title: pADamID-RPE_tracr_10h_r6_LMNB2_sample

description:
Library name: 7122_14_E2071_ID02_10h_RPE1_tracr_LMNB2_R2_CTCATTCTGC-TTGAAGCGGT_S20_R1_001_library
pA-DamID sample from manuscript "Megabase-scale detachment of genome-nuclear lamina interactions is required for efficient repair of double stranded breaks"


title: pADamID-RPE_tracr_10h_r2_gH2AX_sample

status: Public on Jun 24 2025

type: SRA

city: Amsterdam

first: Xabier

last: Vergara

state: North Holland

address: Plesmalaan 121

department: Molecular Genetics

country: Netherlands

institute: Netherlands Cancer Institute

description:
Library name: 7122_18_E2071_ID06_10h_RPE1_tracr_gH2AX_R2_GCATAGCCAA-TGGTTCCTGG_S25_R1_001_library
pA-DamID sample from manuscript "Megabase-scale detachment of genome-nuclear lamina interactions is required for efficient repair of double stranded breaks"

library_source: genomic

data_processing:
We processed the DNA sequencing data using the previously published computational pipeline (https://github.com/vansteensellab/pADamID_ABCB1_Novaseq)
Assembly: hg38
Supplementary files format and content: There are two processed data formats: (1) -gatc.counts.txt.gz, read counts per gatc sequence in the genome used for domainograms and (2) -20kb.bw, bigwig file at 20kb resolution
Library strategy: DamID-Seq

molecule: genomic DNA

organism: Homo sapiens

growth_protocol: Culturing methods per cell line are described in the manuscript

extract_protocol:
genomic DNA was extracted using the Bioline kit (details in methods section)
We followed pA-DamID library preparation protocol used for NOVAseq (details in methods section)

treatment_protocol: Trearment per sample are described in the manuscript

tag: cell line

tag: cell type

value: hTERT-immortalized retinal pigment epithelial

tag: genotype

value: wildtype

tag: antibody

tag: transfection

tag: timepoint

tag: treatment

tag: batch


title: pADamID-RPE_cr6_10h_r6_LMNB2_sample

description:
Library name: 7122_20_E2071_ID08_10h_RPE1_ABCB1_LMNB2_R2_GCGATGCAGA-TCTTCGTGTA_S27_R1_001_library
pA-DamID sample from manuscript "Megabase-scale detachment of genome-nuclear lamina interactions is required for efficient repair of double stranded breaks"


title: pADamID-RPE_cr6_10h_r2_Dam_sample

description:
Library name: 7122_19_E2071_ID07_10h_RPE1_ABCB1_Dam_R2_ACGTGCATCG-CAGTCAGTTG_S26_R1_001_library
pA-DamID sample from manuscript "Megabase-scale detachment of genome-nuclear lamina interactions is required for efficient repair of double stranded breaks"


title: pADamID-RPE_cr6_10h_r2_H3K9me2_sample

description:
Library name: 7122_21_E2071_ID09_10h_RPE1_ABCB1_H3K9me2_R2_GTGCTATCGA-TTAAGCACCG_S22_R1_001_library
pA-DamID sample from manuscript "Megabase-scale detachment of genome-nuclear lamina interactions is required for efficient repair of double stranded breaks"


title: pADamID-RPE_cr6_10h_r1_H3K9me2_sample

description:
Library name: 7070_21_E2061_ABCB1_H3K9me2_F10_GTGGAGGTAG-ATCGCGTCAC_S21_R1_001_library
pA-DamID sample from manuscript "Megabase-scale detachment of genome-nuclear lamina interactions is required for efficient repair of double stranded breaks"


title: pADamID-RPE_tracr_10h_r5_LMNB2_sample

description:
Library name: 7070_12_E2061_tracr_LMNB2_D7_CTTGCGAAGA-AATGACGCGG_S1_R1_001_library
pA-DamID sample from manuscript "Megabase-scale detachment of genome-nuclear lamina interactions is required for efficient repair of double stranded breaks"


title: pADamID-RPE_tracr_10h_r2_H3K9me2_sample

description:
Library name: 7122_15_E2071_ID03_10h_RPE1_tracr_H3K9me2_R2_AACAGTGACT-ATCGCAGTGT_S16_R1_001_library
pA-DamID sample from manuscript "Megabase-scale detachment of genome-nuclear lamina interactions is required for efficient repair of double stranded breaks"


title: pADamID-RPE_cr6_10h_r1_H3K9me3_sample

description:
Library name: 7070_19_E2061_ABCB1_H3K9me3_C8_AGTCGACGTA-CCATGGAACA_S19_R1_001_library
pA-DamID sample from manuscript "Megabase-scale detachment of genome-nuclear lamina interactions is required for efficient repair of double stranded breaks"


title: pADamID-RPE_tracr_10h_r2_Dam_sample

description:
Library name: 7122_13_E2071_ID01_10h_RPE1_tracr_Dam_R2_CACACTGTTG-TGCATTGGTT_S19_R1_001_library
pA-DamID sample from manuscript "Megabase-scale detachment of genome-nuclear lamina interactions is required for efficient repair of double stranded breaks"


title: pADamID-RPE_cr6_10h_r1_Dam_sample

description:
Library name: 7070_17_E2061_ABCB1_dam_only_A8_AGTGGTAGCA-TGGTGTTGAC_S17_R1_001_library
pA-DamID sample from manuscript "Megabase-scale detachment of genome-nuclear lamina interactions is required for efficient repair of double stranded breaks"


title: pADamID-RPE_tracr_10h_r1_H3K9me2_sample

description:
Library name: 7070_14_E2061_tracr_H3K9me2_F7_AACGACATCT-GTCTTGGAAT_S6_R1_001_library
pA-DamID sample from manuscript "Megabase-scale detachment of genome-nuclear lamina interactions is required for efficient repair of double stranded breaks"


title: pADamID-RPE_cr6_10h_r5_LMNB2_sample

description:
Library name: 7070_18_E2061_ABCB1_LMNB2_B8_TATCCAGTTC-TGAGCTACGT_S18_R1_001_library
pA-DamID sample from manuscript "Megabase-scale detachment of genome-nuclear lamina interactions is required for efficient repair of double stranded breaks"


title: pADamID-RPE_tracr_10h_r1_gH2AX_sample

description:
Library name: 7070_16_E2061_tracr_gH2AX_H7_GTCATCGCGT-CCGACAAGGA_S10_R1_001_library
pA-DamID sample from manuscript "Megabase-scale detachment of genome-nuclear lamina interactions is required for efficient repair of double stranded breaks"


title: pADamID-RPE_tracr_10h_r1_Dam_sample

description:
Library name: 7070_11_E2061_tracr_dam_only_C7_CCACGATAAC-CATGCCTGAC_S15_R1_001_library
pA-DamID sample from manuscript "Megabase-scale detachment of genome-nuclear lamina interactions is required for efficient repair of double stranded breaks"


title: ChIPMNase-HEK293T_BZ1_6h

city: Wuhan

first: Yin

last: Zhinang

state: Hubei

address: Donghu road 185

country: China

institute: Wuhan University

description: Library name: Sample 77

data_processing:
ChIP-MNase reads were aligned to the mouse genome using Bowtie version 1.1.2. Only uniquely mapping reads with up to two mismatches within the 150 bp reads were considered for further analysis.
Assembly: hg38
Supplementary files format and content: bigWig

source_name: Derived from embryonic kidney

growth_protocol: HEK293T cells were cultured in high-glucose DMEM (Life Technologies) supplemented with 10% FBS (LONSERA S711-001), 1% penicillin/streptomycin (Gibco), and L-glutamine (Gibco) at 37°C in a 5% CO₂ atmosphere.

extract_protocol:
Briefly, HEK293T cells expressing K/C-III were fixed with 4% formaldehyde for 10 minutes at room temperature and then quenched with glycine. The fixed cells were lysed in L1 buffer (50 mM Tris-HCl pH 8.0, 2 mM EDTA, 0.1% NP-40, 10% glycerol, 1× protease inhibitors, 1 mM PMSF, 2 mM DTT) on ice for 5 minutes. Following centrifugation, the nuclear pellet was resuspended in ice-cold wash buffer D (50 mM Tris–HCl pH 8.0, 0.1 mM EDTA, 5 mM Mg acetate, 5 mM DTT, 25% glycerol) and incubated for 5 minutes before centrifuging at 2,000g for 5 minutes. The pellet was resuspended in 400 μL MNase buffer (10 mM Tris–HCl pH 7.4, 15 mM NaCl, 60 mM KCl, 1 mM CaCl₂, 250 mM sucrose, 0.5 mM DTT) and underwent two freeze-thaw cycles in liquid nitrogen to disrupt nuclei. Chromatin was sonicated with a Diagenode Bruptor Plus (low-power mode, 8 cycles of 30 seconds ON and 30 seconds OFF).
Next, 2 U of MNase was used to digest fixed chromatin at 25°C for 30 minutes with shaking at 1200 rpm. Digestion was halted with EDTA, and 1 mL of buffer V (50 mM Tris pH 7.4, 50 mM NaCl, 5 mM EDTA) was added. The supernatant was pre-cleaned with rProtein A/G beads (Smart Lifesciences, SA032005). Samples were incubated overnight at 4°C with 5 μg H3K4me2 antibody and 15 μL rProtein A/G beads. Beads were washed three times with MNase buffer, followed by a second MNase digestion (15 μL MNase buffer containing 2 U MNase) at 25°C for 30 minutes with shaking. The reaction was stopped with 34 mM EDTA and treated with proteinase K. DNA was purified by phenol-chloroform extraction and ethanol precipitation.
ChIP-MNase libraries were prepared using the NEBNext Ultra II DNA library prep kit for Illumina.

tag: tissue

value: Derived from embryonic kidney

value: immortalized cell line

value: K/C-III express

value: treated with BZ1 for 6 hours


title: ChIPMNase-HEK293T_DMSO

description: Library name: Sample 78

value: treated with DMSO for 12 hours


title: CUT&RUN-HEK293T-KAT6A-dWH1

description: Library name: Sample 53

data_processing:
CUT&RUN reads were aligned to the human or mouse genome with Bowtie2 with the following options: —very-sensitive —no-discordant —no-mixed –X 700 –dovetail.
Peak calling was performed with MACS2 using IgG samples as background.
Coverage signal profiles in bigwig format were generated using the bamCoverage function from deepTools with a Counts-Per-Million per-sample normalization.
These profiles were visualized using deepTools computeMatrix and plotHeatmap functions.
Assembly: hg38, mm10
Supplementary files format and content: bigWig
Library strategy: CUT&Run

growth_protocol:
HEK293T cells were cultured in high-glucose DMEM (Life Technologies) supplemented with 10% FBS (LONSERA S711-001), 1% penicillin/streptomycin (Gibco), and L-glutamine (Gibco) at 37°C in a 5% CO₂ atmosphere.
K/C-III leukemia cells were cultured in Retronectin-coated plates (Takata T100A) with RPMI 1640 medium (Gibco) supplemented with 1% penicillin/streptomycin, 10% FBS (Gibco), and murine SCF, IL-6, and IL-3. Cell viability was assessed with a Bio-Rad TC20 automated cell counter.

extract_protocol:
Briefly, freshly harvested cells (1×10⁶) were bound to CoA beads 4FF (Smart Lifesciences), resuspended in antibody binding buffer, and incubated overnight with primary antibodies. CUT&RUN experiments with leukemia cells were performed using ex vivo-isolated AML cells from leukemic mice. The samples were then washed and bound to homemade pA/G-MNase. Chromatin digestion was initiated by the addition of CaCl₂ and stopped after 30 minutes with STOP buffer containing chelating agents. Samples were incubated for 30 minutes at 37°C to release CUT&RUN fragments and then treated for 1 hour at 50°C with proteinase K. A purification step was performed using SRPI beads.
Library preparation was done using the NEBNext Ultra II DNA Library Prep Kit for Illumina, followed by sequencing on a NovaSeq 6000 to achieve a depth of at least 10 million paired-end 150 bp reads per sample.

value: deletion of the WH1 domain

value: untreated


title: ChIPMNase-HEK293T_BZ1_12h

description: Library name: Sample 76

value: treated with BZ1 for 12 hours


title: CUT&RUN-HEK293T-KAT6A-G657E

description: Library name: Sample 54

value: KAT6A-NT1 mutants


title: CUT&RUN-HEK293T-KAT6A-NT-1-780

description: Library name: Sample 55

value: KAT6A-NT1 express


title: CUT&RUN-HEK293T-KAT6A-dMYST

description: Library name: Sample 52

value: deletion of the MYST domain


title: CUT&RUN-HEK293T-shGFP-antiKAT6A

description: Library name: Sample 47

value: GFP knockdown


title: CUT&RUN-HEK293T-shBPTF-antiKAT6A-rep2

description: Library name: Sample 45

value: BPTF knockdown


title: CUT&RUN-HEK293T-shGFP-antiBPTF

description: Library name: Sample 46


title: CUT&RUN-HEK293T-shBPTF-antiBPTF-rep2

description: Library name: Sample 43


title: CUT&RUN-HEK293T-shBPTF-antiKAT6A-rep1

description: Library name: Sample 44


title: CUT&RUN-HEK293T-shBPTF-antiBPTF-rep1

description: Library name: Sample 42


title: pADamID-RPE_tracr_10h_r1_H3K9me3_sample

description:
Library name: 7070_13_E2061_tracr_H3K9me3_E7_TGGCACGAAC-CCTGACTCTT_S3_R1_001_library
pA-DamID sample from manuscript "Megabase-scale detachment of genome-nuclear lamina interactions is required for efficient repair of double stranded breaks"


title: CUT&RUN-HEK293T-KPIII

description: Library name: Sample 40

value: K/P-III express


title: CUT&RUN-HEK293T-MSCV-Vector

description: Library name: Sample 41

value: MSCV-Vector express


title: CUT&RUN-HEK293T-KCIII

description: Library name: Sample 39


title: CUT&RUN-HEK293T-KAT6A-TIF2

description: Library name: Sample 38

value: KAT6A-TIF2 express


title: CUT&RUN-HEK293T-KAT6A-NCOA3

description: Library name: Sample 36

value: KAT6A-NCOA3 express


title: CUT&RUN-HEK293T-KAT6A-NT1

description: Library name: Sample 37

value: Derived from embryonic kidney


title: HCT116_HPLM_24_hr_Entinostat_rep1

city: Cleveland

first: Leah

last: Gates

state: OH

address: 10900 Euclid Avenue

country: USA

institute: Case Western Reserve University

description: Library name: Sample 65

library_source: transcriptomic

data_processing:
Transcript Quantification with Salmon (version 0.8.2)
Alignment of ChIPseq reads was done with Rsubread (version 1.30.6)
Normalization and rlog transformation of raw read counts in genes were performed using DESeq2 (version 1.20.0)
Assembly: BSgenome.Hsapiens.UCSC.hg19 (version 1.4.3) and TxDb.Hsapiens.UCSC.hg19.knownGene (version 3.4.0)
Assembly: hg19
Supplementary files format and content: counts, bigwigs

molecule: polyA RNA

growth_protocol: HCT-116 cells were grown in DMEM medium or human plasma like media (HPLM) with 10% fetal bovine serum and 1% penicillin/streptomycin. When cells were grown in HPLM, cells were washed in PBS and cultured in HPLM for at least three days prior to experiments. Caco-2 cells were grown in Eagle's Minimum Essential Medium supplemented with 2 mM GlutaMAX, 1 mM sodium pyruvate, 20% FBS, and 1% penicillin/streptomycin.

