Berlin Institute of Health Center for Regenerative Therapies

hyb_protocol: After bisulfite conversion, the gDNA, was fragmented, hybridized, and stained as per the guidelines of the Infinium HD protocol.

scan_protocol: Bead arrays were scanned using the iScan.

data_processing:
The raw intensity data files (IDAT) were preprocessed using minfi version 1.42.0 by quantile normalization. Probes were filtered based on not meeting the detection p-value threshold against the background (p<0.01), being reported as cross-reactive, revisions of Illumina's manifest (Infinium MethylationEPIC v1.0 13.03.2020), or being at a SNP, using the minfi function dropLociWithSnps.
Quantile normalized, filtered based on p-value and croos-reactivity. Beta values, between 0-1.

label: Cy3 and Cy5

source_name: FKBP12KO Treg

label_protocol: Infinium HD Methylation Assay Reference Guide.

extract_protocol: genomic DNA was extracted using Zymo’s Quick-DNA MicroPREP Kit (Zymo Research) following instructions provided by the manufacturer. Isolated genomic DNA was subjected to bisulfite conversion using Zymo’s EZ DNA Methylation-Gold Kit (Zymo Research) according to manufacturer's instructions.

value: FKBP12KO Treg

tag: donor

value: male


title: SLE2_TCR

description:
Library name: SLE2_TCR
10x Genomics

source_name: PBMC

value: PBMC


title: In vivo, Uninjured brain, rep 1

description:
Library name: RNA19
Intact cortical tissue (CD171-).


title: MOCK [GZ_19]

source_name: MOCK

value: MOCK


title: PAG035_Inf_E2

source_name: PAG035 Inf E2 Malaria Symptomatic stage mRNA Year2 Sample


title: SLE1_TCR

description:
Library name: SLE1_TCR
10x Genomics


title: In vivo, Injured brain, rep 3

description:
Library name: RNA18
Cortical stab-wound lesion core collected 1 day post-injury (CD171-).

value: cortical stab-wound injury, 1 day post-injury


title: PAG034_Inf_E2

source_name: PAG034 Inf E2 Malaria Symptomatic stage mRNA Year2 Sample

value: Blood


title: Treg WT [GZ_18]

source_name: Treg WT

value: Treg WT


title: In vivo, Injured brain, rep 2

description:
Library name: RNA17
Cortical stab-wound lesion core collected 1 day post-injury (CD171-).

value: cortex

value: WT


title: PAG121_Inf_E2

source_name: PAG121 Inf E2 Malaria Symptomatic stage mRNA Year2 Sample


title: PAG031_Inf_E2

source_name: PAG031 Inf E2 Malaria Symptomatic stage mRNA Year2 Sample


title: iNKs and reference samples sub-library 8

city: Stevenage

first: Marina

last: Tarunina

state: Hertfordshire

address: Plasticell Ltd., Stevenage Bioscience Catalyst, Gunnels Wood Road

institute: Plasticell Ltd.

description:
Library name: LIB_8
Parse Biosciences Evercode WT v2

data_processing:
Read and barcode demultiplexing and quantification were run using the Parse Biosciences split-pipe pipeline v. 1.2.0.
Assembly: Ensembl GRCh38 reference genome release 108
Supplementary files format and content: count matrix

source_name: human iPSC, iNKs, PB-CD34+ cells, UCB-CD34+ cells, PBMC and PBMC-NK cells

extract_protocol:
iPSCs were thawed and recovered for one passage before fixation. PB-CD34+ cells were thawed and recovered overnight before fixation. UCB-CD34+ cells were thawed and recovered overnight before fixation. Donor PBMCs were thawed and recovered overnight before fixation. PBMC-NK were isolated from thawed and recovered donor PBMCs using NK cell Isolation Kit, human (Miltenyi Biotec), according to manufacturer’s protocol. iNKs were collected from differentiation experiment for fixation. All cells were fixed using EvercodeTM Cell Fixation v2 (Parse Biosciences), according to manufacturer’s protocol V2.1.2.
Libraries for single cell RNA sequencing (scRNA-seq) were prepared from fixed cells using EvercodeTM WT v2 (Parse Biosciences), according to manufacturer’s protocol V2.2.2. Number of fixed cells used for sample preparation was calculated using Parse Biosciences EvercodeTM WT Sample Loading Table v2 (Parse Biosciences), with targeted 2750 barcoded cells for each control sample (i.e. iPSC, PB-CD34+, UCB-CD34+, PBMC and PBMC-NK samples) and targeted 4125 barcoded cells for each iNK sample.


