title: experiment AdapPrim, condition blocked adapter , original P5 , extended P7, rep 1, sample 3

description: Library name: AdapPrim_1_bne_sample3


title: experiment AdapPrim, condition blocked adapter , original P5 , extended P7, rep 2, sample 13

status: Public on Aug 19 2025

type: SRA

city: Martinsried

first: Wolfgang

last: Enard

state: Bavaria

address: Grossshaderner Str.2, Anthropology Human Genomics, AG Enard

department: Anthropology and human genomics

country: Germany

institute: LMU Munich

description: Library name: AdapPrim_2_bne_sample13

library_source: transcriptomic

data_processing:
Quality assessment of the fastq data files was conducted using fastqc (v 0.11.5) [2], followed by polyA trimming using cutadapt (v 4.1) [3]. Subsequent read filtering, mapping, and counting were performed using the zUMIs pipeline (v 2.9.7) [4], with reads mapped to the mouse genome (mm10). Fastq files were sample-demultiplexed using deML [5].
2 Andrews, S. (2010). FastQC: A quality control tool for high throughput sequence data. Available at: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/
3 Martin, M. (2011). Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet. journal, 17(1), 10-12.
4 Parekh, S., Ziegenhain, C., Vieth, B., Enard, W., & Hellmann, I. (2018). zUMIs- A fast and flexible pipeline to process RNA sequencing data with UMIs. GigaScience, 7(6), giy059.
5 Gabriel Renaud, Udo Stenzel, Tomislav Maricic, Victor Wiebe, Janet Kelso (2015) deML: robust demultiplexing of Illumina sequences using a likelihood-based approach, Bioinformatics, Volume 31, Issue 5, March 2015, Pages 770–772, https://doi.org/10.1093/bioinformatics/btu719
Assembly: GRCm39
Supplementary files format and content: processed data files contain the Barcode (BC) of each sample with the associated counts (N) per feature (type), e.g. Intergenic, Intron, Exon, Ambiguity and Unmapped.

molecule: polyA RNA

organism: Mus musculus

source_name: brain

extract_protocol:
prime-seq - tissue lysis and homogenization in RLT+ buffer + 1 % B-Mercaptoethanol
prime-seq, the prime-seq original protocol  [1] , the original protocol with adaptions and the new, improved protocol  version (Pförtner et al, this study)
1 Janjic, A., Wange, L.E., Bagnoli, J.W. et al. Prime-seq, efficient and powerful bulk RNA sequencing. Genome Biol 23, 88 (2022). https://doi.org/10.1186/s13059-022-02660-8

tag: tissue

value: brain


title: experiment AdapPrim, condition blocked adapter , original P5 , extended P7, rep 1, sample 4

description: Library name: AdapPrim_1_bne_sample4


title: experiment AdapPrim, condition blocked adapter , original P5 , extended P7, rep 1, sample 23

description: Library name: AdapPrim_1_bne_sample23


title: experiment AdapPrim, condition blocked adapter , original P5 , extended P7, rep 1, sample 22

description: Library name: AdapPrim_1_bne_sample22


title: experiment AdapPrim, condition blocked adapter , original P5 , extended P7, rep 1, sample 19

description: Library name: AdapPrim_1_bne_sample19


title: experiment AdapPrim, condition blocked adapter , original P5 , extended P7, rep 1, sample 20

description: Library name: AdapPrim_1_bne_sample20


title: experiment AdapPrim, condition blocked adapter , original P5 , extended P7, rep 1, sample 24

description: Library name: AdapPrim_1_bne_sample24


title: experiment AdapPrim, condition blocked adapter , original P5 , extended P7, rep 2, sample 15

description: Library name: AdapPrim_2_bne_sample15


title: experiment AdapPrim, condition blocked adapter , original P5 , extended P7, rep 1, sample 21

description: Library name: AdapPrim_1_bne_sample21


title: experiment AdapPrim, condition blocked adapter , original P5 , extended P7, rep 2, sample 17

description: Library name: AdapPrim_2_bne_sample17


title: experiment AdapPrim, condition blocked adapter , original P5 , extended P7, rep 1, sample 16

description: Library name: AdapPrim_1_bne_sample16


title: experiment AdapPrim, condition blocked adapter , original P5 , extended P7, rep 1, sample 17

description: Library name: AdapPrim_1_bne_sample17


title: experiment AdapPrim, condition blocked adapter , original P5 , extended P7, rep 1, sample 18

description: Library name: AdapPrim_1_bne_sample18


title: experiment AdapPrim, condition blocked adapter , original P5 , extended P7, rep 1, sample 12

description: Library name: AdapPrim_1_bne_sample12


title: experiment AdapPrim, condition blocked adapter , original P5 , extended P7, rep 1, sample 15

description: Library name: AdapPrim_1_bne_sample15


title: experiment AdapPrim, condition blocked adapter , original P5 , extended P7, rep 1, sample 11

description: Library name: AdapPrim_1_bne_sample11


title: experiment AdapPrim, condition blocked adapter , original P5 , extended P7, rep 1, sample 8

description: Library name: AdapPrim_1_bne_sample8


title: experiment AdapPrim, condition blocked adapter , original P5 , extended P7, rep 1, sample 14

description: Library name: AdapPrim_1_bne_sample14


title: experiment AdapPrim, condition blocked adapter , original P5 , extended P7, rep 1, sample 10

description: Library name: AdapPrim_1_bne_sample10


title: experiment AdapPrim, condition blocked adapter , original P5 , extended P7, rep 1, sample 1

description: Library name: AdapPrim_1_bne_sample1


title: DSS colitis JUPfl/fl rep1

city: Würzburg

first: Tom

last: Gräfenhan

address: Josef-Schneider-Str. 2, Bau D15

department: Core Unit SysMed

institute: University of Wuerzburg

data_processing:
Base calling with Illumina NextSeq RTA v3.10.30 (NextSeq 2000).
Demultiplexed FASTQ files were generated with bcl2fastq2 v2.20.0.422 (Illumina).
Illumina reads were quality- and adapter-trimmed via Cutadapt version 2.5 using a cutoff Phred score of 20 in NextSeq mode, and reads without any remaining bases were discarded (command line parameters: --nextseq-trim=20 -m 1 -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC).
Processed reads were subsequently mapped to the mouse genome (GRCm38.p6) using STAR v2.7.2b with default parameters.
Read counts on exon level summarized for each gene were generated using featureCounts v1.6.4 from the Subread package.
Multi-mapping and multi-overlapping reads were counted strand-specific and reversely stranded with a fractional count for each alignment and overlapping feature (command line parameters: -s 2 -t exon -M -O --fraction).
The count output was utilized to identify differentially expressed genes using DESeq2 10 version 1.24.0.
Read counts were normalized by DESeq2 and fold-change shrinkage was applied by setting the parameter “betaPrior=TRUE”.
Assembly: GRCm38.p6
Supplementary files format and content: csv; table containing raw read counts

source_name: mouse gut

extract_protocol:
RNA from murine intestines or organoids for bulk sequencing was isolated using TRIZOL.
RNA quality was checked using a 2100 Bioanalyzer with the RNA 6000 Nano kit (Agilent Technologies). The RIN for all samples was ≥7.7. DNA libraries suitable for sequencing were prepared from 300 ng of total RNA for four samples and appx 200 ng for two samples with lower concentrations, with oligo-dT capture beads for poly-A-mRNA enrichment using the TruSeq.

value: mouse gut


title: DSS colitis JUPfl/fl rep2


title: iVilCre ERT2JUPfl/fl rep3


title: organoid iVilCre ERT2JUPfl/fl rep3

tag: cell type

value: organoid generated out of mouse gut


title: organoid iVilCre ERT2JUPfl/fl rep2


title: iVilCre ERT2JUPfl/fl rep2


title: organoid JUPfl/fl rep 3


title: organoid JUPfl/fl rep 2


title: experiment AdapPrim, condition blocked adapter , original P5 , extended P7, rep 1, sample 2

description: Library name: AdapPrim_1_bne_sample2


title: organoid JUPfl/fl rep 1


title: organoid JUPfl/fl rep2


title: organoid JUPfl/fl rep3


title: organoid JUPfl/fl rep1


title: organoid iVilCre ERT2JUPfl/fl rep1


title: uninfected_shDMAP1_2_BC969

city: Jupiter

first: Susana

middle: T

last: Valente

state: FL

address: 130 Scripps Way

department: Immunology and Microbiology

country: USA

institute: The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology

description:
Donor BC969, uninfected CD4+Tcells, Amt+
672_36

data_processing:
FastQC
Pseudoalignment by Salmon v 0.14.1 using the --validateMappings flag using a decoy-aware index of the GRCh38 transcriptome with the HIV-R7/E-/GFP or HIVGKO transcript added to the end.
The resulting quantification files were read into R (version 4.2.3) using the tximport function from the R package tximport (1.26.1)
Differential expression analysis was done using edgeR.
Raw counts were converted to a DGEList object using DGEList(), lowly expressed transcripts were removed using filterByExpr() and normalization factors were calculated using calcNormFactors().  Normalized counts were converted to log2 counts per million using cpm() and fit to the contrast of interest using lmFit().  Differential expression values were calculated using eBayes(trend=TRUE) and summarized with topTable().
Assembly: GRCh38 transcriptome with the HIV-R7/E-/GFP or HIVGKO transcript added to the end as an extra transcript
Supplementary files format and content: Salmon quantification files in a .sf format

organism: Homo sapiens

source_name: primary CD4+ T cells

growth_protocol: For primary CD4+ T cells: Human PBMCs from 3 healthy donors were obtained from Buffy coats by density centrifugation and CD4+ T cells isolated by negative selection. Cells were then activated with 1:2 ratio with Dynabeads™ Human T-Activator in the presence of 6 ng/ml IL-2, 36 ng/ml IL-7 and 36 ng/ml IL-15. The cells were cultured in RPMI 1640 media supplemented with 1xMEM vitamin solution, 1xNEAA, 1x Sodium Pyruvate , 1xPen/Strep/L-glut, 0.01M HEPES pH 8.0, 1xL-Asp/L-Arg/Folic acid mix (house-made), and 10% FBS. Jurkat and J-Lat 10.6 cells were maintained in RPMI 1640 supplemented with 2.0 mM L-glutamine/100 U/ml penicillin/100 µg/ml streptomycin and 10% heat-inactivated FBS (complete RPMI) and cultured at 37°C and 5% CO2.

extract_protocol:
For primary CD4+ T cells: total RNA was isolated using RNeasy Micro kit which includes an on column DNase treatment. For Jurkat and J-Lat 10.6 cells: Total RNA was extracted from cells using the Qiagen RNeasy kit. RNA was DNase treated using the TURBO DNA-freeTM kit.
For primary CD4+ T cells: Two days post activation of primary CD4+ T cells, non-tissue culture treated 24-well plates were coated with RetroNectin (RN) overnight at 4˚C (RetroNectin® Recombinant Human Fibronectin Fragment). RN was removed, plates washed w

treatment_protocol: For primary CD4+ T cells: Two days post activation of primary CD4+ T cells, non-tissue culture treated 24-well plates were coated with RetroNectin (RN) overnight at 4˚C (RetroNectin® Recombinant Human Fibronectin Fragment). RN was removed, plates washed with PBS and then blocked with sterile 2% BSA in PBS for 30 min at room temperature. Plates were washed with PBS and then GaLV-pseudotyped LMPd was loaded onto the RN (2,000 x g, 2 h at 32˚C). Unbound virus was washed off with PBS and 5x10^5 activated T cells were added at a density of 1x10^6/ml on top of the LMPd-coated plates, concentrated HIVGKO was added on top and centrifuged at 2000 x g for 5 mins to facilitate attachment to the virus and RN, then placed in an incubator overnight. The next day, cells were detatched from the RN and maintained at 1.5x10^6/ml for 9 days in T cell media prior to FACS isolation for RNA-seq analysis. For Jurkat and J-Lat 10.6 cells: cells were transduced with an MOI of 0.3 of LMPd shRNAmirs (two independent shRNAmirs per gene were used as biological replicates). Two days post transduction, transduced cells were FACS isolated and cultured for a further seven days before RNA was extracted.

value: primary CD4+ T cells

tag: treatment


title: experiment AdapPrim, condition blocked adapter , original P5 , extended P7, rep 1, sample 13

description: Library name: AdapPrim_1_bne_sample13


title: uninfected_shCD19_4_BC969

description:
Donor BC969, uninfected CD4+Tcells, Amt+
672_34


title: hiPSC-CMs, HCM, rep1

city: Saint-Petersburg

first: Margarita

last: Sorokina

address: Akkuratova 2

country: Russia

institute: Almazov National Medical Research Centre

description:
Library name: Sample 3
HCM_1

data_processing:
Read quality was checked for each sample using FastQC v0.11.9.
Sequenced reads were mapped to the human genome using mapper STAR v2.7 with reference genome GRCh38.p13 and annotation GENCODE (gencode.v41.primary_assembly)
Aligned reads were count with featureCounts program v1.6.4.
Further analysis were made using DESeq2, fgsea и clusterProfiler R packages, as well as MSigDB and phantasus online tools.
Assembly: GRCh38.p13
Supplementary files format and content: tab-delimited text file includes matrix of raw counts for each of 4 Samples

molecule: total RNA

source_name: hiPSC-CMs

growth_protocol: Mononuclear cells (MNCs) of the HCM patient were electroporated with episomal vectors (0.5 μg each, Addgene IDs #41855-41858, #41813-41814) using Neon Transfection System (Thermo Fisher Scientific, Waltham, MA, USA), program: 1650 V, 10 ms, 3 times. All reprogramming steps were performed according to the Epi5™ Episomal iPSC Reprogramming Kit user guide (Thermo Fisher Scientific, Waltham, MA, USA). Primary iPSC colonies were picked manually, transferred on a feeder layer, and maintained in KnockOut DMEM supplemented with 15% KnockOut Serum Replacement (KoSR), 0.1 mM Non-Essential Amino Acid (NEAA), 1× penicillin-streptomycin, 1 mM GlutaMAX (all Thermo Fisher Scientific, Waltham, MA, USA), 0.05 mM 2-mercaptoethanol (Amresco, Solon, OH, USA), and 10 ng/ml bFGF (SCI-store, Moscow, Russia). Cells were cultured at 37°C in 5% CO2 and passaged at a ratio of 1:10 every 3-5 days with TrypLE™ Express Enzyme (Thermo Fisher Scientific, Waltham, MA, USA).