extract_protocol:
RNA was harvested using RNA isolation kits and genomic DNA was isolated following immunoprecipitation of sonicated chromatin.
Libraries were generated using NEBNext Ultra II kits following the manufacturer's protocol.

treatment_protocol: HCT-116 and Caco-2 cells were treated with different short chain fatty acids (SCFAs) or inhibitors for 6 or 24 hours prior to RNA isolation. For ChIP-seq experiments, cells were treated with 5 mM butyrate or 5 mM propionate for 24 hours prior to fixation.

value: Colorectal carcinoma

value: Wild type

value: 1 uM Entinostat for 24 hours


title: HCT116_HPLM_24_hr_DMSO_Butyrate_rep3

description: Library name: Sample 64

value: 5 mM butyrate and 0.1% DMSO for 24 hours


title: HCT116_HPLM_24_hr_Entinostat_rep3

description: Library name: Sample 67


title: HCT116_HPLM_24_hr_A485_Butyrate_rep1

description: Library name: Sample 71

value: 5 mM butyrate and 1 uM A485 for 24 hours


title: HCT116_HPLM_24_hr_A485_rep1

description: Library name: Sample 68

value: 1 uM A485 for 24 hours


title: HCT116_HPLM_24_hr_A485_rep3

description: Library name: Sample 70


title: HCT116_HPLM_24_hr_A485_Butyrate_rep2

description: Library name: Sample 72


title: HCT116_HPLM_24_hr_A485_rep2

description: Library name: Sample 69


title: HCT116_HPLM_24_hr_Entinostat_rep2

description: Library name: Sample 66


title: HCT116_HPLM_24_hr_A485_Butyrate_rep3

description: Library name: Sample 73


title: HCT116_HPLM_24_hr_DMSO_Butyrate_rep1

description: Library name: Sample 62


title: HCT116_HPLM_24hr_Untreated_rep3

description: Library name: Sample 58

value: Untreated


title: HCT116_HPLM_24_hr_DMSO_rep3

description: Library name: Sample 61

value: 0.1% DMSO for 24 hours


title: HCT116_HPLM_24_hr_DMSO_rep1

description: Library name: Sample 59


title: HCT116_HPLM_24_hr_DMSO_rep2

description: Library name: Sample 60


title: HCT116_HPLM_24hr_Untreated_rep2

description: Library name: Sample 57


title: HCT116_HPLM_24hr_SCFAs_1to1to1_rep3

description: Library name: Sample 52

value: 5 mM acetate, butyrate, and propionate (1.67 mM each) mix for 24 hours


title: HCT116_HPLM_24hr_SCFAs_1to1to1_rep2

description: Library name: Sample 51


title: HCT116_HPLM_24hr_SCFAs_1to1to1_rep1

description: Library name: Sample 50


title: HCT116_HPLM_24hr_Propionate_rep3

description: Library name: Sample 49

value: 5 mM propionate for 24 hours


title: HCT116_HPLM_24hr_Butyrate_rep3

description: Library name: Sample 46

value: 5 mM butyrate for 24 hours


title: HCT116_HPLM_24hr_Butyrate_rep2

description: Library name: Sample 45


title: HCT116_HPLM_24hr_Butyrate_rep1

description: Library name: Sample 44


title: HCT116_HPLM_24hr_Acetate_rep3

description: Library name: Sample 43

value: 5 mM acetate for 24 hours


title: HCT116_HPLM_24hr_SCFAs_3to1to1_rep1

description: Library name: Sample 53

value: 3 mM acetate, 1 mM butyrate, and 1 mM propionate mix for 24 hours


title: HCT116_HPLM_24hr_NaCl_rep2

description: Library name: Sample 39

value: 5 mM NaCl for 24 hours


title: HCT116_HPLM_24hr_Acetate_rep1

description: Library name: Sample 41


title: HCT116_HPLM_24hr_NaCl_rep3

description: Library name: Sample 40


title: HCT116_HPLM_24hr_Acetate_rep2

description: Library name: Sample 42


title: HCT116_HPLM_24hr_NaCl_rep1

description: Library name: Sample 38


title: EVTd8_PPARG_KD1_rep1

city: AUSTIN

first: Qingqing

last: Guo

state: TX

address: 2506 Speedway

institute: The University of Texas at Austin

description:
Library name: EVTd8_PPARG_KD1_rep1
EVTd8_PPARG_KD_Raw_count.txt

data_processing:
All sequencing reads were trimmed using Trim Galore v0.6.10 and aligned to the human reference genome (hg38) with STAR (version 2.7.11b).
Alignments were then filtered using Samtools (version 1.17) with MAPQ score >= 10.
Raw counts were quantified using featureCounts from the Subread package (version 2.0.6).
Assembly: hg38
Supplementary files format and content: Raw counts quantified using featureCounts

source_name: Placenta

extract_protocol:
Total RNA was extracted from cells using the RNeasy Plus Mini Kit (Qiagen) (74136). The mRNA was enriched using the NEBNext® Poly(A) mRNA Magnetic Isolation Module kit (E7490L).
The RNAs-seq libraries were constructed using the NEBNext® Ultra™ RNA Library Prep Kit for Illumina (E7770L) and NEBNext Multiplex Oligos for Illumina (E7600S) following the manufacturer’s protocol. RNA-seq was conducted as paired-end 150 bp sequencing on the NovaSeq 6000 (Illumina).

value: Placenta

value: Human trophoblast stem cells

value: Cells were infected with PPARG shRNA_1 lentivirus from EVT differentiation day 1 to day 8.


title: EVTd8_PPARG_KD2_rep1

description:
Library name: EVTd8_PPARG_KD2_rep1
EVTd8_PPARG_KD_Raw_count.txt

value: Cells were infected with PPARG shRNA_2 lentivirus from EVT differentiation day 1 to day 8.


title: EVTd8_PPARG_KD1_rep2

description:
Library name: EVTd8_PPARG_KD1_rep2
EVTd8_PPARG_KD_Raw_count.txt


title: EVTd8_PPARG_KD2_rep2

description:
Library name: EVTd8_PPARG_KD2_rep2
EVTd8_PPARG_KD_Raw_count.txt


title: HCT116_HPLM_24hr_Untreated_rep1

description: Library name: Sample 56

value: Colorectal carcinoma

value: Wild type


title: HCT116_HPLM_24hr_SCFAs_3to1to1_rep2

description: Library name: Sample 54


title: HCT116_HPLM_24hr_SCFAs_3to1to1_rep3

description: Library name: Sample 55


title: Input_EVTd8

description:
Library name: Input_EVTd8
Input DNA collected from EVT day 8 chromatin for ChIP-seq normalization.

data_processing:
All data reads were trimmed with Trim Galore (version 0.6.10) and mapped to the hg38 human reference genome using Bowtie2 (version 2.5.1) with default parameters.
The alignments were further filtered with Samtools (version 1.17) with MAPQ >= 10.
PCR duplicates were subsequently eliminated with Picard Tools (version 2.27.2).
Peaks were detected utilizing MACS3 (version 3.0.0b3) with a false discovery rate (FDR) < 0.05.
RPGC-normalized bigwig files were produced using the deepTools bamCoverage (version 3.5.2).
Assembly: hg38
Supplementary files format and content: RPGC-normalized bigwig files

extract_protocol:
ChIP were performed by cross-linking proteins to DNA using 1% formaldehyde solution. Immunoprecipitated DNA was sequenced using Illumina sequencers.
Pull-downed DNAs were applied for the generation of sequencing libraries using the NEBNext Ultra II DNA Library Prep Kit (E7103L) and NEBNext Multiplex Oligos for Illumina (E7600S) following the manufacturer’s protocol.

value: Cells under control conditions on EVT day 8.


title: Input_EVTd4

description:
Library name: Input_EVTd4
Input DNA collected from EVT day 4 chromatin for ChIP-seq normalization.

value: Cells under control conditions on EVT day 4.


title: TSC_PPARG_rep2

description:
Library name: TSC_PPARG_rep2
Undifferentiated TSCs were harvested for PPARG ChIP-seq.

value: Cells under control conditions (undifferentiated TSCs).


title: Input_EVTd6

description:
Library name: Input_EVTd6
Input DNA collected from EVT day 6 chromatin for ChIP-seq normalization.

value: Cells under control conditions on EVT day 6.


title: HCT116_HPLM_24hr_Propionate_rep1

description: Library name: Sample 47


title: HCT116_HPLM_24hr_Propionate_rep2

description: Library name: Sample 48


title: EVTd6_PPARG_rep2

description:
Library name: EVTd6_PPARG_rep2
EVT day 6 cells were harvested for PPARG ChIP-seq.


title: EVTd8_PPARG_rep2

description:
Library name: EVTd8_PPARG_rep2
EVT day 8 cells were harvested for PPARG ChIP-seq.


title: EVTd8_PPARG_rep1

description:
Library name: EVTd8_PPARG_rep1
EVT day 8 cells were harvested for PPARG ChIP-seq.


title: EVTd6_PPARG_rep1

description:
Library name: EVTd6_PPARG_rep1
EVT day 6 cells were harvested for PPARG ChIP-seq.


title: EVTd4_PPARG_rep1

description:
Library name: EVTd4_PPARG_rep1
EVT day 4 cells were harvested for PPARG ChIP-seq.


title: Input_TSC

description:
Library name: Input_TSC
Input DNA collected from undifferentiated chromatin for ChIP-seq normalization.


title: Input_EVTd2

description:
Library name: Input_EVTd2
Input DNA collected from EVT day 2 chromatin for ChIP-seq normalization.

value: Cells under control conditions on EVT day 2.


title: TSC_PPARG_rep1

description:
Library name: TSC_PPARG_rep1
Undifferentiated TSCs were harvested for PPARG ChIP-seq.


title: EVTd8_Untreated_Ctrl_rep2

description:
Library name: EVTd8_Untreated_Ctrl_rep2
RNA-seq

value: Cells were differentiated into EVTs for 8 days under control (untreated) conditions.


title: EVTd8_Untreated_Ctrl_rep1

description:
Library name: EVTd8_Untreated_Ctrl_rep1
RNA-seq


title: EVTd8_DMOG_500uM_rep1

description:
Library name: EVTd8_DMOG_500uM_rep1
RNA-seq

value: Cells were treated with 500 μM DMOG from day 3 to day 8 of EVT differentiation.


title: EVTd8_SCH_0.5uM_rep1

description:
Library name: EVTd8_SCH_0.5uM_rep1
RNA-seq

value: Cells were treated with 0.5 μM SCH772984 from day 1 to day 8 of EVT differentiation.


title: EVTd8_T007_D4_rep2

description:
Library name: EVTd8_T007_D4_rep2
RNA-seq

value: Cells were treated with 1 μM T0070907 starting on day 4 of EVT differentiation and maintained until day 8.


title: EVTd8_T007_D6_rep1

description:
Library name: EVTd8_T007_D6_rep1
RNA-seq

value: Cells were treated with 1 μM T0070907 starting on day 6 of EVT differentiation and maintained until day 8.


title: EVTd8_SCH_0.5uM_rep2

description:
Library name: EVTd8_SCH_0.5uM_rep2
RNA-seq


title: EVTd8_T007_Ctrl_rep1

description:
Library name: EVTd8_T007_Ctrl_rep1
RNA-seq

value: Cells were differentiated into EVT for 8 days with DMSO (vehicle control).


title: EVTd8_T007_D3_rep2

description:
Library name: EVTd8_T007_D3_rep2
RNA-seq

value: Placenta

value: Cells were treated with 1 μM T0070907 starting on day 3 of EVT differentiation and maintained until day 8.


title: EVTd8_T007_D4_rep1

description:
Library name: EVTd8_T007_D4_rep1
RNA-seq

value: Human trophoblast stem cells


title: EVTd8_T007_D2_rep2

description:
Library name: EVTd8_T007_D2_rep2
RNA-seq

value: Cells were treated with 1 μM T0070907 starting on day 2 of EVT differentiation and maintained until day 8.


title: EVTd8_T007_D1_rep2

description:
Library name: EVTd8_T007_D1_rep2
RNA-seq

value: Cells were treated with 1 μM T0070907 starting on day 1 of EVT differentiation and maintained until day 8.