title: 02idSERSECLIP2

description: biol rep 2

value: SerRS (SCBT, #sc-271032)


title: Tcon [GZ_17]

source_name: Tcon

value: Tcon


title: iNKs and reference samples sub-library 7

description:
Library name: LIB_7
Parse Biosciences Evercode WT v2

value: human iPSC, iNKs, PB-CD34+ cells, UCB-CD34+ cells, PBMC and PBMC-NK cells


title: PAG030_Inf_E2

source_name: PAG030 Inf E2 Malaria Symptomatic stage mRNA Year2 Sample

value: Malaria Symptomatic stage


title: In vivo, Injured brain, rep 1

description:
Library name: RNA16
Cortical stab-wound lesion core collected 1 day post-injury (CD171-).

value: 2-3 months old


title: FKBP12KO Treg [GZ_16]

value: female


title: iNKs and reference samples sub-library 6

description:
Library name: LIB_6
Parse Biosciences Evercode WT v2


title: MOCK [GZ_15]


title: In vitro, Reactive culture, rep 3

description:
Library name: RNA15
In vitro reactive culture (RC) generated from lesion cores dissected 1 day after cortical stab-wound injury (A/P -1.6 mm to -2.5 mm, M/L ±1.5 mm to ±2.5 mm, and D/V 0.5 mm) and cultured for 6 days. Whole culture collected for RNA-seq (CD171+, ACSA-2+).

value: reactive culture (injured cortex cultured 6 days in vitro)


title: iNKs and reference samples sub-library 5

description:
Library name: LIB_5
Parse Biosciences Evercode WT v2


title: PAG021_Inf_E2

source_name: PAG021 Inf E2 Malaria Symptomatic stage mRNA Year2 Sample


title: Treg WT [GZ_14]


title: iNKs and reference samples sub-library 4

description:
Library name: LIB_4
Parse Biosciences Evercode WT v2


title: PAG020_Inf_E2

source_name: PAG020 Inf E2 Malaria Symptomatic stage mRNA Year2 Sample


title: In vitro, Reactive culture, rep 1

description:
Library name: RNA13
In vitro reactive culture (RC) generated from lesion cores dissected 1 day after cortical stab-wound injury (A/P -1.6 mm to -2.5 mm, M/L ±1.5 mm to ±2.5 mm, and D/V 0.5 mm) and cultured for 6 days. Whole culture collected for RNA-seq (CD171+, ACSA-2+).

source_name: cortex


title: Tcon [GZ_13]


title: PAG019_Inf_E2

source_name: PAG019 Inf E2 Malaria Symptomatic stage mRNA Year2 Sample


title: FKBP12KO Treg [GZ_12]


title: iNKs and reference samples sub-library 2

description:
Library name: LIB_2
Parse Biosciences Evercode WT v2


title: RAW-POPC-Chol3

first: Antonio

last: De Maio

address: 9500 Gilman dr

institute: UC San Diego

description: Library name: sample 9

data_processing:
Sequencing reads were aligned to the mouse genome (mm10) using the STAR v2.5.1a aligner.
Read quantification was performed with RSEM v1.3.0 and GENCODE annotation (Mus_musculus.GRCm38.68.gtf). The R BioConductor packages edgeR and limma were used to implement the limma-voom method for differential expression analysis.
Significance was defined by using an adjusted p-value cut-off of 0.05 after multiple testing corrections using a moderated t-statistic in Limma.
Functional enrichment of the differentially expressed genes was performed using the Bioconductor GSVA package for implementing GSEA, Signaling Pathway Impact Analysis with the Bioconductor package SPIA and overrepresentation analysis in WebGestalt.
Assembly: mm10
Supplementary files format and content: tab-delimited CSV file include FPKM values for each sample

extract_protocol:
Total RNA isolation was performed using RNeasy Mini Kit according to the manufacturer’s protocol (Qiagen, Valencia, CA). RNA sequencing libraries were then generated from 1 µg of RNA using the TruSeq® Stranded Total RNA Library Prep Gold Sample Prep Kit following the manufacturer’s instructions (Illumina, San Diego, CA).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: RAW26.7 macrophages were incubated with POPC liposomes for 1 hour containing or not free cholesterol (n=3). Control cells were treated with vehicle (PBS) in the same conditions (n-3).

