title: R9_HRO761

city: Geneva

first: Sotirios

middle: G.

last: Ntallis

address: 30 quai Ernest-Ansermet

department: Department of Molecular and Cellular Biology

country: Switzerland

institute: University of Geneva

description: Library name: Sample 4

data_processing:
100-bp single end reads were aligned to the reference human genome Human GRCh37/hg19 (repetitive regions masked) using bwa v.0.7.17, retaining only the reads with the highest quality score.
Non-aligned and non-primary reads (flags 4 and 256) were removed using samtools (Li et al., 2009)
BAM files were converted to BigWig format with bamCoverage (deepTools 3.5.6; Ramirez et al., 2016)  with a mapping quality cutoff of 30, 10 kb resolution, and a 40 kb smoothing window.
Read tracks were visualized using IGV (Thorvaldsdóttir et al., 2013).
Assembly: Human GRCh37/hg19
Supplementary files format and content: BigWig files

source_name: Human cell line

growth_protocol: HCT116 cells were maintained in McCoy’s 5A medium (Thermo Scientific, Cat. No. 16600082) supplemented with 10% fetal bovine serum (FBS) (Invitrogen, Cat. No. 10500), 100U/mL penicillin, and 100μg/mL streptomycin (1/100 dilution; Invitrogen, Cat. No. 15140-122).

extract_protocol:
After fixation with 90% Methanol in PBS, the cells were permeabilized with 0.2% Triton-X in PBS and EdU was coupled to a cleavable biotin-azide linker (Azide-PEG(3+3)-S-S-biotin) using the Click-it Kit. Purification of genomic DNA was then performed by phenol-chloroform extraction and ethanol precipitation and subjected to EdU-labelled DNA isolation. (Macheret and Halazonetis 2018)
Purified EdU-labeled DNA was used for library preparation with TrueSeq ChIP Library Preparation Kit (Illumina) and high-throughput 100-bp single-end sequencing was performed on Illumina Hi-Seq 4000 sequencer.

treatment_protocol: EdU-seq samples were treated with 2mM thymidine for 18hrs and were subsequently released in presence of DMSO or 100nM HRO761 for 6 or 9hrs (R6_ and R9_ samples, respectively). 25μM EdU was added 30min before collection.

value: Human cell line

value: Human Colorectal Carcinoma Cells


title: CD45 negative cell fraction from the spleen of a P.chabaudi infected mouse, mouse 2

status: Public on Jul 28 2026

type: SRA

city: Bonn

first: Elvira

last: Mass

address: Carl-Troll-Str. 31

department: Developmental Biology of the Immune System

country: Germany

institute: Life & Medical Sciences Institute, University of Bonn

description:
Library name: CD45neg_Malaria1
10X Genomics

library_source: transcriptomic single cell

data_processing:
The raw sequencing data was  processed with the ‘count’ command of the Cell Ranger software (v7.1.0) provided by 10X Genomics using the refdata-gex-mm10-2020-A reference genome.  All other options were used as per default.
Assembly: refdata-gex-mm10-2020-A
Supplementary files format and content: Tab-delimited text files include cell-barcode names (barcodes.tsv) as well as gene names (features.tsv) corresponding to the count data in matrix.mtx.

molecule: total RNA

organism: Mus musculus

source_name: spleen

extract_protocol:
FACS/MACS enrichment
ChromiumNext GEMSingle Cell 3ʹ Reagent Kits v3.1 (Dual Index)

tag: tissue

value: spleen

tag: age

value: 5-6 months

tag: cell type

tag: genotype

value: Tnfrsf11aCre; Rosa26LSL-YFP; Ms4a3FlpO; Rosa26FSF-tdTomato

tag: treatment

tag: condition

value: Malaria


title: Pta1 degron, Pta1 Mut ura, Auxin, Rep2

city: Oxford

first: Abigail

last: Southers

address: South Parks Road

department: Biochemistry

country: United Kingdom

institute: University of Oxford

description: Library name: mut24hraux_rep2

library_source: transcriptomic

data_processing:
Reads trimmed and quality controlled with fastp (0.20.0)
Reads were aligned to concatenated genome of S.pombe and S. cerevisiae using STAR (2.7.3a)
Reads were split to each of the organisms keeping all alignments with samtools and bash command line
Reads which had too distant pairs were further filtered using a custom script
Aligned, filtered files were sorted and indexed using samtools
Bigwig files were prepared and separated by strand with bedtools genomecov (including -bg -strand -du -split -scale options). As scaling factor spike-in value was used. Bedgraphs were sorted and transformed to bigwigs using bedGraphToBigWig.
Assembly: ASM294v2 from pombase.org
Supplementary files format and content: bigwig with normalised coverage using spiked-in reads for plus strand
Supplementary files format and content: bigwig with normalised coverage using spiked-in reads for minus strand

organism: Schizosaccharomyces pombe

source_name: yeast

growth_protocol: Strains were grown in YES media (with reduced uracil to 10mg/L) to OD600=~0.5

extract_protocol:
Total RNAs were extracted by a standard hot phenol method from 4-thiouracil labelled cells (S.pombe mixed with S.cerevisiae as a spike-in).
Library was prepared following TT-seq (chem) protocol. Briefly, RNA was treated with DNAse, subjected to NaOH fragmentation, followed by RNA biotinylation and purification on streptavidin beads. Purified RNA (50ng) was used in library preparation following manufacture recommendations for NEBNext ultra II directional RNA library prep kit for Illumina.

treatment_protocol: Auxin (1 mM final) treatment for 24 hours at 25°C. Non treated cells were grown at 30°C.Thiouracil labelling (5 mM final) for 6 minutes. Cells harvested and snap-frozen in liquid nitrogen

tag: cell line

value: yeast

value: h- ade6::(Padh15-skp1-AtTIR1-2NLS) ura4-D18 Pta1:HYG-mAID-FLAG ura4::WT-Pta1-V5

value: auxin treated


title: R9_DMSO

description: Library name: Sample 3

library_source: genomic

molecule: genomic DNA

organism: Homo sapiens


title: CD45 negative cell fraction from the spleen of a PBS treated control mouse, mouse 99

description:
Library name: CD45neg_Ctrl99
10X Genomics

value: PBS

value: Ctrl


title: Pta1 degron, Pta1 Mut ura, Auxin, Rep1

description: Library name: mut24hraux_rep1


title: R6_HRO761

description: Library name: Sample 2


title: Nur77_HA_Ctrl2

city: Amsterdam

first: Claudia

last: van Tiel

address: Meibergdreef 15

department: Medical Biochemistry

country: Netherlands

institute: Amsterdam UMC

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Skewer 0.2.2
Reads were aligned to the mouse genome mm10 by HISAT2 2.1.0
Tag directories were created using the makeTagDirectory command in HOMER
BigWigs were produced from HOMER tag directories
Nur77 binding peaks were identified by using HOMER peak calling with default settings, Pol II and H3K27ac binding was called using the regions setting (broad peaks)
For the peak files, the reproducible peaks in three or two biological replicates were merged using HOMER’s mergePeaks.pl script. The BigWigs were merged using bigwigAverage from deepTools2
Assembly: mm10
Supplementary files format and content: tab-delimited text files with identiified peaks (except for input samples), bigWig files

growth_protocol: The RAW264.7 macrophage stable cell lines with doxycyclin-inducible expression of HA-tagged Nur77 or GFP were seeded at a density of 3.75x10^5 cells/ml and after two days Nur77 or GFP expression was induced by incubation with 50ng/ml doxycyclin for 18 h

extract_protocol:
Only for the Nur77 ChIP, cells were crosslinked directly in culture flasks with 2mM Di(N-succinimidyl) glutarate in PBS for 30 min at room temperature. For all ChIP targets including Nur77, cells were then crosslinked with 1% formaldehyde for 10 minutes at room temperature. After quenching and cell lysis, the chromatin was sonicated into approximately 400bp fragments using a Bioruptor Pico (Diagenode) for 4 cycles (double cross-linked) or 3 cycles (single cross-linked) of 10sec on and 50sec off. Immunoprecipitation was performed using HA (for Nur77),  RNA polymerase, or H3K27ac antibody
Strrand-specific ChIP seq libraries were prepared using the KAPA hyperprep kit protocol. Concentration and fragment size of chromatin was confirmed using the Tapestation4200 (Agilent).

treatment_protocol: Cells were stimulated with 500 ng/ml LPS for 0 and 1h

value: macrophages

value: untreated

tag: chip antibody

value: HA (Diagenode, C15200190)


title: R6_DMSO

description: Library name: Sample 1


title: Pta1 degron, Pta1 WT ura, Auxin, Rep1

description: Library name: wt24hraux_rep1

value: h- ade6::(Padh15-skp1-AtTIR1-2NLS) ura4-D18 Pta1:HYG-mAID-FLAG ura4::AAA-V5


title: CD45 negative cell fraction from the spleen of a PBS treated control mouse, mouse 2

description:
Library name: CD45neg_Ctrl2
10X Genomics


title: Nur77_HA_Ctrl1


title: Healthy_RNA_006

status: Public on Jul 27 2026

city: Miami

first: Qin

last: Yang

state: FL

address: 1501 NW 10th Avenue

department: Sylvester Comprehensive Cancer Center

country: USA

institute: University of Miami Miller School of Medicine

description: Library name: Healthy_RNA_006

data_processing:
The quality of the resulting reads was assessed using FastQC (v0.11.8) and multiQC (1.11). Then all reads were processed using Trim Galore (version 0.6.2) to trim to paired end 50 basepairs and remove adapters.
The resulting reads were aligned to the hg19 Gencode v19 reference genome using the STAR aligner (version 2.7.6a) with specific parameters: outFilterType=BySJout, outFilterMultimapNmax=20, alignSJoverhangMin=8, alignSJDBoverhangMin=1, outFilterMismatchNmax=999, alignIntronMin=20, alignIntronMax=1000000, alignMatesGapMax=1000000, and alignEndsType=EndToEnd.
Gene expression was quantified using featureCounts (v2.0.1), which was run in paired-end mode with the hg19 gencode annotation file (excluding entries for ribosomal RNA).
Differential expression analysis was performed using DESeq2 (v1.32.0) with a multifactor design that accounted for both the donor's condition and any batch effects. Genes with an absolute fold change of at least 1.5 and a p-value adjusted for multiple comparisons of less than or equal to 0.05 were considered significant.
Assembly: hg19
Supplementary files format and content: featureCounts files

source_name: Bone marrow

extract_protocol:
RNA extracted from the CD34+ fraction was employed for RNA-seq. To guarantee RNA quality, Tapestation was utilized prior to library preparation. The RNA was treated with Illumina Ribo-Zero
For library preparation, we used the Nugen Ovation Solo RNA-seq ultra-low input kit, following the manufacturer's instructions. Subsequently, the prepared libraries were sequenced on an Illumina NextSeq platform. These libraries were paired-end and they were strand-specific.

value: Bone marrow

value: Healthy


title: Healthy_RNA_004

description: Library name: Healthy_RNA_004


title: Healthy_RNA_003

description: Library name: Healthy_RNA_003


title: Healthy_RNA_005

description: Library name: Healthy_RNA_005


title: Healthy_RNA_001

description: Library name: Healthy_RNA_001


title: MDS_AZA_097

data_processing:
The quality of the resulting reads was assessed using FastQC (v0.11.8) and multiQC (1.11). Then all reads were processed using Trim Galore (version 0.6.2) to trim to paired end 50 basepairs and remove adapters.
The resulting reads were aligned to the hg19 Gencode v19 reference genome using the STAR aligner (version 2.7.6a) with specific parameters: outFilterType=BySJout, outFilterMultimapNmax=20, alignSJoverhangMin=8, alignSJDBoverhangMin=1, outFilterMismatchNmax=999, alignIntronMin=20, alignIntronMax=1000000, alignMatesGapMax=1000000, and alignEndsType=EndToEnd.
Gene expression was quantified using featureCounts (v2.0.1), which was run in paired-end mode with the hg19 gencode annotation file (excluding entries for ribosomal RNA).
Differential expression analysis was performed using DESeq2 (v1.32.0) with a multifactor design that accounted for both the donor's condition and any batch effects. Genes with an absolute fold change of at least 1.5 and a p-value adjusted for multiple comparisons of less than or equal to 0.05 were considered significant.
Assembly: hg19
Supplementary files format and content: featureCounts  files

tag: individual

value: MDS patient

tag: Sex

value: Male

tag: responder

value: NonResp


title: MDS_AZA_096


title: MDS_AZA_095

value: Female


title: MDS_AZA_059

value: Responder


title: MDS_AZA_058


title: MDS_AZA_057


title: MDS_AZA_060


title: MDS_AZA_056


title: MDS_AZA_055


title: MDS_AZA_052


title: MDS_AZA_051


title: MDS_AZA_050


title: MDS_AZA_047


title: MDS_AZA_046


title: MDS_AZA_045


title: MDS_AZA_044


title: MDS_AZA_010


title: MDS_AZA_038


title: MDS_AZA_002


title: MDS_AZA_009


title: MDS_AZA_013


title: MDS_AZA_017


title: MDS_AZA_016


title: MDS_AZA_015


title: K562 cells with drug treatments, gene expression

city: New York

first: Isabella

last: Grabski

state: NY

address: 101 Avenue of the Americas

institute: New York Genome Center

description:
Library name: K562_drug_GEX
Gene expression via 10x Flex probes

library_source: other

data_processing:
Data were processed as described at https://phospho-seq.com/post/protocol_5/FlexPlexProtocol.pdf and by using the scripts provided at https://phospho-seq.com/files/quant.ipynb.
Data were processed with Cell Ranger.
Assembly: GRCh38
Supplementary files format and content: Seurat object (RDS)

molecule: other

extract_protocol:
Extraction was done according to the protocols for 10x Flex v1.
Extraction was done according to the protocols for 10x Genomics Chromium Single Cell 3’ Gene Expression v3.1 with Feature Barcoding technology for CRISPR screening.
Libraries were constructed according to the protocol described at https://phospho-seq.com/post/protocol\_6/FlexPlexProtocol.pdf.
Libraries were constructed according to the protocols for 10x Genomics Chromium Single Cell 3’ Gene Expression v3.1 with Feature Barcoding technology for CRISPR screening.
Libraries were constructed according to the protocol described at https://phospho-seq.com/post/protocol\_6/FlexPlexProtocol.pdf.