title: EVTd8_T007_D1_rep1

description:
Library name: EVTd8_T007_D1_rep1
RNA-seq


title: TSC_T007_Ctrl_rep2

description:
Library name: TSC_T007_Ctrl_rep2
RNA-seq

value: TSCs were treated with vehicle (DMSO) and maintained for 72 hours.


title: TSC_T007_Ctrl_rep1

description:
Library name: TSC_T007_Ctrl_rep1
RNA-seq


title: EVTd2_PPARG_rep2

description:
Library name: EVTd2_PPARG_rep2
EVT day 2 cells were harvested for PPARG ChIP-seq.


title: EVTd4_PPARG_rep2

description:
Library name: EVTd4_PPARG_rep2
EVT day 4 cells were harvested for PPARG ChIP-seq.


title: EVTd8_T007_D2_rep1

description:
Library name: EVTd8_T007_D2_rep1
RNA-seq


title: EVTd8_DMOG_500uM_rep2

description:
Library name: EVTd8_DMOG_500uM_rep2
RNA-seq


title: EVTd8_T007_Ctrl_rep2

description:
Library name: EVTd8_T007_Ctrl_rep2
RNA-seq


title: TSC_T007_3uM_rep1

description:
Library name: TSC_T007_3uM_rep1
RNA-seq

value: TSCs were treated with 3 μM T0070907 and maintained for 72 hours.


title: TSC_T007_1uM_rep2

description:
Library name: TSC_T007_1uM_rep2
RNA-seq

value: TSCs were treated with 1 μM T0070907 and maintained for 72 hours.


title: EVTd8_T007_D6_rep2

description:
Library name: EVTd8_T007_D6_rep2
RNA-seq


title: TSC_T007_10uM_rep1

description:
Library name: TSC_T007_10uM_rep1
RNA-seq

value: TSCs were treated with 10 μM T0070907 and maintained for 72 hours.


title: P. knowlesi in culture, Nycodenz gradient

city: Antwerp

first: Pieter

last: Monsieurs

address: Nationalestraat 155

country: Belgium

institute: Institute of Tropical Medicine

library_source: transcriptomic single cell

data_processing:
BeeNet v1.1 was used to map sequencing reads to an updated PKNH reference (downloaded from PlasmoDB version 62 (58)) with default parameters and an expected number of cells of 60,000. As 3’UTR annotations are absent for most P. knowlesi genes, the annotations of the 3′UTR were added in a systematic manner to enhance the accuracy of read assignments to the annotated transcript: for each protein-coding gene, the 3′UTR region was annotated by adding 2500 base pairs downstream of the stop codon. In cases where the newly designated 3′UTR overlapped with other genomic elements, the 3’UTR was truncated to avoid overlap. The resulting TCM and RCM files were read into R (version 4.2.1) and converted into a Seurat object using Seurat 4.2 (59). The single-cell data from 6 samples were merged into one Seurat object. Cells with less than 600 reads per cell or less than 300 expressed genes per cell were filtered out. Doublets were removed using scrublet (version 0.2.3, (60)) Preliminary analysis (PCA analysis and clustering analysis) before excluding potential doublets showed that one cluster was significantly enriched with scrublet-predicted doublets, and as such the entire cluster was also removed from the single-cell dataset. Count data were normalized using regularized negative binomial regression (SCTransform). After principal component analysis, the Uniform Manifold Approximation and Projection (UMAP) dimensional reduction technique was applied for visualization of the single-cell transcriptomes using the first 20 principal components (61). Clustering of cells was performed on the PCA output using a resolution of 0.25.
Assembly: P. knowlesi A1-H1 strain from PlasmoDB
Supplementary files format and content: RCM and TCM files ouput from the BeeNet software, which can be used as input for the Seurat pipeline

organism: Plasmodium knowlesi

source_name: culture

growth_protocol: P. knowlesi A1-H.1 strain parasites were maintained between 0.5 and 10% parasitemia in culture medium consisting of RPMI-1640 (Westburg Life Sciences) supplemented with 0.32 g/L sodium bicarbonate, 5.0 g/L Albumax II (Invitrogen, cat: 11021-029), 2.0 g/L D-glucose, 25mM HEPES, 0.05g/L hypoxanthine, 0.005 g/L gentamicin, 2mM L-glutamine with 10% (v/v) heat-inactivated horse serum (Invitrogen) at 3% hematocrit (HCT). Parasites were continuously cultured in O+ blood and incubated at 37°C under atmospheric conditions of 90% N2, 5% O2, 5% CO2. Parasitemia was determined using thin smear slides stained with 10% Giemsa stain for 10 minutes.

extract_protocol:
Resuspended enriched iRBC pellets were further diluted in PBS-BSA to a concentration of 60,000 cells/mL using a Scepter 3.0 cell counter (Merck). 1mL of cell suspension was loaded into each HIVE to settle into the pico-wells via gravity or using a centrifuge according to modified manufacturer’s directions. The incubation time for the HIVE loading was increased from 30 minutes to 1 hour at room temperature (gravity) and from 3 to 5 minutes (centrifuge). HIVEs were stored at -20°C until library preparation to mimic using a -20°C freezer in the field.
Library preparation was conducted following manufacturer’s directions with 10 extra PCR cycles added to the whole transcriptome amplification (WTA). All samples were sequenced by on a NovaSeq6000 (Broad Institute, USA) according to the manufacturer’s recommendations. Sequencing data has been deposited in the NCBI sequencing read archive.

treatment_protocol: A P. knowlesi infected red blood cell (iRBC) pellet of 5% parasitemia was diluted to 50% HCT. 0.75mL of diluted culture was loaded onto 5mL of either 70% Nycodenz (N) (Serumwerk Bernburg, 18003) or 60% Percoll (P) (CAT NO) density gradient and centrifuged at 900g for 12 minutes (brake 0) for Nycodenz or 2400rpm for 10 minutes (brake 0) for Percoll, to separate iRBCs from non-iRBCs. The interfaces of the gradients were washed in 10mL medium without serum. The enriched iRBC pellets were resuspended in 2mL PBS-BSA buffer (PBS with 0.5% BSA).

value: culture

tag: strain

value: Nycodenz


title: EVTd8_T007_D3_rep1

description:
Library name: EVTd8_T007_D3_rep1
RNA-seq


title: TSC_T007_0.3uM_rep2

description:
Library name: TSC_T007_0.3uM_rep2
RNA-seq

value: TSCs were treated with 0.3 μM T0070907 and maintained for 72 hours.


title: P. knowlesi in blood, Nycodenz, gravity

description: P. knowlesi in blood, Nycodenz, gravity

source_name: blood

value: blood

value: Nycodenz, gravity


title: P. knowlesi in blood, Nycodenz, centrifuge

value: Nycodenz, centrifuged


title: TSC_T007_1uM_rep1

description:
Library name: TSC_T007_1uM_rep1
RNA-seq


title: P. knowlesi in blood, MACS column, centrifuged

value: MACS, centrifuged


title: EVTd8_shCtrl_rep2

description:
Library name: EVTd8_shCtrl_rep2
RNA-seq

value: Cells were infected with non-targeting control shRNA lentivirus 3–20 h after EVT induction to control for shRNA delivery.


title: EVTd8_T007_D0_rep2

description:
Library name: EVTd8_T007_D0_rep2
RNA-seq

value: Placenta

value: Cells were treated with 1 μM T0070907 starting on day 0 of EVT differentiation and maintained until day 8.


title: uninfected glands - biol repl 6

description: Library name: 031

data_processing:
Adapter trimming was performed using Cutadapt according to trimming instructions provided for the NEXTflex kit.Read mapping was performed using Bowtie1 (-k 100 --best --strata). For samples from uninfected flies, mapping was performed using the Glossina morsitans Yale genome (GmorY1), obtained from VectorBase - release 63.24 For samples isolated from the infected flies, mapping was performed using a merged genome index comprising the GmorY1 genome and the Trypanosoma brucei TREU927 (TbT927) genome, obtained from TriTrypDB - release 63. To annotate reads per read length (for visualizing the distribution of RNA type like rRNA, sRNA, mRNA, etc. according to their length), reads were sorted for each category, mapped, and annotated per read length. For this, gff annotation files for both reference genomes were downloaded from VectorBase and TriTrypDB. Gff files were merged and harmonised using scripts from the AGAT suite. The featureCounts program was subsequently used for assigning reads to gene features (allowing overlapping annotations and multiple feature assignment; -M -O arguments). Additional mapping statistics were obtained using Qualimap v. 2.3. Mapping results were summarized using MultiQC.Taxonomic read classification to check for potential contamination or check the presence of symbiotic species, was done using Kraken2, with the pre-built Kraken2-Microbial database (version September 2018).Output analysis and visualisation was done with KronaTools.
Assembly: Glossina morsitans morsitans GmorY1
Supplementary files format and content: Raw read counts of all detected miRNAs in the 32 samples.

molecule: total RNA

organism: Glossina morsitans morsitans

source_name: glands

extract_protocol:
RNA from these 32 pooled samples was extracted using the miRNeasy Micro kit of Qiagen
SmallRNA libraries were constructed using he NEXTflex Small RNA-Seq Kit (Perkin-Elmer, Waltham, MA, USA)

treatment_protocol: Tsetse flies (Glossina morsitans morsitans) were available from the colony at the Institute of Tropical Medicine, Antwerp. The tsetse fly colony is maintained on defibrinated bovine/sheep blood using an in vitro feeding system, at 25±0.5°C and a relative humidity of 65%-75%. To obtain infected flies, freshly emerged male tsetse flies were fed for their first blood meal with defibrinated sheep blood (E&O Laboratories LTD-UK) containing the T. brucei brucei AnTat1.1 bloodstream parasites (around 5.106 tryps./ml) and supplemented with 10 mM reduced L-glutathione to increase trypanosome infection establishment in the tsetse midgut.21 The bloodstream trypanosomes were collected by heart puncture from cyclophosphamide-immune suppressed mice at day 7 after the initial trypanosome inoculation. Then, the flies were further maintained for four weeks while feeding three times a week on uninfected defibrinated sheep blood. Thirty days after the initial blood meal, flies that carried a metacyclic trypanosome infection in the salivary glands were selected by induced probing on a microscopic slide and subsequent examination of the fly spit by phase-contrast microscopy (400x). Salivary glands were dissected in ice-cold sterile physiological H2O and the saliva was allowed to flow out for at least two hours. Then, salivary glands, saliva, and metacyclic parasites were obtained separately by sequential centrifugation.  Salivary glands and saliva of uninfected male flies (control group) of the same age and with the same feeding history were also sampled at this stage. All samples (infected and uninfected) were obtained from two independent infection- collection cycles, yielding samples each derived from a pool of 35 flies. At the end, six pools of salivary gland, saliva, and metacyclic parasite samples were obtained from the infected flies.  From the uninfected flies, seven pools of salivary gland and saliva samples were obtained.

value: glands

value: uninfected


title: EVTd2_PPARG_rep1

description:
Library name: EVTd2_PPARG_rep1
EVT day 2 cells were harvested for PPARG ChIP-seq.

value: Human trophoblast stem cells

value: Cells under control conditions on EVT day 2.


title: P. knowlesi in blood, MACS column, gravity

value: MACS, gravity


title: EVTd8_T007_D0_rep1

description:
Library name: EVTd8_T007_D0_rep1
RNA-seq


title: TSC_T007_0.3uM_rep1

description:
Library name: TSC_T007_0.3uM_rep1
RNA-seq


title: EVTd8_shCtrl_rep1

description:
Library name: EVTd8_shCtrl_rep1
RNA-seq


title: uninfected glands - biol repl 5

description: Library name: 030


title: TSC_T007_3uM_rep2

description:
Library name: TSC_T007_3uM_rep2
RNA-seq

value: TSCs were treated with 3 μM T0070907 and maintained for 72 hours.


title: EVTd8_shPPARG_rep2

description:
Library name: EVTd8_shPPARG_rep2
RNA-seq

value: PPARG KD1 shRNA lentiviral infection was performed 3–20 h after EVT induction to achieve sustained PPARG knockdown during differentiation.


title: P. knowlesi in culture, Percoll gradient

value: culture

value: Percoll


title: uninfected saliva - biol repl 7

description: Library name: 029

source_name: saliva

value: saliva


title: EVTd8_shPPARG_rep1

description:
Library name: EVTd8_shPPARG_rep1
RNA-seq


title: uninfected saliva - biol repl 6

description: Library name: 028


title: EVTd8_shPPARG_DLX6Rescue_rep2

description:
Library name: EVTd8_shPPARG_DLX6Rescue_rep2
RNA-seq

value: PPARG KD1 shRNA lentiviral infection was performed 3–20 h after EVT induction to achieve sustained PPARG knockdown during differentiation, and DLX6 overexpression was induced from day 1 of differentiation.


title: TSC_T007_10uM_rep2

description:
Library name: TSC_T007_10uM_rep2
RNA-seq

value: TSCs were treated with 10 μM T0070907 and maintained for 72 hours.


title: uninfected saliva - biol repl 5

description: Library name: 027


title: EVTd8_shPPARG_DLX6Rescue_rep1

description:
Library name: EVTd8_shPPARG_DLX6Rescue_rep1
RNA-seq


title: infected saliva - biol repl 6

description: Library name: 026

value: infected


title: TSC_shPPARG_Rescue15_rep2

description:
Library name: TSC_shPPARG_Rescue15_rep2
RNA-seq

value: TSCs were infected with PPARG KD1 shRNA lentivirus and post 72 hours shRNA-resistant PPARG was Dox-induced for 3 days, induced with 15 ng/mL Dox.