value: Macrophages

value: POPC liposomes-Chol


title: MOCK [GZ_11]

value: male


title: PAG018_Inf_E2

source_name: PAG018 Inf E2 Malaria Symptomatic stage mRNA Year2 Sample


title: iNKs and reference samples sub-library 1

description:
Library name: LIB_1
Parse Biosciences Evercode WT v2


title: PAG016_Inf_E2

source_name: PAG016 Inf E2 Malaria Symptomatic stage mRNA Year2 Sample


title: Treg WT [GZ_10]


title: Degos_3_CSF_PostRuxo_Wk_12_TCR

state: MD

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.0.0 or v6.0.2
Assembly: GRCh38-2020-A
Supplementary files format and content: Tab-separated values files and matrix files
Library strategy: scTCR-seq

source_name: CSF

extract_protocol:
Skin biopsy from Degos disease patients and healthy volunteers were washed with PBS and digested enzymatically using whole skin dissociation kit (Miltenyi Biotec).  Following mechanical dissociation and filteration, cells were resuspended in 500 μL of complete RPMI-1640 with 10% FBS before sorting. Skin live cells were enriched by fluorescence-activated cell sorting (FACS) using Sytox green. Peripheral blood mononuclear cells (PBMCs) from blood were isolated according to desity centrifugation method. PBMCs and CSF samples were subjected to ACK lysis treatment to remove RBCs. Finally, single cell suspensions prepared from skin, PBMCs and CSF were counted and and cell concentration was adjusted in the range of 700-1200 cells/ul with the viability of > 70% before being used for single-cell capturing. cDNA was generated using 5' 10X kit and subsequenctly used for gene expression library and single cell TCR library preparation.
Single cell TCR library construction was performed in accordance with 10X Genomics protocol (10X Chromium 5' v2 or 5'-HT kit).

value: CSF


title: RAW-POPC3

description: Library name: sample 6

value: POPC liposomes


title: Tcon [GZ_09]


title: PAG014_Inf_E2

source_name: PAG014 Inf E2 Malaria Symptomatic stage mRNA Year2 Sample


title: RAW-POPC2

description: Library name: sample 5


title: FKBP12KO Treg [GZ_08]

source_name: FKBP12KO Treg

value: FKBP12KO Treg


title: PAG008_Inf_E2

source_name: PAG008 Inf E2 Malaria Symptomatic stage mRNA Year2 Sample

value: Blood


title: Degos_3_PBMC_PostRuxo_Wk_12_TCR

description: 10x Genomics

source_name: PBMC

value: PBMC


title: RAW-POPC1

description: Library name: sample 4


title: PAG007_Inf_E2

source_name: PAG007 Inf E2 Malaria Symptomatic stage mRNA Year2 Sample


title: MOCK [GZ_07]

source_name: MOCK

value: MOCK


title: RAW-CTL3

description: Library name: sample 3

value: PBS


title: Degos_3_CSF_PostRuxo_Wk_12_Rep1

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.0.0 or v6.0.2
Assembly: GRCh38-2020-A
Supplementary files format and content: Tab-separated values files and matrix files

extract_protocol:
Skin biopsy from Degos disease patients and healthy volunteers were washed with PBS and digested enzymatically using whole skin dissociation kit (Miltenyi Biotec).  Following mechanical dissociation and filteration, cells were resuspended in 500 μL of complete RPMI-1640 with 10% FBS before sorting. Skin live cells were enriched by fluorescence-activated cell sorting (FACS) using Sytox green. PBMCs from blood were isolated according to desity centrifugation method. PBMCs and CSF samples were subjected to ACK lysis treatment to remove RBCs. Finally, single cell suspensions prepared from skin, PBMCs and CSF were counted and and cell concentration was adjusted in the range of 700-1200 cells/ul with the viability of > 70% before being used for single-cell RNA-sequencing.
Library construction was performed in accordance with 10X Genomics protocol (10X Chromium 5' v2 or 5'-HT kit).


title: RAW-CTL2

description: Library name: sample 2


title: PAG005_Inf_E2

source_name: PAG005 Inf E2 Malaria Symptomatic stage mRNA Year2 Sample


title: Tcon [GZ_05]


title: PAG002_Inf_E2

source_name: PAG002 Inf E2 Malaria Symptomatic stage mRNA Year2 Sample


title: RAW-CTL1

description: Library name: sample 1


title: cGAS sample 3_m (new)

status: Public on Jun 10 2026

city: Jerusalem

first: Itamar

last: Harel

address: Givat Ram

department: Genetics

country: Israel

institute: The Hebrew University of Jerusalem

description: Library name: cGAS sample 3_m (new)