extract_protocol:
Total RNA was isolated from the cells with an Extract RNA kit (Evrogen, Russia)
RNA-libraries were constructed using TruSeq Stranded mRNA library prep kit.

treatment_protocol: hiPSC were differentiated into mature cardiomyocytes (45 days), according to a previously published protocol (https://doi.org/10.1002/cm.21922).

value: hiPSC-CMs

tag: genotype

value: MYPN mutation

value: cardio differentiation


title: hiPSC-CMs, healthy donor, rep2

description:
Library name: Sample 2
Donor_2

value: Healthy Donor


title: hiPSC-CMs, HCM, rep2

description:
Library name: Sample 4
HCM_2


title: hiPSC-CMs, healthy donor, rep1

description:
Library name: Sample 1
Donor_1


title: uninfected_shEP400_4_BC923

description:
Donor BC923, uninfected CD4+Tcells, Amt+
672_31


title: uninfected_shCD19_4_BC923

description:
Donor BC923, uninfected CD4+Tcells, Amt+
672_30


title: DSS colitis JUPfl/fl rep3


title: uninfected_shEP400_4_BC969

description:
Donor BC969, uninfected CD4+Tcells, Amt+
672_35


title: uninfected_shDMAP1_2_BC923

description:
Donor BC923, uninfected CD4+Tcells, Amt+
672_32


title: iVilCre ERT2JUPfl/fl rep1


title: uninfected_shDMAP1_2_BC920

description:
Donor BC920, uninfected CD4+Tcells, Amt+
672_28


title: uninfected_shEP400_4_BC920

description:
Donor BC920, uninfected CD4+Tcells, Amt+
672_27


title: tar of cells in epithelial (epi) cell dataset isolated from female mice

city: Huddinge

first: Lars

last: Muhl

address: Blickagången 6

department: MedH

country: Sweden

institute: Karolinska Institutet

description:
Library name: Sample8
Smart-seq2

library_source: transcriptomic single cell

data_processing:
bcl2fastq - demultiplexing
sequenced reads were trimmed for adaptor sequence, and then mapped to the mouse reference genome (GRCm38 / mm10) using TapHat2, Bowtie1 or Bowtie2.
raw read counts per gene were calculated using featureCounts from subread
for analysis, all raw counts from all cells of each of the sample-plates were combined into one expression matrix file
counts data was processed and analyzed using Seurat and pagoda2 packages in R-software
Assembly: GRCm38 (mm10)
Supplementary files format and content: tab-deliminated txt file as expression matrix including non-normalized counts of all samples

source_name: liver

extract_protocol:
FACS into 384well plate of single cells from dissociation of mouse liver in Miltenyi's skeletal muscle dissociation kit (supplemented with collagenase IV-S).
RNA libraries were prepared using the Smart-Seq2 protocol at SICOF Huddinge, Sweden.

value: liver

tag: Sex

value: female

value: epithelial cells


title: productive_shDMAP1_2_BC969

description:
Donor BC969, productively infected with HIVGKO (Amt+GFP+mKO2+)
672_23


title: uninfected_shCD8B_3_BC920

description:
Donor BC920, uninfected CD4+Tcells, Amt+
672_25


title: productive_shEP400_4_BC969

description:
Donor BC969, productively infected with HIVGKO (Amt+GFP+mKO2+)
672_21


title: latent_shDMAP1_2_BC969

description:
Donor BC969, latently infected with HIVGKO (Amt+GFP-mKO2+)
672_24


title: tar of cells in immune (imm) cell dataset isolated from male mice

description:
Library name: Sample5
Smart-seq2

value: male

value: immune cells


title: uninfected_shCD19_4_BC920

description:
Donor BC920, uninfected CD4+Tcells, Amt+
672_26


title: tar of cells in immune (imm) cell dataset isolated from female mice

description:
Library name: Sample6
Smart-seq2


title: tar of cells in epithelial (epi) cell dataset isolated from male mice

description:
Library name: Sample7
Smart-seq2


title: productive_shCD19_4_BC969

description:
Donor BC969, productively infected with HIVGKO (Amt+GFP+mKO2+)
672_19


title: tar of cells in mesenchymal (mes) cell dataset isolated from male mice

description:
Library name: Sample1
Smart-seq2

value: mesenchymal cells


title: tar of cells in endothelial (endo) cell dataset isolated from male mice

description:
Library name: Sample3
Smart-seq2

value: endothelial cells


title: productive_shCD8B_3_BC969

description:
Donor BC969, productively infected with HIVGKO (Amt+GFP+mKO2+)
672_17


title: latent_shCD8B_3_BC969

description:
Donor BC969, latently infected with HIVGKO (Amt+GFP-mKO2+)
672_18


title: latent_shDMAP1_2_BC923

description:
Donor BC923, latently infected with HIVGKO (Amt+GFP-mKO2+)
672_16


title: uninfected_shCD8B_3_BC923

description:
Donor BC923, uninfected CD4+Tcells, Amt+
672_29


title: latent_shEP400_4_BC923

description:
Donor BC923, latently infected with HIVGKO (Amt+GFP-mKO2+)
672_14


title: productive_shEP400_4_BC923

description:
Donor BC923, productively infected with HIVGKO (Amt+GFP+mKO2+)
672_13


title: uninfected_shCD8B_3_BC969

description:
Donor BC969, uninfected CD4+Tcells, Amt+
672_33


title: Control

city: Brisbane

first: Juliet

last: French

address: 300 Herston Rd

country: Australia

institute: QIMRB

description: Library name: Control

library_source: genomic

data_processing:
Raw sequencing data were checked for quality using FastQC v0.11.5 and adapters trimmed using Cutadapt v1.13. Paired-end reads were aligned to the hg19 human reference genome using Bowtie2 v2.2.9 and filtered using PicardTools v2.19.0. MACS2 v2.1.2 was used to call peaks representing regions of enriched H3K27ac signal. Global signal tracks were generated with bamCompare (deepTools) and visualized with the Integrative Genomics Viewer (IGV) browser. Enriched peaks were assigned to genes within a 5 kb linear distance and over-represented pathway terms were determined using the ReactomePA Bioconductor package v1.9.4.
Assembly: HG38
Supplementary files format and content: Peak file with called peaks

molecule: genomic DNA

source_name: Breast

extract_protocol:
T47D cells were cross-linked with 1% formaldehyde (Merck) at 37oC for 10 min, rinsed with phosphate buffered saline (PBS; TMO) containing 5% bovine serum albumin (BSA; Scientifix) and harvested in PBS containing protease inhibitor cocktail (PIC; Roche). Harvested cells were centrifuged for 2 min at 3,000 rpm. Cell pellets were resuspended in lysis buffer (1% sodium dodecyl sulfate (SDS; Merck), 10 mM EDTA (TMO), 50 mM Tris-HCl, pH 8.1, PIC) and sonicated three times for 15 s at 70% duty cycle (Branson SLPt) then centifuged at 13,000 rpm for 15 min. Supernatants were resuspended in dilution buffer (1% Triton X-100, 2 mM EDTA, 150 mM NaCl, 20 mM Tris-HCl, pH 8.1).
For ChIPseq, libraries were prepared using the NEBNext Ultra II DNA library prep kit (NEB), according to manufacturer’s instructions. Samples were barcoded and run

treatment_protocol: H3k27ac ChiP antibody (Abcam; ab4729)

value: Breast

tag: cell line

value: Mammary epithelial

tag: chip antibody


title: GuideB

description: Library name: GuideB


title: g3'EC1

description: Library name: g3’EC1


title: latent_shCD19_4_BC923

description:
Donor BC923, latently infected with HIVGKO (Amt+GFP-mKO2+)
672_12


title: g3'EC2

description: Library name: g3’EC2


title: latent_shEP400_4_BC969

description:
Donor BC969, latently infected with HIVGKO (Amt+GFP-mKO2+)
672_22


title: productive_shDMAP1_2_BC923

description:
Donor BC923, productively infected with HIVGKO (Amt+GFP+mKO2+)
672_15


title: latent_shCD19_4_BC969

description:
Donor BC969, latently infected with HIVGKO (Amt+GFP-mKO2+)
672_20


title: tar of cells in endothelial (endo) cell dataset isolated from female mice

description:
Library name: Sample4
Smart-seq2


title: tar of cells in mesenchymal (mes) cell dataset isolated from female mice

description:
Library name: Sample2
Smart-seq2


title: GuideA

description: Library name: GuideA


title: productive_shCD19_4_BC923

description:
Donor BC923, productively infected with HIVGKO (Amt+GFP+mKO2+)
672_11


title: productive_shDMAP1_2_BC920

description:
Donor BC920, productively infected with HIVGKO (Amt+GFP+mKO2+)
672_7


title: GuideControl

description: Library name: GuideControl


title: latent_shDMAP1_2_BC920

description:
Donor BC920, latently infected with HIVGKO (Amt+GFP-mKO2+)
672_8


title: productive_shCD8B_3_BC923

description:
Donor BC923, productively infected with HIVGKO (Amt+GFP+mKO2+)
672_9


title: ChIP-seq U2OS siRING1B Input

city: Hershey

first: Zhonghua

last: Gao

state: PA

address: 700 HMC Cres Rd

department: Biochemistry

institute: Pennsylvania State University

description: Library name: ChIP-seq Sample 21

data_processing:
For ChIP-seq samples, alignment was performed using BWA and mm10 (mouse) and hg38 (human) were used as reference genomes. Samtools was used to generate bam/sam files. Deeptools were used for bigwig file and visualization. MACS2 was used for peak calling using default parameters.
Assembly: mm10, hg38
Supplementary files format and content: For ChIP-seq, BigWig (.bw) files containing read density data of respective immunoprecipitated proteins at mapped genomic loci.

growth_protocol: ESCs and NPCs were cultured in basic stem cell media (DMEM, 15% FBS, 1 X non-essential amino acids, 0.1 mM β-mercaptoethanol, 0.5 X penicillin/streptomycin, 1X sodium pyruvate). For ESCs, 0.003 µg/mL LIF, 1 µM PD0325901 (PD), and 3 µM Chir99021 (CH) were added to the media. For NPCs, 5 µM retinoic acid was added starting from day 4 of differentiation until day 8. U2OS cells were cultured on standard attachment cell culture plates in DMEM, 10% FBS, 10% newborn calf serum (NCS), and 0.5X penicillin/streptomycin.

extract_protocol:
For ChIP-seq samples, cells were cross-linked with 1% formaldehyde for 8 minutes at room temperature. After washing, cells were sonicated with Diagenode Bioruptor in ChIP lysis buffer. Samples were cleaned up for immunoprecipitation using protein G agarose beads with antibodies of interest. Bound protein-DNA complexes were collected from beads and reverse crosslinked before being purified for DNA. Futher procedure details are described in the main associated article.
The ChIP-seq libraries were constructed using the sparQ DNA Library Prep kit.

treatment_protocol: NPCs were cultured in basic stem cell media with 5 µM retinoic acid (RA) starting from day 4 of differentiation until day 8. U2OS cells were transfected with either siControl or siRING1B for 2 days before collection.