title: infected saliva - biol repl 5

description: Library name: 025


title: TSC_shPPARG_Rescue15_rep1

description:
Library name: TSC_shPPARG_Rescue15_rep1
RNA-seq


title: uninfected glands - biol repl 7

description: Library name: 032


title: infected metacyclics - biol repl 6

description: Library name: 023

source_name: metacyclics

value: metacyclics


title: TSC_shPPARG_Rescue12.5_rep1

description:
Library name: TSC_shPPARG_Rescue12.5_rep1
RNA-seq

value: Placenta

value: TSCs were infected with PPARG KD1 shRNA lentivirus and post 72 hours shRNA-resistant PPARG was Dox-induced for 3 days, induced with 12.5 ng/mL Dox.


title: TSC_shCtrl_rep2

description:
Library name: TSC_shCtrl_rep2
RNA-seq

value: TSCs were infected with non-targeting control shRNA lentivirus and maintained under self-renewal conditions.


title: infected metacyclics - biol repl 4

description: Library name: 021


title: TSC_shCtrl_rep1

description:
Library name: TSC_shCtrl_rep1
RNA-seq


title: infected glands - biol repl 6

description: Library name: 020

value: glands


title: TSC_shPPARG_rep2

description:
Library name: TSC_shPPARG_rep2
RNA-seq

value: Human trophoblast stem cells

value: TSCs were infected with PPARG KD1 shRNA lentivirus and maintained under self-renewal conditions.


title: infected glands - biol repl 5

description: Library name: 019


title: infected glands - biol repl 4

description: Library name: 018


title: TSC_shPPARG_rep1

description:
Library name: TSC_shPPARG_rep1
RNA-seq


title: uninfected saliva - biol repl 4

description: Library name: 017

value: uninfected


title: dTETv4_H3K4me3

city: Sydney

first: Merlin

last: Crossley

state: NSW

address: UNSW

department: BABS

country: Australia

institute: University of New South Wales

description: Library name: dTETv4_H3K4me3

data_processing:
BWA mem mapping to hg19
Assembly: hg19
Supplementary files format and content: bw files
Library strategy: CUT&Run

growth_protocol: Cells cultured in Phase 1 media include IMDM (Thermo Fisher Scientific, Waltham, MA, USA), 3% human AB serum (Atlanta Biologicals, Flowery Branch, GA, USA, S40110), 2% human blood type AB plasma (SeraCare, Milford, MA, USA 1810-0001), 1 penicillin/streptomycin, 3 units/mL erythropoietin (EPOGEN; Amgen, Thousand Oaks, CA, USA # 55513-144-01), 3 units/mL heparin (Sagent Pharmaceuticals, Schaumburg, IL, USA # 25021-401-02), 200 μg/mL holo-transferrin (Millipore Sigma, Burlington, MA, USA T0665), 10 ng/mL human SCF, and 1 ng/mL human interleukin-3 (IL-3; R&D systems, Minneapolis, MN, USA, 203-IL/CF) for 7 days.

extract_protocol: Library construction for DNA sequencing was performed using a NEBNext UltraII DNA Library Prep Kit from NEB (E7645S). Indexed samples were analyzed by paired-end NGS using an Illumina NextSeq Mid-Output (150 cycles) Kit.

treatment_protocol: CD34+ cell were electroporated with Cas9+ NT/UHRF1 gRNA1 or HBG promoter gRNA1-6+TETv4 /dTETv4 mRNA

value: WT

value: electroporated  with dTETv4 mRNA and HBG promoter sgRNA1-9


title: dTETv4_NFY

description: Library name: dTETv4_NFY

value: electroporated  with dTETv4 mRNA and HBG promoter sgRNA1-10


title: uninfected saliva - biol repl 3

description: Library name: 016


title: dTETv4_BCL11A

description: Library name: dTETv4_BCL11A

value: electroporated  with dTETv4 mRNA and HBG promoter sgRNA1-7


title: infected saliva - biol repl 3

description: Library name: 015

value: saliva


title: infected saliva - biol repl 2

description: Library name: 014


title: TETv4_NFY

description: Library name: TETv4_NFY

value: HBG promoter demethylation

value: electroporated with TETv4 mRNA and HBG promoter sgRNA1-9


title: infected metacyclics - biol repl 3

description: Library name: 013

value: infected


title: infected saliva - biol repl 4

description: Library name: 024


title: infected glands - biol repl 3

description: Library name: 012


title: TETv4_GATA1

description: Library name: TETv4_GATA1

value: electroporated with TETv4 mRNA and HBG promoter sgRNA1-7


title: TETv4_H3K4me3

description: Library name: TETv4_H3K4me3

value: electroporated with TETv4 mRNA and HBG promoter sgRNA1-8


title: infected glands - biol repl 2

description: Library name: 010


title: infected metacyclics - biol repl 2

description: Library name: 011

value: metacyclics


title: infected metacyclics - biol repl 5

description: Library name: 022


title: TETv4_BCL11A

description: Library name: TETv4_BCL11A

value: electroporated with TETv4 mRNA and HBG promoter sgRNA1-6


title: TSC_shPPARG_Rescue12.5_rep2

description:
Library name: TSC_shPPARG_Rescue12.5_rep2
RNA-seq

value: Placenta

value: TSCs were infected with PPARG KD1 shRNA lentivirus and post 72 hours shRNA-resistant PPARG was Dox-induced for 3 days, induced with 12.5 ng/mL Dox.


title: uninfected glands - biol repl 3

description: Library name: 008

value: glands


title: uninfected glands - biol repl 4

description: Library name: 009


title: infected metacyclics - biol repl 1

description: Library name: 007


title: infected glands - biol repl 1

description: Library name: 006


title: uninfected glands - biol repl 2

description: Library name: 005


title: dTETv4_GATA1

description: Library name: dTETv4_GATA1

value: electroporated  with dTETv4 mRNA and HBG promoter sgRNA1-8


title: uninfected glands - biol repl 1

description: Library name: 004

value: uninfected


title: infected saliva - biol repl 1

description: Library name: 003


title: uninfected saliva - biol repl 1

description: Library name: 001


title: uninfected saliva - biol repl 2

description: Library name: 002


title: SIO_MTF_WT_Zn3

city: Providence

first: Geongoo

last: Han

address: 171 Meeting St.

institute: Brown University

description:
Library name: sv_ry_mtf1_ko_sio_rna12
SIO_Zn_WT3

data_processing:
Adapter and low-quality sequences were trimmed from the raw sequence reads using Trimmomatic (v0.36)
Trimmed sequences were aligned to the mm10 mouse genome and reads per gene was counted using STAR (v2.7.3a)
Gene count was normalized in DESeq2 v1.38.1
Assembly: mm10
Supplementary files format and content: tab-delimited text file raw counts for all samples
Supplementary files format and content: tab-delimited text file normalized counts by DESeq2 for all samples

organism: Mus musculus

source_name: small intestinal organoid

extract_protocol:
RNA from small intestinal organoid was extracted using the RNeasy Mini Kit (Qiagen).
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification.

value: small intestinal organoid

value: WT

value: Zn


title: Huh7-Lunet,NA,none,Mock,rep5

city: Princeton

first: Aaron

middle: E

last: Lin

state: NJ

address: Washington Road

department: Molecular Biology

institute: Princeton University

description:
Library name: sMPS088.l1
sMPS088.l1

data_processing:
Reads were demultiplexed using Picard v2.25.6, from within viral-core v2.3.1 with the read structure ‘5S8B15M8B101T’ and Q20M1 mismatch tolerance.
Demultiplexed reads were mapped to the human genome hg38, plus the HCV/Jc1 isolate reference (derived from GenBank OQ726018.1), using STAR v2.7.11b.
Uniquely mapped reads were counted based on the GENCODE comprehensive gene annotation on the primary assembly, plus the positive-sense ('JC1GENE1') and negative-sense ('JC1GENE2') HCV RNA, using htseq-count v2.0.5.
Assembly: hg38, GENCODE release 39
Supplementary files format and content: Counts matrix of genes (hg38, v39) x all 96 samples

growth_protocol: Cells were maintained in Dulbecco’s Modified Eagle’s Medium (DMEM, Thermo Fisher Scientific, Waltham, MA, USA) containing 10% (v/v) heat-inactivated fetal bovine serum (FBS) (Bio-Techne, Minneapolis, MN, USA) and 1% (v/v) penicillin/streptomycin (Corning Inc., Corning, NY, USA) at 37 °C with 5% (v/v) CO2

extract_protocol:
At indicated timepoints post-transduction, cells were trypsinized, centrifuged at 2000 rpm for 3 min at 4 °C, washed once with DPBS, and resuspended in 200 μL H2O with 133 μL lysis/binding buffer (Applied Biosystems, Waltham, MA, USA). Timepoints were frozen on dry-ice and stored at −20 °C until RNA extraction. RNA extraction was performed using the KingFisher Flex System (Thermo Fisher Scientific, Waltham, MA, USA). Samples were subsequently treated with 12 μL of 1X DNase I (RNase-free) (New England Biolabs, Ipswich, MA, USA) for 30 min at 37 °C. Samples were re-extracted from this reaction using 0.8X SPRIselect (Beckman Coulter, Brea, CA) and quantified via NanoDrop spectrophotometer (Thermo Fisher Scientific, Waltham, MA, USA).
Up to 25 ng total RNA was used per sample for gene expression profiling. Bulk RNA-barcoding and sequencing (BRB-Seq) was performed with minor modifications. At the reverse transcription (RT) step, Template Switching RT Enzyme Mix (New England Biolabs, Ipswich, MA, USA), along with a uniquely barcoded oligo(dT)30 primer was used for each sample, modified with the Illumina TruSeq Read 1 priming site instead of Nextera Read 1. The remainder of the BRB-Seq protocol was followed, pooling up to 24 first-strand cDNAs into a single tube, followed by Gubler-Hoffman nick translation cDNA synthesis, and tagmented cDNA with in-house-produced Tn5(62). cDNAs were amplified for 14–15 PCR cycles using a P5-containing primer and a distinct multiplexed i7 indexing primer  (Chromium i7 Multiplex Kit, 10X Genomics, Pleasanton, CA). Size-selection was performed using 0.65X SPRIselect (Beckman Coulter, Brea, CA), and libraries were sequenced on one flowcell of a NovaSeq SP v1.5 flowcell (Illumina, San Diego, CA) with 28 cycles Read 1, 8 cycles Read i7, and 101 cycles Read 2.

treatment_protocol: HCV infections were conducted in a 10cm plate with 1E6 Huh7-Lunet cells seeded per plate 12 hrs pre-infection. Cells were infected at an MOI of 1 and expanded over the course of a week. On day 6 post-infection, 24-well plates were seeded with 3E4 cells per well. On day 7, cells were transduced with 500 μL 1:5 diluted lentivirus.

value: hepatoma

tag: time post-transduction

tag: transgene

tag: virus

value: Mock

tag: rna conc

tag: replicate


title: Huh7-Lunet,72h,mmRTP4,Mock,rep6

description:
Library name: sMPS095.l1
sMPS095.l1


title: Huh7-Lunet,72h,blank,HCVJc1,rep6

description:
Library name: sMPS092.l1
sMPS092.l1

value: blank


title: Huh7-Lunet,NA,none,Mock,rep6

description:
Library name: sMPS096.l1
sMPS096.l1


title: Huh7-Lunet,72h,mmRTP4,HCVJc1,rep6

description:
Library name: sMPS094.l1
sMPS094.l1


title: Huh7-Lunet,24h,mmRTP4,HCVJc1,rep6

description:
Library name: sMPS091.l1
sMPS091.l1


title: Huh7-Lunet,24h,hsRTP4,HCVJc1,rep6

description:
Library name: sMPS090.l1
sMPS090.l1


title: Huh7-Lunet,24h,blank,HCVJc1,rep6

description:
Library name: sMPS089.l1
sMPS089.l1


title: Huh7-Lunet,72h,mmRTP4,Mock,rep5

description:
Library name: sMPS087.l1
sMPS087.l1


title: Huh7-Lunet,72h,hsRTP4,HCVJc1,rep6

description:
Library name: sMPS093.l1
sMPS093.l1


title: Huh7-Lunet,72h,mmRTP4,HCVJc1,rep5

description:
Library name: sMPS086.l1
sMPS086.l1


title: SIO_MTF_WT_Zn2

description:
Library name: sv_ry_mtf1_ko_sio_rna11
SIO_Zn_WT2


title: SIO_MTF_WT_Zn1

description:
Library name: sv_ry_mtf1_ko_sio_rna10
SIO_Zn_WT1


title: SIO_MTF_KO_Zn2

description:
Library name: sv_ry_mtf1_ko_sio_rna8
SIO_Zn_KO2

value: KO


title: Huh7-Lunet,72h,hsRTP4,HCVJc1,rep5

description:
Library name: sMPS085.l1
sMPS085.l1


title: Huh7-Lunet,72h,blank,HCVJc1,rep5

description:
Library name: sMPS084.l1
sMPS084.l1


title: SIO_MTF_KO_Zn3

description:
Library name: sv_ry_mtf1_ko_sio_rna9
SIO_Zn_KO3


title: Huh7-Lunet,24h,blank,HCVJc1,rep5

description:
Library name: sMPS081.l1
sMPS081.l1


title: Huh7-Lunet,24h,mmRTP4,HCVJc1,rep5

description:
Library name: sMPS083.l1
sMPS083.l1


title: SIO_MTF_WT3

description:
Library name: sv_ry_mtf1_ko_sio_rna6
SIO_WT3

value: control


title: Huh7-Lunet,24h,hsRTP4,HCVJc1,rep5

description:
Library name: sMPS082.l1
sMPS082.l1


title: SIO_MTF_WT2

description:
Library name: sv_ry_mtf1_ko_sio_rna5
SIO_WT2


title: Huh7-Lunet,72h,mmRTP4,Mock,rep4

description:
Library name: sMPS079.l1
sMPS079.l1


title: SIO_MTF_KO_Zn1

description:
Library name: sv_ry_mtf1_ko_sio_rna7
SIO_Zn_KO1


title: Huh7-Lunet,NA,none,Mock,rep4

description:
Library name: sMPS080.l1
sMPS080.l1


title: SIO_MTF_WT1

description:
Library name: sv_ry_mtf1_ko_sio_rna4
SIO_WT1


title: Huh7-Lunet,72h,mmRTP4,HCVJc1,rep4

description:
Library name: sMPS078.l1
sMPS078.l1


title: SIO_MTF_KO3

description:
Library name: sv_ry_mtf1_ko_sio_rna3
SIO_KO3


title: SIO_MTF_KO2

description:
Library name: sv_ry_mtf1_ko_sio_rna2
SIO_KO2


title: Huh7-Lunet,72h,hsRTP4,HCVJc1,rep4

description:
Library name: sMPS077.l1
sMPS077.l1


title: SIO_MTF_KO1

description:
Library name: sv_ry_mtf1_ko_sio_rna1
SIO_KO1


title: HEK 293T cells, CAT-seq Enrich, rep2

city: Beijing

first: Qidong

last: Deng

address: No.5 Yiheyuan Road Haidian District, Beijing 100871 P.R. China

department: School of Life Sciences

institute: Peking university

description: HEK_293T_CAT-seq_Input_Enrich_Reads_Count.txt

data_processing:
Raw reads were trimmed with Trim Galore!(v0.6.7) to remove low-quality bases and adapters and subsequently aligned to the Homo sapiens genome (Ensembl GRCh38.107) or Mus musculus(GRCm38.98) by HISAT2 (v2.2.1) with with ‘-rna-strandness RF’ parameters.After the low-quality reads were filtered out by SAMtools (v1.9), fragments mapped on the exons were processed using featureCounts (v2.0.2) to obtain the gene expression matrix.The R/Bioconductor package DESeq2 (v1.36.0) was used for data normalization and differential expression analysis.
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: HEK 293T

growth_protocol: HEK 293T cell line was cultured in DMEM medium (Gibco) supplemented with 10% fetal bovine serum and 1% penicillin/ streptomycin at 37°C under 5% CO2.