title: MDS_AZA_007


title: K562 cells with drug treatments, hashes

description:
Library name: K562_drug_HTO
Hashtag-derived oligonucleotide (HTO)

data_processing:
Data were processed as described at https://phospho-seq.com/post/protocol\_6/FlexPlexProtocol.pdf.
Data were processed with Cell Ranger.
Assembly: GRCh38
Supplementary files format and content: Seurat object (RDS)

molecule: protein


title: K562 cells with drug treatments, proteins

description:
Library name: K562_drug_ADT
Antibody-derived oligonucleotide (ADT)


title: K562 cells with CRISPRi perturbations, guide capture

description:
Library name: K562_CRISPRi_GDO
Guide-derived oligonucleotide (GDO)

data_processing:
Data were processed with Cell Ranger.
Assembly: GRCh38
Supplementary files format and content: Seurat object (RDS)

extract_protocol:
Extraction was done according to the protocols for 10x Genomics Chromium Single Cell 3’ Gene Expression v3.1 with Feature Barcoding technology for CRISPR screening.
Libraries were constructed according to the protocols for 10x Genomics Chromium Single Cell 3’ Gene Expression v3.1 with Feature Barcoding technology for CRISPR screening.


title: K562 cells with CRISPRi perturbations, gene expression

description: Library name: K562_CRISPRi_GEX

molecule: polyA RNA


title: A549 cells with siRNA knockdowns, hashes

description:
Library name: A549_siRNA_HTO
Hashtag-derived oligonucleotide (HTO)

data_processing:
Data were processed as described at https://phospho-seq.com/post/protocol_5/FlexPlexProtocol.pdf and by using the scripts provided at https://phospho-seq.com/files/quant.ipynb.
Assembly: GRCh38
Supplementary files format and content: Seurat object (RDS)

extract_protocol:
Extraction was done according to the protocols for 10x Flex v1.
Libraries were constructed according to the protocol described at https://phospho-seq.com/post/protocol\_6/FlexPlexProtocol.pdf.


title: A549 cells with siRNA knockdowns, gene expression

description:
Library name: A549_siRNA_GEX
Gene expression via 10x Flex probes


title: 4-1BB/z, hCD45+mCD45-GFP-CD33+CD3-CD19-

city: Tokyo

first: Satoshi

last: Yamazaki

address: 4 Chome-6-1 Shirokanedai, Minato City

country: Japan

institute: The Institute of Medical Science, The University of Tokyo

description: Library name: 4-1BB/zCD33

data_processing:
RNA quality was assessed using NanoDrop 2000 and Agilent Bioanalyzer prior to Sequencing. Bulk RNA sequencing was performed on the Illumina NextSeq 500 platform by Tsukuba i-Laboratory LLP. Raw sequencing data were obtained as FASTQ files. Data processing and downstream analysis were performed using CLC Genomics Workbench (Qiagen). Reads were aligned to the human reference genome hg19 (GRCh37). Gene annotations within the analysis workflow were based on GENCODE annotations.
Assembly: hg19 (GRCh37)
Supplementary files format and content: CSV file with gene-level RNA-sequencing expression values for CAR-engineered immune populations. Rows correspond to genes and columns correspond to samples.

source_name: SPLEEN (NOG-w41 differentiated human cord-blood CD34+ cells)

growth_protocol: NOG-w41 mouse-derived splenocytes were thawed and maintained in Roswell Park Memorial Institute-1640 (RPMI-1640), 1% bovine serum albumin (BSA) (Wako, Osaka, Japan, catalogue # 019-23293, lot # LKH4780), 1% P/S as the basal medium. Antigen-specific activation was performed with basal medium supplemented with human CD19/Leu-12 protein (His-Tag), biotinylated (Sino Biological, catalogue #11880-H08H-B), added at a concentration of 1µg/ml.

extract_protocol:
Cells were sorted directly into TRIZOL LS for cell lysis and total RNA was extracted using the TAKARA SMARTer RNA extraction protocol (SMARTer Stranded Total RNA-Seq Kit, Takara Bio) according to the manufacturer’s instructions.
cDNA libraries were prepared using the TAKARA SMARTer Stranded Total RNA-Seq Kit (Takara Bio) and the high-output kit v2 (Illumina), following the manufacturer’s protocol.

treatment_protocol: Antigen-specific CAR activation was performed with basal medium supplemented with human CD19/Leu-12 protein (His-Tag), biotinylated (Sino Biological, catalogue #11880-H08H-B), added at a concentration of 1µg/ml for 24 hours at 37°C.

value: GFP-

value: CD19 antigen stimulation for 24 hours


title: 4-1BB/z, hCD45+mCD45-GFP-CD19+CD3-CD33-

description: Library name: 4-1BB/zCD19

value: SPLEEN (NOG-w41 differentiated human cord-blood CD34+ cells)


title: HiC on OVCAR8 ko2 cells

city: Bethesda

first: Elena

last: Pugacheva

state: MD

department: NIAID

institute: NIH

description: Library name: HiC_OVCAR8_ko2

data_processing:
ChIP-seq and  ATAC-seq: paired-end reads were aligned to the UCSC human hg38 genome using Bowtie version 2 under default parameters with options “–very-sensitive -X 2000” .
Bowtie output files (SAM) were converted into BAM files using the "samtools view" option in Samtools,
ChIP-seq,  and ATAC-seq peaks were called using Model-based Analysis for ChIP-seq (MACS3) using default parameters.
HiC: Hi-C data were processed using the Juicer pipeline and aligned to the human reference genome (hg38) using BWA-MEM. Hi-C pair files (.pairs.gz) were generated from the aligned BAM files using Pairtools with default parameters. The .pairs.gz files were converted into .hic contact matrix files using Juicer.
Assembly: hg38
Supplementary files format and content: ChIP-seq, ATAC-seq: bigwig
Supplementary files format and content: HiC data: HIC files
Supplementary files format and content: RNA-seq data: Raw counts for each gene .tab

growth_protocol: OVCAR8 wild type (wt) and BORIS knockout (ko) cells were maintained in RPMI 1640 supplemented with 10% FBS, 1% penicillin/streptomycin

extract_protocol:
ChIP-seq protocol: 2x106 asynchronously growing cells were crosslinked with 1% formaldehyde for 10 min at room temperature, followed by quenching with 125 mM glycine for 10 min, washed twice with 1×phosphate buffered saline (PBS), and resuspended in chromatin immunoprecipitation (ChIP) lysis buffer (150 mM NaCl, 1 % Triton X-100, 0.1 % SDS, 20 mM Tris–HCl pH8.0, 2 mM EDTA). Chromatin was sheared to 200–600 bp and immunoprecipitated with 5 μg of antibody. Immunoprecipitated DNA was purified with QIAquick columns (ZymaResearch).
ChIP-seq libraries were prepared using TruSeq ChIP Sample Preparation Kit (Illumina, Inc., USA) or NEBNext UltraII DNA Library Prep Kit for Illumina (BioLabs, catalog # E7645S).  Libraries were amplified using 15 cycles on the thermocycler. Post amplification libraries were size selected at 250-450bp in length using Agencourt AMPure XP beads from Beckman Coulter. Libraries were validated using the Agilent High Sensitivity DNA Kit.
ATAC-seq libraries were prepared from 50,000 OVCAR8 cells. Nuclei were isolated by lysis in cold buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl_2, and 0.1% IGEPAL CA-630) and subjected to tagmentation using Tn5 transposase (Illumina) for 40 min at 37°C. Tagmented DNA was purified using DNA Clean & Concentrator-5 columns (Zymo Research), amplified with NEBNext High-Fidelity 2× PCR Master Mix (New England Biolabs), and size-selected using 1.8× AMPure XP beads (Beckman Coulter).
RNA-seq: Total RNA was extracted from OVCAR8 cells using TRIzol reagent according to the manufacturer's protocol. RNA-seq libraries were prepared according to the manufacturer's protocol using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs, E7760S).
Hi-C libraries were prepared using the Arima-HiC Kit (Arima Genomics) according to the manufacturer's instructions. Briefly, 5 million OVCAR8 cells were crosslinked with 2% formaldehyde in growth medium for 10 min at room temperature, and the reaction was quenched with 0.125 M glycine for 10 min. Cells were washed twice with phosphate-buffered saline (PBS), snap-frozen, and stored at −80°C until nuclei isolation.

value: High-Grade Serous Ovarian Carcinoma

value: homozygous deletion of ZF1-4 (Exon #4-5) in BORIS gene (clone#2, ko2)

value: CRISPR–Cas9 knockout of exon 4-5 of BORIS gene


title: 4-1BB/z, hCD45+mCD45-GFP-CD3+CD19-CD33-

description: Library name: 4-1BB/zCD3


title: HiC on OVCAR8 WT cells

description: Library name: HiC_OVCAR8_WT

value: wild type


title: RNA-seq on OVCAR8ko2 cells

description: Library name: RNA-seq_OVCAR8_ko2


title: 4-1BB/z, hCD45+mCD45-GFP+CD56+CD3-

description: Library name: 4-1BB/zGFPCD56


title: 4-1BB/z, hCD45+mCD45-GFP+CD33+CD3-CD19-

description: Library name: 4-1BB/zGFPCD33


title: 4-1BB/z, hCD45+mCD45-GFP+CD3+CD19-CD33-

description: Library name: 4-1BB/zGFPCD3


title: RNA-seq on OVCAR8 WT cells

description: Library name: RNA-seq_OVCAR8_WT


title: ATAC-seq on OVCAR8ko2 cells

description: Library name: ATAC-seq_OVCAR8_ko2


title: CD3z, hCD45+mCD45-GFP-CD33+CD3-CD19-

description: Library name: CD3zCD33


title: ATAC-seq on OVCAR8 ko1 cells

description: Library name: ATAC-seq_OVCAR8_ko1

value: homozygous deletion of ZF1-4 (Exon #4-5) in BORIS gene (clone#1, ko1)


title: CD3z, hCD45+mCD45-GFP-CD19+CD3-CD33-

description: Library name: CD3zCD19


title: CD3z, hCD45+mCD45-GFP-CD56+CD3-

description: Library name: CD3zCD56


title: ATAC-seq on OVCAR8 WT cells

description: Library name: ATAC-seq_OVCAR8_WT


title: Input for ChIP-seq on OVCAR8WT cells

description: Library name: Input_OVCAR8_WT


title: CD3z, hCD45+mCD45-GFP-CD3+CD19-CD33-

description: Library name: CD3zCD3


title: Input for ChIP-seq on OVCAR8 ko1 cells

description: Library name: Input_OVCAR8_ko1


title: CD3z, hCD45+mCD45-GFP+CD33+CD3-CD19-

description: Library name: CD3zGFPCD33

value: CD3z (GFP+)


title: Input for ChIP-seq on OVCAR8 ko2 cells

description: Library name: Input_OVCAR8_ko2


title: ChIP-seq on OVCAR8 ko2 cells with SMC3 antibodies

description: Library name: ChIP_OVCAR8_ko2_SMC3

value: rabbit polyclonal antibody against SMC3 (Abcam, ab#9263)


title: CD3z, hCD45+mCD45-GFP+CD19+CD3-CD33-

description: Library name: CD3zGFPCD19


title: CD3z, hCD45+mCD45-GFP+CD3+CD19-CD33-

description: Library name: CD3zGFPCD3


title: ChIP-seq on OVCAR8 ko2 cells with H3K4me3 antibodies

description: Library name: ChIP_OVCAR8_ko2_H3K4me3

value: rabbit polyclonal to Histone H3 (tri methyl K4) (Abcam, ab8580)


title: 2B4/z, hCD45+mCD45-GFP-CD19+CD3-CD33-

description: Library name: 2B4/zCD19


title: ChIP-seq on OVCAR8 ko2 cells with H2AZ antibodies

description: Library name: ChIP_OVCAR8_ko2_H2AZ

value: rabbit polyclonal antibody against histone H2A.Z (Abcam, ab4174)


title: 2B4/z, hCD45+mCD45-GFP-CD56+CD3-

description: Library name: 2B4/zCD56


title: ChIP-seq on OVCAR8 ko2 cells with CTCF antibodies

description: Library name: ChIP_OVCAR8_ko2_CTCF

value: mouse monoclonal antibody against CTCF (Santa Cruz, (B-5):sc-271514)


title: 2B4/z, hCD45+mCD45-GFP-CD3+CD19-CD33-

description: Library name: 2B4/zCD3


title: 2B4/z, hCD45+mCD45-GFP+CD33+CD3-CD19-

description: Library name: 2B4/zGFPCD33


title: ChIP-seq on OVCAR8 ko1 cells with SMC3 antibodies

description: Library name: ChIP_OVCAR8_ko1_SMC3


title: ChIP-seq on OVCAR8 ko1 cells with RAD21 antibodies

description: Library name: ChIP_OVCAR8_ko1_RAD21

value: rabbit monoclonal antibody against RAD21 (Abcam, ab217678)


title: 2B4/z, hCD45+mCD45-GFP+CD56+CD3-

description: Library name: 2B4/zGFPCD56


title: ChIP-seq on OVCAR8 ko1 cells with H3K4me3 antibodies

description: Library name: ChIP_OVCAR8_ko1_H3K4me3


title: 2B4/z, hCD45+mCD45-GFP+CD3+CD19-CD33-

description: Library name: 2B4/zGFPCD3


title: CD3z, hCD45+mCD45-GFP+CD56+CD3-

description: Library name: CD3zGFPCD56


title: ChIP-seq on OVCAR8 ko2 cells with RAD21 antibodies

description: Library name: ChIP_OVCAR8_ko2_RAD21


title: ChIP-seq on OVCAR8 ko1 cells with H3K27ac antibodies

description: Library name: ChIP_OVCAR8_ko1_H3K27ac

value: rabbit polyclonal to Histone H3 (acetyl K27) (Abcam, ab4729)


title: 2B4/z, hCD45+mCD45-GFP-CD33+CD3-CD19-

description: Library name: 2B4/zCD33


title: ChIP-seq on OVCAR8 ko2 cells with H3K27ac antibodies

description: Library name: ChIP_OVCAR8_ko2_H3K27ac


title: AAV2CBE, biol_rep2

city: Madison

first: Kinjal

last: Majumder

state: WI

address: 1525 Linden Drive

department: Oncology

institute: University of Wisconsin

description: Library name: Sample2

data_processing:
Reads aligned to human hg38 genome using Bowtie2
Aligned V3C-seq samples were sorted using Samtools, and the resulting aligned and sorted Bam files were converted to Bedgraph files using BEDtools.
Regions that were shared between independent biological replicates of these experiments were determined using BEDtools BEDtools Intersect intervals
Mapped reads were partitioned into bins corresponding to HindIII restriction fragments across the human genome, such that each read was allocated to the fragment defined by its genomic position. Based on this, the top 150 HindIII fragments that had the highest number of reads were sorted and used.
Assembly: Human hg38
Supplementary files format and content: bedgraph
Library strategy: V3C-seq

source_name: Kidney

growth_protocol: Human embryonic kidney cells (HEK293T) in Dulbecco’s modified Eagle’s medium (DMEM, high glucose; Gibco) supplemented with 5% Serum Plus and 50 µg/ml gentamicin (Gibco). All cells were cultured at 37°C and 5% CO2.