value: Osteosarcoma cells

value: RING1B knock-down

value: siRING1B siRNA


title: latent_shCD8B_3_BC923

description:
Donor BC923, latently infected with HIVGKO (Amt+GFP-mKO2+)
672_10

value: primary CD4+ T cells


title: ChIP-seq U2OS siControl Input

description: Library name: ChIP-seq Sample 19

value: Vehicle control

value: siControl siRNA


title: productive_shEP400_4_BC920

description:
Donor BC920, productively infected with HIVGKO (Amt+GFP+mKO2+)
672_5


title: ChIP-seq U2OS siRING1B Ctcf

description: Library name: ChIP-seq Sample 22


title: latent_shEP400_4_BC920

description:
Donor BC920, latently infected with HIVGKO (Amt+GFP-mKO2+)
672_6


title: latent_shCD19_4_BC920

description:
Donor BC920, latently infected with HIVGKO (Amt+GFP-mKO2+)
672_4


title: ChIP-seq U2OS siControl Ctcf

description: Library name: ChIP-seq Sample 20


title: latent_shCD8B_3_BC920

description:
Donor BC920, latently infected with HIVGKO (Amt+GFP-mKO2+)
672_2


title: productive_shCD19_4_BC920

description:
Donor BC920, productively infected with HIVGKO (Amt+GFP+mKO2+)
672_3


title: P118NEG

city: Geneva

first: Celine

last: Delucinge

address: 1 rue Michel Servet

department: iGE3 Genomics Platform

country: Switzerland

institute: University of Geneva

description: Library name: Sample 9

data_processing:
Illumina bcl2fastq software (v.2.20.0) used for basecalling.
Sequenced reads were mapped to UCSC hg38 whole genome using STAR v2.7.0f with default parameters
Raw counts are produced by htseq-count (HTSeq v.0.9.1)
Normalization and differential expression analysis were performed with edgeR v.3.38.4
Assembly: UCSC hg38
Supplementary files format and content: rawcounts.txt = tab-delimited text files include rawcount values for each Sample
Supplementary files format and content: log2normcounts.txt = tab-delimited text files include normalized expression values(log 2 cpm = count per millions) for each Sample

growth_protocol: fresh PBMC isolation, FACS sorted c-Met+ CD4 T cells

extract_protocol:
Venous blood was collected in vacutainer K2E tubes containing EDTA (Becton Dickinson) and CSF was collected in 15 mL Falcon tubes via lumbar puncture from MS and NIND patients. CSF was collected and kept on ice until processing, then centrifuged at 400 g for 10 minutes. The cell pellet was gently resuspended in ice-cold phosphate-buffered saline (PBS; Thermo-Fisher #10010072) for flow cytometry staining, performed within 2 hours after lumbar puncture. Whole blood was processed for the isolation of PBMCs by density gradient centrifugation using Ficoll Paque Plus (GE Healthcare). A fraction of PBMCs was resuspended in ice-cold PBS for flow cytometric analysis, and the remaining cells were cryopreserved using 10% DMSO in fetal bovine serum (Gibco) and stored in liquid nitrogen. CD4 T cells were magnetically isolated from PBMCs using CD4 microbeads (Miltenyi Biotec), stained with anti-human CD3 (UCHT1, Biolegend), anti-human CD4 (SK3, BD Biosciences), anti-human c-Met (95106, R&D), and DAPI, and sorted on a FACSAria™ II to >95% purity for use in transmigration assays and RNA isolation for bulk RNA sequencing. FACS-sorted T cell subsets were washed with PBS and resuspended in RNA lysis solution with 1% DTT, and total RNA was extracted using the Nucleospin RNA kit (Macherey-Nagel). Complementary DNA was synthesized from total RNA using a reaction mix containing Tris-aminoMethane (200 mM), KCl (500 mM), MgCl₂ (0.2 M; Sigma-Aldrich), DTT (100 mM; Invitrogen), random hexamers (50 mM; Invitrogen), oligo(dT)₁₅ primer (100 mg/ml; Promega), dNTP mix (10 mM; Promega), RNAsin (40 U/ml; Promega), and SuperScript™ II (200 U/ml; Invitrogen). After incubation at 42 °C for 50 minutes and inactivation at 99 °C for 3 minutes, cDNA was diluted and stored at −20 °C until use. Bulk RNA sequencing was performed on sorted c-Met⁻ and c-Met⁺ CD4 T cells using the SMART-Seq v4 kit (Clontech) for reverse transcription and cDNA amplification according to the manufacturer’s instructions, starting with 1 ng total RNA. 200 pg of cDNA were used for library preparation with the Nextera XT kit (Illumina), and library molarity and quality were assessed with the Qubit and Tapestation using a DNA High Sensitivity chip (Agilent Technologies). Libraries were sequenced on a NovaSeq 6000 Illumina sequencer for SR100 reads, with an average depth of approximately 35 million reads per sample.
Illumina TruSeq HT stranded mRNA

tag: subject


title: P115POS

description: Library name: Sample 8


title: P120NEG

description: Library name: Sample 11


title: J-Lat 10.6, shEP400, input, ChIP, unstimulated, Rep2

description:
712_41
shEP400_input_n_of_2_NORMsort.bw

data_processing:
FASTQC
Read trimming with trim_galore (--paired --length 24 --stringency 3)
Align with bowtie2 (-p 16 --no-mixed --no-discordant -1)
Removed duplicates with samtools
Peaks were called with macs2 (callpeak  --broad -f BAMPE -g hs -q 0.05 -B)
For visualization, bam files for replicates were merged using samtools, deepTools was used to convert BAM files to bedgraph format (bamCoverage), and and then the bdg files were normalized across samples to library size prior to conversion to bigwig format (bedGraphToBigWig).
Assembly: custom genome GRCh38 with HIV-R7/E-/GFP inserted into chromosome 9 at position 136,468,578, shifting the remaining chromosome 9 by 10,200 bp (the length of the HIV insertion), including a repeat of the “ACAAA” sequence in the SEC16A intron that became duplicated upon HIV integration
Supplementary files format and content: bigWig
Supplementary files format and content: broadPeak

source_name: J-Lat 10.6 cells

growth_protocol: J-Lat 10.6 cells were maintained in RPMI 1640 supplemented with 2.0 mM L-glutamine/100 U/ml penicillin/100 µg/ml streptomycin and 10% heat-inactivated FBS (complete RPMI) and cultured at 37°C and 5% CO2.

extract_protocol:
Native ChIP was performed using MNase to fragment chromatin to mono-to pentanucleosomes sizes.
ChIP DNA libraries for next-generation sequencing on the Illumina platform were constructed based on the protocol of NEB Next Ultra II DNA Library Prep Kit (#E7103, NEB) using NEBNext Multiplex Oligos for Illumina (96 Unique Dual Index Primer Pairs, # E6440S)

treatment_protocol: Cells were transduced with the indicated shRNAs in pMKO.1-puro. Two days post transduction cells were selected with 4 µg/ml puromycin for one week, after which cells were collected for Native ChIP-seq

value: J-Lat 10.6 cells

value: unstimulated


title: P115NEG

description: Library name: Sample 7


title: P112NEG

description: Library name: Sample 5


title: J-Lat 10.6, shDMAP1, H2A.Z, ChIP, TNFa, Rep2

description:
712_39
shDMAP1_TNF_H2AZ_n_of_2_NORMsort.bw

value: H2A.Z (Abcam, #Ab4174)

value: TNFa


title: J-Lat 10.6, shDMAP1, input, ChIP, unstimulated, Rep2

description:
712_42
shDMAP1_input_n_of_2_NORMsort.bw


title: P118POS

description: Library name: Sample 10


title: P112POS

description: Library name: Sample 6


title: Control 03, Kidney

city: Hamburg

first: Christian

last: Krebs

state: Hamburg

address: Martinistraße 52

institute: UKE

description:
Library name: C03
Single Cell 3' v3.1 (10x Genomics)

data_processing:
Cell Ranger software (v7.1.0, 10x Genomics) was used to process cellular barcodes and align reads to the GRCh38-2020-A reference genome.All quality control and preprocessing steps were performed in Scanpy and python.
Assembly: GRCh38-2020-A
Supplementary files format and content: filtered_gene_bc_matrices_h5.h5 : files output from CellRanger

source_name: Kidney

extract_protocol:
For single nucRNA-sequencing, snap frozen biopsies were thawed and chopped using a fresh razor blade. After adding 200 µl lysis buffer (1 mM DTT, 0.1% Triton X-100, 0.2 U/µl SUPERaseIN RNAse Inhibitor and 0.4 U/µl RNasin® Plus Ribonuclease Inhibitor in Nuclei PURE Lysis Buffer), the tissue homogenized 60 times using a pestle on ice. Next, the lysate was supplemented with additional 3.8 ml lysis buffer and incubated on ice for 25 min. Lysis efficiency was assessed using an optical microscope. After incubation, a 30 µm strainer was used to filter the lysate and washed with 1 ml lysis buffer. The lysate was centrifuged at 500 g (5 min, 4°C) and the supernatant was discarded. 5 ml washing buffer (0.01% BSA, 0.4 U/µl SUPERaseIN RNAse Inhibitor and 0.4 U/µl RNasin® Plus Ribonuclease Inhibitor in PBS) were added to the pellet and transferred to a falcon tube coated with 0.1% BSA in PBS and centrifuged (500 g, 5 min, 4°C). Resuspension buffer (1% BSA and 0.4 U/µl RNasin® Plus Ribonuclease Inhibitor in PBS) was added to the pellet. 40,000 nuclei were loaded onto a Chip G for GEM generation using the Chromium Single Cell 3’ v3.1 kit (10X Genomics). Reverse transcription, barcoding, complementary DNA amplification and purification for library preparation were performed as specified in the manufacturer's protocol. Sequencing was performed on a NovaSeq 6000 platform (Illumina) at a target read depth of 25,000 by Novogene.
libaries were constructed according to manufacturer specifications

value: Kidney

tag: subject status

value: control

value: Cells from Kidney cortex


title: Control 02, Kidney

description:
Library name: C02
Single Cell 3' v3.1 (10x Genomics)


title: Control 04, Kidney

description:
Library name: C04
Single Cell 3' v3.1 (10x Genomics)


title: J-Lat 10.6, shCD8B, H2A.Z, ChIP, TNFa, Rep2

description:
712_37
shCD8B_TNF_H2AZ_n_of_2_NORMsort.bw


title: J-Lat 10.6, shEP400, H2A.Z, ChIP, TNFa, Rep2

description:
712_38
shEP400_TNF_H2AZ_n_of_2_NORMsort.bw


title: Patient 11, Kidney

description:
Library name: P11
Single Cell 3' v3.1 (10x Genomics)

value: individuals with ANCA-associated glomerulonephritis


title: Control 01, Kidney

description:
Library name: C01
Single Cell 3' v3.1 (10x Genomics)


title: J-Lat 10.6, shCD8B, H2A.Z, ChIP, unstimulated, Rep2

description:
712_34
shCD8B_NS_H2AZ_n_of_2_NORMsort.bw


title: J-Lat 10.6, shEP400, H2A.Z, ChIP, unstimulated, Rep2

description:
712_35
shEP400_NS_H2AZ_n_of_2_NORMsort.bw


title: P120POS

description: Library name: Sample 12


title: Patient 10, Kidney

description:
Library name: P10
Single Cell 3' v3.1 (10x Genomics)


title: productive_shCD8B_3_BC920

description:
Donor BC920, productively infected with HIVGKO (Amt+GFP+mKO2+)
672_1


title: J-Lat 10.6, shDMAP1, H3.3, ChIP, TNFa, Rep2

description:
712_33
shDMAP1_TNF_H3_3_n_of_2_NORMsort.bw


title: Patient 08, Kidney

description:
Library name: P08
Single Cell 3' v3.1 (10x Genomics)


title: J-Lat 10.6, shEP400, H3.3, ChIP, TNFa, Rep2

description:
712_32
shEP400_TNF_H3_3_n_of_2_NORMsort.bw


title: Patient 07, Kidney

description:
Library name: P07
Single Cell 3' v3.1 (10x Genomics)


title: Patient 06, Kidney

description:
Library name: P06
Single Cell 3' v3.1 (10x Genomics)


title: J-Lat 10.6, shEP400, H3.3, ChIP, unstimulated, Rep2

description:
712_29
shEP400_NS_H3_3_n_of_2_NORMsort.bw


title: J-Lat 10.6, shDMAP1, H3.3, ChIP, unstimulated, Rep2

description:
712_30
shDMAP1_NS_H3_3_n_of_2_NORMsort.bw


title: J-Lat 10.6, shCD8B, H3.3, ChIP, TNFa, Rep2

description:
712_31
shCD8B_TNF_H3_3_n_of_2_NORMsort.bw


title: Patient 09, Kidney

description:
Library name: P09
Single Cell 3' v3.1 (10x Genomics)


title: J-Lat 10.6, shCD8B, input, ChIP, unstimulated, Rep2

description:
712_40
shCD8B_input_n_of_2_NORMsort.bw


title: J-Lat 10.6, shCD8B, H3.3, ChIP, unstimulated, Rep2

description:
712_28
shCD8B_NS_H3_3_n_of_2_NORMsort.bw


title: J-Lat 10.6, shDMAP1, AcH4, ChIP, TNFa, Rep2

description:
712_27
shDMAP1_TNF_AcH4_n_of_2_NORMsort.bw

value: pan-AcH4 (Millipore, #06-598)


title: Patient 05, Kidney

description:
Library name: P05
Single Cell 3' v3.1 (10x Genomics)


title: Patient 04, Kidney

description:
Library name: P04
Single Cell 3' v3.1 (10x Genomics)


title: J-Lat 10.6, shEP400, AcH4, ChIP, TNFa, Rep2

description:
712_26
shEP400_TNF_AcH4_n_of_2_NORMsort.bw


title: Patient 03, Kidney

description:
Library name: P03
Single Cell 3' v3.1 (10x Genomics)


title: J-Lat 10.6, shDMAP1, H2A.Z, ChIP, unstimulated, Rep2

description:
712_36
shDMAP1_NS_H2AZ_n_of_2_NORMsort.bw


title: Patient 02, Kidney

description:
Library name: P02
Single Cell 3' v3.1 (10x Genomics)


title: J-Lat 10.6, shCD8B, AcH4, ChIP, TNFa, Rep2

description:
712_25
shCD8B_TNF_AcH4_n_of_2_NORMsort.bw


title: Patient 01, Kidney

description:
Library name: P01
Single Cell 3' v3.1 (10x Genomics)


title: J-Lat 10.6, shDMAP1, AcH4, ChIP, unstimulated, Rep2

description:
712_24
shDMAP1_NS_AcH4_n_of_2_NORMsort.bw


title: J-Lat 10.6, shEP400, AcH4, ChIP, unstimulated, Rep2

description:
712_23
shEP400_NS_AcH4_n_of_2_NORMsort.bw


title: J-Lat 10.6, shCD8B, AcH4, ChIP, unstimulated, Rep2

description:
712_22
shCD8B_NS_H2AZ_n_of_2_NORMsort.bw


title: J-Lat 10.6, shEP400, input, ChIP, unstimulated, Rep1

description:
712_20
shEP400_input_n_of_2_NORMsort.bw


title: D10_Z_P_bilomics1

city: Rehovot

first: Tal

last: Barkai

address: Herzl St 234

department: Molecular Cell Biology

country: Israel

institute: Weizmann Institute of Science

description: Library name: Sample 28

data_processing:
Illumina output sequencing raw files were converted to FASTQ files using the UTAP pipeline. To obtain the UMI counts table, UTAP for SCRB-seq was used with CUTADAPT, and FASTQ files were aligned to the human reference genome (GRCh38).
Assembly: GRCh38
Supplementary files format and content: UMI counts table

source_name: NGT fluid

extract_protocol:
Tri-reagent was added at a ratio of 1:3, and samples were thawed on ice and thoroughly mixed every few minutes. Samples with a significant presence of solid content underwent additional centrifugation at this stage at 500g for 5 minutes at 4°C. Ethanol was added at a ratio of 1:1 to the supernatant, and extraction was continued according to the manufacturer’s instruction of Direct-zol micro prep kit (ZYMO research, R2052).
The mcSCRBseq protocol(Bagnoli et al, 2018) was used with minor modifications.