extract_protocol:
Cells grown in cell culture dishes at ~90% confluency were incubated with 50 nM photocatalyst in fresh medium at 37°C under 5% CO2 for 30 min, washed with PBS for three times, incubated with 50 µM QMPAB-2 in culture medium for 30 min and washed twice with PBS. After washing, cells were maintained in fresh medium at 37°C under 5% CO2 for 5 min and illuminated with blue LED (4 mW cm-2; λmax ∼460 nm) for 15 min at room temperature. Cells were placed about 5 cm from the light source. After illumination, cells were immediately collected using cell scraper and lysed with TRIzol reagent. Cellular total RNA purification was operated following the manufacture protocol by isopropanol precipitation.Total RNA was extracted using TRIzol reagent(Invitrogen).
RNA libraries were prepared using SMARTer Stranded Total RNA-Seq Kit v2(Takara). Labeled RNA was captured using Dynabeads MyOne Streptavidin C1 (Invitrogen).

value: HEK 293T

value: Human kidney epithelial cells

value: CAT-seq+


title: Huh7-Lunet,24h,mmRTP4,HCVJc1,rep4

description:
Library name: sMPS075.l1
sMPS075.l1


title: Huh7-Lunet,72h,mmRTP4,HCVJc1,rep3

description:
Library name: sMPS070.l1
sMPS070.l1


title: Huh7-Lunet,24h,hsRTP4,HCVJc1,rep4

description:
Library name: sMPS074.l1
sMPS074.l1


title: Huh7-Lunet,NA,none,Mock,rep3

description:
Library name: sMPS072.l1
sMPS072.l1


title: HEK 293T cells, CAT-seq Enrich, rep1


title: Huh7-Lunet,72h,blank,HCVJc1,rep4

description:
Library name: sMPS076.l1
sMPS076.l1


title: HEK 293T cells, CAT-seq Input, rep2

value: CAT-seq-


title: Huh7-Lunet,24h,blank,HCVJc1,rep4

description:
Library name: sMPS073.l1
sMPS073.l1


title: Huh7-Lunet,72h,hsRTP4,HCVJc1,rep3

description:
Library name: sMPS069.l1
sMPS069.l1


title: Huh7-Lunet,72h,mmRTP4,Mock,rep3

description:
Library name: sMPS071.l1
sMPS071.l1


title: Huh7-Lunet,72h,blank,HCVJc1,rep3

description:
Library name: sMPS068.l1
sMPS068.l1


title: HEK 293T cells, CAT-seq Input, rep1


title: HCT116_HPLM_24_hr_DMSO_Butyrate_rep2

description: Library name: Sample 63

value: Colorectal carcinoma

value: Wild type

value: 5 mM butyrate and 0.1% DMSO for 24 hours


title: Huh7-Lunet,24h,mmRTP4,HCVJc1,rep3

description:
Library name: sMPS067.l1
sMPS067.l1


title: Huh7-Lunet,24h,hsRTP4,HCVJc1,rep3

description:
Library name: sMPS066.l1
sMPS066.l1


title: Control CMO

city: Freiburg

first: Maximilian

last: Frosch

address: Breisacher Str. 64

department: Institute of Neuropathology

country: Germany

institute: University Medical Center Freiburg

description: Library name: Control CMO

data_processing:
Fastq files were further processed using the Cell Ranger v7.1.0 pipeline (10x Genomics) for demultiplexing, read alignment
Assembly: GRCh38p13, Gencode v35, hg38
Supplementary files format and content: Fastq files, filtered feature-barcode matrices, Seurat objects

source_name: Brain

extract_protocol:
snRNA-seq using 10x was conducted on nuclei extracted from frozen brain specimen
cDNA amplification and library preparation were conducted following the manufacturer’s instructions (Chromium Next GEM Single Cell 3' Kit v3.1 (10x Genomics))

value: Brain


title: Huh7-Lunet,24h,blank,HCVJc1,rep3

description:
Library name: sMPS065.l1
sMPS065.l1


title: Sandhoff GEX

description: Library name: Sandhoff GEX


title: Sandhoff CMO

description: Library name: Sandhoff CMO


title: Control GEX

description: Library name: Control GEX


title: Huh7-Lunet,NA,none,Mock,rep2

description:
Library name: sMPS064.l1
sMPS064.l1


title: Y-ZT6-2

city: HangZhou

first: Wang

last: Zhijie

state: ZheJiang

address: No. 618, Fengqi East Road

department: Department of Retina Center

institute: Eye Hospital and School of Ophthalmology

description: Library name: Y-ZT6-2

data_processing:
Raw reads were trimmed and quality-controlled using FastQC software (v0.23.4). Clean reads were aligned to the mouse genome (Mus_musculus.GRCm39) using HISAT2 (v2.2.1). Raw read counts and reads per kilobase per million mapped reads (RPKM) values were quantified using Subread (v2.0.6)
Assembly: Mus_musculus.GRCm39
Supplementary files format and content: tab-delimited csv file includes RPKM value for each Sample

source_name: retina

extract_protocol:
At each time point, four mice from each group were euthanized by cervical dislocation, and the right eyes were enucleated. Under dim red light, the anterior segments were removed, and the retinas were carefully dissected.
Total RNA was isolated from retina tissues using TRIzol reagent according to the manufacturer’s instructions. RNA integrity was assessed using the Nano 6000 Assay Kit on the Bioanalyzer 2100 system. mRNA was enriched from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was performed using divalent cations at elevated temperatures in First Strand Synthesis Reaction buffer. Approximately 2 μg of total RNA was used to synthesize first-strand cDNA using random hexamer primers, and second-strand cDNA synthesis was subsequently conducted with DNA polymerase I and RNase H. After end-repair of DNA fragments, adaptors with hairpin-loop structures were ligated for hybridization. The cDNA fragments, preferentially 370-420 bp in length, were PCR-amplified with Phusion High-Fidelity DNA polymerase and universal PCR primers.