extract_protocol:
Cells were crosslinked with 1% formaldehyde, and reaction was quenched with glycine. Cells were then lysed and chromatin was digested with HindIII (NEB; R3104) before intramolecular ligation in dilute conditions with T4 DNA ligase (NEB; M0202). DNA was purified before undergoing secondary digest with NlaIII (NEB; R0125) and circularization with T4 DNA ligase under dilute conditions. Viral-host interactions were enriched through inverse and nested inverse PCR amplification steps with primers complementary to wtAAV2.
Libraries were prepared using NEBNext Ultra II DNA Library Prep Kit and sequenced using single-end sequencing on an Illumina NextSeq platform spiked with 25% phiX spike-in to increase library complexity.

treatment_protocol: Cell were seeded at 2.5*10^6 high glucose DMEM supplementet with with 5% Serum Plus and 50 µg/ml gentamicin. Cells were infected with wtAAV2 for 24hrs.

value: Kidney

value: HEK 293T

value: Human Embryonic Kidney


title: ChIP-seq on OVCAR8 ko1 cells with H2AZ antibodies

description: Library name: ChIP_OVCAR8_ko1_H2AZ


title: AAV2CBE, biol_rep1

description: Library name: Sample1


title: ChIP-seq on OVCAR8 ko1 cells with CTCF antibodies

description: Library name: ChIP_OVCAR8_ko1_CTCF


title: ChIP-seq on OVCAR8 ko1 cells with BORIS antibodies

description: Library name: ChIP_OVCAR8_ko1_BORIS

value: rabbit recombinant monoclonal BORIS antibody (Abcam, EP12204)


title: PRO-seq, HG03645, IFNB, 1 hour, rep 2

city: Boulder

first: Robin

middle: D.

last: Dowell

state: CO

address: 596 UCB

department: Molecular, Cellular and Developmental Biology

institute: University of Colorado Boulder

data_processing:
PRO-seq datasets were processed using the Nextflow pipeline found in https://github.com/Dowell-Lab/Nascent-Flow.
Read quality was assessed using FastQC (v0.11.5).
Read quality and adapter trimming was done using BBMap (v38.05) bbduk with options ktrim=r, qtrim=10, k=23, mink=11, hdist=1, maq=10, minlen=25, literal=AAAAAAAAAAAAAAAAAAAAAAA, ref= The FASTA file containing common adapters found in https://github.com/Dowell-Lab/Nascent-Flow/blob/master/bin/adapters.fa.
Mapping was done using HISAT2 (v2.1.0) with options --very-sensitive --no-spliced-alignment.
SAM to BAM conversion was done using Samtools (v1.8).
Bigwigs were obtained using deepTools (v3.0.1) bamCoverage with options --binSize 1 --normalizeUsing RPKM --filterRNAstrand reverse (for pos file) or forward (for neg file) --scaleFactor 1 (for pos file) or -1 (for neg file).
Assembly: Human (Homo sapiens) datasets were mapped to hs1.
Supplementary files format and content: The *.pos.bigwig and *.neg.bigwig files are bigwig visualization files for each of the two DNA strands, normalized for coverage using deepTools using --normalizeUsing RPKM.
Library strategy: PRO-seq

growth_protocol: The human LCLs were cultured in RPMI-1640 media (Gibco 72400-047) using 15% FBS (Gibco 10437-028) and 100 units/mL Penicillin-Streptomycin (Gibco 15140-122) in vent-cap T-25 flasks (Corning 430639), and kept at a confluency between 400,000 cells/mL to 800,000 cells/mL during cell culture at 37°C with 5% CO2.

extract_protocol:
Nuclei isolation was done as described in [Core2008] (https://doi.org/10.1126/science.1162228) with some modifications. Briefly, LCL cultures ranging from 3 to 25 million cells were used for each condition. After each culture was treated for 1 hour, the cultures were washed twice with ice-cold PBS. Then, the cell pellets were carefully resuspended in 6 mL of lysis buffer (0.1% DEPC-DI water with 10 mM Tris-HCl pH 7.4, 2 mM MgCl2, 3 mM CaCl2, 0.5% IGEPAL, 10% Glycerol, 1 mM DTT, Invitrogen Ref. AM2696 SUPERase-IN RNAse inhibitor, and with Roche Ref. 11836170001 protease inhibitor cocktail) and centrifuged for 15 minutes at 4°C at 1000 x g. The pellets were carefully resuspended in 1 mL lysis buffer using Finntip wide orifice pipette tips (Thermo Scientific Ref. 9405163), were mixed with 4 mL more of lysis buffer, and centrifuged a second time for 15 minutes at 4°C at 1000 x g. The pellets were carefully resuspended a second time in 1 mL lysis buffer using Finntip wide orifice pipette tips, transferred to low binding 1.7 mL eppendorf tubes (Costar Ref. 3207), and centrifuged for 5 minutes at 4°C at 1000 x g. The pellets were carefully resuspended using Finntip wide orifice pipette tips in 500 μL freezing buffer (0.1% DEPC-DI water with 50 mM Tris-HCl pH 8.0, 5 mM MgCl2, 40% Glycerol, 0.1 mM EDTA pH 8.0, and SUPERase-IN RNAse inhibitor), and centrifuged for 2 minutes at 4°C at 2000 x g. The resulting nuclei pellets were resuspended a final time in 110 μL of freezing buffer using Finntip wide orifice pipette tips. We mixed 10 μL of the resuspended nuclei with 990 μL of PBS for counting the nuclei yield. The remaining 100 μL resuspended nuclei were snap-frozen in liquid nitrogen and stored at -70°C before being used for the PRO-seq nuclear-run on reactions.
PRO-seq datasets were prepared as described in [Fant2020] (https://doi.org/10.1016/j.molcel.2020.03.008), which in turn is a modified protocol from [Mahat2016] (https://doi.org/10.1016/j.molcel.2020.03.008). Briefly, between 2 to 18 million nuclei per dataset were used for the PRO-seq transcription run-on using a mixture of rNTP and Biotin-11-CTP (Biotin-11-CTP at 0.025 mM from PerkinElmer Ref. NEL542001EA; rCTP at 0.025 mM from Promega Ref. E604B, rATP at 0.125 mM Ref. E601B, rGTP at 0.125 mM Ref. E603B, and rUTP at 0.125 mM Ref. E6021). 1% of S2 Drosophila melanogaster nuclei relative to the number of the sample nuclei were added during the run-on reaction as a normalization spike-in. Total RNA was extracted using a phenol/chloroform precipitation. Isolated RNA was fragmented using base hydrolysis with NaOH. Biotinylated fragmented nascent transcripts were isolated using a first streptavidin Dynabeads M-280 (Invitrogen Ref. 11206D) pull down, and the VRA3 RNA adaptor was ligated at their 3’ end. A second streptavidin bead pull down was performed, followed by the enzymatic modifications of the RNA fragment 5’ ends with a pyrophosphohydrolase and a polynucleotide kinase, and the VRA5 RNA adaptor was ligated at their fixed 5’ ends. A third streptavidin bead pull down was performed, followed by the reverse transcription of the resulting adaptor-ligated libraries. The libraries were cleaned up with AMPure XP beads (Beckman Coulter Ref. A63881). Then, the libraries were amplified using 13 PCR cycles, and cleaned up again with another round of AMPure XP beads. The resulting library concentrations were measured with the Qubit dsDNA high sensitivity assay (Invitrogen Ref. Q32851), and their size distributions assessed using the Agilent High Sensitivity D1000 ScreenTape. The 1st replicates were processed on 2021/01/01, the 2nd replicates were processed on 2021/03/02, the 3rd replicates (only Dave, Ethan, and Eric LCLs) were processed on 2022/06/21.

treatment_protocol: Each of the human LCLs were treated for 1 hour prior to the nuclei isolation with human IFN-β at 100 ng/mL (Kingfisher Biotech Ref. RP1788H-100 Lot. KU4428KU), or with BSA as negative control for a final concentration 0.00004% BSA, similar to that of the IFN-β treatments. 3 T-25 cultures per LCLs were used per treatment. The 1st replicates were processed on 2020/12/25, 2nd replicates were processed on 2021/03/01, and the 3rd replicates (only Dave, Ethan, and Eric LCLs) were processed on 2022/06/19. All cultures and treatments were processed in parallel.

value: Female

value: Lymphoblastoid cell line

value: WT

value: IFNB

tag: time

value: 1 hour


title: PRO-seq, HG03645, IFNB, 1 hour, rep 1


title: PRO-seq, HG03077, IFNB, 1 hour, rep 2

value: Male


title: ChIP-seq on OVCAR8 ko2 cells with BORIS antibodies

description: Library name: ChIP_OVCAR8_ko2_BORIS

value: High-Grade Serous Ovarian Carcinoma

value: homozygous deletion of ZF1-4 (Exon #4-5) in BORIS gene (clone#2, ko2)

value: CRISPR–Cas9 knockout of exon 4-5 of BORIS gene


title: ChIP-seq on OVCAR8 WT cells with SMC3 antibodies

description: Library name: ChIP_OVCAR8_WT_SMC3

value: wild type

value: rabbit polyclonal antibody against SMC3 (Abcam, ab#9263)


title: ChIP-seq on OVCAR8 WT cells with RAD21 antibodies

description: Library name: ChIP_OVCAR8_WT_RAD21

value: rabbit monoclonal antibody against RAD21 (Abcam, ab217678)


title: PRO-seq, HG03077, IFNB, 1 hour, rep 1


title: ChIP-seq on OVCAR8 WT cells with H3K4me3 antibodies

description: Library name: ChIP_OVCAR8_WT_H3K4me3

value: rabbit polyclonal to Histone H3 (tri methyl K4) (Abcam, ab8580)


title: PRO-seq, HG02150, IFNB, 1 hour, rep 2


title: 2B4/z, hCD45+mCD45-GFP+CD19+CD3-CD33-

description: Library name: 2B4/zGFPCD19

value: SPLEEN (NOG-w41 differentiated human cord-blood CD34+ cells)

value: CD19 antigen stimulation for 24 hours


title: ChIP-seq on OVCAR8 WT cells with H3K27ac antibodies

description: Library name: ChIP_OVCAR8_WT_H3K27ac

value: rabbit polyclonal to Histone H3 (acetyl K27) (Abcam, ab4729)


title: PRO-seq, HG02150, IFNB, 1 hour, rep 1


title: ChIP-seq on OVCAR8 WT cells with H2AZ antibodies

description: Library name: ChIP_OVCAR8_WT_H2AZ

value: rabbit polyclonal antibody against histone H2A.Z (Abcam, ab4174)


title: PRO-seq, GM19024, IFNB, 1 hour, rep 2

value: Female


title: Nur77_HA_Ctrl3

value: macrophages

value: untreated

value: HA (Diagenode, C15200190)


title: ChIP-seq on OVCAR8 WT cells with CTCF antibodies

description: Library name: ChIP_OVCAR8_WT_CTCF

value: mouse monoclonal antibody against CTCF (Santa Cruz, (B-5):sc-271514)


title: PRO-seq, GM19024, IFNB, 1 hour, rep 1

value: Lymphoblastoid cell line

value: WT

value: IFNB

value: 1 hour


title: PRO-seq, GM18530, IFNB, 1 hour, rep 2

value: Male


title: ChIP-seq on OVCAR8 WT cells with BORIS antibodies

description: Library name: ChIP_OVCAR8_WT_BORIS

value: High-Grade Serous Ovarian Carcinoma

value: wild type

value: rabbit recombinant monoclonal BORIS antibody (Abcam, EP12204)


title: Healthy_RNA_002

description: Library name: Healthy_RNA_002

value: Bone marrow

value: Healthy


title: iMSN C15, CELF5 siRNA, rep 6

city: Cambridge

first: Chesna

last: Apere

state: Massachusetts

address: 455 Main St

department: Biology

institute: Whitehead Institute for Biomedical Research

description:
Library name: C15_CELF5_6
Column name in Counts_gene_SCR_CELF5.txt: celf5_R6

data_processing:
Reads were filtered with FastQC (v0.11.9) and trimmed using fastp (v0.23.4). Trimmed reads were aligned to the GRCh38/hg38 reference genome with STAR (v2.7.1a).
Gene counts were obtained using featureCounts (v2.0.1) with GENCODE Release 46 gene annotations.
Differential gene expression analysis was performed using edgeR (v3.40.2).
Assembly: GRCh38/hg38
Supplementary files format and content: raw counts, txt format or tsv

source_name: AAVS1 dCas9-KRAB ZIM3 AG07657 iPSC clone

growth_protocol: See manuscript methods for details on iPSC differentiations

extract_protocol:
iMSNs were adherent and scraped into QIAzol directly from the tissue culture vessel. Total RNA was extracted with the QIAgen miRNeasy Mini kit protocol.
RNA libraries for RNA seq were prepared using Watchmaker-mRNA kit.