value: NGT fluid


title: D74_Z_P_P_B_bilomics7

description: Library name: Sample 30


title: H2_Z_P_bilomics4

description: Library name: Sample 31


title: D52_Z_A_P_B_bilomics6

description: Library name: Sample 29


title: C7_Z_P_bilomics1

description: Library name: Sample 27


title: J-Lat 10.6, shDMAP1, input, ChIP, unstimulated, Rep1

description:
712_21
shDMAP1_input_n_of_2_NORMsort.bw


title: J-Lat 10.6, shCD8B, input, ChIP, unstimulated, Rep1

description:
712_19
shCD8B_input_n_of_2_NORMsort.bw


title: C6_Z_P_bilomics1

description: Library name: Sample 26


title: C50_Z_P_bilomics7

description: Library name: Sample 23


title: C56_Z_P_Q_bilomics8

description: Library name: Sample 24


title: C58_Z_P_bilomics10

description: Library name: Sample 25


title: J-Lat 10.6, shDMAP1, H2A.Z, ChIP, unstimulated, Rep1

description:
712_15
shDMAP1_NS_H2AZ_n_of_2_NORMsort.bw


title: E.coli-RNAseq

city: Heidelberg

first: Jiří

last: Koubek

address: INF 345

department: ZMBH

institute: Heidelberg University

description: Library name: E.coli-RNAseq

data_processing:
demultiplexed libraries were trimmed via cutadapt to remove universal linkers
unique molecular identifiers were extracted
rRNA sequences were removed by alignment against known rRNA
rRNA-depleted reads were aligned to corresponding genome
Assembly: E.coli GCA_000499485.1, yeast GCA_000146045.2, mouse GRCm39, GCA_000001635.9, human GRCh38p10, GCA_000001405.25
Supplementary files format and content: hdf5 files contain p-site assigned reads

organism: Escherichia coli

extract_protocol:
total RNA was extracted via phenol:chlorophorm extraction
libraries were prepared according to Ingolia et al (2009) and by a method described within the accompanying manuscript

tag: strain


title: J-Lat 10.6, shCD8B, H2A.Z, ChIP, TNFa, Rep1

description:
712_16
shCD8B_TNF_H2AZ_n_of_2_NORMsort.bw


title: J-Lat 10.6, shEP400, H2A.Z, ChIP, unstimulated, Rep1

description:
712_14
shEP400_NS_H2AZ_n_of_2_NORMsort.bw


title: LNA in L2 and RT

description: Library name: L2-RT

data_processing:
demultiplexed libraries were trimmed via cutadapt to remove universal linkers
unique molecular identifiers were extracted
rRNA sequences were removed by alignment against known rRNA
rRNA-depleted reads were aligned to corresponding genome
Assembly: E.coli GCA_000499485.1, yeast GCA_000146045.2, mouse GRCm39, GCA_000001635.9, human GRCh38p10, GCA_000001405.25
Supplementary files format and content: hdf5 files contain p-site assigned reads
Library strategy: Ribo-Seq


title: J-Lat 10.6, shCD8B, H2A.Z, ChIP, unstimulated, Rep1

description:
712_13
shCD8B_NS_H2AZ_n_of_2_NORMsort.bw


title: C45_Z_P_bilomics7

description: Library name: Sample 22


title: LNA in RT

description: Library name: RT


title: J-Lat 10.6, shEP400, H3.3, ChIP, TNFa, Rep1

description:
712_11
shEP400_TNF_H3_3_n_of_2_NORMsort.bw


title: C42_Z_P_bilomics7

description: Library name: Sample 21


title: J-Lat 10.6, shCD8B, H3.3, ChIP, TNFa, Rep1

description:
712_10
shCD8B_TNF_H3_3_n_of_2_NORMsort.bw


title: LNA in L2 ligation

description: Library name: L2


title: J-Lat 10.6, shDMAP1, H3.3, ChIP, unstimulated, Rep1

description:
712_9
shDMAP1_NS_H3_3_n_of_2_NORMsort.bw


title: J-Lat 10.6, shEP400, H3.3, ChIP, unstimulated, Rep1

description:
712_8
shEP400_NS_H3_3_n_of_2_NORMsort.bw


title: noLNA

description: Library name: ctrl


title: J-Lat 10.6, shDMAP1, H2A.Z, ChIP, TNFa, Rep1

description:
712_18
shDMAP1_TNF_H2AZ_n_of_2_NORMsort.bw


title: J-Lat 10.6, shEP400, H2A.Z, ChIP, TNFa, Rep1

description:
712_17
shEP400_TNF_H2AZ_n_of_2_NORMsort.bw


title: E.coli-TT-replicate2

description: Library name: ecoli-tt-rep2


title: C40_Z_P_bilomics7

description: Library name: Sample 19


title: J-Lat 10.6, shEP400, AcH4, ChIP, TNFa, Rep1

description:
712_5
shEP400_TNF_AcH4_n_of_2_NORMsort.bw


title: J-Lat 10.6, shDMAP1, AcH4, ChIP, TNFa, Rep1

description:
712_6
shDMAP1_TNF_AcH4_n_of_2_NORMsort.bw


title: C3_Z_P_bilomics1

description: Library name: Sample 18


title: J-Lat 10.6, shDMAP1, AcH4, ChIP, unstimulated, Rep1

description:
712_3
shDMAP1_NS_AcH4_n_of_2_NORMsort.bw


title: C38_Z_P_bilomics6

description: Library name: Sample 17


title: J-Lat 10.6, shEP400, AcH4, ChIP, unstimulated, Rep1

description:
712_2
shEP400_NS_AcH4_n_of_2_NORMsort.bw


title: J-Lat 10.6, shCD8B, AcH4, ChIP, TNFa, Rep1

description:
712_4
shCD8B_TNF_AcH4_n_of_2_NORMsort.bw


title: J-Lat 10.6, shCD8B, H3.3, ChIP, unstimulated, Rep1

description:
712_7
shCD8B_NS_H3_3_n_of_2_NORMsort.bw


title: J-Lat 10.6, shCD8B, AcH4, ChIP, unstimulated, Rep1

description:
712_1
shCD8B_NS_H2AZ_n_of_2_NORMsort.bw


title: E.coli-TT-new protocol

description: Library name: ecoli-new


title: E.coli-TT-replicate1

description: Library name: ecoli-tt-rep1


title: J-Lat 10.6, input, shDMAP1,unstimulated, Rep2

value: Unstimulated


title: E.coli-TT-standard protocol

description: Library name: ecoli-standard


title: C35_Z_P_bilomics6

description: Library name: Sample 15


title: C37_Z_P_bilomics6

description: Library name: Sample 16


title: J-Lat 10.6, shDMAP1, H3.3, ChIP, TNFa, Rep1

description:
712_12
shDMAP1_TNF_H3_3_n_of_2_NORMsort.bw


title: J-Lat 10.6, input, shEP400,unstimulated, Rep2


title: C41_Z_P_bilomics7

description: Library name: Sample 20


title: J-Lat 10.6, RNAPII, ChIP, shDMAP1, TNFa, Rep2

description:
697-6
shDMAP1_TNF_n_of_2_NORMsort.bw

value: RNA polymerase II (Millipore, #05-623)

value: TNFa stimulated


title: Cryopreserved, Dark, rep3

city: Savonlinna

first: Jaanika

last: Edesi

address: Vipusenkuja 5

country: Finland

institute: Natural Resources Institute Finland LUKE

data_processing:
The quality of reads was assessed by FastQC v. 1.11.2 (Andrews, 2010) with default settings to ensure the per base pair quality score was above 20, and that there were no overrepresented sequences. TopHat (v2.0.8b) and bowtie1 (v 1.1.1) were used to map the reads to the S. tuberosum reference genome taking the annotation into account (genome and annotation: PGSC_DM_v4.03) (The Potato Genome Sequencing Consortium, 2011; Sharma et al., 2013). Reads per gene were counted based on the TopHat output using featureCounts v1.5.0 (Liao et al., 2014) and the annotation as mentioned above.
The DESeq2 (v1.14.1) (Love et al., 2014) in Bioconductor/R package (https://www.bioconductor.org/help/workflows/rnaseqGene/) was used to identify differentially expressed genes (DEGs) between different treatments (control vs. treatments) and by using a negative binomial test (Anders et al., 2010). Computing was done in the Linux shell using the taito.csc.fi platform (https://research.csc.fi). The parameters used in DESeq2 analysis were: mode=“Union”, singleEnd=FALSE, ignore.strand=FALSE, fragments=TRUE. False discovery rate-adjusted p-value (FDR) was estimated based on Benjamini Hochberg correction (Benjamini and Hochberg, 1995), and significance levels were corrected accordingly during DESeq2 analysis. Changes in gene expression with an FDR (padj value) of <0.05 were considered significant.
Assembly: PGSC_DM_v4.03
Supplementary files format and content: Text files with read count information for each sample*gene combination

organism: Solanum tuberosum

source_name: in vitro shoot tips

growth_protocol: In vitro plants were multiplied by nodal cuttings in 250 ml jars (Combiness) containing MS medium (Murashige and Skoog, 1962) supplemented with 2% sucrose and 0.64% (w/v) agar (pH 5.7). Each jar contained 30 plants. The jars were closed with lids including 0.2 mm filters to enable gas exchange and placed in a growth chamber illuminated by cool white fluorescent tubes (Philips TL-D 840) with a 16/8-h light/dark photoperiod (40 µmol m-2s-1) at 22 ± 1°C.

extract_protocol:
For cryopreservation, shoot tips (2–3 mm) of 3.5-week-old in vitro plants were aseptically dissected under a stereomicroscope. The non-cryopreserved control shoot tips were trimmed to 1 mm. The explants were placed onto 4.5-cm sterile filter papers moistened with 2 ml of liquid MS medium for overnight. Cryopreservation was carried out using the DMSO-droplet method. Briefly, before cryopreservation, shoot tips were treated with cryoprotectant solution (10% DMSO (v/v)) in MS medium containing 30% sucrose for 2 h at room temperature (RT) before being transferred into droplets of 2.5 µl cryoprotectant solution on aluminium foil strips (0.5 x 1.5 cm). After that, the shoot tips were flash-frozen in liquid nitrogen (LN). The shoot tips were kept in LN for 1 h. After that, the shoot tips were rewarmed quickly by transferring the aluminium foil strips into liquid MS medium (50 ml) for 1.5 h at RT. After thawing, the cryopreserved samples (+) were placed on regeneration medium (MS with 0.5 mg/l zeatin riboside, 0.2 mg/l gibberellic acid (GA3), 0.5 mg/l indole acetic acid (IAA), and 30 g/l sucrose) on small Petri dishes (5.5 cm in diameter) and were allowed to regenerate for 48 h in total darkness. After the 48-h dark-incubation, the cryopreserved (+) samples were exposed to three different light conditions: total darkness (D), cool white fluorescent tubes (CW) and a combination of blue and red LEDs (90% red, 10% blue) (RB). The non-cryopreserved control samples (-) were only exposed to CW light. The light treatments lasted for 16 h, after which the samples (ten shoot tips per each treatment with three biological replicates) were collected into RNALater and stored at -80oC until RNA extraction. The intensity of both RB and CW was 40 µmol m-2s-1.
Approximately 1 µg total RNA (RIN >7.4) was used for library preparation using Illumina’s TruSeq Stranded mRNA Library Prep Kit (Illumina, San Diego, CA, USA) following the manufacturer’s instructions. Quality of the libraries was assessed using an Agilent Bioanalyzer 2100 and concentrations with Qubit® Fluorometric Quantitation (Life Technologies). The obtained 12 libraries were pooled and run in one lane using an Illumina HiSeq2500 in high-output, paired-ended, 100 cycle mode, followed by read extraction (FastQ format) using bcl2fastq v1.8.4 (supported by Illumina).