value: retina

tag: group

value: Young

tag: time


title: Y-ZT6-3

description: Library name: Y-ZT6-3


title: Y-ZT6-4

description: Library name: Y-ZT6-4


title: Y-ZT6-1

description: Library name: Y-ZT6-1


title: Huh7-Lunet,72h,mmRTP4,HCVJc1,rep2

description:
Library name: sMPS062.l1
sMPS062.l1

tag: cell line


title: Y-ZT22-3

description: Library name: Y-ZT22-3


title: Y-ZT22-4

description: Library name: Y-ZT22-4


title: Y-ZT22-2

description: Library name: Y-ZT22-2


title: Huh7-Lunet,72h,hsRTP4,HCVJc1,rep2

description:
Library name: sMPS061.l1
sMPS061.l1

tag: cell type


title: Huh7-Lunet,72h,blank,HCVJc1,rep2

description:
Library name: sMPS060.l1
sMPS060.l1


title: Huh7-Lunet,24h,mmRTP4,HCVJc1,rep2

description:
Library name: sMPS059.l1
sMPS059.l1


title: Huh7-Lunet,24h,blank,HCVJc1,rep2

description:
Library name: sMPS057.l1
sMPS057.l1


title: Y-ZT2-4

description: Library name: Y-ZT2-4


title: Huh7-Lunet,NA,none,Mock,rep1

description:
Library name: sMPS056.l1
sMPS056.l1


title: Huh7-Lunet,24h,hsRTP4,HCVJc1,rep2

description:
Library name: sMPS058.l1
sMPS058.l1


title: Y-ZT2-3

description: Library name: Y-ZT2-3


title: Y-ZT2-1

description: Library name: Y-ZT2-1


title: Huh7-Lunet,72h,mmRTP4,Mock,rep1

description:
Library name: sMPS055.l1
sMPS055.l1


title: Huh7-Lunet,72h,mmRTP4,HCVJc1,rep1

description:
Library name: sMPS054.l1
sMPS054.l1


title: Y-ZT18-4

description: Library name: Y-ZT18-4


title: Y-ZT18-3

description: Library name: Y-ZT18-3


title: Huh7-Lunet,72h,blank,HCVJc1,rep1

description:
Library name: sMPS052.l1
sMPS052.l1


title: Huh7-Lunet,72h,hsRTP4,HCVJc1,rep1

description:
Library name: sMPS053.l1
sMPS053.l1


title: Y-ZT18-2

description: Library name: Y-ZT18-2


title: Y-ZT18-1

description: Library name: Y-ZT18-1


title: Y-ZT14-4

description: Library name: Y-ZT14-4


title: Huh7-Lunet,24h,mmRTP4,HCVJc1,rep1

description:
Library name: sMPS051.l1
sMPS051.l1


title: Huh7-Lunet,24h,hsRTP4,HCVJc1,rep1

description:
Library name: sMPS050.l1
sMPS050.l1


title: Huh7-Lunet,72h,mmRTP4,Mock,rep2

description:
Library name: sMPS063.l1
sMPS063.l1


title: Y-ZT14-3

description: Library name: Y-ZT14-3


title: Huh7-Lunet,24h,blank,HCVJc1,rep1

description:
Library name: sMPS049.l1
sMPS049.l1


title: Y-ZT14-2

description: Library name: Y-ZT14-2


title: Y-ZT22-1

description: Library name: Y-ZT22-1


title: Y-ZT14-1

description: Library name: Y-ZT14-1


title: Y-ZT10-4

description: Library name: Y-ZT10-4


title: Huh7-Lunet,72h,blank,Mock,rep6

description:
Library name: sMPS048.l1
sMPS048.l1


title: Huh7-Lunet,72h,hsRTP4,Mock,rep6

description:
Library name: sMPS047.l1
sMPS047.l1


title: Y-ZT2-2

description: Library name: Y-ZT2-2


title: Y-ZT10-3

description: Library name: Y-ZT10-3


title: Huh7-Lunet,12h,mmRTP4,HCVJc1,rep6

description:
Library name: sMPS043.l1
sMPS043.l1


title: Huh7-Lunet,48h,mmRTP4,HCVJc1,rep6

description:
Library name: sMPS046.l1
sMPS046.l1


title: Y-ZT10-2

description: Library name: Y-ZT10-2


title: Huh7-Lunet,48h,hsRTP4,HCVJc1,rep6

description:
Library name: sMPS045.l1
sMPS045.l1


title: AG-ZT6-4

description: Library name: AG-ZT6-4

value: Aging


title: Y-ZT10-1

description: Library name: Y-ZT10-1


title: Huh7-Lunet,48h,blank,HCVJc1,rep6

description:
Library name: sMPS044.l1
sMPS044.l1


title: Huh7-Lunet,12h,hsRTP4,HCVJc1,rep6

description:
Library name: sMPS042.l1
sMPS042.l1


title: Huh7-Lunet,12h,blank,HCVJc1,rep6

description:
Library name: sMPS041.l1
sMPS041.l1


title: Huh7-Lunet,72h,blank,Mock,rep5

description:
Library name: sMPS040.l1
sMPS040.l1


title: AG-ZT6-2

description: Library name: AG-ZT6-2


title: AG-ZT22-3

description: Library name: AG-ZT22-3


title: Huh7-Lunet,48h,hsRTP4,HCVJc1,rep5

description:
Library name: sMPS037.l1
sMPS037.l1


title: Huh7-Lunet,48h,mmRTP4,HCVJc1,rep5

description:
Library name: sMPS038.l1
sMPS038.l1


title: AG-ZT6-3

description: Library name: AG-ZT6-3


title: AG-ZT6-1

description: Library name: AG-ZT6-1


title: AG-ZT22-1

description: Library name: AG-ZT22-1


title: Huh7-Lunet,48h,blank,HCVJc1,rep5

description:
Library name: sMPS036.l1
sMPS036.l1


title: Huh7-Lunet,12h,mmRTP4,HCVJc1,rep5

description:
Library name: sMPS035.l1
sMPS035.l1


title: AG-ZT2-4

description: Library name: AG-ZT2-4


title: AG-ZT22-2

description: Library name: AG-ZT22-2


title: Huh7-Lunet,12h,hsRTP4,HCVJc1,rep5

description:
Library name: sMPS034.l1
sMPS034.l1


title: AG-ZT2-2

description: Library name: AG-ZT2-2


title: AG-ZT2-3

description: Library name: AG-ZT2-3


title: Huh7-Lunet,12h,blank,HCVJc1,rep5

description:
Library name: sMPS033.l1
sMPS033.l1


title: AG-ZT2-1

description: Library name: AG-ZT2-1


title: Huh7-Lunet,72h,blank,Mock,rep4

description:
Library name: sMPS032.l1
sMPS032.l1


title: Huh7-Lunet,72h,hsRTP4,Mock,rep4

description:
Library name: sMPS031.l1
sMPS031.l1


title: AG-ZT18-3

description: Library name: AG-ZT18-3


title: Huh7-Lunet,48h,mmRTP4,HCVJc1,rep4

description:
Library name: sMPS030.l1
sMPS030.l1


title: AG-ZT18-2

description: Library name: AG-ZT18-2


title: AG-ZT18-1

description: Library name: AG-ZT18-1


title: Huh7-Lunet,12h,mmRTP4,HCVJc1,rep4

description:
Library name: sMPS027.l1
sMPS027.l1


title: Huh7-Lunet,48h,blank,HCVJc1,rep4

description:
Library name: sMPS028.l1
sMPS028.l1


title: AG-ZT22-4

description: Library name: AG-ZT22-4


title: Huh7-Lunet,72h,hsRTP4,Mock,rep5

description:
Library name: sMPS039.l1
sMPS039.l1


title: Huh7-Lunet,12h,hsRTP4,HCVJc1,rep4

description:
Library name: sMPS026.l1
sMPS026.l1


title: AG-ZT14-3

description: Library name: AG-ZT14-3


title: AG-ZT14-1

description: Library name: AG-ZT14-1


title: AG-ZT14-2

description: Library name: AG-ZT14-2


title: Huh7-Lunet,72h,blank,Mock,rep3

description:
Library name: sMPS024.l1
sMPS024.l1


title: Huh7-Lunet,12h,blank,HCVJc1,rep4

description:
Library name: sMPS025.l1
sMPS025.l1


title: Huh7-Lunet,72h,hsRTP4,Mock,rep3

description:
Library name: sMPS023.l1
sMPS023.l1


title: AG-ZT10-3

description: Library name: AG-ZT10-3


title: AG-ZT10-2

description: Library name: AG-ZT10-2


title: Huh7-Lunet,48h,mmRTP4,HCVJc1,rep3

description:
Library name: sMPS022.l1
sMPS022.l1


title: AG-ZT10-4

description: Library name: AG-ZT10-4


title: Huh7-Lunet,48h,hsRTP4,HCVJc1,rep3

description:
Library name: sMPS021.l1
sMPS021.l1


title: AG-ZT10-1

description: Library name: AG-ZT10-1


title: Huh7-Lunet,48h,blank,HCVJc1,rep3

description:
Library name: sMPS020.l1
sMPS020.l1


title: ATAC-seq-MouseLeukemiaCells-DMSO_6h

description: Library name: ATAC-seq-MouseLeukemiaCells-DMSO_6h

data_processing:
ATAC-seq reads were aligned to the mouse genome, and alignments were processed with Bowtie using the command options -m 1 -v 2, allowing only uniquely mapping reads with up to two mismatches within the 150 bp reads
BigWig files were generated using the ‘bamCoverage’ function in Deeptools
Assembly: mm10
Supplementary files format and content: bigWig

source_name: Derived from spleen

growth_protocol: K/C-III leukemia cells were cultured in Retronectin-coated plates (Takata T100A) with RPMI 1640 medium (Gibco) supplemented with 1% penicillin/streptomycin, 10% FBS (Gibco), and murine SCF, IL-6, and IL-3. Cell viability was assessed with a Bio-Rad TC20 automated cell counter.

extract_protocol:
Briefly, 2.5× 104 mouse leukemia cells were treated and centrifuged at 600 g for 5 minutes at room temperature for each reaction. The cell pellet was resuspended in 50 μL lysis buffer containing 10 mM Tris-HCl (pH 7.5), 10 mM NaCl, 3 mM MgCl₂, 0.1% NP-40, 0.1% Tween-20, and 0.02% digitonin, and centrifuged at 500 g for 10 minutes at 4°C. After centrifugation, the cell pellet was processed immediately for the transposition reaction, resuspended in 50 μL transposase mixture containing 25 μL 2× TD buffer, 22.5 μL nuclease-free water, and 2.5 μL Tn5 transposase. The mixture was incubated for 30 minutes at 37°C with mixing at 1,000 rpm. The transposed DNA was purified and amplified using NEBNext high-fidelity 2× PCR master mix with custom Nextera PCR primers.
The transposed DNA was purified and amplified using NEBNext high-fidelity 2× PCR master mix with custom Nextera PCR primers. The optimal number of PCR cycles was determined by qPCR, and the DNA libraries were size-selected and sequenced on the NovaSeq 6000 platform.

value: Derived from spleen

value: HSPCs

value: hematopoietic stem and progenitor cells

tag: genotype

value: K/C-III leukemia cells

value: treated with DMSO for 6 hours


title: ATAC-seq-MouseLeukemiaCells-A485_6h

description: Library name: ATAC-seq-MouseLeukemiaCells-A485_6h

value: treated with A485 for 6 hours


title: Huh7-Lunet,12h,blank,HCVJc1,rep3

description:
Library name: sMPS017.l1
sMPS017.l1

value: hepatoma

value: blank


title: AG-ZT14-4

description: Library name: AG-ZT14-4


title: ATAC-seq-MouseLeukemiaCells-BZ1_6h

description: Library name: ATAC-seq-MouseLeukemiaCells-BZ1_6h

value: treated with BZ1 for 6 hours


title: Huh7-Lunet,12h,hsRTP4,HCVJc1,rep3

description:
Library name: sMPS018.l1
sMPS018.l1


title: Huh7-Lunet,48h,hsRTP4,HCVJc1,rep4

description:
Library name: sMPS029.l1
sMPS029.l1


title: ATAC-seq-MouseLeukemiaCells-A485_0h

description: Library name: ATAC-seq-MouseLeukemiaCells-A485_0h


title: Huh7-Lunet,72h,hsRTP4,Mock,rep2

description:
Library name: sMPS015.l1
sMPS015.l1

value: Mock


description: Library name: ChIP-seq-MouseLeukemiaCells-DMSO-antiWDR5

data_processing:
ChIP-seq reads were aligned to the mouse genome using Bowtie version 1.1.2. Only uniquely mapping reads with up to two mismatches within the 150 bp reads were considered for further analysis.
Assembly: mm10
Supplementary files format and content: bigWig

extract_protocol:
Briefly, cells were crosslinked with 1% paraformaldehyde for 10 min and were quenched with glycine for 5 min at room temperature. Fixed chromatin was sonicated with a Covaris Focused-ultrasonicator for 6 min and immunoprecipitated with the indicated antibody and Dynabeads Protein G.
Library preparation was carried out using the NEBNext Ultra II DNA Library Prep Kit for Illumina, followed by sequencing on a NovaSeq 6000.


title: Huh7-Lunet,48h,mmRTP4,HCVJc1,rep2

description:
Library name: sMPS014.l1
sMPS014.l1


title: Huh7-Lunet,72h,blank,Mock,rep2

description:
Library name: sMPS016.l1
sMPS016.l1


description: Library name: ChIP-seq-MouseLeukemiaCells-BZ1-antiPolII


description: Library name: ChIP-seq-MouseLeukemiaCells-DMSO-antiH3K4me2


title: Huh7-Lunet,48h,hsRTP4,HCVJc1,rep2

description:
Library name: sMPS013.l1
sMPS013.l1


description: Library name: ChIP-seq-MouseLeukemiaCells-DMSO-antiH3K4me1


title: Huh7-Lunet,48h,blank,HCVJc1,rep2

description:
Library name: sMPS012.l1
sMPS012.l1


title: Huh7-Lunet,12h,hsRTP4,HCVJc1,rep2

description:
Library name: sMPS010.l1
sMPS010.l1


description: Library name: ChIP-seq-MouseLeukemiaCells-BZ1-antiH3K4me2


title: Huh7-Lunet,12h,mmRTP4,HCVJc1,rep2

description:
Library name: sMPS011.l1
sMPS011.l1


description: Library name: ChIP-seq-MouseLeukemiaCells-BZ1-antiH3K4me1


description: Library name: ChIP-seq-MouseLeukemiaCells-BZ1-antiWDR5


title: Huh7-Lunet,72h,blank,Mock,rep1

description:
Library name: sMPS008.l1
sMPS008.l1


description: Library name: ChIP-seq-MouseLeukemiaCells-DMSO-antiPolII


description: Library name: ChIP-seq-MouseLeukemiaCells-DMSO-antiMLL


title: Huh7-Lunet,12h,mmRTP4,HCVJc1,rep3

description:
Library name: sMPS019.l1
sMPS019.l1


title: Huh7-Lunet,72h,hsRTP4,Mock,rep1

description:
Library name: sMPS007.l1
sMPS007.l1


title: Huh7-Lunet,12h,blank,HCVJc1,rep2

description:
Library name: sMPS009.l1
sMPS009.l1


description: Library name: ChIP-seq-MouseLeukemiaCells-DMSO-antiBPTF


title: Huh7-Lunet,48h,mmRTP4,HCVJc1,rep1

description:
Library name: sMPS006.l1
sMPS006.l1


title: Huh7-Lunet,48h,hsRTP4,HCVJc1,rep1

description:
Library name: sMPS005.l1
sMPS005.l1


description: Library name: ChIP-seq-MouseLeukemiaCells-A485-antiMLL


title: Huh7-Lunet,48h,blank,HCVJc1,rep1

description:
Library name: sMPS004.l1
sMPS004.l1


description: Library name: ChIP-seq-MouseLeukemiaCells-A485-antiBPTF


description: Library name: ChIP-seq-MouseLeukemiaCells-A485-antiPolII


title: Huh7-Lunet,12h,mmRTP4,HCVJc1,rep1

description:
Library name: sMPS003.l1
sMPS003.l1


title: Huh7-Lunet,12h,hsRTP4,HCVJc1,rep1

description:
Library name: sMPS002.l1
sMPS002.l1


title: CUT&RUN-MouseLeukemiaCells-antiSMARC1

description: Library name: Sample 85

value: untreated


title: Huh7-Lunet,12h,blank,HCVJc1,rep1

description:
Library name: sMPS001.l1
sMPS001.l1


title: CUT&RUN-MouseLeukemiaCells-antiKCIII

description: Library name: Sample 84


title: CUT&RUN-MouseLeukemiaCells-antiH3K4Me3

description: Library name: Sample 82


title: DKFZ-BT66-OFF_100nM trametinib 24h_Rep3

city: Jena

first: Romain

last: Sigaud

address: Am Klinikum 1

department: Pediatrics and Adolescent Medicine

institute: UKJ

description: Library name: Sample 15

data_processing:
Fastq files were  submitted to the RNAseqWorkflow pipeline on the OTP platform for automated reads trimming, mapping to the hg38/GRCh38.p13 human genome, annotated to ENSEMBL version 84, and calculation of TPM per transcript.
Assembly: hg38/GRCh38.p13 human genome
Supplementary files format and content: Tab-delimited text files include TPM values for each Sample

source_name: Patient-derived pilocytic astrocytoma cell line

growth_protocol: Pilocytic astrocytoma cell lines (DKFZ-BT66) were cultured in Astrocyte Basal Medium (ABM, cat. no. CC-3187, Lonza) plus supplement (Astrocyte Growth Medium BulletKit, cat.no. CC-3186, Lonza) with 1 µg/ml doxycycline (cat. no. sc-337691, Santa Cruz) to induce cell proliferation.  All cells were cultured under 5% CO2 atmosphere, at 37°C.

extract_protocol:
RNA extraction was performed using the RNeasy Mini Kit (cat. no. 74104, Qiagen) with on-column DNase digestion according to the manufacturer’s instructions.
Samples were rRNA depleted using QIAseq FastSelect (Human/Mouse/Rat 96rxns). cDNA synthesis was achieved with the NEBNext RNA First Strand Synthesis and NEBNext Ultra Directional RNA Second Strand Synthesis Modules (New England BioLabs). The remaining steps of library preparation were done using the NEBNext Ultra II DNA Library Prep Kit for Illumina (New England BioLabs)

treatment_protocol: Cells were treated with 100nM trametinib (in DMSO) for 15min, 1h, 6h or 24h.