value: medium spiny neurons

value: CELF5 siRNA


title: PRO-seq, GM18530, IFNB, 1 hour, rep 1


title: iMSN C15, CELF5 siRNA, rep 5

description:
Library name: C15_CELF5_5
Column name in Counts_gene_SCR_CELF5.txt: celf5_R5

value: AAVS1 dCas9-KRAB ZIM3 AG07657 iPSC clone

value: Female


title: MDS_AZA_098

value: MDS patient

value: Responder


title: PRO-seq, GM18489, IFNB, 1 hour, rep 2


title: iMSN C15, CELF5 siRNA, rep 4

description:
Library name: C15_CELF5_4
Column name in Counts_gene_SCR_CELF5.txt: celf5_R4


title: iMSN C15, CELF5 siRNA, rep 3

description:
Library name: C15_CELF5_3
Column name in Counts_gene_SCR_CELF5.txt: celf5_R3


title: PRO-seq, GM18489, IFNB, 1 hour, rep 1


title: MDS_AZA_053


title: PRO-seq, GM12878, IFNB, 1 hour, rep 2


title: iMSN C15, CELF5 siRNA, rep 2

description:
Library name: C15_CELF5_2
Column name in Counts_gene_SCR_CELF5.txt: celf5_R2


title: PRO-seq, GM12878, IFNB, 1 hour, rep 1


title: iMSN C15, CELF5 siRNA, rep 1

description:
Library name: C15_CELF5_1
Column name in Counts_gene_SCR_CELF5.txt: celf5_R1


title: PRO-seq, Ethan, IFNB, 1 hour, rep 3

source_name: Ethan

value: Ethan

value: Trisomy 21


title: iMSN C15, Scr control, rep 6

description:
Library name: C15_SCR6
Column name in Counts_gene_SCR_CELF5.txt: scr_R6

value: scr control


title: PRO-seq, Ethan, IFNB, 1 hour, rep 2

value: Lymphoblastoid cell line

value: IFNB


title: iMSN C15, Scr control, rep 5

description:
Library name: C15_SCR5
Column name in Counts_gene_SCR_CELF5.txt: scr_R5


title: PRO-seq, Ethan, IFNB, 1 hour, rep 1

value: Male

value: 1 hour


title: iMSN C15, Scr control, rep 4

description:
Library name: C15_SCR4
Column name in Counts_gene_SCR_CELF5.txt: scr_R4


title: PRO-seq, Eric, IFNB, 1 hour, rep 3

source_name: Eric

value: Eric

value: WT


title: iMSN C15, Scr control, rep 3

description:
Library name: C15_SCR3
Column name in Counts_gene_SCR_CELF5.txt: scr_R3


title: PRO-seq, Eric, IFNB, 1 hour, rep 2


title: iMSN C15, Scr control, rep 2

description:
Library name: C15_SCR2
Column name in Counts_gene_SCR_CELF5.txt: scr_R2


title: PRO-seq, Eric, IFNB, 1 hour, rep 1


title: iMSN C6, CELF5 siRNA, rep 6

description:
Library name: C6_CELF5_6
Column name in Counts_gencode_CELF5i.tsv : celf5_R6

source_name: AG07657 iPSCs

value: AG07657 iPSCs


title: PRO-seq, Dave, IFNB, 1 hour, rep 3

source_name: Dave

value: Dave


title: iMSN C15, Scr control, rep 1

description:
Library name: C15_SCR1
Column name in Counts_gene_SCR_CELF5.txt: scr_R1

value: medium spiny neurons


title: iMSN C6, CELF5 siRNA, rep 5

description:
Library name: C6_CELF5_5
Column name in Counts_gencode_CELF5i.tsv : celf5_R5

value: CELF5 siRNA


title: PRO-seq, Dave, IFNB, 1 hour, rep 1


title: PRO-seq, Dave, IFNB, 1 hour, rep 2


title: iMSN C6, CELF5 siRNA, rep 4

description:
Library name: C6_CELF5_4
Column name in Counts_gencode_CELF5i.tsv : celf5_R4


title: A549 cells with siRNA knockdowns, proteins

description:
Library name: A549_siRNA_ADT
Antibody-derived oligonucleotide (ADT)


title: PRO-seq, HG03645, BSA, 1 hour, rep 2

value: BSA


title: iMSN C6, CELF5 siRNA, rep 3

description:
Library name: C6_CELF5_3
Column name in Counts_gencode_CELF5i.tsv : celf5_R3

value: Female


title: PRO-seq, HG03645, BSA, 1 hour, rep 1


title: iMSN C6, CELF5 siRNA, rep 2

description:
Library name: C6_CELF5_2
Column name in Counts_gencode_CELF5i.tsv : celf5_R2


title: 4-1BB/z, hCD45+mCD45-GFP-CD56+CD3-

description: Library name: 4-1BB/zCD56

value: SPLEEN (NOG-w41 differentiated human cord-blood CD34+ cells)

value: GFP-

value: CD19 antigen stimulation for 24 hours


title: PRO-seq, HG03077, BSA, 1 hour, rep 2


title: iMSN C6, CELF5 siRNA, rep 1

description:
Library name: C6_CELF5_1
Column name in Counts_gencode_CELF5i.tsv : celf5_R1


title: PRO-seq, HG03077, BSA, 1 hour, rep 1


title: iMSN C6, Scr control, rep 6

description:
Library name: C6_SCR6
Column name in Counts_gencode_CELF5i.tsv : scr_R6


title: PRO-seq, HG02150, BSA, 1 hour, rep 2


title: iMSN C6, Scr control, rep 4

description:
Library name: C6_SCR4
Column name in Counts_gencode_CELF5i.tsv : scr_R4


title: PRO-seq, HG02150, BSA, 1 hour, rep 1


title: iMSN C6, Scr control, rep 5

description:
Library name: C6_SCR5
Column name in Counts_gencode_CELF5i.tsv : scr_R5


title: 4-1BB/z, hCD45+mCD45-GFP+CD19+CD3-CD33-

description: Library name: 4-1BB/zGFPCD19


title: RNA-seq on OVCAR8 ko1 cells

description: Library name: RNA-seq_OVCAR8_ko1

value: High-Grade Serous Ovarian Carcinoma

value: homozygous deletion of ZF1-4 (Exon #4-5) in BORIS gene (clone#1, ko1)

value: CRISPR–Cas9 knockout of exon 4-5 of BORIS gene


title: PRO-seq, GM19024, BSA, 1 hour, rep 2

value: Lymphoblastoid cell line


title: iMSN C6, Scr control, rep 3

description:
Library name: C6_SCR3
Column name in Counts_gencode_CELF5i.tsv : scr_R3

value: scr control


title: PRO-seq, GM19024, BSA, 1 hour, rep 1

value: 1 hour


title: iMSN C6, Scr control, rep 2

description:
Library name: C6_SCR2
Column name in Counts_gencode_CELF5i.tsv : scr_R2


title: PRO-seq, GM18530, BSA, 1 hour, rep 2

value: Male


title: PRO-seq, GM18530, BSA, 1 hour, rep 1

value: WT


title: iMSN C6, Scr control, rep 1

description:
Library name: C6_SCR1
Column name in Counts_gencode_CELF5i.tsv : scr_R1

value: AG07657 iPSCs


title: PRO-seq, GM18489, BSA, 1 hour, rep 2


title: K562 5 day cold (4C) rep2

first: Tara

last: Thakurta

state: MA

address: 455 Main Street

institute: Whitehead Institute

description:
Library name: L511_186
core BL8; count-matrix column L511_186

data_processing:
Read alignment with STAR v2.7.1a (paired-end; --outSAMtype BAM SortedByCoordinate).
Gene-level read quantification with featureCounts (Subread).
Differential expression analysis with DESeq2 (R).
Assembly: Human (K562): GRCh38, Ensembl release 93 (Homo_sapiens.GRCh38.93.canonical). Hamster (BHK-21): BCM_Maur_2.0, GCF_017639785.1 (Mesocricetus auratus).
Supplementary files format and content: Tab-delimited gene-level raw count matrices (genes x samples): BHK21_featureCounts.matrix.txt (hamster BHK-21, 6 samples) and K562_raw_counts.matrix.txt (human K562, 9 samples). DESeq2 differential expression result tables (cold vs 37 C) are provided as supplementary processed files.

growth_protocol: Cell lines were maintained at 37 C, 5% CO2, and 95% relative humidity.

extract_protocol:
Cell pellets were lysed and homogenized using QIAshredder columns (Qiagen), and RNA was extracted using the RNeasy Mini Kit (Qiagen) with on-column DNase digestion, according to the manufacturer's instructions.
Libraries were prepared using the NEBNext Ultra II kit. In brief, 1 ug of RNA per sample underwent Poly(A) selection before fragmentation and random priming followed by first- and second-strand complementary DNA synthesis. Following cDNA synthesis, NEBNext Multiplex Oligos for Illumina (96 Unique Dual Index Primer Pairs, NEB E6441A) were ligated before PCR enrichment. All libraries were pooled to a final concentration of 2 nM and sequenced on a NovaSeq 6000.

treatment_protocol: For cold exposure experiments, cells were subsequently transferred to 4 C for up to 5 days. At the time of collection, cells were collected (with gentle scraping for adherent BHK-21 lines) and pelleted by centrifugation. Per-sample timepoints are given in the treatment column.

value: 5 day cold (4C)


title: K562 5 day cold (4C) rep3

description:
Library name: L511_187
core BL9; count-matrix column L511_187


title: PRO-seq, GM12878, BSA, 1 hour, rep 2


title: PRO-seq, GM18489, BSA, 1 hour, rep 1


title: K562 5 day cold (4C) rep1

description:
Library name: L511_185
core BL7; count-matrix column L511_185


title: K562 24 hour cold (4C) rep3

description:
Library name: L511_184
core BL6; count-matrix column L511_184

value: 24 hour cold (4C)


title: PRO-seq, GM12878, BSA, 1 hour, rep 1


title: PRO-seq, Ethan, BSA, 1 hour, rep 3

value: Ethan

value: Trisomy 21


title: K562 24 hour cold (4C) rep2

description:
Library name: L511_183
core BL5; count-matrix column L511_183


title: K562 24 hour cold (4C) rep1

description:
Library name: L511_182
core BL4; count-matrix column L511_182


title: PRO-seq, Ethan, BSA, 1 hour, rep 2

value: BSA


title: K562 37C control rep3

description:
Library name: L511_181
core BL3; count-matrix column L511_181

value: 37C control


title: PRO-seq, Eric, BSA, 1 hour, rep 3

value: Eric


title: PRO-seq, Ethan, BSA, 1 hour, rep 1


title: K562 37C control rep1

description:
Library name: L511_179
core BL1; count-matrix column L511_179


title: K562 37C control rep2

description:
Library name: L511_180
core BL2; count-matrix column L511_180


title: PRO-seq, Eric, BSA, 1 hour, rep 2


title: HiC 3hrs rep2 seq2

city: Mexico City

first: Mayra

last: Furlan-Magaril

state: Mexico City

address: Circuito exterior s/n

department: Molecular Genetics

country: Mexico

institute: IFC-UNAM

description: Library name: Sample 8

data_processing:
Hi-C experiments were processed following the HiC-Pro (v2.11.1) with default parameters. The alignment of the reads was performed with Bowtie2 v2.3.4.1 against the hg19 human genome. The normalized ICE matrices were generated with same number of valid pairs and computed at 20kb resolution.
Assembly: hg19
Supplementary files format and content: Tabular separated data with chromatin interactions counts

extract_protocol:
HiC in nuclei were performed with 2x106 cells. The cells were fixed with formaldehyde 2%. Chromatin was digested with HindIII enzyme for 0.25, 1, 3 and 12 hours. The 5′ overhangs were filled with dCTP, dGTP, dTTP and Biotin-14-dATP and re-ligated in nuclei. DNA fragments were purified and sonicated in COVARIS S220. The DNA were selected using Ampure SPRI Beads to get 300-600bp fragments. The pull-down was performed with Dynabeads MyOne Streptavidine C1.
The libraries were marked with Illumina TrueSeq DNA Adapters and amplified using Taq Phusion NEB. The paired-end sequencing was performed in a Illumina NovaSeq 6000.


title: PRO-seq, Eric, BSA, 1 hour, rep 1


title: HiC 3hrs rep1 seq2

description: Library name: Sample 7


title: PRO-seq, Dave, BSA, 1 hour, rep 3

value: Dave


title: PRO-seq, Dave, BSA, 1 hour, rep 2


title: HiC 1hr rep2 seq2

description: Library name: Sample 6


title: HiC 1hr rep1 seq2

description: Library name: Sample 5


title: PRO-seq, Dave, BSA, 1 hour, rep 1


title: HiC 12hrs rep2 seq2

description: Library name: Sample 4


title: 10E_minCHO_rep1_in

city: Barcelona

first: Elisabet

last: Tinto-Font

address: c/Rossello 153

department: Malaria

country: Spain

institute: ISGlobal

description:
Library name: 10E_minCHO_rep1_in
10E_minCHO_rep1_in

data_processing:
ChIP-seq data analysis was carried out using custom scripts written in Python (v3.7.16), as previously described (Michel-Todó, L., 2023. PMID: 36515553). ChIP-seq reads were trimmed using the bbduk command from BBmap (v36.99) software. The 3' end was trimmed if it had a quality score < 6 and reads shorter than 10 bp after trimming were discarded. Quality control of raw reads was performed using FastQC (v0.11.9) and contamination with non-P. falciparum reads was checked with FastqScreen (v0.14.0).  Bowtie2 (v2.4.5) was used to align reads to the Plasmodium falciparum 3D7 reference genome (PlasmoDB v67) using the parameters: --very-sensitive --local -5 4 -3 4 -I 50 -X 2000, which are different from the default ones. SAMtools (v1.15) was used for compressing, sorting and filtering-out < 5 mapping quality reads, from the alignment files. PCR duplicates were removed using GATK (v4.4.0.0) MarkDuplicates command. Normalized coverage (log₂-transformed enrichment of IP over input) was calculated at 10-bp resolution using the bamCompare function from DeepTools (v3.5.1), with the parameters: --normalizeUsing RPKM -bs 10 --smoothLength 200 --pseudocount 10. Negative values were set to -1 to avoid the detection of apparent differential coverage in non-heterochromatic regions. Normalized log₂(IP/input) coverage values were used to generate bedgraph tracks.
Assembly: Plasmodium falciparum 3D7 reference genome (PlasmoDB v67)
Supplementary files format and content: Bedgraph tracks (.bdg): normalized log₂(IP/input) coverage values

organism: Plasmodium falciparum

growth_protocol: Parasites were cultured in B+ or O+ erythrocytes at a 3% hematocrit under standard conditions in RPMI-1640-based media, supplemented with 0.5% Albumax II (Gibco, 11021037) and 2 mM choline chloride (Sigma-Aldrich, C7527), and maintained in a shaking incubator with a 5% CO₂, 3% O₂, and balance N₂ atmosphere. All cultures were kept at 37ºC, except for parasite lines in which pfap2-hs was disrupted and control cultures grown in parallel , which were maintained at 35ºC because at 37ºC they show reduced growth (Tintó-Font, E., et al., 2021; PMID:34400833). Tight synchronization to a 5 h age window was achieved by purification of late stages in 63% Percoll gradients (GE Healthcare, 17-0891-01) followed by sorbitol lysis 5 h later (Sigma-Aldrich, S3889). For ChIP-seq experiments, erythrocyte were filtered with Plasmodipur (R-Biopharm Nederland B.V., 8011FILTER) to remove leukocytes before using them for parasite cultures.