value: in vitro shoot tips

value: Agrie Dzeltenie


title: J-Lat 10.6, input, shCD8B,unstimulated, Rep2


title: C33_Z_P_bilomics6

description: Library name: Sample 14


title: Cryopreserved, Dark, rep2


title: C32_Z_A_bilomics7

description: Library name: Sample 13


title: J-Lat 10.6, RNAPII, ChIP, shEP400, unstimulated, Rep2

description:
697-2
shEP400_NS_n_of_2_NORMsort.bw


title: Cryopreserved, Dark, rep1


title: J-Lat 10.6, RNAPII, ChIP, shCD8B, TNFa, Rep2

description:
697-4
shCD8B_TNF_n_of_2_NORMsort.bw


title: MDA_PCa_2b cells, input, replicate 2

city: Bethesda

first: David

last: Takeda

state: MD

address: 37 Convent Drive

department: National Cancer Institute

institute: National Institutes of Health

data_processing:
Reads were aligned to hg19 after filtering for ENCODE blacklist regions using bwa (0.7.17) and converted to BAM format using Samtools (1.17).
Duplicate reads removed using Picard (2.27.3) and peaks identified with MACS2 (2.2.7.1) with q value cutoff of 0.01.
Input subtracted bigWig files were generated using Deeptools (3.5.1).
Assembly: hg19
Supplementary files format and content: input normalized bigWig (except for input samples)

growth_protocol: LNCaP: RPMI with 10% fetal bovine serum in humidified atmosphere with 5% CO2 at 37C; MDA_PCa_2b: F-12K Medium with 20% fetal calf serum, 25 ng/ml cholera toxin, 10 ng/ml mouse EGF, 0.005 mM phosphoethanolamine, 100 pg/ml hydrocortisone, 45 nM sodium selenite, 0.005 mg/ml human recombinant insulin in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Cells or tissues were fixed with 2 mM DSG for 10 min and 1% paraformaldehyde for 10 min followed by quenching with glycine. Chromatin was isolated and sonicated using Diagenode Pico sonicator.
ChIP-seq libraries were prepared using NEB Next Ultra II DNA Library Prep Kit for Illumina and amplified libraries purified using NEB purification beads. Libraries were validated using Agilent Tapestation.


title: J-Lat 10.6, RNAPII, ChIP, shCD8B, unstimulated, Rep2

description:
697-1
shCD8B_NS_n_of_2_NORMsort.bw


title: Cryopreserved, RB Leds, rep2


title: J-Lat 10.6, RNAPII, ChIP, shDMAP1, unstimulated, Rep2

description:
697-3
shDMAP1_NS_n_of_2_NORMsort.bw


title: MDA_PCa_2b cells, input, replicate 1


title: MDA_PCa_2b cells, FOXA1, ChIP, replicate 2

value: FOXA1 (Abcam, #ab23738)


title: Cryopreserved, RB Leds, rep1


title: MDA_PCa_2b cells, FOXA1, ChIP, replicate 1


title: C27_Z_P_Bilomics5

description: Library name: Sample 10


title: C25_Z_P_Bilomics5

description: Library name: Sample 9


title: C30_Z_P_Bilomics5

description: Library name: Sample 11


title: LNCaP cells, input, replicate 1

source_name: LNCaP

value: LNCaP


title: LNCaP cells, FOXA1, ChIP, replicate 2


title: Cryopreserved, cool white fluorescent, rep3


title: LNCaP cells, input, replicate 2


title: LNCaP cells, FOXA1, ChIP, replicate 1


title: C21_Z_P_bilomics4

description: Library name: Sample 8


title: C20_Z_A_bilomics4

description: Library name: Sample 7


title: swr1Δ-expA-input-2

city: Vienna

first: Jian Yi

last: Kok

address: Dr.-Bohr-Gasse 3

country: Austria

institute: GMI - Gregor Mendel Institute of Molecular Plant Biology

description:
Library name: 207823
Experiment A

data_processing:
Alignments, quality control, and initial processing of the raw fastq files from the sequencing run were performed using the dev version of the nf-core/chipseq pipeline (https://github.com/nf-core/chipseq) with default parameters.
Assembly: ASM294v2
Supplementary files format and content: Provided are bigWig files representing the read-depth normalized ChIP-seq output and input control for each sample. Additionally, input-normalized bigWig files for each sample are also provided.

organism: Schizosaccharomyces pombe

growth_protocol: Cells were revived from frozen (-70 ºC) stocks on YES plates at 32 ºC. Cells were then grown to saturation in YES at 32 ºC, subcultured and grown to mid-log (OD600 ~ 0.5) before being harvested.

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis with beads via a Precellys homogenizer, chromatin was sonicated with a E220 focused ultra-sonicator (Covaris).
ChIP-seq libraries were prepared using the NEBNext Ultra II library preparation kit for Illumina complemented with custom synthesized barcoded sequencing adapters provided by the Vienna BioCenter Core Facilities Next Generation Sequencing Facility. PCR was performed as a 50 µl reaction using the Q5 polymerase (NEB). Samples were PCR-amplified to the beginning of the logarithmic phase, as determined using a small-scale qPCR reaction run in parallel (typically around 8-10 cycles). Following quality control by Agilent Fragment Analyzer and quantification by RT-qPCR using a Kapa Library Quantification Kit, libraries were sequenced at the Vienna BioCenter Core Facilities Next Generation Sequencing Core Facility on an Illumina sequencer.

treatment_protocol: No treatment was used.

value: h+ ade6-M216 ura4-D18 leu1-32 swr1del::kanMX


title: swr1Δ-expA-input-1

description:
Library name: 207752
Experiment A


title: Cryopreserved, cool white fluorescent, rep2


title: C31_Z_P_Bilomics5

description: Library name: Sample 12


title: Cryopreserved, RB Leds, rep3


title: irc20Δ-expA-input-1

description:
Library name: 207751
Experiment A

value: h+ ade6-M216 ura4-D18 leu1-32 irc20del::kanMX


title: snf22Δ-expA-input-2

description:
Library name: 207821
Experiment A

value: h+ ade6-M216 ura4-D18 leu1-32 snf22del::hygMX


title: irc20Δ-expA-input-2

description:
Library name: 207822
Experiment A


title: Non-cryopreserved, cool white fluorescent, rep3


title: C1_Z_P_bilomics10

description: Library name: Sample 6


title: Non-cryopreserved, cool white fluorescent, rep2


title: C17_Z_P_bilomics4

description: Library name: Sample 5


title: rrp2Δ-expA-input-2

description:
Library name: 207820
Experiment A

value: h+ ade6-M216 ura4-D18 leu1-32 rrp2del::kanMX


title: C14_Z_P_bilomics3

description: Library name: Sample 4


title: C12_Z_P_bilomics4

description: Library name: Sample 3


title: rrp2Δ-expA-input-1

description:
Library name: 207749
Experiment A


title: snf22Δ-expA-input-1

description:
Library name: 207750
Experiment A


title: rrp1Δ-expA-input-2

description:
Library name: 207819
Experiment A

value: h+ ade6-M216 ura4-D18 leu1-32 rrp1del::kanMX


title: rrp1Δ-expA-input-1

description:
Library name: 207748
Experiment A


title: mit1Δ-expA-input-1

description:
Library name: 207826
Experiment A

value: h+ ade6-M216 ura4-D18 leu1-32 mit1del::kanMX


title: C11_Z_P_bilomics3

description: Library name: Sample 2


title: hrp1Δhrp3Δ-expA-2

description:
Library name: 243100
Experiment A

data_processing:
Data processing, including alignment and QC, was performed using the nf-core/mnaseseq pipeline (https://github.com/nf-core/mnaseseq), with further analysis using Deeptools (v3.3.1).
Assembly: ASM294v2
Supplementary files format and content: Provided are bigWig files representing the read-depth normalized and smoothed MNase-seq data for each sample.

extract_protocol:
MNase-seq was performed by adapting a published protocol (Lanterman et. al, 2009). Briefly, cells were fixed with formaldehyde, and converted to spheroplasts using Zymolyase. Chromatin was digested with MNase, and DNA was extracted using phenol-chloroform and ethanol precipitation. Mononucleosomal DNA was size-selected via agarose gel extraction.
Library preparation was performed using the NEBNext Ultra II kit (NEB Cat. No. E7645L) with custom barcoded adapters. Libraries were quality-checked using an Agilent Fragment Analyzer and quantified with a Kapa Library Quantification Kit (Roche Cat. No. KK4903). Sequencing was conducted on an Illumina sequencer.

value: h+ ade6-M216 ura4-D18 leu1-32 hrp1del::kanMX hrp3del


title: mit1Δ-expA-input-2

description:
Library name: 207812
Experiment A


title: C10_Z_P_bilomics3

description: Library name: Sample 1


title: hrp3Δ-expA-input-2

description:
Library name: 207811
Experiment A

value: h+ ade6-M216 ura4-D18 leu1-32 hrp3del::kanMX


title: hrp1Δhrp3Δ-expA-1

description:
Library name: 232119
Experiment A


title: Cryopreserved, cool white fluorescent, rep1


title: J-Lat 10.6, RNAPII, ChIP, shEP400, TNFa, Rep2

description:
697-5
shEP400_TNF_n_of_2_NORMsort.bw

value: J-Lat 10.6 cells


title: hrp3Δ-expA-input-1

description:
Library name: 207741
Experiment A


title: hrp1Δ-expA-input-2

description:
Library name: 207810
Experiment A

value: h+ ade6-M216 ura4-D18 leu1-32 hrp1del::kanMX


title: hrp1Δ-expA-input-1

description:
Library name: 207740
Experiment A


title: swr1Δ-expA-1

description:
Library name: 232118
Experiment A


title: fft3Δ-expA-input-2

description:
Library name: 207809
Experiment A

value: h+ ade6-M216 ura4-D18 leu1-32 fft3del::kanMX


title: HME1_Myc_MSL3ko_EdU_HUseq_Rep2

city: London

first: Paola

last: Scaffidi

address: 1 Midland Road

country: United Kingdom

institute: Francis Crick Institute

description: Library name: HME1_Myc_MSL3ko_EdU_HUseq_Rep2

data_processing:
EdU-HUseq reads were aligned to the hg38 genome using nf-core/chipseq pipeline version 2.0.0 with bwa aligner.
BigWig files were generated within the nf-core/chipseq pipeline
Assembly: hg38
Supplementary files format and content: bigWig of aligned samples for genome browser visualization

growth_protocol: hTert-HME1 (ME16C, American Type Culture Collection (ATCC) CRL-4010) were grown in DMEM/F12 (Thermo Fisher, 11330057) with the addition of 2% Fetal Bovine Serum (FBS, Gibco 16000-044), 100 U/ml penicillin and 100 μg/mL streptomycin (Thermo Fisher 15140122), 20ng/ml EGF (Merck, E9644), 0.5μg/ml Hydrocortisone (Merck, H0888), 10ug/ml rh Insulin (Merck, I9278).

extract_protocol:
Stable Ctrl-KO, MSL3-KO and Myc overexpressing HME1 cells were seeded in T150 flasks. When 50% confluency was reached, cells were treated with 2μM Palbociclib (Universal Biologicals, S116) for 20 hours to synchronize them in G1/S. Cells were washed twice with medium and treated with 10mM Hydroxyurea (Merck Life Science, H8627) for 7 hours to stop them at the entry of S phase. After two washes with medium, cells were released in medium containing 25μM EdU (Universal Biologicals, 10540) for 90 minutes. Cells were collected and fixed in 90% MetOH. EdU-labelled DNA was isolated as previously described[5]. Briefly, cells were permeabilized in 0.2% Triton-X100 in PBS for 30 minutes and EdU was detected using a biotin-azide click reaction by incubating cells in click-it reaction cocktail (100 mM TrisHCl pH 8, 4mM CuSO4, 100mM sodium-L-ascorbate, 50µM Biotin Azide - Thermo Fisher Scientific, B10184) for 30 minutes. After washes, cells were incubated in lysis buffer (10 mM Tris-HCl, pH 8, 10 mM EDTA, 0.5% SDS, 0.2 mg/ml Proteinase K) for 3 hours at 50ºC. DNA was purified using phenol/chloroform/isoamyl alcohol, resuspended in TE and sonicated using Bioruptor Pico. EdU-labelled DNA was captured using Dynabeads MyOne Streptavidin C1 (Thermo Fisher Scientific, 65001), washed and eluted from beads using 2% β-mercaptoethanol. DNA was purified with solid-phase reversible immobilization (SPRI) beads (Agencourt AMPure XP, Beckman Coulter), and then quantified with QuantiFluor (Promega, E2670). For HighResEdU-HUseq sample, stable Ctrl-KO HME1 cells were seeded in T150 flasks. When 50% confluency was reached, cells were treated with 100ng/ml Nocodazole (Merck Life Science, SML1665) for 8 hours. Cells in mitosis were detached by shake-off in the same culture medium, pelleted, washed once with PBS and plated in medium containing 25μM EdU (Universal Biologicals, 10540) and 10mM Hydroxyurea (Merck Life Science, H8627). After 16 hours, cells were collected and fixed in 90% MetOH. EdU-labelled DNA isolation and library preparation were carried out as described for EdU-HUseq.
DNA libraries were prepared using the NEBNext UltraII DNA Library Prep Kit for Illumina (New England Biolabs, E7645L).