value: Senescent cells

value: KIAA1549::BRAF fusion

value: 100nM trametinib 24h


title: DKFZ-BT66-OFF_100nM trametinib 24h_Rep2

description: Library name: Sample 14

value: Patient-derived pilocytic astrocytoma cell line


title: CUT&RUN-MouseLeukemiaCells-antiH3K4Me2

description: Library name: Sample 81


title: DKFZ-BT66-OFF_100nM trametinib 24h_Rep1

description: Library name: Sample 13


title: CUT&RUN-MouseLeukemiaCells-antiH3K27ac

description: Library name: Sample 80


title: CUT&RUN-MouseLeukemiaCells-antiBPTF

description: Library name: Sample 79


title: DKFZ-BT66-OFF_100nM trametinib 6h_Rep2

description: Library name: Sample 11

value: 100nM trametinib 6h


title: DKFZ-BT66-OFF_100nM trametinib 6h_Rep3

description: Library name: Sample 12


title: CUT&RUN-MouseLeukemiaCells-DMSO-antiMLL

description: Library name: Sample 61


title: 9022-MND50-1

city: Shanghai

first: Guoming

last: Ma

address: 100 Haike Road, Zhangjiang Hi-Tech Park

department: Interdisciplinary Research Center on Biology and Chemistry

institute: Chinese Academy of Science

description: Library name: R17029182LR01

data_processing:
The reads were aligned to the GRCh37 reference genome with HISAT2 (v.2.2.1) after removing the adapter sequences and low-quality reads using Trimmomatic (v.0.39)45. Read counts were quantified using FeatureCounts in Rsubread (v.2.0.1)46 using GENCODE GTF annotation version 19.
Assembly: GRCh37
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

extract_protocol:
TRIzol (Invitrogen) was used to extract total RNA. DNA digestion and reverse transcription were performed using the Hifair™ III 1st Strand cDNA Synthesis SuperMix for qPCR (YEASEN) according to the manufacturer’s instructions. qPCR was performed on cDNA using qPCR SYBR Green Master Mix (UNIQ) with a QuantStudio 7 Flex Real-Time PCR System according to the manufacturer’s instructions. The relative expression levels of target genes were measured using the ddCt method normalizing to control gene expression. ACTIN was used as a reference in the ALS-SOD1, ALS-FUS, and ALS-TARDBP subgroups. TFRC was used as a reference in the ALS-C9orf72. The primers used for qPCR are listed in Table S2.
RNA purification, reverse transcription, and library construction were performed in Mingma Technologies Co., Ltd. (Shanghai, China) according to the manufacturer’s instructions. RNA integrity were measured using an Agilent 2100 Bioanalyzer (Agilent). The mRNA-focused sequencing libraries from total RNA were prepared using the VAHTS mRNA-seq v3 Library Prep Kit (VAHTS, NR611). PolyA mRNA was purified from total RNA and then fragmented. The final cDNA libraries were sequenced on  an Illumina HiSeq PE150 sequencing system following Illumina protocols provided by Mingma Technologies Co., Ltd. in Shanghai.


title: 9022-NPC-3

description: Library name: R17030744LR01


title: 9022-MND50-2

description: Library name: R17029183LR01


title: 9022-MND50-3

description: Library name: R17029184LR01


title: 9022-MND28-2

description: Library name: R17029180LR01


title: 9022-MND28-1

description: Library name: R17029179LR01


title: DKFZ-BT66-OFF_100nM trametinib 1h_Rep3

description: Library name: Sample 9

value: 100nM trametinib 1h


title: CUT&RUN-MouseLeukemiaCells-DMSO-antiKC-III

description: Library name: Sample 60

value: Derived from spleen


title: 9022-NPC-2

description: Library name: R17030743LR01


title: CUT&RUN-MouseLeukemiaCells-antiIgG

description: Library name: Sample 83

value: HSPCs


title: 9022-IPS-2

description: Library name: R17030740LR01


title: CUT&RUN-MouseLeukemiaCells-DMSO-antiBPTF

description: Library name: Sample 59

value: hematopoietic stem and progenitor cells


title: 9022-IPS-1

description: Library name: R17030739LR01


title: CUT&RUN-MouseLeukemiaCells-BZ1-antiMLL

description: Library name: Sample 58

value: K/C-III leukemia cells


title: 9021-NPC-2

description: Library name: R17030749LR01


title: CUT&RUN-MouseLeukemiaCells-BZ1-antiKC-III

description: Library name: Sample 57


title: 9021-NPC-1

description: Library name: R17030748LR01


title: 9022-NPC-1

description: Library name: R17030742LR01


title: 9022-MND28-3

description: Library name: R17029181LR01


title: 9021-MND50-3

description: Library name: R18004475LR01


title: DKFZ-BT66-OFF_100nM trametinib 15min_Rep3

description: Library name: Sample 6

value: 100nM trametinib 15min


title: 9021-MND50-2

description: Library name: R17029189LR01


title: DKFZ-BT66-OFF_100nM trametinib 6h_Rep1

description: Library name: Sample 10


title: CUT&RUN-MouseLeukemiaCells-BZ1-antiBPTF

description: Library name: Sample 56


title: 9021-MND50-1

description: Library name: R17029188LR01


title: DKFZ-BT66-OFF_100nM trametinib 1h_Rep1

description: Library name: Sample 7


title: 9021-NPC-3

description: Library name: R17030750LR01


title: 9022-IPS-3

description: Library name: R17030741LR01


title: DKFZ-BT66-OFF_100nM trametinib 15min_Rep1

description: Library name: Sample 4


title: CUT&RUN-MouseLeukemiaCells-DMSO-antihaloKCIII

description: Library name: Sample 51

value: treated with DMSO for 6 hours


title: 9021-MND28-1

description: Library name: R17029185LR01


title: DKFZ-BT66-OFF_100nM trametinib 1h_Rep2

description: Library name: Sample 8


title: CUT&RUN-MouseLeukemiaCells-DMSO-antiH3K27ac

description: Library name: Sample 50


title: DKFZ-BT66-OFF_Ctrl_Rep3

description: Library name: Sample 3

value: DMSO control


title: 9021-MND28-3

description: Library name: R17029187LR01


title: CUT&RUN-MouseLeukemiaCells-A485-antihaloKCIII

description: Library name: Sample 49

value: treated with A485 for 6 hours


title: DKFZ-BT66-OFF_Ctrl_Rep2

description: Library name: Sample 2


title: 9021-IPS-2

description: Library name: R18007939LR01


title: 9021-IPS-1

description: Library name: R17030745LR01


title: CUT&RUN-MouseLeukemiaCells-A485-antiH3K27ac

description: Library name: Sample 48


title: DKFZ-BT66-OFF_Ctrl_Rep1

description: Library name: Sample 1


title: 7189-NPC-2

description: Library name: R17030761LR01


title: RNAseq-MouseLeukemiaCells-BZ1-6h-rep2

description: Library name: RNAseq-MouseLeukemiaCells-BZ1-6h-rep2

data_processing:
The sequencing data were aligned to the mm10 mouse genome, normalized (RPM), and visualized using the UCSC genome browser.
Differential gene expression analysis was performed with HTSeq-count (version 0.12.3) and DESeq2 (version 1.32.0)
Gene ontology enrichment analysis was conducted using Metascape.
Assembly: mm10
Supplementary files format and content: bigWig

growth_protocol: Primary murine HSPCs, isolated using CD117 MicroBeads, and K/C-III and K/P-III leukemia cells were cultured in Retronectin-coated plates (Takata T100A) with RPMI 1640 medium (Gibco) supplemented with 1% penicillin/streptomycin, 10% FBS (Gibco), and murine SCF, IL-6, and IL-3. Cell viability was assessed with a Bio-Rad TC20 automated cell counter.

extract_protocol:
Mouse leukemia cells isolated from leukemic mice, MP cells (Lin-, c-Kit+), and c-Kit-enriched HSPCs were lysed with Trizol (Ambion 15596018) for total RNA extraction. mRNA from 2 µg of total RNA was enriched with VAHTS mRNA capture beads and fragmented to 200-500 nt lengths using 2× ProtoScript II buffer.
Strand-specific RNA-seq libraries were prepared and sequenced with 150 bp paired-end reads on the NovaSeq 6000 platform.

value: treated with BZ1 for 6 hours


title: 7189-NPC-1

description: Library name: R17030760LR01


title: DKFZ-BT66-OFF_100nM trametinib 15min_Rep2

description: Library name: Sample 5


title: CD34_UHRF1gRNA1_H3K9ac

description: Library name: CD34_UHRF1gRNA1_H3K9ac

value: UHRF1 KO

value: electroporated with Cas9 and UHRF1 sgRNA5


title: 7189-MND50-1

description: Library name: R17029200LR01


title: CD34_UHRF1gRNA1_H3K4me3

description: Library name: CD34_UHRF1gRNA1_H3K4me3

value: electroporated with Cas9 and UHRF1 sgRNA4


title: 9021-MND28-2

description: Library name: R17029186LR01


title: 7189-MND28-2

description: Library name: R17029198LR01


title: 9021-IPS-3

description: Library name: R17030747LR01


title: CD34_UHRF1gRNA1_GATA1

description: Library name: CD34_UHRF1gRNA1_GATA1

value: electroporated with Cas9 and UHRF1 sgRNA2


title: 7189-IPS-3

description: Library name: R17030759LR01


title: CD34_UHRF1gRNA1_H3K27ac

description: Library name: CD34_UHRF1gRNA1_H3K27ac

value: electroporated with Cas9 and UHRF1 sgRNA3


title: 6751-NPC-3

description: Library name: R18001289LR01


title: 7189-NPC-3

description: Library name: R17030762LR01


title: 7189-IPS-2

description: Library name: R17030758LR01


title: 7189-MND28-1

description: Library name: R17029197LR01


title: CD34_UHRF1gRNA1_NFYA

description: Library name: CD34_UHRF1gRNA1_NFYA

value: electroporated with Cas9 and UHRF1 sgRNA6


title: RNAseq-MouseLeukemiaCells-BZ1-6h-rep1

description: Library name: RNAseq-MouseLeukemiaCells-BZ1-6h-rep1


title: RNAseq-MouseLeukemiaCells-BZ1-0h-rep2

description: Library name: RNAseq-MouseLeukemiaCells-BZ1-0h-rep2

value: treated with DMSO for 12 hours


title: RNAseq-MouseLeukemiaCells-BZ1-0h-rep1

description: Library name: RNAseq-MouseLeukemiaCells-BZ1-0h-rep1


title: 6751-MND50-3

description: Library name: R17029232LR01


title: 6751-NPC-1

description: Library name: R17030730LR01


title: 7189-MND50-3

description: Library name: R17029202LR01


title: 6751-NPC-2

description: Library name: R17030731LR01


title: 6751-MND50-2

description: Library name: R17029231LR01


title: RNAseq-MouseLeukemiaCells-BZ1-12h-rep2

description: Library name: RNAseq-MouseLeukemiaCells-BZ1-12h-rep2

value: treated with BZ1 for 12 hours


title: 7189-MND50-2

description: Library name: R17029201LR01


title: CD34_UHRF1gRNA1_BCL11A

description: Library name: CD34_UHRF1gRNA1_BCL11A

value: electroporated with Cas9 and UHRF1 sgRNA1


title: 7189-MND28-3

description: Library name: R17029199LR01


title: RNAseq-MouseLeukemiaCells-A485_6h_rep2

description: Library name: RNAseq-MouseLeukemiaCells-A485_6h_rep2

value: Derived from spleen

value: HSPCs


title: CD34_NT_NFYA

description: Library name: CD34_NT_NFYA

value: WT

value: electroporated with Cas9 and NT sgRNA


title: CD34_NT_H3K9ac

description: Library name: CD34_NT_H3K9ac


title: 6751-MND28-3

description: Library name: R17029229LR01


title: 7189-IPS-1

description: Library name: R17030757LR01


title: 6751-MND50-1

description: Library name: R17029230LR01


title: RNAseq-MouseLeukemiaCells-A485_6h_rep1

description: Library name: RNAseq-MouseLeukemiaCells-A485_6h_rep1

value: hematopoietic stem and progenitor cells

value: K/C-III leukemia cells


title: RNAseq-MouseLeukemiaCells-A485_12h_rep3

description: Library name: RNAseq-MouseLeukemiaCells-A485_12h_rep3

value: treated with A485 for 12 hours


title: 6751-MND28-2

description: Library name: R17029228LR01


title: CD34_NT_H3K4me3

description: Library name: CD34_NT_H3K4me3


title: CD34_NT_H3K27ac

description: Library name: CD34_NT_H3K27ac


title: RNAseq-MouseLeukemiaCells-BZ1-12h-rep1

description: Library name: RNAseq-MouseLeukemiaCells-BZ1-12h-rep1


title: RNAseq-MouseLeukemiaCells-A485_6h_rep3

description: Library name: RNAseq-MouseLeukemiaCells-A485_6h_rep3

value: treated with A485 for 6 hours


title: 6751-IPS-3

description: Library name: R17030729LR01


title: 6751-IPS-2

description: Library name: R17030728LR01


title: RNAseq-MouseLeukemiaCells-A485_12h_rep2

description: Library name: RNAseq-MouseLeukemiaCells-A485_12h_rep2


title: CD34_NT_GATA1

description: Library name: CD34_NT_GATA1


title: 6751-IPS-1

description: Library name: R17030727LR01


title: RNAseq-MouseLeukemiaCells-A485_12h_rep1

description: Library name: RNAseq-MouseLeukemiaCells-A485_12h_rep1


title: 41003B-NPC-3

description: Library name: R17030780LR01


title: CD34_NT_BCL11A

description: Library name: CD34_NT_BCL11A


title: 41003B-NPC-2

description: Library name: R17030779LR01


title: RNAseq-MouseLeukemiaCells-A485_0h_rep3

description: Library name: RNAseq-MouseLeukemiaCells-A485_0h_rep3


title: 41003B-NPC-1

description: Library name: R17030778LR01


title: 41003B-MND50-3

description: Library name: R17030696LR01


title: RNAseq-MouseLeukemiaCells-A485_0h_rep2

description: Library name: RNAseq-MouseLeukemiaCells-A485_0h_rep2


title: CD34_UHRF1gRNA1_ATAC

description: Library name: CD34_UHRF1gRNA1_ATAC

data_processing:
ATAC-seq analysis was performed using the Hemtools atac_seq pipeline (PMID: 34341563) (https://hemtools.readthedocs.io/en/latest/content/NGS_pipelines/atac_seq.html).
Assembly: hg19
Supplementary files format and content: bw

growth_protocol: and then cultured in Phase 1 media include IMDM (Thermo Fisher Scientific, Waltham, MA, USA), 3% human AB serum (Atlanta Biologicals, Flowery Branch, GA, USA, S40110), 2% human blood type AB plasma (SeraCare, Milford, MA, USA 1810-0001), 1 penicillin/streptomycin, 3 units/mL erythropoietin (EPOGEN; Amgen, Thousand Oaks, CA, USA # 55513-144-01), 3 units/mL heparin (Sagent Pharmaceuticals, Schaumburg, IL, USA # 25021-401-02), 200 μg/mL holo-transferrin (Millipore Sigma, Burlington, MA, USA T0665), 10 ng/mL human SCF, and 1 ng/mL human interleukin-3 (IL-3; R&D systems, Minneapolis, MN, USA, 203-IL/CF) for 7 days.