extract_protocol:
ChIP-seq was performed using tightly synchronized cultures at the mid-trophozoite stage: 33–38 hpi, or 37–42 hpi for the ap2-hs KO line, to account for their slower IDC progression (Tintó-Font, E., et al., 2021; PMID:34400833), unless otherwise stated. Chromatin was extracted from ~30–45 ml at ~2% parasitemia and immunoprecipitated as previously described (Llorà-Batlle, O., 2020. PMID: 32577509). Briefly, after saponin lysis and formaldehyde cross-linking, chromatin was extracted using the MAGnify Chromatin Immunoprecipitation System (Life Technologies, 492024). Sonication was performed with a Covaris M220 sonicator to generate ~150–200 bp fragments. For immunoprecipitation, 2 μg of chromatin and 4 μg of anti-H3K9me3 antibody (Diagenode, C15410193) were used. An equal sample was processed in parallel as input, with no immunoprecipitation. The resulting DNA was quantified using Qubit HS before library preparation.
Library preparation was performed using 5 ng of DNA, as previously described (Llorà-Batlle, O., 2020. PMID: 32577509). NEBNext multiplex oligonucleotides for Illumina (NEB, E7335, E7500 and E7710) were used, and 9 cycles of amplification were performed with the Kapa HiFi HotStart PCR kit (Roche, 7958889001). All purification steps were carried out using AMPure XP beads (Beckman Coulter, 082A63881). Quality and concentration of all libraries was determined using a Tapestation 4200 (Agilent). We obtained ~8-19 million 150 bp paired-end reads per sample using a NextSeq500 System (Illumina).

treatment_protocol: Sexual conversion was induced by three different methods: choline depletion, dihydroartemisinin (DHA; Sigma-Aldrich, D7439) treatment or heat shock (HS). For induction by choline depletion, the regular RPMI medium with Albumax II and a 2 mM choline supplement was replaced by the same medium without the choline supplement in cultures at the early ring stage (0-5 h post-invasion, hpi) and cultures were placed in static conditions in a hypoxia chamber for the rest of the experiment. For induction of sexual conversion by DHA or HS, tightly synchronized cultures (0-5 hpi) were placed in static conditions in a hypoxia chamber, and left undisturbed until the early trophozoite stage (25-30 hpi for most experiments; 29-34 hpi for experiments with transgenic lines in which ap2hs was disrupted, to account for their slower growth), when they were exposed to a 3 h of 10 nM DHA pulse or maintained for 3 h at 41.5 ºC (placing the full hypoxia chamber in an incubator at 41.5 ºC), respectively. After exposure, DHA was removed from the medium by centrifugation or cultures were placed back in an incubator at the normal growth temperature. Medium  was refreshed at ~33 hpi to all conditions. A control condition was always kept in parallel until the end of the experiment

value: choline depletion

tag: biological replicate


title: HiC 12hrs rep1 seq2

description: Library name: Sample 3


title: 10E_minCHO_rep1_IP

description:
Library name: 10E_minCHO_rep1_IP
10E_minCHO_rep1_IP

value: H3K9me3 (Diagenode, C15410193)


title: HiC 0.25hrs rep2 seq2

description: Library name: Sample 2


title: 10E_plusCHO_rep1_in

description:
Library name: 10E_plusCHO_rep1_in
10E_plusCHO_rep1_in

value: control choline


title: HiC 0.25hrs rep1 seq2

description: Library name: Sample 1


title: 10E_plusCHO_rep1_IP

description:
Library name: 10E_plusCHO_rep1_IP
10E_plusCHO_rep1_IP


title: MONO-MAC-6 A9 72 h_3_3

city: Gainesville

first: Chandra Kumar

last: Maharjan

state: Florida

address: 1333 Center Drive Rm BG003

department: Pathology, Immunology and Laboratory Medicine

institute: University of Florida

description:
Library name: Sample36
name in file: monomac72A3_3

data_processing:
Each sample was sequenced 3 times and pair-end. The sequencing data was aligned using kallisto. Zero expressing genes were removed from analysis. The DEG was analyzed using limma package in R and pathway analysis was done using GSEA.
Assembly: Alignment was done using kallisto using homo sapiens GRCh38
Supplementary files format and content: The processed data is in tab-delimited txt format, The files contain samples names with their transcripts per million (TPM)

source_name: Cell line

growth_protocol: MOLM-13 and MONO-MAC-6 cells were maintained in RPMI medium supplemented with 10% FBS and antibiotics in humidified atmosphere with 5% CO2 and 37 C

extract_protocol:
RNA was harvested using NucleoSpin RNA, Mini kit from Macherey-Nagel and at least 900 ng per sample was used for library preparation
RNA was sent to the University of Florida Interdisciplinary Center for Biotechnology Research Gene Expression and Genotyping Core (RRID: SCR_019145). RNA concentration was determined by Qubit and quality was determined using a Bioanalyzer RNA assay. Samples with a RIN score ≥ 8 were used for library preparation. Library preparation was done using the NEBNext Poly(A) mRNA isolation module (New England Biolabs) and NEBNext Ultra II Library prep Kit (New England Biolabs). Libraries were sequenced at 150 paired end reads at 25 million reads/sample using an Illumina Novaseq 6000 (Illumina)

treatment_protocol: Cells were treated with DMSO or A9 PROTAC (at 0.125 uM for MOLM-13 and 0.25 uM for MONO-MAC-6) cells for 72 before RNA isolation

value: Cell line

value: AML

value: A9 PROTAC


title: 10E_ap2hsKO_minCHO_rep1_in

description:
Library name: 10E_ap2hsKO_minCHO_rep1_in
10E_ap2hsKO_minCHO_rep1_in

value: ap2-hs knockout


title: MONO-MAC-6 A9 72 h_3_2

description:
Library name: Sample35
name in file: monomac72A3_2

value: WT


title: 10E_ap2hsKO_minCHO_rep1_IP

description:
Library name: 10E_ap2hsKO_minCHO_rep1_IP
10E_ap2hsKO_minCHO_rep1_IP


title: 10E_ap2hsKO_plusCHO_rep1_in

description:
Library name: 10E_ap2hsKO_plusCHO_rep1_in
10E_ap2hsKO_plusCHO_rep1_in


title: MONO-MAC-6 A9 72 h_3_1

description:
Library name: Sample34
name in file: monomac72A3_1


title: MONO-MAC-6 A9 72 h_2_3

description:
Library name: Sample33
name in file: monomac72A2_3


title: 10E_ap2hsKO_plusCHO_rep1_IP

description:
Library name: 10E_ap2hsKO_plusCHO_rep1_IP
10E_ap2hsKO_plusCHO_rep1_IP


title: MONO-MAC-6 A9 72 h_2_2

description:
Library name: Sample32
name in file: monomac72A2_2


title: 10E, minCHO, rep2

description:
Library name: 10E_minCHO_rep2
10E, minCHO, rep2

data_processing:
RNA-seq data analysis was carried out using custom scripts written in Python (v3.11.5) and R (v4.3.2). Trimming, quality control and contamination check of raw reads were performed as for ChIP-seq. Trimmed reads were mapped to the P. falciparum 3D7 reference transcriptome (PlasmoDB v67) using STAR (v2.7.10b) with the following parameters: --outFilterType Normal --outFilterMultimapNmax 20 --outMultimapperOrder Random --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax 0.05 --alignIntronMin 20 --alignIntronMax 5000 --alignMatesGapMax 10000. Alignments were sorted, compressed and indexed using SAMtools (v1.15).  Gene-level quantification was performed using featureCounts (Rsubread v2.16.1), based on the GTF annotation file from PlasmoDB (v67).
Assembly: Plasmodium falciparum 3D7 reference genome (PlasmoDB v67)
Supplementary files format and content: Raw counts: gene-level quantification in counts. Tab-separated file.

extract_protocol:
RNA was harvested from  tyghtly synchronized cultures at the mid trophozoite stage (33–38 hpi, unless stated otherwise) at ~2 % parasitemia using 20 pellet volumes of TRIrizol (Life Technologies, 15596018). RNA of ap2-hs KO was collected at 37-42 hpi to account for their slower IDC progression (Tintó-Font, E., et al., 2021; PMID:34400833). RNA extraction and treatment with DNase was performed as previously described [Casas-Vila, N., Pickford, A., et al. 2021. PMID: 34313989]. rRNA depletion of 5 μg of RNA was performed using the Rneasy Pure mRNA Bead Kit (Qiagen, 180244) following manufacturers’ instructions, and eluted in 18 μl of nuclease-free water. rRNA-depleted RNA was fragmented to ~100-400 bp using the NEBNext Magnesium RNA Fragmentation Module (NEB, E6150S), by adding 2 μl of fragmentation buffer, incubating for 4 min at 94 ºC, placing on ice and immediately adding 2 μl of stop solution. Fragmented RNA was cleaned up using the RNeasy MinElute CleanUp Kit (Qiagen, 74204) and eluted in 11 μl of nuclease-free water. For the first-strand cDNA synthesis, the SuperScript III Reverse Transcriptase kit (Invitrogen, 18080093) was used. Each sample was pre-incubated for 10 min at 70 ºC with 1.25 μl of AT-biased random primers (IDT) and 1 μl of actinomycin (Gibco, 11805017) and then for 2 min at 37 ºC with 8 μl of mastermix containing 1x first-strand buffer, 25 mM DTT, 1.25 mM dNTP (NEB, N0447S) and 1 μl RNasin Plus Ribonuclease inhibitor (40 U/ μl) (Promega, N2611).Next, 1 μl of Superscript III (200 U/ μl) was added to each sample, and incubated for 10 min at 37 ºC, followed by 1 h at 42 ºC. Second-strand cDNA synthesis was achieved by incubating the product of the previous reaction for 2 h at 16 ºC with 55 μl of a mastermix containing 1x second-strand buffer (Invitrogen, 10812014), 0.27 mM dNTP custom mix (10 mM dACG/dU) (Invitrogen, 10297018; Thermo Scientific, R0133), 0.1 μl Ambion RNase H (10 U/μl) (Invitrogen, AM2292), 2 μl DNA Polymerase I (10 U/μl) (Promega, M205A) and 0.5 μl E. coli DNA ligase (10 U/μl) (NEB, M0205S). The final cleanup was performed using the MinElute PCR purification kit (Qiagen, 28006), eluting in 10 μl nuclease-free water. The resultant cDNA was quantified by Qubit HS before library preparation.
Library preparation was performed using 5 ng of DNA, as previously described (Llorà-Batlle, O., 2020. PMID: 32577509). NEBNext multiplex oligonucleotides for Illumina (NEB, E7335, E7500 and E7710) were used, and 9 cycles of amplification were performed with the Kapa HiFi HotStart PCR kit (Roche, 7958889001). All purification steps were carried out using AMPure XP beads (Beckman Coulter, 082A63881). Quality and concentration of all libraries was determined using a Tapestation 4200 (Agilent). We obtained ~8-19 million 150 bp paired-end reads per sample using a NextSeq500 System (Illumina).