tag: pull down

value: EdU

value: immortalized mammary epithelial cells

value: MSL3 KO + Myc overexpression


title: HME1_Myc_MSL3ko_EdU_HUseq_Rep1

description: Library name: HME1_Myc_MSL3ko_EdU_HUseq_Rep1


title: Non-cryopreserved, cool white fluorescent, rep1

value: in vitro shoot tips

value: Agrie Dzeltenie


title: irc20Δ-expA-2

description:
Library name: 243098
Experiment A


title: swr1Δ-expA-2

description:
Library name: 243099
Experiment A


title: fft2Δ-expA-input-2

description:
Library name: 207808
Experiment A

value: h+ ade6-M216 ura4-D18 leu1-32 fft2del::kanMX


title: fft3Δ-expA-input-1

description:
Library name: 207739
Experiment A


title: HME1_MSL3ko_H4K16acAb3_Rep2

description: Library name: HME1_MSL3ko_H4K16acAb3_Rep2

data_processing:
ChIPseq reads were aligned to the hg38 genome using nf-core/chipseq pipeline version 2.0.0 with bwa aligner. In the case of H4K16ac ChIP, reads were aligned to a composite genome containing Homo sapiens hg38 and Drosophila melanogaster BDGP6 genome assemblies
BigWig files were generated within the nf-core/chipseq pipeline
For H4K16ac datasets only: replicates were merged using SAMtools merge. Scaling factors from Drosophila reads were used to generate BigWig files through deepTools bamCoverage and WT over MSL KO corrected BigWig files were obtained through bigwigCompare with parameters --operation subtract --skipNAs -bs 1 --skipZeroOverZero.
Assembly: hg38
Supplementary files format and content: bigWig of aligned samples for genome browser visualization
Supplementary files format and content: For H4K16ac datasets only: bigWig of corrected signal after replicate merging and removal of non-specific signal retained in the KO samples

extract_protocol:
2x106 cells per pull down were cross-linked using 1% formaldehyde for 10 min. The reaction was stopped by incubation for 5 min with 0.125M glycine. After nuclear extraction and chromatin shearing by sonication, lysates were incubated overnight at 4°C with protein G Dynabeads (Thermo Fisher Scientific, 10003D) coupled with one of the following antibodies: anti-H4K16ac (Millipore, 07-329, 5g), anti-H4K16ac (Cell Signaling Technology, 13534; 1g) anti-H3K36me3 (Cell Signaling Technology, 4909S, 5l). After immunoprecipitation, beads were recovered using a magnet and washed; chromatin was eluted and cross-links reverted overnight at 65°C. DNA was purified with solid-phase reversible immobilization (SPRI) beads (Agencourt AMPure XP, Beckman Coulter), and then quantified with QuantiFluor (Promega, E2670). For H4K16ac pull-downs, Drosophila spike-in was added to normalize signal between Ctrl-KO and MSL3-KO cells. S2 Drosophila cells were processed as described above and lysates were quantified using DC Protein Assay Kit I (Bio-Rad Laboratories Ltd, 5000111). 5% chromatin was added to HME1 lysates and pull-down was carried on.
DNA libraries were prepared using the NEBNext UltraII DNA Library Prep Kit for Illumina (New England Biolabs, E7645L).

value: Abcam, Ab109463

value: MSL3 KO


title: fft1Δ-expA-input-2

description:
Library name: 207807
Experiment A

value: h+ ade6-M216 ura4-D18 leu1-32 fft1del::hygMX


title: HME1_MSL3ko_H4K16acAb3_Rep1

description: Library name: HME1_MSL3ko_H4K16acAb3_Rep1


title: irc20Δ-expA-1

description:
Library name: 232117
Experiment A

value: h+ ade6-M216 ura4-D18 leu1-32 irc20del::kanMX


title: fft1Δ-expA-input-1

description:
Library name: 207737
Experiment A


title: fft2Δ-expA-input-1

description:
Library name: 207738
Experiment A


title: snf22Δ-expA-2

description:
Library name: 243097
Experiment A

value: h+ ade6-M216 ura4-D18 leu1-32 snf22del::hygMX


title: HME1_WT_H4K16acAb3_Rep2

description: Library name: HME1_WT_H4K16acAb3_Rep2

value: Ctrl KO


title: wt-expA-input-1

description:
Library name: 207754
Experiment A


title: HME1_WT_H4K16acAb3_Rep1

description: Library name: HME1_WT_H4K16acAb3_Rep1


title: wt-expA-H3K36me3-2

description:
Library name: 207783
Experiment A


title: snf22Δ-expA-1

description:
Library name: 232116
Experiment A


title: wt-expA-H3K36me3-1

description:
Library name: 207733
Experiment A


title: rrp2Δ-expA-1

description:
Library name: 232115
Experiment A

value: h+ ade6-M216 ura4-D18 leu1-32 rrp2del::kanMX


title: rrp2Δ-expA-2

description:
Library name: 243096
Experiment A


title: swr1Δ-expA-H2A.Z-1

description:
Library name: 207842
Experiment A

value: h+ ade6-M216 ura4-D18 leu1-32 swr1del::kanMX


title: irc20Δ-expA-H2A.Z-1

description:
Library name: 207841
Experiment A


title: CScreen_Rapa_CD79B

city: bethesda

first: Seolkyoung

last: Jung

address: 10 Center Dr

department: NIAMS

institute: NIH

description: Library name: CScreen_Rapa_CD79B

data_processing:
base calling: illumina CASAVA 1.8.2
CRISPR screen: build index on artificial genome which have  specific sgRNA sequence and common template sequence with stagger sequence
CRISPR screen: bowtie/1.1.2 with -S -m 1 -p 4 -a --best --strata -n 2 -l 80
CRISPR screen: samtools idxstats and custom perl script to generate table for counts and fraction on each gene
Assembly: hg19
Supplementary files format and content: Tab-separated values files
Library strategy: CRISPR screen

growth_protocol: SU-DHL-4 cells with doxycycline inducible Cas9 were described previously (Phelan et al. 2018). Cells were cultured in advanced RPMI-1640 media supplemented with 5% FBS (Gemini), 1% GlutaMAX, and 1% Penicillin-Streptomycin (Thermo Fisher Scientific). Peripheral blood mononuclear cells from healthy blood donors (NIH blood bank) were isolated over Ficoll and cryopreserved. All cells were cultured at 37°C and 5% CO2 in a humidified incubator.

extract_protocol:
CRISPR screens: SU-DHL-4 reporter cells were transduced with the Brunello library. For each screen, 6 replicates with 15 million cells (90 million in total) were transduced at a density of 5 million cells/ml in a 6 well plate. The amount of virus was adjusted according to the viral titer to obtain a multiplicity of infection (MOI) of 0.3. Cells were transduced by spinfection (1,460g for 90 min and 30°C) in the presence of 6 µg/ml polybrene. Infected cells were puromycin selected 24h post infection at a final concentration of 4 µg/ml. On day 3 post infection, the MOI was verified and cells were split in medium containing 200 ng/ml doxycycline. Cells were split every other day with fresh doxycycline containing medium. On day 10 post infection, for each of the six replicates 60 million cells were sorted using BD FACS Aria or Fusion cell sorters based on reporter fluorescence to capture the bottom and top 5% expressing cells. On average, for each screen 286 million cells were sorted yielding ~9 million low or high expressing cells (Table S1B). For the three mTORC1 inhibited CRISPR screens in BTG2, CD79B and OCAB reporter cell lines, 5 nM rapamycin was added on day 8 and cells were sorted on day 10 as for the other screens. Genomic DNA from sorted cells was extracted using DNeasy Blood and Tissue kit (Qiagen) according to the manufacturer’s instructions.
CRISPR screen Libraries were prepared using staggered GeCKO readout primers following the recommended instructions (Shalem et al. 2014). Deep sequencing was performed on NextSeq550 and NovaSeq6000 (Illumina) using 75bp single-end reads.

treatment_protocol: Inhibitor treatments: SU-DHL-4 or primary B cells were seeded at 0.2 million cells/ml and treated with DMSO or inhibitors. Inhibitors were purchased from MedChemExpress or Selleck Chemicals and dissolved in DMSO. Inhibitors were titrated and used at the following concentrations: rapamycin (5 nM), MK2206 (250 nM), AS1842856 (50 nM), LY2090314 (2 nM), CHIR99021 (1 µM). After two days of treatment, cells were analyzed by flow cytometry or harvested for RNA-seq.

value: B cell lymphoma

value: Rapamycin


title: irc20Δ-expA-H2A.Z-2

description:
Library name: 207802
Experiment A


title: rrp1Δ-expA-2

description:
Library name: 243095
Experiment A

value: h+ ade6-M216 ura4-D18 leu1-32 rrp1del::kanMX


title: snf22Δ-expA-H2A.Z-2

description:
Library name: 207801
Experiment A


title: CScreen_Rapa_BTG2

description: Library name: CScreen_Rapa_BTG2


title: CScreen_Rapa_OCAB

description: Library name: CScreen_Rapa_OCAB


title: snf22Δ-expA-H2A.Z-1

description:
Library name: 207840
Experiment A


title: rrp1Δ-expA-1

description:
Library name: 232114
Experiment A


title: rrp2Δ-expA-H2A.Z-2

description:
Library name: 207800
Experiment A


title: rrp2Δ-expA-H2A.Z-1

description:
Library name: 207839
Experiment A


title: CMK cells, untreated, replicate 2

city: suzhou

first: yang

last: yang

address: zhongnan road

country: China

institute: soochow university

description: Library name: Sample 4

data_processing:
Illumina Casava2.19 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and then mapped to hg38 whole genome and GENCODE v29 using STAR 2.7.10a with parameters --outFilterMismatchNoverReadLmax 0.04 --outFilterMultimapNmax 1
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using stringtie v2.1.7. Gene differential expression were calculated using DESeq2 v1.40.2.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include read counts and expression values of each gene for each sample and differential expression values between treatment group and control group.

source_name: CMK

extract_protocol:
Cells were harvested, and total RNA was extracted with TRIzol (Invitrogen) according to the manufacturer's protocol.  FastPure Cell/Tissue Total RNA Isolation Kit V2(( Vazyme , RC112-01)  was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: CMK

value: AML cells


title: wt-expA-input-2

description:
Library name: 207825
Experiment A


title: mit1Δ-expA-2

description:
Library name: 243088
Experiment A

value: h+ ade6-M216 ura4-D18 leu1-32 mit1del::kanMX


title: rrp1Δ-expA-H2A.Z-2

description:
Library name: 207799
Experiment A


title: CMK cells, untreated, replicate 1

description: Library name: Sample 3


title: mit1Δ-expA-H2A.Z-1

description:
Library name: 207806
Experiment A


title: CMK cells, SB-743921 treated,4nmol, replicate 2

description: Library name: Sample 2

value: 4nmol SB-743921 for 24hr


title: hrp3Δ-expA-2

description:
Library name: 243087
Experiment A

value: h+ ade6-M216 ura4-D18 leu1-32 hrp3del::kanMX


title: hrp3Δ-expA-1

description:
Library name: 232107
Experiment A


title: CMK cells, SB-743921 treated, 4nmol, replicate 1

description: Library name: Sample 1


title: hrp1Δ-expA-H2A.Z-2

description:
Library name: 207790
Experiment A

value: h+ ade6-M216 ura4-D18 leu1-32 hrp1del::kanMX


title: rrp1Δ-expA-H2A.Z-1

description:
Library name: 207838
Experiment A


title: swr1Δ-expA-H2A.Z-2

description:
Library name: 207803
Experiment A


title: SUDHL4_mRNA_WT_sgIRF8_r3

description: Library name: SUDHL4_mRNA_WT_sgIRF8_r3

data_processing:
base calling: illumina CASAVA 1.8.2
CRISPR screen: build index on artificial genome which have  specific sgRNA sequence and common template sequence with stagger sequence
CRISPR screen: bowtie/1.1.2 with -S -m 1 -p 4 -a --best --strata -n 2 -l 80
CRISPR screen: samtools idxstats and custom perl script to generate table for counts and fraction on each gene
ChIP-Seq_density: alignment: bowtie-1.1.1/bowtie -S -m 1 -p 20 -a --best --strata -n 2 -l 50
ChIP-Seq_density: filtering (uniquely aligned reads): samtools-0.1.19-1.2/samtools view -S -b -F4
ChIP-Seq_density: normalized tag density: custom script, maximum 2 reads with the same start position allowed
mRNA-Seq_density:alignment: gsnap --use-sarray=0 --novelsplicing=0 --use-splicing refseq.splices.iit --format=sam -B 4
mRNA-Seq_density: filtering: samtools-1.2/samtools view -S -b -F132 -q 20
mRNA-Seq density: normalized tag density: bedtools-2.25/genomeCoverageBed -ibam -bg -split -scale normalization_factor, ucsc-314/bedGraphToBigWig
Assembly: hg19
Supplementary files format and content: Tab-separated values files
Supplementary files format and content: bigwig file

growth_protocol: SU-DHL-4 cells with doxycycline inducible Cas9 were described previously (Phelan et al. 2018). Cells were cultured in advanced RPMI-1640 media supplemented with 5% FBS (Gemini), 1% GlutaMAX, and 1% Penicillin-Streptomycin (Thermo Fisher Scientific). Peripheral blood mononuclear cells from healthy blood donors (NIH blood bank) were isolated over Ficoll and cryopreserved. Naïve CD19+ human B cells were isolated with EasySep Human Naïve B Cell Isolation Kit according to the manufacture’s instructions (Stemcell Technologies). Isolated B cells were grown in IMDM media supplemented with 10% FBS (Gemini), 50 µM of beta-mercaptoethanol, and 1% Penicillin-Streptomycin (Thermo Fisher Scientific). All cells were cultured at 37°C and 5% CO2 in a humidified incubator.