data_processing:
Quality control and adapter trimming of the fastq sequence files were performed with FastQC (v0.11.8), fastx-toolkits (v0.0.13), Trim Galore! (v0.6.4), and Cutadapt (3.4). Options were set to remove Illumina TruSeq adapters and end sequences to retain high-quality bases with phred score > 20 and a remaining length > 20 bp. Successful processing was verified by re-running FastQC. Reads was mapped and quantified to the killifish genome Nfu_20140520 using STAR 2.7.6a. Differential gene expression between rag2 mutant and WT fish was performed using the edgeR package (v3.32.1).
Assembly: Nfu_20140520
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

organism: Nothobranchius furzeri

source_name: Brain

growth_protocol: Fish were grown at 28°C in a central filtration recirculating system with a 12 h light/dark cycle at the Hebrew University of Jerusalem (Aquazone ltd, Israel). Fish were fed with live Artemia until the age of 2 weeks (#109448, Primo), and starting week 3, fish were fed three times a day on weekdays (and once a day on weekends), with GEMMA Micro 500 Fish Diet (Skretting Zebrafish, USA), supplemented with Artemia once a day.

extract_protocol:
Livers were isolated as described in (Astre et al. 2022)
Library preparation was performed using KAPA mRNA HyperPrep Kit (ROCHE-08105936001) according to the recommended protocols. Library quantity and pooling were measured by Qubit (dsDNA HS, Q32854), Size selection at 4% agarose gel. Library quality was measured by Tape Station (HS, 5067-5584). Libraries were sequenced by NextSeq 2000 P4, 300 cycle,75 bp single-end (Illumina, 20100992) with ~30 million reads per sample.

value: Brain

value: cGAS mutant

value: 3 months

value: Male


title: cGAS sample 2_m (new)

description: Library name: cGAS sample 2_m (new)


title: cGAS sample 1_m (new)

description: Library name: cGAS sample 1_m (new)


title: cGAS sample 1_f (new)

description: Library name: cGAS sample 1_f (new)

value: Female


title: WT sample L33 liver

source_name: Liver

extract_protocol:
Brain and liver were isolated as described in (Astre et al. 2022)
Library preparation was performed using KAPA mRNA HyperPrep Kit (ROCHE-08105936001) according to the recommended protocols. Library quantity and pooling were measured by Qubit (dsDNA HS,Q32854), Size selection at 4% agarose gel. Library quality was measured by Tape Station (HS,5067-5584). Libraries were sequenced by NextSeq 2000 P2, 100 cycle,75 bp single-end (Illumina, 20024906) with ~40 million reads per sample.

value: Liver

value: WT


title: WT sample 4_f (new)

description: Library name: WT sample 4_f (new)


title: cGAS sample 2_f (new)

description: Library name: cGAS sample 2_f (new)


title: WT sample 3_m (new)

description: Library name: WT sample 3_m (new)


title: WT sample L7 liver


title: Blm sample L30 liver

value: Blm1 mutant


title: Blm sample L3 liver


title: WT sample 4 liver

value: 2 months


title: Blm sample L29 liver


title: WT sample 4 brain


title: cGAS sample 3_f (new)

description: Library name: cGAS sample 3_f (new)