title: MONO-MAC-6 A9 72 h_2_1

description:
Library name: Sample31
name in file: monomac72A2_1


title: 10E, plusCHO, rep2

description:
Library name: 10E_plusCHO_rep2
10E, plusCHO, rep2


title: 10E_ap2hs_KO, minCHO, rep2

description:
Library name: 10E_ap2hs_KO_minCHO_rep2
10E_ap2hs_KO, minCHO, rep2


title: MONO-MAC-6 A9 72 h_1_3

description:
Library name: Sample30
name in file: monomac72A1_3


title: MONO-MAC-6 A9 72 h_1_2

description:
Library name: Sample29
name in file: monomac72A1_2


title: 10E_ap2hs_KO, plusCHO, rep2

description:
Library name: 10E_ap2hs_KO_plusCHO_rep2
10E_ap2hs_KO, plusCHO, rep2


title: MONO-MAC-6 A9 72 h_1_1

description:
Library name: Sample28
name in file: monomac72A1_1


title: 10E, minCHO, rep1

description:
Library name: 10E_minCHO_rep1
10E, minCHO, rep1


title: MONO-MAC-6 DMSO 72 h_3_3

description:
Library name: Sample27
name in file: monomac72V3_3

value: Vehicle


title: 10E, plusCHO, rep1

description:
Library name: 10E_plusCHO_rep1
10E, plusCHO, rep1


title: 10E_ap2hs_KO, minCHO, rep1

description:
Library name: 10E_ap2hs_KO_minCHO_rep1
10E_ap2hs_KO, minCHO, rep1


title: MONO-MAC-6 DMSO 72 h_3_2

description:
Library name: Sample26
name in file: monomac72V3_2


title: MONO-MAC-6 DMSO 72 h_3_1

description:
Library name: Sample25
name in file: monomac72V3_1


title: 10E_ap2hs_KO, plusCHO, rep1

description:
Library name: 10E_ap2hs_KO_plusCHO_rep1
10E_ap2hs_KO, plusCHO, rep1


title: MONO-MAC-6 DMSO 72 h_2_3

description:
Library name: Sample24
name in file: monomac72V2_3


title: ap2hs_KO, minCHO, rep2

description:
Library name: ap2hs_KO_minCHO_rep2
ap2hs_KO_minCHO_rep2


title: MONO-MAC-6 DMSO 72 h_2_2

description:
Library name: Sample23
name in file: monomac72V2_2


title: ap2hs_KO, plusCHO, rep2

description:
Library name: ap2hs_KO_plusCHO_rep2
ap2hs_KO_plusCHO_rep2


title: ap2hs_KO, minCHO, rep1

description:
Library name: ap2hs_KO_minCHO_rep1
ap2hs_KO_minCHO_rep1


title: MONO-MAC-6 DMSO 72 h_2_1

description:
Library name: Sample22
name in file: monomac72V2_1


title: MONO-MAC-6 DMSO 72 h_1_3

description:
Library name: Sample21
name in file: monomac72V1_3


title: ap2hs_KO, plusCHO, rep1

description:
Library name: ap2hs_KO_plusCHO_rep1
ap2hs_KO_plusCHO_rep1


title: MONO-MAC-6 DMSO 72 h_1_2

description:
Library name: Sample20
name in file: monomac72V1_2


title: F12, minCHO, rep2

description:
Library name: F12_minCHO_rep2
F12_minCHO_rep2


title: MONO-MAC-6 DMSO 72 h_1_1

description:
Library name: Sample19
name in file: monomac72V1_1


title: F12, plusCHO, rep2

description:
Library name: F12_plusCHO_rep2
F12_plusCHO_rep2


title: MOLM-13 A9 72 h_3_3

description:
Library name: Sample18
name in file: molm72hA3_3


title: F12, minCHO, rep1

description:
Library name: F12_minCHO_rep1
F12_minCHO_rep1


title: MOLM-13 A9 72 h_3_2

description:
Library name: Sample17
name in file: molm72hA3_2


title: F12, plusCHO, rep1

description:
Library name: F12_plusCHO_rep1
F12_plusCHO_rep1


title: gdv1as_shKO, minCHO, rep2

description:
Library name: gdv1as_shKO_minCHO_rep2
gdv1as_shKO_minCHO_rep2

value: gdv1-as knockout


title: MOLM-13 A9 72 h_3_1

description:
Library name: Sample16
name in file: molm72hA3_1


title: MOLM-13 A9 72 h_2_3

description:
Library name: Sample15
name in file: molm72hA2_3


title: gdv1as_shKO, plusCHO, rep2

description:
Library name: gdv1as_shKO_plusCHO_rep2
gdv1as_shKO_plusCHO_rep2


title: MOLM-13 A9 72 h_2_2

description:
Library name: Sample14
name in file: molm72hA2_2


title: gdv1as_shKO, minCHO, rep1

description:
Library name: gdv1as_shKO_minCHO_rep1
gdv1as_shKO_minCHO_rep1


title: MOLM-13 A9 72 h_1_3

description:
Library name: Sample12
name in file: molm72hA1_3


title: gdv1as_shKO, plusCHO, rep1

description:
Library name: gdv1as_shKO_plusCHO_rep1
gdv1as_shKO_plusCHO_rep1


title: MOLM-13 A9 72 h_2_1

description:
Library name: Sample13
name in file: molm72hA2_1


title: gdv1_KO, minCHO, rep2

description:
Library name: gdv1_KO_minCHO_rep2
gdv1_KO_minCHO_rep2

value: gdv1 knockout


title: MOLM-13 A9 72 h_1_2

description:
Library name: Sample11
name in file: molm72hA1_2


title: MOLM-13 A9 72 h_1_1

description:
Library name: Sample10
name in file: molm72hA1_1


title: gdv1_KO, plusCHO, rep2

description:
Library name: gdv1_KO_plusCHO_rep2
gdv1_KO_plusCHO_rep2


title: gdv1_KO, minCHO, rep1

description:
Library name: gdv1_KO_minCHO_rep1
gdv1_KO_minCHO_rep1


title: gdv1_KO, plusCHO, rep1

description:
Library name: gdv1_KO_plusCHO_rep1
gdv1_KO_plusCHO_rep1


title: MOLM-13 DMSO 72 h_3_3

description:
Library name: Sample9
name in file: molm72hV3_3


title: gdv1as_OE, minCHO, rep2

description:
Library name: gdv1as_OE_minCHO_rep2
gdv1as_OE_minCHO_rep2

value: gdv1-as overexpression


title: MOLM-13 DMSO 72 h_3_2

description:
Library name: Sample8
name in file: molm72hV3_2


title: MOLM-13 DMSO 72 h_3_1

description:
Library name: Sample7
name in file: molm72hV3_1


title: MOLM-13 DMSO 72 h_2_3

description:
Library name: Sample6
name in file: molm72hV2_3


title: gdv1as_OE, minCHO, rep1

description:
Library name: gdv1as_OE_minCHO_rep1
gdv1as_OE_minCHO_rep1


title: gdv1as_OE, plusCHO, rep2

description:
Library name: gdv1as_OE_plusCHO_rep2
gdv1as_OE_plusCHO_rep2


title: MOLM-13 DMSO 72 h_2_2

description:
Library name: Sample5
name in file: molm72hV2_2


title: gdv1as_OE, plusCHO, rep1

description:
Library name: gdv1as_OE_plusCHO_rep1
gdv1as_OE_plusCHO_rep1


title: MOLM-13 DMSO 72 h_2_1

description:
Library name: Sample4
name in file: molm72hV2_1


title: gdv1as_KO, minCHO, rep2

description:
Library name: gdv1as_KO_minCHO_rep2
gdv1as_KO_minCHO_rep2


title: MOLM-13 DMSO 72 h_1_3

description:
Library name: Sample3
name in file: molm72hV1_3


title: gdv1as_KO, plusCHO, rep2

description:
Library name: gdv1as_KO_plusCHO_rep2
gdv1as_KO_plusCHO_rep2


title: MOLM-13 DMSO 72 h_1_2

description:
Library name: Sample2
name in file: molm72hV1_2


title: gdv1as_KO, minCHO, rep1

description:
Library name: gdv1as_KO_minCHO_rep1
gdv1as_KO_minCHO_rep1


title: gdv1as_KO, plusCHO, rep1

description:
Library name: gdv1as_KO_plusCHO_rep1
gdv1as_KO_plusCHO_rep1


title: MOLM-13 DMSO 72 h_1_1

description:
Library name: Sample1
name in file: molm72hV1_1


title: 1.2Bcorr, minCHO rep2

description:
Library name: 1.2Bcorr_minCHO rep2
1.2Bcorr_minCHO rep2

value: gdv1 fixed


title: LV_d7.5_KO_cl14_R1

city: Vienna

first: Stefan

middle: M.

last: Jahnel

address: Dr. Bohrgasse 3

country: Austria

institute: IMBA

description: Library name: 223066_7.5_KO-7.5_cl14_R1

data_processing:
Initial R1 read processing was performed using BBDuk v38.06 by removing adapter, polyA and low-quality bases from the 3' end (ref=polyA.fa.gz,truseq.fa.gz k=13 ktrim=r useshortkmers=t mink=5 qtrim=r trimq=10 minlength=20) and filtering for abundant sequences included in the iGenomes UCSC hg38 reference (human rDNA, human mitochondrial chromosome, phiX174 genome, adapter) (k=31). The processed R1 reads were analyzed using genome and gene annotation for the GRCh38 assembly obtained from Homo sapiens Ensembl release 94. Reads were aligned to the genome using star v2.6.0c and reads in genes were counted with featureCounts (subread v1.6.2).
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file with raw counts for each sample

source_name: cardiac (cardioid)

growth_protocol: Generation of cardioids To generate cardioids, hPSCs at ~70% confluency were seeded at 25-35k cells per well (24-well plates, TPP #92024) in E8 + ROCKi (5 µM). 24 hours after seeding (d0) cells were induced using mesoderm induction media. 36-40 hours later (d1.5) cells were dissociated using 2 minutes incubation in TrypLE Express and reseeded into ultra-low attachment 96-well plates (Corning #7007) at 15-20k cells/well in Cardiac Mesoderm Patterning Media 1 supplemented with ROCKi (5 µM). After seeding, cells were spun down at 200g for 4 minutes. 24 hours later (d2.5) media was replaced with Cardiac Mesoderm Patterning Media 1 without ROCKi. The following two days (d3.5-d4.5) medium was changed daily to Cardiac Mesoderm Patterning Media 2. For the subsequent two days medium was changed daily to Cardiomyocyte Differentiation Media. All media formulations are described below.  Cardioid compartment-specific differentiation media All differentiation media are based on chemically defined medium (CDM) consisting of 5 mg/ml bovine serum albumin (Europa BiosciencesEQBAH70) in 50% IMDM (Gibco #21980065) plus 50% Ham’s F12 Nutrient-MIX (Gibco #31765068), supplemented with 1% concentrated Lipids (Gibco #11905031) 0.004% Monothioglycerol (Sigma #M6145-100ML) and 15 mg/ml of Transferrin (Roche #10652202001), 1X Antibiotic-Antimycotic (Thermo Scientific #15240062).  Mesoderm Induction Media (d0-d1.5) Left ventricular cardioid (LV): CDM containing FGF2-G3 (5.5 ng/mL, Qk053), LY294002 (5 µM, Tocris #1130), Activin A (5ng/ml, Cambridge University), BMP4 (10 ng/ml, R&D Systems RD-314-BP-050), and CHIR99021 (3 µM, R&D Systems RD-4423/50) Atrial cardioid (A): CDM containing FGF2-G3 (5.5 ng/mL), LY294002 (5 µM), Activin A (50 ng/ml), BMP4 (10 ng/ml), and CHIR99021 (4 µM)  Cardiac Mesoderm Patterning Media 1 (d1.5-d3.5) LV: CDM containing BMP4 (10 ng/ml), FGF2-G3 (1.466 ng/mL), Insulin (10 µg/ml), C59 (2 µM, Tocris #5148/10) and Retinoic Acid (50 nM, Sigma Aldrich #R2625). A: CDM containing SB 431542 (10 µM, Tocris #1614), XAV939 (5 µM, SelleckChem #S1180) and Retinoic Acid (500 nM).  Cardiac Mesoderm Patterning Media 2 (d3.5-d5.5) LV: CDM containing BMP4 (10 ng/ml), FGF2-G3 (1.466 ng/mL), Insulin (10 µg/ml), C59 (2 µM) and Retinoic Acid (50 nM). A: CDM containing BMP4 (10 ng/ml), FGF2-G3 (1.466 ng/mL), Insulin (10 µg/ml), XAV939 (5 µM) and Retinoic Acid (500 nM).  Co-development Patterning Media (d3.5-d5.5) CDM containing BMP4 (10 ng/ml), FGF2-G3 (1.466 ng/mL), Insulin (10 µg/ml), C59 (2 µM) and Retinoic Acid (500 nM).  Cardiomyocyte Differentiation Media (d5.5-d7.5) LV&A: CDM containing BMP4 (10 ng/ml), FGF2-G3 (1.466 ng/mL) and Insulin (10 µg/ml)

extract_protocol:
A total of 8 cardioids were pooled per replicate and condition. For each condition cardioids from at least 3 biological replicates were included. RNA was extracted using an in-house RNA bead isolation kit semi-automated using KingFisher devices (KingFisher Duo Prime).
Libraries were prepared according to the manufacturer’s instruction using QuantSeq 3‘ mRNA-Seq Library Prep Kit for Illumina (FWD) (Lexogen #015). Samples were checked for adequate size distribution with a fragment analyzer (Advanced Analytical Technologies, Inc). The RNA-seq library was submitted to the Vienna Biocenter Core Facilities (VBCF) Next-Generation-Sequencing (NGS) facility for sequencing (NovaSeq SP SR100 XP).

value: cardiac (cardioid)