extract_protocol:
CRISPR screens:
SU-DHL-4 reporter cells were transduced with the Brunello library. For each screen, 6 replicates with 15 million cells (90 million in total) were transduced at a density of 5 million cells/ml in a 6 well plate. The amount of virus was adjusted according to the viral titer to obtain a multiplicity of infection (MOI) of 0.3. Cells were transduced by spinfection (1,460g for 90 min and 30°C) in the presence of 6 µg/ml polybrene. Infected cells were puromycin selected 24h post infection at a final concentration of 4 µg/ml. On day 3 post infection, the MOI was verified and cells were split in medium containing 200 ng/ml doxycycline. Cells were split every other day with fresh doxycycline containing medium. On day 10 post infection, for each of the six replicates 60 million cells were sorted using BD FACS Aria or Fusion cell sorters based on reporter fluorescence to capture the bottom and top 5% expressing cells. On average, for each screen 286 million cells were sorted yielding ~9 million low or high expressing cells (Table S1B). For the three mTORC1 inhibited CRISPR screens in BTG2, CD79B and OCAB reporter cell lines, 5 nM rapamycin was added on day 8 and cells were sorted on day 10 as for the other screens. Genomic DNA from sorted cells was extracted using DNeasy Blood and Tissue kit (Qiagen) according to the manufacturer’s instructions.
RNA-seq
Cells were either unperturbed, transduced with sgRNA, or treated with inhibitors as described above. Cells were split every other day and seeded at 200,000 cells/ml the day before harvest. Inhibitor treated cells were harvested on day 2 post-treatment and sgRNA transduced cells on day 10 post-infection. On the day of harvest, half a million cells were pelleted and lysed in 100 µl of the Ambion RNAqueous lysis solution. RNA was extracted and treated with DNase according to the RNAqueous-Micro Total RNA Isolation Kit protocol (Thermo Fisher Scientific). RNA-seq libraries were prepared from 500 ng of RNA using NEBNext Poly(A) mRNA Magnetic Isolation and NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs).
ChIP-seq
Cells for ChIP-seq analysis were either unperturbed or transduced with sgRNA for 10 days before harvesting. The day before harvest, cells were diluted to 200,000 cells/ml. Cultured cells were fixed at room temperature for 10 min with 1% formaldehyde (Sigma) and the reaction was quenched with 125 mM glycine (Sigma). Fixed cells were washed with PBS, snap-frozen, and stored at -80°C until further processing. For ChIP, 20 million cells were resuspended in 1 ml of RIPA buffer (10 mM Tris pH 7.6, 1 mM EDTA, 0.1% SDS, 0.1% sodium deoxycholate, 1% Triton X-100, and freshly added Complete Mini EDTA free proteinase inhibitor (Roche)). Chromatin was sheared by sonication on ice using a Branson Sonifier with an amplitude of 35% and 12 cycles of 20 sec sonication followed by 30 sec of pause. Supernatant was precleared with 20 µl Dynabeads Protein A (Thermo Fisher Scientific) for 1 hour at 4°C under rotation. Precleared chromatin was incubated with BRD4 (Abcam, ab128874) or FLI1 (Abcam, ab133485) antibody overnight at 4°C under rotation. The antibody-protein solution was then captured with 40 µl of Dynabeads Protein A for 1 hour at 4°C under rotation. Antibody-bound beads were washed twice with RIPA buffer, twice with RIPA buffer containing 0.3 M NaCl, once with LiCl buffer (0.25M LiCl, 0.5% NP-40, 0.5% sodium deoxycholate), once with TE pH 8.0 containing 0.2% Triton X-100, and once with TE pH 8.0. Crosslinks were reversed by incubating the beads at 65°C for 4 hours in the presence of 0.3% SDS and 1 mg/ml Proteinase K (Thermo Fisher Scientific). ChIP DNA was column purified with ChIP DNA Clean and Concentrator kit (Zymo research).
RNA-seq
Libraries were prepared from 500 ng of RNA using NEBNext Poly(A) mRNA Magnetic Isolation and NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs). Single 50 cycles of sequencing data were acquired on HiSeq3000, NovaSeq6000, NovaSeqXplus (illumina).
ChIP-Seq
Libraries were prepared using the Ovation Ultralow Library System V2. Single 50 cycles of sequencing data were acquired on NextSeq550, NovaSeq6000 (illumina)
CRISPR screen
Libraries were prepared using staggered GeCKO readout primers following the recommended instructions (Shalem et al. 2014). Deep sequencing was performed on NextSeq550 and NovaSeq6000 (Illumina) using 75bp single-end reads.

treatment_protocol:
primary human B cells:
Cells were activated with 100 ng/ml MEGACD40L (Enzo Life Sciences), 1 µg/ml CpG oligodeoxynucleotide ODN 2006 (Invivogen), 50 ng/ml human IL-2, 50 ng/ml human IL-10, and 10 ng/ml human IL-15 (all interleukins from PeproTech). Every other day the medium was fully removed and cells diluted in fresh activation medium.
Inhibitor treatments:
SU-DHL-4 or primary B cells were seeded at 0.2 million cells/ml and treated with DMSO or inhibitors. Inhibitors were purchased from MedChemExpress or Selleck Chemicals and dissolved in DMSO. Inhibitors were titrated and used at the following concentrations: rapamycin (5 nM), MK2206 (250 nM), AS1842856 (50 nM), LY2090314 (2 nM), CHIR99021 (1 µM). After two days of treatment, cells were analyzed by flow cytometry or harvested for RNA-seq.

value: WT


title: hrp3Δ-expA-H2A.Z-2

description:
Library name: 207791
Experiment A


title: SUDHL4_mRNA_WT_sgIRF8_r2

description: Library name: SUDHL4_mRNA_WT_sgIRF8_r2


title: hrp3Δ-expA-H2A.Z-1

description:
Library name: 207831
Experiment A


title: hrp1Δ-expA-2

description:
Library name: 243086
Experiment A


title: hrp1Δ-expA-1

description:
Library name: 232106
Experiment A


title: fft3Δ-expA-2

description:
Library name: 243085
Experiment A

value: h+ ade6-M216 ura4-D18 leu1-32 fft3del::kanMX


title: mit1Δ-expA-1

description:
Library name: 232108
Experiment A


title: SUDHL4_mRNA_WT_sgIRF8_r1

description: Library name: SUDHL4_mRNA_WT_sgIRF8_r1


title: fft3Δ-expA-H2A.Z-2

description:
Library name: 207789
Experiment A


title: mit1Δ-expA-H2A.Z-2

description:
Library name: 207792
Experiment A


title: fft1Δ-expA-H2A.Z-2

description:
Library name: 207787
Experiment A

value: h+ ade6-M216 ura4-D18 leu1-32 fft1del::hygMX


title: fft2Δ-expA-H2A.Z-1

description:
Library name: 207828
Experiment A

value: h+ ade6-M216 ura4-D18 leu1-32 fft2del::kanMX


title: fft1Δ-expA-H2A.Z-1

description:
Library name: 207827
Experiment A


title: fft2Δ-expA-H2A.Z-2

description:
Library name: 207788
Experiment A


title: SUDHL4_mRNA_WT_sgNTC_r3

description: Library name: SUDHL4_mRNA_WT_sgNTC_r3

value: sgNTC


title: fft3Δ-expA-1

description:
Library name: 232105
Experiment A


title: wt-expA-H2A.Z-2

description:
Library name: 207805
Experiment A


title: hrp1Δ-expA-H2A.Z-1

description:
Library name: 207830
Experiment A


title: SUDHL4_mRNA_WT_sgNTC_r1

description: Library name: SUDHL4_mRNA_WT_sgNTC_r1


title: hrp1Δhrp3Δ-expB-2

description:
Library name: 194825
Experiment B

data_processing:
Alignments, quality control, and initial processing of the raw fastq files or bam files from the sequencing run were performed using a custom pipeline.
Raw count files for each gene were subsequently generated using Kallisto.
Assembly: ASM294v2
Supplementary files format and content: Raw count tsv files for each sample are provided.

extract_protocol:
Total RNA was extracted from yeast cells using a standard hot acid phenol protocol, followed by phenol-chloroform-isopropanol (PCI) extraction and DNase digestion
RNA-seq libraries were prepared with polyA-tail enrichment using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina, followed by using the NEBNext Ultra II library preparation kit for Illumina complemented with custom synthesized barcoded sequencing adapters provided by the Vienna BioCenter Core Facilities Next Generation Sequencing Facility. PCR was performed as a 50 µl reaction using the Q5 polymerase (NEB). Samples were PCR-amplified to the beginning of the logarithmic phase, as determined using a small-scale qPCR reaction run in parallel (typically around 8-10 cycles). Following quality control by Agilent Fragment Analyzer and quantification by RT-qPCR using a Kapa Library Quantification Kit, libraries were sequenced at the Vienna BioCenter Core Facilities Next Generation Sequencing Core Facility on an Illumina sequencer.

value: h+ ade6-M216 ura4-D18 leu1-32 hrp1del::kanMX hrp3del


title: fft3Δ-expA-H2A.Z-1

description:
Library name: 207829
Experiment A


title: hrp1Δhrp3Δ-expB-3

description:
Library name: 194845
Experiment B


title: hrp1Δhrp3Δ-expB-1

description:
Library name: 194805
Experiment B


title: wt-expA-H2A.Z-1

description:
Library name: 207844
Experiment A


title: fft2Δ-expA-1

description:
Library name: 232104
Experiment A


title: SUDHL4_mRNA_WT_sgFLI1_r3

description: Library name: SUDHL4_mRNA_WT_sgFLI1_r3


title: fft1Δ-expA-1

description:
Library name: 232103
Experiment A


title: fft1Δ-expA-2

description:
Library name: 243083
Experiment A


title: SUDHL4_mRNA_WT_sgFLI1_r2

description: Library name: SUDHL4_mRNA_WT_sgFLI1_r2


title: hrp1Δ-expB-3

description:
Library name: 194846
Experiment B


title: hrp3Δ-expB-3

description:
Library name: 194847
Experiment B


title: hrp3Δ-expB-1

description:
Library name: 194807
Experiment B


title: hrp3Δ-expB-2

description:
Library name: 194827
Experiment B


title: SUDHL4_mRNA_WT_sgFLI1_r1

description: Library name: SUDHL4_mRNA_WT_sgFLI1_r1


title: hrp1Δ-expB-1

description:
Library name: 194806
Experiment B


title: hrp1Δ-expB-2

description:
Library name: 194826
Experiment B


title: wt-expB-3

description:
Library name: 194844
Experiment B


title: SUDHL4_mRNA_WT

description: Library name: SUDHL4_mRNA_WT

value: no


title: wt-expB-1

description:
Library name: 194804
Experiment B


title: SUDHL4_mRNA_WT_sgNTC_r2

description: Library name: SUDHL4_mRNA_WT_sgNTC_r2


title: wt-expA-1

description:
Library name: 232102
Experiment A


title: hrp1Δhrp3Δ-expC-input-1

description:
Library name: 275934
Experiment C


title: fft2Δ-expA-2

description:
Library name: 243084
Experiment A


title: ChIPseq_WT_FLI1_sgFLI1

description: Library name: ChIPseq_WT_FLI1_sgFLI1

value: Abcam, ab133485


title: hrp3Δ-expC-input-1

description:
Library name: 275933
Experiment C


title: snf22Δ-expA-b2-3

description:
Library name: 206648
Experiment A, batch 2

value: h+ ade6-M216 ura4-D18 leu1-32 snf22del::hygMX


title: CScreen_TP53

description: Library name: CScreen_TP53

data_processing:
base calling: illumina CASAVA 1.8.2
CRISPR screen: build index on artificial genome which have  specific sgRNA sequence and common template sequence with stagger sequence
CRISPR screen: bowtie/1.1.2 with -S -m 1 -p 4 -a --best --strata -n 2 -l 80
CRISPR screen: samtools idxstats and custom perl script to generate table for counts and fraction on each gene
ChIP-Seq_density: alignment: bowtie-1.1.1/bowtie -S -m 1 -p 20 -a --best --strata -n 2 -l 50
ChIP-Seq_density: filtering (uniquely aligned reads): samtools-0.1.19-1.2/samtools view -S -b -F4
ChIP-Seq_density: normalized tag density: custom script, maximum 2 reads with the same start position allowed
mRNA-Seq_density:alignment: gsnap --use-sarray=0 --novelsplicing=0 --use-splicing refseq.splices.iit --format=sam -B 4
mRNA-Seq_density: filtering: samtools-1.2/samtools view -S -b -F132 -q 20
mRNA-Seq density: normalized tag density: bedtools-2.25/genomeCoverageBed -ibam -bg -split -scale normalization_factor, ucsc-314/bedGraphToBigWig
Assembly: hg19
Supplementary files format and content: Tab-separated values files
Supplementary files format and content: bigwig file
Library strategy: CRISPR screen

value: B cell lymphoma


title: fft1Δ-expA-b2-3

description:
Library name: 206639
Experiment A, batch 2


title: snf22Δ-expA-b2-2

description:
Library name: 206647
Experiment A, batch 2


title: CScreen_TNIP1

description: Library name: CScreen_TNIP1


title: hrp1Δ-expC-input-1

description:
Library name: 275932
Experiment C


title: hrp1Δhrp3Δ-expC-H2BK119ub-1

description:
Library name: 275926
Experiment C


title: wt-expA-b2-1

description:
Library name: 206634
Experiment A, batch 2


title: wt-expB-2

description:
Library name: 194824
Experiment B


title: wt-expA-b2-2

description:
Library name: 206635
Experiment A, batch 2


title: ChIPseq_WT_FLI1_sgNTC

description: Library name: ChIPseq_WT_FLI1_sgNTC


title: hrp3Δ-expC-H2BK119ub-1

description:
Library name: 275925
Experiment C


title: hrp1Δhrp3Δ-2

description: Library name: 206658

data_processing:
Data analysis was conducted using a custom Nextflow pipeline (https://github.com/Gregor-Mendel-Institute/PROalign) for QC, alignment, and read processing, generating strand-specific bigwig files for downstream analysis.
Assembly: ASM294v2
Supplementary files format and content: Provided are strand-specific bigWig files representing the read-depth normalized PRO-seq signal for each sample.
Library strategy: PRO-Seq

extract_protocol:
Cells were permeabilized in ice-cold yeast permeabilization buffer, and subjected to a run-on reaction with biotin-labeled nucleotides at 30 ºC. RNA was extracted using the Norgen RNA Extraction Kit, treated with NaOH, and cleaned via ethanol precipitation. Final RNA was resuspended in DEPC-treated water for downstream analysis.
RNA was processed using streptavidin bead-based purification and ligation of 3’ and 5’ adapters. Reverse transcription was performed with Maxima H Minus RT, followed by PCR amplification to the logarithmic phase. Libraries were sequenced at the Vienna BioCenter Core Facilities.