title: WT sample 3 liver


title: WT sample 3 brain


title: WT sample 2 liver


title: WT sample 1 liver


title: WT sample 2 brain


title: dKO sample 4 liver

value: ATMcGAS double mutant


title: dKO sample 3 liver


title: dKO sample 2 liver


title: dKO sample 1 brain


title: dKO sample 4 brain


title: ATM sample 4 brain

value: ATM mutant


title: ATM sample 3 liver


title: ATM sample 3 brain


title: ATM sample 2 liver


title: ATM sample 2 brain


title: ATM sample 1 liver


title: ATM sample 1 brain


title: Flavopiridol_treated_Spt5_Cut&Run_replicate_2

city: New York

first: Feiyue

last: Lu

state: NY

department: Institute for Systems Genetics

institute: NYU School of Medicine

description: Library name: Flavopiridol_treated_Spt5_Cut_Run_replicate_2

data_processing:
Paired-end CUT&RUN sequencing reads were assessed with FastQC (Babraham Bioinformatics - FastQC A Qu...) using default criteria, then adapter and quality trimming were performed using Trim Galore (Trim Galore: A wrapper tool around Cu...) in paired-end mode. Trimmed reads were aligned with Bowtie2 (Langmead and Salzberg 2012)(local, very-sensitive-local) to an E. coli reference genome to quantify spike-in reads and to a custom Drosophila melanogaster genome: starting from the dm6 assembly, we swapped the histone locus repeats for a single instance of the consensus sequence of the ~ 5kb repeated unit, followed by a stretch of unspecified bases to retain the register of Chr. 2L regions downstream of the histone locus with the dm6 assembly. This procedure prevents the undesirable exclusion of histone locus reads that do not map unambiguously to a unique repeat. As a result, reads from the ~110 histone repeats pile up on a single unit, ensuring ample read depth and providing an average profile of the repeat unit. Alignments were processed with SAMtools (Danecek et al. 2021), including sorting/indexing and filtering by a minimum mapping quality, and reads mapping to the mitochondrial genome were removed. Spike-in normalization was applied by computing a per-sample scaling factor from the number of mapped E. coli reads, and scaled genome-wide coverage tracks were generated using deepTools (Ramírez et al. 2016) bamCoverage. Replicates were then averaged to generate a mean bigWig track, and background-corrected bigWigs were produced by subtracting from each coverage track the coverage track obtained from non-Halo-expressing negative-control ovaries submitted to the same biological treatment and processed identically. Signal around transcription start sites was summarized with deepTools computeMatrix and visualized using plotHeatmap and plotProfile.  For gene-level quantification, CUT&RUN signal was first summarized per gene and per sample as a single numeric value (summed signal across the gene), and these values were then aggregated across all samples for the genes of interest. For each gene, background signal was estimated separately for each treatment using the matched negative-control samples and averaged across replicates, then subtracted from the corresponding experimental samples to obtain background-corrected gene signals. To calculate the summary matrix used for plotting, the background-corrected control condition for each comparison was scaled to 1 by dividing both the control and treatment background-corrected signals by the mean background-corrected control signal computed across replicates for that gene. Results were then visualized as replicate-level points with the mean indicated for each condition.
Assembly: dm6
Supplementary files format and content: .bw
Library strategy: CUT&Run

source_name: adult ovaries

extract_protocol:
CUT&RUN libraries were prepared using the CUTANA™ CUT&RUN Kit (EpiCypher, Cat. No. 14-1048) following the manufacturer’s instructions with minor modifications. In brief, ovaries were harvested from 0-6 hr old adult females fattened with yeast paste for 8-10 hrs to reach development Stage 10. Four pairs of ovaries were collected per replicate, with two to four replicates prepared per genotype per condition. For drug-treated conditions, ovaries were incubated in growth media containing either 500 μM TRI or 500 nM FP for 35 min. To allow for antibody binding in situ, cells were permeabilized in buffer containing 0.05% digitonin. The ovaries were incubated with rabbit polyclonal Halotag antibody (Promega G9281; 1:100) at 4°C overnight. The w1118 line, lacking HaloTag expression, served as a negative control. Following antibody incubation, pAG-MNase (EpiCypher, Cat. No. 15-1016) was added to bind the antibody-labeled chromatin. Targeted digestion was activated by the addition of 100 mM CaCl2. To normalize read counts across conditions, 0.1 ng of E. coli Spike-in DNA (EpiCypher, Cat. No. 18-1401) was added to each reaction within the Stop Buffer master mix used to halt MNase activity.
CUT&RUN-enriched DNA was isolated from the supernatant and purified using 1.66x SPRIselect beads (Beckman Coulter, Cat. No. 21-1405). Purified DNA was quantified via Qubit fluorometer. Sequencing libraries were generated using universal i5 and uniquely barcoded i7 primers with 14 PCR cycles. All subsequent library purifications were performed using 1.66x SPRIselect beads to eliminate residual primers and concentrate the samples. Final library quality and fragment distribution—targeting a peak at ~300 bp representing mononucleosomes plus sequencing adapters—were confirmed via Bioanalyzer prior to paired-end sequencing on an Illumina NextSeq 550.

value: adult ovaries

value: Flavopiridol


title: dKO sample 3 brain


title: Triptolide_treated_Spt5_Cut&Run_replicate_2

description: Library name: Triptolide_treated_Spt5_Cut_Run_replicate_2

value: Triptolide


title: dKO sample 1 liver


title: DMSO_treated_Spt5_Cut&Run_replicate_2

description: Library name: DMSO_treated_Spt5_Cut_Run_replicate_2

value: DMSO


title: Flavopiridol_treated_Spt5_Cut&Run_replicate_1

description: Library name: Flavopiridol_treated_Spt5_Cut_Run_replicate_1


title: Triptolide_treated_Spt5_Cut&Run_replicate_1

description: Library name: Triptolide_treated_Spt5_Cut_Run_replicate_1


title: DMSO_treated_Spt5_Cut&Run_replicate_1

description: Library name: DMSO_treated_Spt5_Cut_Run_replicate_1


title: ATM sample 4 liver


title: Flavopiridol_treated_Pol2_Cut&Run_replicate_4

description: Library name: Flavopiridol_treated_Pol2_Cut_Run_replicate_4