value: iPSC WTC-11

value: cardiomyocytes

value: cardioid differentiation


title: LV_d7.5_KO_cl4_R3

description: Library name: 223064_7.5_KO-7.5_cl4_R3


title: 1.2Bcorr, plusCHO rep2

description:
Library name: 1.2Bcorr_plusCHO rep2
1.2Bcorr_plusCHO rep2


title: LV_d4.5_WT_TNT2

description: Library name: 223063_4.5_WT-4.5_TNT2

value: cardiac progenitor


title: 1.2Bcorr, minCHO, rep1

description:
Library name: 1.2Bcorr_minCHO_rep1
1.2Bcorr_minCHO_rep1

value: choline depletion


title: LV_d4.5_KO_cl51_R1

description: Library name: 223062_4.5_KO-4.5_cl51_R1


title: 1.2Bmut, minCHO rep2

description:
Library name: 1.2Bmut_minCHO rep2
1.2Bmut_minCHO rep2

value: gdv1 mutation


title: LV_d4.5_KO_cl46_R1

description: Library name: 223061_4.5_KO-4.5_cl46_R1


title: 1.2Bcorr, plusCHO, rep1

description:
Library name: 1.2Bcorr_plusCHO_rep1
1.2Bcorr_plusCHO_rep1

value: control choline


title: 1.2Bmut, plusCHO rep2

description:
Library name: 1.2Bmut_plusCHO rep2
1.2Bmut_plusCHO rep2


title: LV_d4.5_WT_cl43_WT_UT

description: Library name: 223060_4.5_WT-4.5_cl43_WT_UT


title: LV_d4.5_KO_cl14_R1

description: Library name: 223059_4.5_KO-4.5_cl14_R1


title: 1.2Bmut, minCHO, rep1

description:
Library name: 1.2Bmut_minCHO_rep1
1.2Bmut_minCHO_rep1


title: 1.2Bmut, plusCHO, rep1

description:
Library name: 1.2Bmut_plusCHO_rep1
1.2Bmut_plusCHO_rep1


title: NF54, 38hpi, minCHO

description:
Library name: NF54_38hpi_minCHO
NF54_38hpi_minCHO


title: LV_d4.5_KO_cl4_R3

description: Library name: 223057_4.5_KO-4.5_cl4_R3


title: LV_d2.5_WT_TNT2

description: Library name: 223056_2.5_WT-2.5_TNT2


title: LV_d2.5_KO_cl51_R1

description: Library name: 223055_2.5_KO-2.5_cl51_R1


title: NF54, 38hpi, plusCHO

description:
Library name: NF54_38hpi_plusCHO
NF54_38hpi_plusCHO


title: LV_d2.5_KO_cl46_R1

description: Library name: 223054_2.5_KO-2.5_cl46_R1


title: NF54, 33hpi, minCHO

description:
Library name: NF54_33hpi_minCHO
NF54_33hpi_minCHO


title: LV_d2.5_WT_cl43_WT_UT

description: Library name: 223053_2.5_WT-2.5_cl43_WT_UT


title: LV_d2.5_KO_cl14_R1

description: Library name: 223052_2.5_KO-2.5_cl14_R1


title: NF54, 23hpi, minCHO

description:
Library name: NF54_23hpi_minCHO
NF54_23hpi_minCHO


title: NF54, 33hpi, plusCHO

description:
Library name: NF54_33hpi_plusCHO
NF54_33hpi_plusCHO


title: LV_d2.5_KO_cl4_R3

description: Library name: 223050_2.5_KO-2.5_cl4_R3


title: LV_d1.5_WT_TNT2

description: Library name: 223049_1.5_WT-1.5_TNT2


title: NF54, 23hpi, plusCHO

description:
Library name: NF54_23hpi_plusCHO
NF54_23hpi_plusCHO


title: NF54, 10hpi, minCHO

description:
Library name: NF54_10hpi_minCHO
NF54_10hpi_minCHO


title: LV_d1.5_KO_cl51_R1

description: Library name: 223048_1.5_KO-1.5_cl51_R1


title: LV_d1.5_KO_cl46_R1

description: Library name: 223047_1.5_KO-1.5_cl46_R1


title: NF54, 10hpi, plusCHO

description:
Library name: NF54_10hpi_plusCHO
NF54_10hpi_plusCHO


title: NF54, HS, rep2

description:
Library name: NF54_HS_rep2
NF54_HS_rep2

value: heat shock exposure


title: LV_d1.5_WT_cl43_WT_UT

description: Library name: 223046_1.5_WT-1.5_cl43_WT_UT


title: NF54, ctrl, rep2

description:
Library name: NF54_ctrl_rep2
NF54_ctrl_rep2

value: control heat shock


title: LV_d1.5_KO_cl14_R1

description: Library name: 223045_1.5_KO-1.5_cl14_R1


title: LV_d1.5_KO_cl4_R3

description: Library name: 223043_1.5_KO-1.5_cl4_R3


title: NF54, HS, rep1

description:
Library name: NF54_HS_rep1
NF54_HS_rep1


title: NF54 ctrl, rep1

description:
Library name: NF54 ctrl_rep1
NF54 ctrl_rep1


title: LV_d7.5_HAse_d2.5-7.5_TNNT2_R3

description: Library name: 223042_7.5_HAse_d2.5-7.5_HAse_d2.5_TNT2


title: NF54, plusDHA, rep3

description:
Library name: NF54_plusDHA_rep3
NF54_plusDHA_rep3

value: DHA treatment


title: LV_d7.5_HAse_d1.5-7.5_TNNT2_R3

description: Library name: 223041_7.5_HAse_d1.5-7.5_HAse_d1.5_TNT2

value: WT


title: NF54, plusDHA, rep2

description:
Library name: NF54_plusDHA_rep2
NF54_plusDHA_rep2


title: LV_d7.5_untreated_TNNT2_R3

description: Library name: 223040_7.5_HAse-7.5_HAse_ctrl_TNT2


title: NF54, minDHA, rep2

description:
Library name: NF54_minDHA_rep2
NF54_minDHA_rep2

value: control DHA


title: LV_d4.5_HAse_d2.5-4.5_TNNT2_R3

description: Library name: 223039_4.5_HAse_d2.5-4.5_HAse_d2.5_TNT2


title: NF54plusDHA, rep4

description:
Library name: NF54plusDHA_rep4
NF54plusDHA_rep4


title: LV_d4.5_HAse_d1.5-4.5_TNNT2_R3

description: Library name: 223038_4.5_HAse_d1.5-4.5_HAse_d1.5_TNT2


title: NF54minDHA, rep4

description:
Library name: NF54minDHA_rep4
NF54minDHA_rep4


title: LV_d4.5_untreated_TNNT2_R3

description: Library name: 223037_4.5_HAse-4.5_HAse_ctrl_TNT2


title: A7, minCHO, rep2

description:
Library name: A7_minCHO_rep2
A7_minCHO_rep2


title: LV_d2.5_HAse_d1.5-2.5_TNNT2_R3

description: Library name: 223036_2.5_HAse_d1.5-2.5_HAse_d1.5_TNT2


title: LV_d7.5_HAse_d2.5-7.5_WT_R2

description: Library name: 223034_7.5_HAse_d2.5-7.5_HAse_d2.5_WT


title: A7, minCHO, rep1

description:
Library name: A7_minCHO_rep1
A7_minCHO_rep1


title: A7, plusCHO, rep2

description:
Library name: A7_plusCHO_rep2
A7_plusCHO_rep2


title: A7, plusCHO, rep1

description:
Library name: A7_plusCHO_rep1
A7_plusCHO_rep1


title: LV_d7.5_HAse_d1.5-7.5_WT_R2

description: Library name: 223033_7.5_HAse_d1.5-7.5_HAse_d1.5_WT


title: LV_d2.5_untreated_TNNT2_R3

description: Library name: 223035_2.5_HAse-2.5_HAse_TNT2


title: E5, minCHO, rep2

description:
Library name: E5_minCHO_rep2
E5_minCHO_rep2


title: E5, plusCHO, rep2

description:
Library name: E5_plusCHO_rep2
E5_plusCHO_rep2


title: LV_d7.5_untreated_WT_R2

description: Library name: 223032_7.5_HAse-7.5_HAse_ctrl_WT


title: E5, minCHO, rep1

description:
Library name: E5_minCHO_rep1
E5_minCHO_rep1


title: LV_d4.5_HAse_d1.5-4.5_WT_R2

description: Library name: 223030_4.5_HAse_d1.5-4.5_HAse_d1.5_WT


title: LV_d4.5_HAse_d2.5-4.5_WT_R2

description: Library name: 223031_4.5_HAse_d2.5-4.5_HAse_d2.5_WT


title: E5, plusCHO, rep1

description:
Library name: E5_plusCHO_rep1
E5_plusCHO_rep1


title: LV_d4.5_untreated_WT_R2

description: Library name: 223029_4.5_HAse-4.5_HAse_ctrl_WT


title: NF54, minCHO, rep3

description:
Library name: NF54_minCHO_rep3
NF54_minCHO_rep3


title: LV_d2.5_HAse_d1.5-2.5_WT_R2

description: Library name: 223028_2.5_HAse_d1.5-2.5_HAse_d1.5_WT


title: NF54, plusCHO, minDHA, rep3

description:
Library name: NF54_plusCHO_minDHA_rep3
NF54_plusCHO_rep3

value: control choline, control DHA


title: LV_d2.5_untreated_WT_R2

description: Library name: 223027_2.5_HAse-2.5_HAse_WT


title: NF54, minCHO, rep2

description:
Library name: NF54_minCHO_rep2
NF54_minCHO_rep2


title: LV_d7.5_HAse_d2.5-7.5_TNNI1_R1

description: Library name: 223026_7.5_HAse_d2.5-7.5_HAse_d2.5_TNI1


title: LV_d7.5_HAse_d1.5-7.5_TNNI1_R1

description: Library name: 223025_7.5_HAse_d1.5-7.5_HAse_d1.5_TNI1


title: NF54, plusCHO, rep2

description:
Library name: NF54_plusCHO_rep2
NF54_plusCHO_rep2


title: LV_d7.5_untreated_TNNI1_R1

description: Library name: 223024_7.5_HAse-7.5_HAse_ctrl_TNI1


title: NF54, minCHO, rep1

description:
Library name: NF54_minCHO_rep1
NF54_minCHO_rep1


title: NF54, plusCHO, rep1

description:
Library name: NF54_plusCHO_rep1
NF54_plusCHO_rep1


title: LV_d4.5_HAse_d2.5-4.5_TNNI1_R1

description: Library name: 223023_4.5_HAse_d2.5-4.5_HAse_d2.5_TNI1


title: PNG_plusCHO_in

description: Library name: PNG_plusCHO_in

source_name: Field Isolate PNG

treatment_protocol: Sexual conversion was induced by three different methods: choline depletion, dihydroartemisinin (DHA; Sigma-Aldrich, D7439) treatment or heat shock (HS). For induction by choline depletion, the regular RPMI medium with Albumax II and a 2 mM choline supplement was replaced by the same medium without the choline supplement in cultures at the early ring stage (0-5 h post-invasion, hpi) and cultures were placed in static conditions in a hypoxia chamber for the rest of the experiment. For induction of sexual conversion by DHA or HS, tightly synchronized cultures (0-5 hpi) were placed in static conditions in a hypoxia chamber, and left undisturbed until the early trophozoite stage (25-30 hpi for most experiments; 30-35 hpi for proteomics experiments; 29-34 hpi for experiments with transgenic lines in which ap2hs was disrupted, to account for their slower growth), when they were exposed to a 3 h of 10 nM DHA pulse or maintained for 3 h at 41.5 ºC (placing the full hypoxia chamber in an incubator at 41.5 ºC), respectively. After exposure, DHA was removed from the medium by centrifugation or cultures were placed back in an incubator at the normal growth temperature. Medium  was refreshed at ~33 hpi to all conditions. A control condition was always kept in parallel until the end of the experiment

value: Field Isolate PNG


title: LV_d4.5_HAse_d1.5-4.5_TNNI1_R1

description: Library name: 223022_4.5_HAse_d1.5-4.5_HAse_d1.5_TNI1


title: PNG_plusCHO_IP

description: Library name: PNG_plusCHO_IP

value: H3K9me3 (Diagenode, C15410193)


title: ap2hsKOminCHO_rep2_in

description: Library name: ap2hsKOminCHO_rep2_in

value: ap2-hs knockout


title: LV_d4.5_untreated_TNNI1_R1

description: Library name: 223021_4.5_HAse-4.5_HAse_ctrl_TNI1

value: cardiac (cardioid)


title: Dd2_plusCHO_in

description: Library name: Dd2_plusCHO_in


title: ap2hsKOminCHO_rep2_IP

description: Library name: ap2hsKOminCHO_rep2_IP


title: LV_d7.5_WT_WT_TU_R2

description: Library name: 223016_7.5_WT-7.5_WT_TU_R2

value: iPSC WTC-11


title: ap2hsKO_plusCHO_rep2_in

description: Library name: ap2hsKO_plusCHO_rep2_in


title: LV_d7.5_WT_WT_R2

description: Library name: 223015_7.5_WT-7.5_WT_R2

value: cardiomyocytes


title: ap2hsKO_plusCHO_rep2_IP

description: Library name: ap2hsKO_plusCHO_rep2_IP


title: ap2hsKOminCHO_rep1_in

description: Library name: ap2hsKOminCHO_rep1_in


title: Dd2_plusCHO_IP

description: Library name: Dd2_plusCHO_IP


title: LV_d2.5_untreated_TNNI1_R1

description: Library name: 223019_2.5_HAse-2.5_HAse_TNI1

value: cardioid differentiation


title: LV_d2.5_HAse_d1.5-2.5_TNNI1_R1

description: Library name: 223020_2.5_HAse_d1.5-2.5_HAse_d1.5_TNI1

value: cardiac progenitor


title: LV_d7.5_KO_cl4_R2

description: Library name: 223017_7.5_KO-7.5_cl4_R2


title: LV_d4.5_WT_WT_TU_R2

description: Library name: 223012_4.5_WT-4.5_WT_TU_R2


title: LV_d4.5_WT_WT_R2

description: Library name: 223011_4.5_WT-4.5_WT_R2


title: LV_d4.5_KO_cl4_R2

description: Library name: 223013_4.5_KO-4.5_cl4_R2


title: LV_d2.5_KO_cl4_R2

description: Library name: 223009_2.5_KO-2.5_cl4_R2


title: ap2hsKO_plusCHO_rep1_in

description: Library name: ap2hsKO_plusCHO_rep1_in


title: ap2hsKO_plusCHO_rep1_IP

description: Library name: ap2hsKO_plusCHO_rep1_IP


title: F12_minCHO_rep2_in

description: Library name: F12_minCHO_rep2_in

value: choline depletion


title: F12_minCHO_rep2_IP

description: Library name: F12_minCHO_rep2_IP


title: LV_d1.5_KO_cl4_R2

description: Library name: 223005_1.5_KO-1.5_cl4_R2


title: LV_d1.5_WT_WT_R2

description: Library name: 223003_1.5_WT-1.5_WT_R2


title: F12_plusCHO_rep2_in

description: Library name: F12_plusCHO_rep2_in


title: ap2hsKOminCHO_rep1_IP

description: Library name: ap2hsKOminCHO_rep1_IP


title: F12_minCHO_rep1_IP

description: Library name: F12_minCHO_rep1_IP


title: LV_d4.5_WT_WT_R1

description: Library name: 222995_4.5_WT-4.5_WT_R1


title: LV_d2.5_WT_WT_TU_R2

description: Library name: 223008_2.5_WT-2.5_WT_TU_R2


title: LV_d7.5_WT_WT_R1

description: Library name: 222999_7.5_WT-7.5_WT_R1


title: LV_d2.5_WT_WT_R2

description: Library name: 223007_2.5_WT-2.5_WT_R2


title: F12_plusCHO_rep2_IP

description: Library name: F12_plusCHO_rep2_IP


title: F12_minCHO_rep1_in

description: Library name: F12_minCHO_rep1_in


title: gdv1as_shKO_minCHO_rep1 _in

description: Library name: gdv1as_shKO_minCHO_rep1 _in

value: gdv1-as knockout


title: LV_d2.5_WT_WT_R1

description: Library name: 222991_2.5_WT-2.5_WT_R1


title: LV_d4.5_WT_WT_TU_R1

description: Library name: 222996_4.5_WT-4.5_WT_TU_R1


title: LV_d4.5_KO_cl4_R1

description: Library name: 222998_4.5_KO-4.5_cl4_R1


title: F12_plusCHO_rep1_in

description: Library name: F12_plusCHO_rep1_in

value: control choline


title: F12_plusCHO_rep1_IP

description: Library name: F12_plusCHO_rep1_IP


title: LV_d2.5_WT_WT_TU_R1

description: Library name: 222994_2.5_WT-2.5_WT_TU_R1


title: gdv1as_shKO_minCHO_rep1 _IP

description: Library name: gdv1as_shKO_minCHO_rep1 _IP


title: gdv1as_shKO_plusCHO_rep1 _IP

description: Library name: gdv1as_shKO_plusCHO_rep1 _IP


title: LV_d2.5_KO_cl4_R1

description: Library name: 222992_2.5_KO-2.5_cl4_R1


title: gdv1_KO_minCHO_rep2_IP

description: Library name: gdv1_KO_minCHO_rep2_IP

value: gdv1 knockout


title: LV_d1.5_WT_WT_R1

description: Library name: 222987_1.5_WT-1.5_WT_R1


title: gdv1_KO_minCHO_rep2_in

description: Library name: gdv1_KO_minCHO_rep2_in


title: gdv1as_shKO_plusCHO_rep1 _in

description: Library name: gdv1as_shKO_plusCHO_rep1 _in


title: Pure DicerKO, Rep3

city: Houston

first: George

last: Calin

state: TX

address: 1515 Bertner Ave

institute: The University of Texas MD Anderson Cancer Center

description: Library name: MIX-6-7

data_processing:
Raw single-end miRNA-seq reads were generated as FASTQ files and assessed for base quality, GC content, and adapter contamination using FastQC.
Adapter sequences and low-quality bases were trimmed, and very short reads removed, using Trim Galore (default settings); only trimmed reads passing quality control were retained for downstream analysis.
Trimmed reads were processed with mapper.pl from the miRDeep2 package to remove reads with ambiguous bases,  collapse identical reads to unique sequences, and align reads to the human reference genome assembly38
Reads were analyzed with miRDeep2.pl using mature miRNA reference sequences mirbase v22, hairpin precursor sequences, and species code hsa to identify and quantify known and candidate novel miRNAs.
Per-miRNA read counts were extracted from the miRDeep2 output for each sample
Assembly: GRCh38
Supplementary files format and content: Comma separated values with samples as columns and miRNAs as rows

growth_protocol: HCT116 colon cancer cells and HS-5 stromal cells were cultured at 37°C in a humidified incubator with 5% CO2. HS-5 cells were maintained in Dulbecco's Modified Eagle's Medium (DMEM; Corning) supplemented with 10% fetal bovine serum (FBS; Corning) and 1% Antibiotic-Antimycotic (Gibco), while HCT116 cells were maintained in McCoy’s 5A medium (Corning) with the same supplements. The Dicer1 knockout (KO) HCT116 cells were cultured under the same conditions with the addition of G-418 selective antibiotic solution (neomycin resistance) to preserve the homogenous KO population.