title: CScreen_SYK

description: Library name: CScreen_SYK


title: hrp1Δhrp3Δ-1

description: Library name: 206653


title: hrp1Δ-expC-H2BK119ub-1

description:
Library name: 275924
Experiment C


title: hrp3Δ-1

description: Library name: 206652


title: CScreen_SPI1

description: Library name: CScreen_SPI1


title: hrp3Δ-2

description: Library name: 206657


title: hrp1Δ-2

description: Library name: 206656


title: wt-expC-H2BK119ub-1

description:
Library name: 275923
Experiment C


title: wt-expA-2

description:
Library name: 243082
Experiment A


title: CScreen_SPIB

description: Library name: CScreen_SPIB


title: wt-2

description: Library name: 206654


title: hrp3-expB-input-2

description:
Library name: 228865
Experiment B

value: h- ade6-M216 ura4-D18 leu1-32 hrp3-13xmyc-kanMX6


title: wt-expC-input-1

description:
Library name: 275931
Experiment C


title: wt-expA-b2-3

description:
Library name: 206636
Experiment A, batch 2


title: CScreen_RB1

description: Library name: CScreen_RB1


title: HEK293-T, 10ng input, new protocol, replicate 2

description: Library name: HEK_10ng_new_rep2


title: hrp1-expB-input-2

description:
Library name: 228867
Experiment B

value: h- ade6-M216 ura4-D18 leu1-32 hrp1-13xmyc-kanMX6


title: HEK293-T, 240ng input, new protocol, replicate 2

description: Library name: HEK_240ng_new_rep2


title: HEK293-T, 240ng input, new protocol, replicate 1

description: Library name: HEK_240ng_new_rep1


title: CScreen_PTPRC

description: Library name: CScreen_PTPRC


title: CScreen_PTEN

description: Library name: CScreen_PTEN


title: HEK293-T, 10ng input, classical protocol, replicate 2

description: Library name: HEK_10ng_classical_rep2


title: CScreen_POU2F2

description: Library name: CScreen_POU2F2


title: HEK293-T, 240ng input, classical protocol, replicate 2

description: Library name: HEK_240ng_classical_rep2


title: CScreen_PLCG2

description: Library name: CScreen_PLCG2


title: wt-1

description: Library name: 206649


title: ChIPseq_WT_Brd4_rep1

description: Library name: ChIPseq_WT_Brd4_rep1

value: Abcam, ab128874


title: CScreen_PIK3AP1

description: Library name: CScreen_PIK3AP1


title: hrp1-expB-myc-2

description:
Library name: 228863
Experiment B

value: anti-Myc 9E10


title: hrp3-expB-myc-1

description:
Library name: 228862
Experiment B; sample failed and excluded from analysis


title: CScreen_REL

description: Library name: CScreen_REL


title: HEK293-T, 10ng input, classical protocol, replicate 1

description: Library name: HEK_10ng_classical_rep1


title: CScreen_BCL6

description: Library name: CScreen_BCL6


title: HEK293-T, 240ng input, classical protocol, replicate 1

description: Library name: HEK_240ng_classical_rep1


title: CScreen_OCAB

description: Library name: CScreen_OCAB


title: HEK293-T, 10ng input, new protocol, replicate 1

description: Library name: HEK_10ng_new_rep1


title: CScreen_PAX5

description: Library name: CScreen_PAX5


title: hrp1-expB-myc-1

description:
Library name: 228864
Experiment B


title: GLA/A4GALT-KO_2

city: Seoul

first: Seung Yun

last: Chae

address: 222 Banpo-daero, Seocho-gu

country: South Korea

institute: The catholic university of korea

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to hg19 (UCSC) whole genome using Bowtie2
Read count extraction using bedtools.
Assembly: hg19
Supplementary files format and content: tab-delimited text files include read count values for each Sample

source_name: Human induced pluripotent stem cells

growth_protocol: PBMCs were transformed into hiPSCs using the CytoTune®-iPS 2.0 Kit (Life Technologies) following the provided guidelines. These cells were sustained in mTeSR1 medium (STEMCELL Technologies) on dishes pre-treated with Corning Matrigel® hESC-Qualified Matrix (1.25%) at 37 °C in a 5% CO2 humidified chamber. After 5-6 days, the hiPSCs were divided at a 1:20 proportion using ReLeSR (STEMCELL Technologies).

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen). 500 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using LEXOGEN Quant-Seq Library Prep Kit (Cat#001.24) standard protocols.

treatment_protocol: The EC differentiation from hiPSC was conducted using the STEMdiff™ Endothelial Cell Differentiation Kit (08005, STEMCELL Technologies, Canada) following the provided guidelines. In brief, hiPSCs were seeded at 5.0 X 10^4 ~ 1.0 X 10^5 density in mTeSR1 medium (05850; STEMCELL Technologies) with 10 µM ROCK inhibitor Y-27632 (1293823; Biogems, CA, USA). The medium switched to STEMdiff™ Mesoderm Induction Medium (05220; STEMCELL Technologies) on day 1 and to STEMdiff™ Endothelial Induction Medium (08006; STEMCELL Technologies) on day 3, refreshed on day 5. By day 7, cells were dissociated with the ACF Cell Dissociation Kit (05426; STEMCELL Technologies), moved to an ACF Cell Attachment Substrate-coated T75 flask (07130; STEMCELL Technologies), and grown in STEMdiff™ Endothelial Expansion Medium until near full confluence.

value: Human induced pluripotent stem cells

value: GLA/A4GALT Knock down

value: Differentiation into endothelial cells


title: hrp3-expB-input-1

description:
Library name: 228866
Experiment B


title: GLA/A4GALT-KO_3


title: GLA/A4GALT-KO_1


title: MMV1545561_rep3

city: Edinburgh

first: Tianchi

last: Zhou

address: Crewe Rd S

institute: University of Edinburgh

description: Library name: S12

data_processing:
The sequencing quality was checked with FastQC (v0.11.9). Low-quality sequences and adapters were trimmed with Cutadapt (v3.5) . Alignment and feature calling was performed with HISAT2 (v2.2.1) , SAMtools (v1.12) and Rsubread (v2.0.1). Differential expression analysis was performed with DESeq2 (v1.36.0).
Assembly: Plasmoduim falciparum 3D7 65
Supplementary files format and content: csv normalised counts

organism: Plasmodium falciparum 3D7

source_name: whole organism

extract_protocol:
Total RNA was extracted from the pellets with RNAzol (Sigma) according to the manufacture’s protocol, quality checked with nanodrop before being snap frozen.
The mRNA were enriched by NEBNext® Poly(A) mRNA Magnetic Isolation Module E7490 (New England Biolabs) for mRNA-Seq library construction.The cDNA library was prepared according to manufacturer’s instructions using the NEBNext® Ultra™ II Directional RNA Library Prep Kit E7760 and NEBNext® Multiplex Oligos E7710 (New England Biolabs). The libraries were purified with Beckman SPRIselect beads (Beckman Coulter). The library quality was checked using Agilent Bioanalyzer. A total of 12 qualified samples were sent for sequencing (Novogene, Illumina NovaSeq 6000 system).

value: whole organism

tag: batch


title: hrp1-expB-input-1

description:
Library name: 228868
Experiment B


title: hrp3-expB-myc-2

description:
Library name: 228861
Experiment B


title: GLA-KO_3

value: GLA Knock down


title: CScreen_PARP1

description: Library name: CScreen_PARP1


title: CScreen_NCOA3

description: Library name: CScreen_NCOA3


title: MMV1545561_rep2

description: Library name: S11


title: MMV085071_rep3

description: Library name: S10


title: WT_2

value: Wild Type


title: WT_3


title: WT_1


title: CScreen_MSH6

description: Library name: CScreen_MSH6


title: GLA-KO_2


title: DMSO_rep3

description: Library name: S8

value: DMSO


title: fft1Δ-expA-b2-2

description:
Library name: 206638
Experiment A, batch 2

value: h+ ade6-M216 ura4-D18 leu1-32 fft1del::hygMX


title: ATAC_BMM cells, MYADM knockout, rep2

city: taipei

first: Tai-Lung

last: Cha

state: taipei

address: 11490 No.161, Sec. 6, Minquan E. Rd., Neihu Dist., Taipei City 114, Taiwan (R.O.

department: National Institute of Cancer Research

country: Taiwan

institute: National Defense Medical Center

description:
Library name: Smaple 52
Column name in ATAC_BMM_pvalue.csv :mKO_BMM

data_processing:
RNAseq:RNA-seq data were aligned to the UCSC reference genome using Bowtie2 (v2.4.5). The human genome (GRCh37/hg19) and mouse genome (GRCm38/mm10) assemblies from the UCSC Genome Browser were used as references. Aligned reads were processed with SAMtools (v1.3) to generate a read count table for each gene.
ATACsaq: Reads were mapped to the human genome (hg19) and mouse genome (mm10) using Bowtie2. PCR duplicates were removed using Picard Tools. For peak calling, biological replicates were merged and processed using MACS2. Peaks from all replicates were further merged using SAMtools. Variance-stabilizing transformation and principal component analysis (PCA) were performed using SeqMonk, based on the DESeq2 model. Visualization of ATAC-seq signals across specific genes was performed using the Integrative Genomics Viewer (IGV).
Assembly: hg19 and mm10
Supplementary files format and content: text files inculed raw counts for each sample
Supplementary files format and content: csv files include FPKM value for each sample

source_name: bone marrow

growth_protocol: Cell lines were cultured in media recommended by the American Type Culture Collection (ATCC) and maintained at 37°C in a humidified incubator with 5% CO₂. Bone marrow cells were isolated from mouse femurs and tibias by PBS flushing, followed by red blood cell lysis with Tris-ammonium chloride. Cells were filtered through a 70-μm strainer and cultured in RPMI-1640 supplemented with 10% heat-inactivated FBS. For stimulation, cells were seeded at 0.5 × 10⁶ cells/ml with 20 ng/ml M-CSF. Fresh cytokine-containing medium was added on day 2, and cells were collected over a 5-day period.

extract_protocol:
Total RNA was extracted using the RNeasy Plus Mini Kit (QIAGEN). RNA-seq libraries were prepared from pretreated RNA using the TruSeq Stranded Total RNA Library Prep Kit (Illumina) according to the manufacturer’s instructions. For ATAC-seq, 1×10⁶ cells were collected, washed with PBS, and lysed in cold ATAC RSB lysis buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl₂, 0.1% NP-40, 0.1%Tween-20, and 0.01% digitonin). Nuclei were washed with ATAC RSB containing 0.1% Tween-20 and resuspended in transposition mix containing Tn5 transposase (Illumina). Transposition was carried out at 37°C for 30 min with shaking at 300 rpm. DNA was purified using the Qiagen MinElute PCR Purification Kit and libraries were amplified using NEBNext PCR master mix (NEB).
RNA-seq libraries were quantified using Qubit (Invitrogen), denatured to single-stranded DNA, loaded onto Illumina flow cells, amplified by in situ cluster generation, and sequenced for 150 cycles on an Illumina HiSeq 2500 platform following the manufacturer's instructions. ATAC-seq libraries were sequenced on an Illumina NextSeq 550 system using paired-end reads.

value: bone marrow

value: mouse bone marrow-derived monocyte

value: MYADM knockout

value: bone marrow-derived monocytes from MYADM knockout mice


title: CQ_rep3

description: Library name: S9

value: CQ


title: ATAC_BMM cells, wild type, rep2

description:
Library name: Smaple 50
Column name in ATAC_BMM_pvalue.csv :mWT_BMM

value: wild-type

value: bone marrow-derived monocytes from wild-type mice


title: ATAC_BMM cells, wild type, rep1

description:
Library name: Smaple 49
Column name in ATAC_BMM_pvalue.csv :mWT_BMM


title: MMV085071_rep2

description: Library name: S7


title: CScreen_MEF2B

description:
Library name: CScreen_MEF2B
processed file: MEF2B_count.txt

value: B cell lymphoma

value: no


title: CScreen_MS4A1

description: Library name: CScreen_MS4A1


title: ATAC_4T1 cells, shRhoA, rep3

description:
Library name: Smaple 48
Column name in ATAC_4T1shRhoA_pvalue.csv :m4T1_shRhoA

source_name: mammary gland

value: mammary gland

value: mouse mammary carcinoma cell

value: RhoA knockdown

value: RhoA knockdown (shRhoA)


title: ATAC_4T1 cells, shRhoA, rep2

description:
Library name: Smaple 47
Column name in ATAC_4T1shRhoA_pvalue.csv :m4T1_shRhoA


title: ATAC_4T1 cells, shRhoA, rep1

description:
Library name: Smaple 46
Column name in ATAC_4T1shRhoA_pvalue.csv :m4T1_shRhoA


title: CQ_rep2

description: Library name: S6

value: whole organism


title: CScreen_MYC

description: Library name: CScreen_MYC


title: GLA-KO_1

value: Human induced pluripotent stem cells

value: GLA Knock down

value: Differentiation into endothelial cells


title: ATAC_4T1 cells, Vector, rep3

description:
Library name: Smaple 45
Column name in ATAC_4T1shRhoA_pvalue.csv :m4T1_shCtrl

value: shRNA control vector


title: ATAC_BMM cells, MYADM knockout, rep1

description:
Library name: Smaple 51
Column name in ATAC_BMM_pvalue.csv :mKO_BMM

value: bone marrow

value: mouse bone marrow-derived monocyte


title: CScreen_MCL1

description: Library name: CScreen_MCL1


title: ATAC_4T1 cells, Vector, rep2

description:
Library name: Smaple 44
Column name in ATAC_4T1shRhoA_pvalue.csv :m4T1_shCtrl