extract_protocol:
Total RNA was extracted from 1 x 106 cells using the Zymo RNA Isolation Mini Kit (Zymo Research). Small RNA concentrations (ng/µL) were quantified using a Qubit 4 Fluorometer (Invitrogen) with the Qubit microRNA Assay Kit (Invitrogen). Sample quality was validated using an Agilent Bioanalyzer (Agilent).
MiRNA sequencing libraries were prepared using the QIAseq miRNA Library Kit (Qiagen) and sequenced on an Illumina platform by SeqMatic LLC.

value: Colorectal cancer


title: gdv1_KO_plusCHO_rep2_IP

description: Library name: gdv1_KO_plusCHO_rep2_IP


title: Fibroblast:DicerKO mix3, 40:60

description: Library name: MIX-6-4

source_name: Mix

value: Mix


title: Fibroblast:DicerKO mix3, 30:70

description: Library name: MIX-6-5


title: LV_d1.5_KO_cl4_R1

description: Library name: 222990_1.5_KO-1.5_cl4_R1


title: Fibroblast:DicerKO mix3, 50:50

description: Library name: MIX-6-3


title: LV_d1.5_WT_WT_TU_R1

description: Library name: 222988_1.5_WT-1.5_WT_TU_R1

value: WT


title: gdv1_KO_plusCHO_rep2_in

description: Library name: gdv1_KO_plusCHO_rep2_in


title: gdv1_KO_minCHO_rep1_IP

description: Library name: gdv1_KO_minCHO_rep1_IP


title: gdv1as_OE_minCHO_rep2_in

description: Library name: gdv1as_OE_minCHO_rep2_in

value: gdv1-as overexpression


title: Fibroblast:DicerKO mix3, 15:85

description: Library name: MIX-6-6


title: Fibroblast:DicerKO mix2, 15:85

description: Library name: MIX-5-6


title: gdv1_KO_minCHO_rep1_in

description: Library name: gdv1_KO_minCHO_rep1_in


title: Fibroblast:DicerKO mix3, 70:30

description: Library name: MIX-6-2


title: gdv1as_OE_minCHO_rep2_IP

description: Library name: gdv1as_OE_minCHO_rep2_IP


title: gdv1as_OE_plusCHO_rep2_in

description: Library name: gdv1as_OE_plusCHO_rep2_in


title: Fibroblast:DicerKO mix2, 40:60

description: Library name: MIX-5-4


title: gdv1_KO_plusCHO_rep1_IP

description: Library name: gdv1_KO_plusCHO_rep1_IP


title: Pure DicerKO, Rep2

description: Library name: MIX-5-7


title: gdv1as_OE_plusCHO_rep2_IP

description: Library name: gdv1as_OE_plusCHO_rep2_IP


title: Fibroblast:DicerKO mix2, 50:50

description: Library name: MIX-5-3


title: Fibroblast:DicerKO mix2, 30:70

description: Library name: MIX-5-5


title: gdv1_KO_plusCHO_rep1_in

description: Library name: gdv1_KO_plusCHO_rep1_in


title: gdv1as_OE_minCHO_rep1_in

description: Library name: gdv1as_OE_minCHO_rep1_in


title: Fibroblast:DicerKO mix1, 15:85

description: Library name: MIX-4-6


title: gdv1as_OE_minCHO_rep1_IP

description: Library name: gdv1as_OE_minCHO_rep1_IP


title: Pure DicerKO, Rep1

description: Library name: MIX-4-7


title: gdv1as_OE_plusCHO_rep1_in

description: Library name: gdv1as_OE_plusCHO_rep1_in


title: gdv1as_KO_minCHO_rep2 _in

description: Library name: gdv1as_KO_minCHO_rep2 _in


title: Fibroblast:DicerKO mix1, 40:60

description: Library name: MIX-4-4


title: gdv1as_KO_minCHO_rep2 _IP

description: Library name: gdv1as_KO_minCHO_rep2 _IP


title: Fibroblast:DicerKO mix1, 30:70

description: Library name: MIX-4-5


title: gdv1as_OE_plusCHO_rep1_IP

description: Library name: gdv1as_OE_plusCHO_rep1_IP


title: gdv1as_KO_plusCHO_rep2_IP

description: Library name: gdv1as_KO_plusCHO_rep2_IP


title: Fibroblast:DicerKO mix2, 70:30

description: Library name: MIX-5-2


title: gdv1as_KO_plusCHO_rep2_in

description: Library name: gdv1as_KO_plusCHO_rep2_in


title: Fibroblast:DicerKO mix1, 50:50

description: Library name: MIX-4-3


title: Pure DicerWT, Rep3

description: Library name: MIX-3-7


title: gdv1as_KO_minCHO_rep1 _in

description: Library name: gdv1as_KO_minCHO_rep1 _in


title: gdv1as_KO_minCHO_rep1 _IP

description: Library name: gdv1as_KO_minCHO_rep1 _IP


title: MN4

city: GuangZhou

first: Li

last: qy

address: Jinan University, No.601, West Huangpu Avenue, Tianhe District, Guangzhou City, Guangdong Province, China

country: China

institute: Jinan University

description:
Library name: Sample 7
Sample was prepared using the Chromium Single Cell 5’ kit, sequenced on Illumina NovaSeq, and aligned using Cell Ranger v4.0.0

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v4.0.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: GRGh38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Blood

extract_protocol:
Human PBMCs were pre-isolated from EDTA anticoagulated peripheral blood via Ficoll density gradient centrifugation and cryopreserved long-term. Cryopreserved PBMCs were quickly thawed at 37 °C, washed with warm RPMI medium to remove DMSO, then purified with cold PBS + 0.04% BSA, and qualified with >90% cell viability.
Library was performed according to the manufacter’s instructions (single cell 5’ v3 protocol, 10x Genomics).Cell suspension was adjusted to 700–1200 cells/μL and loaded onto 10x Genomics Chromium Next GEM Chip G to generate single-cell GEM droplets. Within each GEM, cell lysis, polyA mRNA capture via 16 bp barcode + 12 bp UMI poly(dT) gel bead oligos, and in-droplet reverse transcription were completed for single-cell RNA extraction, following Lianchuan Biotechnology’s 10x scRNA-seq experimental protocol.

value: Blood

tag: group

value: peripheral blood mononuclear cells

value: treatment naïve

tag: disease

value: PMN


title: Fibroblast:DicerWT mix3, 15:85

description: Library name: MIX-3-6


title: gdv1as_KO_plusCHO_rep1 _IP

description: Library name: gdv1as_KO_plusCHO_rep1 _IP

value: H3K9me3 (Diagenode, C15410193)


title: gdv1as_KO_plusCHO_rep1 _in

description: Library name: gdv1as_KO_plusCHO_rep1 _in


title: MN5

description:
Library name: Sample 8
Sample was prepared using the Chromium Single Cell 5’ kit, sequenced on Illumina NovaSeq, and aligned using Cell Ranger v4.0.0


title: MN3

description:
Library name: Sample 6
Sample was prepared using the Chromium Single Cell 5’ kit, sequenced on Illumina NovaSeq, and aligned using Cell Ranger v4.0.0


title: Fibroblast:DicerKO mix1, 70:30

description: Library name: MIX-4-2


title: 1.2Bcorr_plusCHO rep2_in

description: Library name: 1.2Bcorr_plusCHO rep2_in

value: gdv1 fixed


title: MN1

description:
Library name: Sample 4
Sample was prepared using the Chromium Single Cell 5’ kit, sequenced on Illumina NovaSeq, and aligned using Cell Ranger v4.0.0


title: 1.2Bcorr_minCHO_rep1_in

description: Library name: 1.2Bcorr_minCHO_rep1_in


title: 1.2Bcorr_plusCHO rep2_IP

description: Library name: 1.2Bcorr_plusCHO rep2_IP


title: 1.2Bcorr_minCHO rep2_in

description: Library name: 1.2Bcorr_minCHO rep2_in


title: WXT

description:
Library name: Sample 3
Sample was prepared using the Chromium Single Cell 5’ kit, sequenced on Illumina NovaSeq, and aligned using Cell Ranger v4.0.0

value: WXT

value: healthy controls


title: 1.2Bcorr_minCHO_rep1_IP

description: Library name: 1.2Bcorr_minCHO_rep1_IP


title: Fibroblast:DicerWT mix3, 30:70

description: Library name: MIX-3-5


title: MN2

description:
Library name: Sample 5
Sample was prepared using the Chromium Single Cell 5’ kit, sequenced on Illumina NovaSeq, and aligned using Cell Ranger v4.0.0


title: 1.2Bcorr_minCHO rep2_IP

description: Library name: 1.2Bcorr_minCHO rep2_IP


title: HC2

description:
Library name: Sample 2
Sample was prepared using the Chromium Single Cell 5’ kit, sequenced on Illumina NovaSeq, and aligned using Cell Ranger v4.0.0


title: Fibroblast:DicerWT mix3, 40:60

description: Library name: MIX-3-4


title: 1.2Bmut_minCHO rep2_IP

description: Library name: 1.2Bmut_minCHO rep2_IP

value: gdv1 mutation


title: Healthy_007

data_processing:
Reads were trimmed using Trim Galore (version 0.6.2) and aligned to a bisulfite-converted human genome (hg19) using Bowtie2 and Bismark (versions 2.4.1 and 0.23.1, respectively).
After strand collapsing and filtering by coverage (keep loci with reads between 10-400), methylation loci were tiled by window (25bp) and a methylDiff object was created using MethylSig (version 1.5.0) for regions that were present in at least 3 samples per group.
Significant differentially methylated regions (DMRs) were identified as those with an absolute mean methylation difference of ≥ 25 and a DMR q-value of ≤ 0.05.
Assembly: hg19
Supplementary files format and content: genome-wide cytosine report output from bismark
Supplementary files format and content: tab-delimited text files include base-pair resolution information of the read strand and coverage of the methylated and unmethylated Cs in the sequenced DNA for each Sample

extract_protocol:
For the isolation of CD34+ cells from human bone marrow samples, we utilized the Miltenyi MACS magnetic bead purification kit. In a nutshell, 2 mL frozen vials of human mononuclear cells (MNC) were thawed at 37°C, followed by treatment with 200 µL of DNase-I (Roche) at a concentration of 1 mg/mL for 90 seconds. Subsequently, the cells were gently resuspended in Iscove's Modified Dulbecco's Medium (IMDM) containing 40% fetal bovine serum (FBS) to minimize primary human cell mortality. All centrifugation steps were performed at 1500 rpm. After an 8-minute centrifugation, the cells were resuspended in 15 mL of MACS buffer and then incubated with magnetic beads for 50 minutes at 4°C. Following three consecutive washes with MACS buffer (each for 10 minutes at 4°C), the cells were resuspended in 6 mL of MACS buffer and passed through an AUTOMACS instrument using the Posseld program. After another 8-minute centrifugation at 4°C, the cells were resuspended in RTL buffer with beta-mercaptoethanol. DNA and RNA were extracted from the CD34+ fraction using the AllPrep Micro kit (QIAGEN), while the CD34+ depleted fraction was processed with the AllPrep Mini kit.
Prior to adapter ligation, the methylated adapters were diluted to a concentration of 150 nmol/L. During the gel size selection step, fragments falling within the range of 150 to 450 base pairs were excised from the gel.

value: Bone marrow

value: Healthy


title: 1.2Bcorr_plusCHO_rep1_IP

description: Library name: 1.2Bcorr_plusCHO_rep1_IP

value: control choline


title: Fibroblast:DicerWT mix3, 50:50

description: Library name: MIX-3-3


title: 1.2Bcorr_plusCHO_rep1_in

description: Library name: 1.2Bcorr_plusCHO_rep1_in


title: 1.2Bmut_minCHO rep2_in

description: Library name: 1.2Bmut_minCHO rep2_in

value: choline depletion


title: Fibroblast:DicerWT mix3, 70:30

description: Library name: MIX-3-2


title: 1.2Bmut_minCHO_rep1_in

description: Library name: 1.2Bmut_minCHO_rep1_in


title: 1.2Bmut_minCHO_rep1_IP

description: Library name: 1.2Bmut_minCHO_rep1_IP


title: Pure DicerWT, Rep2

description: Library name: MIX-2-7

value: Colorectal cancer


title: Healthy_006


title: HC1

description:
Library name: Sample 1
Sample was prepared using the Chromium Single Cell 5’ kit, sequenced on Illumina NovaSeq, and aligned using Cell Ranger v4.0.0


title: 1.2Bmut_plusCHO rep2_in

description: Library name: 1.2Bmut_plusCHO rep2_in


title: 1.2Bmut_plusCHO_rep1_in

description: Library name: 1.2Bmut_plusCHO_rep1_in


title: 1.2Bmut_plusCHO rep2_IP

description: Library name: 1.2Bmut_plusCHO rep2_IP


title: Healthy_005


title: Pure fibroblast, Rep3

description: Library name: MIX-3-1

value: Fibroblast


title: 1.2Bmut_plusCHO_rep1_IP

description: Library name: 1.2Bmut_plusCHO_rep1_IP


title: NF54_38hpi_minCHO_in

description: Library name: NF54_38hpi_minCHO_in

value: WT


title: Fibroblast:DicerWT mix2, 40:60

description: Library name: MIX-2-4

value: Mix


title: NF54_38hpi_plusCHO_IP

description: Library name: NF54_38hpi_plusCHO_IP


title: NF54_38hpi_minCHO_IP

description: Library name: NF54_38hpi_minCHO_IP


title: Fibroblast:DicerWT mix2, 15:85

description: Library name: MIX-2-6


title: Healthy_002


title: Fibroblast:DicerWT mix2, 70:30

description: Library name: MIX-2-2


title: NF54_23hpi_plusCHO_IP

description: Library name: NF54_23hpi_plusCHO_IP


title: Healthy_001


title: NF54_38hpi_plusCHO_in

description: Library name: NF54_38hpi_plusCHO_in


title: Healthy_003