extract_protocol:
ATAC-seq was performed using the Omni-ATAC protocol. For each sample, 5-6 × 104 cells were lysed with buffer containing 0.1% NP-40, 0.1% Tween-20, and 0.01% digitonin, then the lysate was washed and incubated with Tagment DNA TDE1 Enzyme (Illumina) for 30 min at 37°C. DNA was purified with a Qiagen MinElute PCR Purification Kit.
Library fragments were amplified using NEBNext® High-Fidelity 2X PCR Master Mix (NEB, M0541) and custom primers (table S4) with unique dual indexes. PCR amplification cycles were in accordance with the manufacturer’s instructions. PCR products were purified using AMPure XP beads (Beckman Coulter, A63881) at a 1:1 ratio according to the manufacturer’s instructions. Purified PCR products sized from 150 bp to 1 kb were purified from E-Gel EX Agarose Gels, 2% (Thermo Fisher, G401002). Libraries were pooled and sequenced in paired-end mode by using an Illumina NovaSeq kit.

treatment_protocol: CD34+ cell were electroporated with Cas9+ NT or UHRF1 gRNA1 or HBG promoter gRNA1-6+TETv4 or dTETv4 mRNA

value: day10 erythroid blast

value: UHRF1 KO


title: CD34_NT_ATAC

description: Library name: CD34_NT_ATAC


title: 41003B-MND50-1

description: Library name: R17030694LR01


title: RNAseq-MouseLeukemiaCells-A485_0h_rep1

description: Library name: RNAseq-MouseLeukemiaCells-A485_0h_rep1


title: 41003B-MND28-3

description: Library name: R18001285LR01


title: 6751-MND28-1

description: Library name: R17029227LR01


title: 41003B-MND28-2

description: Library name: R17030692LR01


title: ATAC_dTETv4_HBG

description: Library name: ATAC_dTETv4_HBG

value: electroporated  with dTETv4 mRNA and HBG promoter sgRNA1-7


title: 41003B-MND28-1

description: Library name: R17030691LR01


title: ATAC_TETv4_HBG

description: Library name: ATAC_TETv4_HBG

value: HBG promoter demethylation

value: electroporated with TETv4 mRNA and HBG promoter sgRNA1-6


title: 41003B-IPS-2

description: Library name: R17030776LR01


title: HUDEP2_UHRF1gRNA1KO_rep3

description: Library name: HUDEP2_UHRF1gRNA1KO_rep3

data_processing:
For HUDEP-2 RNA-seq, sequencing data was processed using the nf-core RNAseq workflow (v3.14) with the Kallisto pseudoaligner. Kallisto parameters were set with 100 bootstrap samples, and fragment length set to 75 with a standard deviation of 2 where single end reads were used.
Assembly: hg38
Supplementary files format and content: tsv abundance file - output from kallisto

growth_protocol: Human umbilical cord blood derived 2 (HUDEP2) cells were grown in serum free expansion medium (SFEM, StemSpan) supplemented with 50 ng/µL stem cell factor (In Vitro Technologies), 3 IU/mL erythropoietin (Lonza), 10 µM dexamethasone (Sigma-Aldrich), 1 µg/mL doxycycline (Sigma-Aldrich), and 0.5 mg/mL PSG. All cell cultures were incubated at 37°C in a water jacketed incubator with 5% CO2. CD34+ cells cultured in Phase 1 media include IMDM (Thermo Fisher Scientific, Waltham, MA, USA), 3% human AB serum (Atlanta Biologicals, Flowery Branch, GA, USA, S40110), 2% human blood type AB plasma (SeraCare, Milford, MA, USA 1810-0001), 1 penicillin/streptomycin, 3 units/mL erythropoietin (EPOGEN; Amgen, Thousand Oaks, CA, USA # 55513-144-01), 3 units/mL heparin (Sagent Pharmaceuticals, Schaumburg, IL, USA # 25021-401-02), 200 μg/mL holo-transferrin (Millipore Sigma, Burlington, MA, USA T0665), 10 ng/mL human SCF, and 1 ng/mL human interleukin-3 (IL-3; R&D systems, Minneapolis, MN, USA, 203-IL/CF) for 7 days.

extract_protocol:
HUDEP2 cells were harvested and washed in 1× PBS before lysis and RNA was isolated using TRI™ reagent (Sigma-Aldrich) according to the manufacturer’s instructions. RNA was purified using the RNeasy® Mini Kit and RNase-free DNase set (Qiagen) according to the manufacturer’s instructions. For CD34 cells, RNA samples were extracted with QIAGEN RNeasy micro Plus kit.
Stranded mRNA prep (Illumina) sequencing libraries were generated and RNA sequencing was performed by the Ramaciotti Centre for Genomics using NextSeq 1×75bp high output or NovaSeq 2x100bp flow cells (Illumina). For CD34 cells, RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: CD34+ cell were electroporated with Cas9+ NT/UHRF1 gRNA1

value: erythroid progenitor cell line

value: Cas9+UHRF1 gRNA treated


title: 41003B-IPS-1

description: Library name: R17030775LR01


title: RNAseq-MouseLeukemiaCells-DMSO-rep2

description: Library name: RNAseq-MouseLeukemiaCells-DMSO-rep2

value: treated with DMSO for 12 hours


title: RNAseq-MouseLeukemiaCells-DMSO-rep1

description: Library name: RNAseq-MouseLeukemiaCells-DMSO-rep1


title: HUDEP2_UHRF1gRNA1KO_rep2

description: Library name: HUDEP2_UHRF1gRNA1KO_rep2


title: 40077-NPC-1

description: Library name: R18007940LR01


title: 40077-NPC-3

description: Library name: R17030774LR01


title: HUDEP2_UHRF1gRNA1KO_rep1

description: Library name: HUDEP2_UHRF1gRNA1KO_rep1


title: 40077-NPC-2

description: Library name: R17030773LR01


title: RNAseq-MouseLeukemiaCells-BZ1alone-rep3

description: Library name: RNAseq-MouseLeukemiaCells-BZ1alone-rep3

value: treated with BZ1 for 6 hours


title: RNAseq-MouseLeukemiaCells-BZ1alone-rep2

description: Library name: RNAseq-MouseLeukemiaCells-BZ1alone-rep2

value: Derived from spleen


title: 40077-MND50-3

description: Library name: R17030690LR01


title: 40077-MND50-1

description: Library name: R17030688LR01


title: HUDEP2_NT_rep3

description: Library name: HUDEP2_NT_rep3

value: Cas9+NT gRNAtreated


title: HUDEP2_NT_rep2

description: Library name: HUDEP2_NT_rep2

value: WT


title: 40077-MND50-2

description: Library name: R18001284LR01


title: 41003B-MND50-2

description: Library name: R17030695LR01


title: 40077-MND28-3

description: Library name: R17030687LR01


title: RNAseq-MouseLeukemiaCells-DMSO-rep3

description: Library name: RNAseq-MouseLeukemiaCells-DMSO-rep3

value: HSPCs


title: RNAseq-MouseLeukemiaCells-A485+BZ1-rep3

description: Library name: RNAseq-MouseLeukemiaCells-A485+BZ1-rep3

value: hematopoietic stem and progenitor cells

value: treated with A485 and BZ1 for 6 hours


title: RNAseq-MouseLeukemiaCells-BZ1alone-rep1

description: Library name: RNAseq-MouseLeukemiaCells-BZ1alone-rep1

value: K/C-III leukemia cells


title: 40077-MND28-2

description: Library name: R17030686LR01


title: 41003B-IPS-3

description: Library name: R17030777LR01


title: HUDEP2_NT_rep1

description: Library name: HUDEP2_NT_rep1


title: 40077-IPS-3

description: Library name: R18004474LR01


title: 40077-MND28-1

description: Library name: R17030684LR01


title: HUDEP-2 All Guides Rep3

description: Library name: HUDEP-2 All Guides Rep3

value: transfected with TETv4 plasmid and plasmids containing sgRNAs 1-6


title: 40077-IPS-2

description: Library name: R17030770LR01


title: RNAseq-MouseLeukemiaCells-A485+BZ1-rep2

description: Library name: RNAseq-MouseLeukemiaCells-A485+BZ1-rep2


title: 40077-IPS-1

description: Library name: R17030769LR01


title: RNAseq-MouseLeukemiaCells-A485+BZ1-rep1

description: Library name: RNAseq-MouseLeukemiaCells-A485+BZ1-rep1


title: HUDEP-2 All Guides Rep2

description: Library name: HUDEP-2 All Guides Rep2


title: 39027-NPC-2

description: Library name: R17030767LR01


title: 39027-NPC-3

description: Library name: R17030768LR01


description: Library name: RNAseq-MouseLeukemiaCells-A4851alone-rep3

value: treated with A485 for 6 hours


title: 39027-NPC-1

description: Library name: R17030766LR01


title: HUDEP-2 All Guides Rep1

description: Library name: HUDEP-2 All Guides Rep1


title: 39027-MND50-3

description: Library name: R17030683LR01


description: Library name: RNAseq-MouseLeukemiaCells-A4851alone-rep2


title: 39027-MND50-1

description: Library name: R17030681LR01


title: HUDEP-2 Guide 6 Rep3

description: Library name: HUDEP-2 Guide 6 Rep3

value: transfected with TETv4 plasmid and plasmid containing sgRNA6


title: 39027-MND50-2

description: Library name: R17030682LR01


description: Library name: RNAseq-MouseLeukemiaCells-A4851alone-rep1


title: 39027-MND28-2

description: Library name: R17030679LR01


title: HUDEP-2 Guide 6 Rep2

description: Library name: HUDEP-2 Guide 6 Rep2


title: 39027-MND28-3

description: Library name: R17030680LR01


title: 39027-IPS-3

description: Library name: R17030765LR01


title: RNAseq-Mouse_MPP_rep2

description: Library name: RNAseq-Mouse_MPP_rep2

source_name: Derived from bone marrow

value: Derived from bone marrow

value: untreated


title: HUDEP-2 Guide 6 Rep1

description: Library name: HUDEP-2 Guide 6 Rep1


title: 39027-MND28-1

description: Library name: R17030678LR01


title: 39027-IPS-2

description: Library name: R18001288LR01


title: 39027-IPS-1

description: Library name: R17030763LR01


title: HUDEP-2 Guide 5 Rep3

description: Library name: HUDEP-2 Guide 5 Rep3

value: transfected with TETv4 plasmid and plasmid containing sgRNA5


title: RNAseq-Mouse_KPIII_rep2

description: Library name: RNAseq-Mouse_KPIII_rep2

value: K/P-III leukemia cells


title: HUDEP-2 Guide 5 Rep2

description: Library name: HUDEP-2 Guide 5 Rep2

value: erythroid progenitor cell line


title: RNAseq-Mouse_MPP_rep1

description: Library name: RNAseq-Mouse_MPP_rep1


title: RNAseq-Mouse_KPIII_rep1

description: Library name: RNAseq-Mouse_KPIII_rep1


title: 32947-NPC-3

description: Library name: R17030786LR01


title: 32947-NPC-1

description: Library name: R17030784LR01


title: HUDEP-2 Guide 5 Rep1

description: Library name: HUDEP-2 Guide 5 Rep1


title: 32947-NPC-2

description: Library name: R17030785LR01


title: 32947-MND50-3

description: Library name: R18001287LR01


title: RNAseq-Mouse_KCIII_rep2

description: Library name: RNAseq-Mouse_KCIII_rep2


title: 32947-MND50-2

description: Library name: R17030701LR01


title: 32947-MND50-1

description: Library name: R17030700LR01


title: HUDEP-2 Guide 4 Rep3

description: Library name: HUDEP-2 Guide 4 Rep3

value: transfected with TETv4 plasmid and plasmid containing sgRNA4


title: RNAseq-Mouse_KCIII_rep1

description: Library name: RNAseq-Mouse_KCIII_rep1


title: HUDEP-2 Guide 4 Rep2

description: Library name: HUDEP-2 Guide 4 Rep2


title: 32947-MND28-2

description: Library name: R17030698LR01


title: RNAseq-Mouse_cKit_rep2

description: Library name: RNAseq-Mouse_cKit_rep2


title: 32947-MND28-1

description: Library name: R17030697LR01


title: HUDEP-2 Guide 4 Rep1

description: Library name: HUDEP-2 Guide 4 Rep1


title: 32947-IPS-3

description: Library name: R18007942LR01


title: 32947-MND28-3

description: Library name: R18004479LR01


title: RNAseq-Mouse_cKit_rep1

description: Library name: RNAseq-Mouse_cKit_rep1


title: HUDEP-2 Guide 3 Rep3

description: Library name: HUDEP-2 Guide 3 Rep3

value: transfected with TETv4 plasmid and plasmid containing sgRNA3


title: 32947-IPS-2

description: Library name: R17030782LR01


title: 32947-IPS-1

description: Library name: R17030781LR01


title: 29523-NPC-3

description: Library name: R17030708LR01


title: HUDEP-2 Guide 3 Rep2

description: Library name: HUDEP-2 Guide 3 Rep2


title: 29523-NPC-2

description: Library name: R17030707LR01


title: Gpx4 KO_Mist1+ organoids_ P15_3

first: Fan

last: Chen

address: Yueyang Road, No. 320

institute: Center for Excellence in Molecular Cell Science, CAS

description:
Library name: Sample 27
all.fpkm_anno_1.txt
G-2-15-3

data_processing:
Quality Control: In order to remove technical sequences, including adapters, polymerase chain reaction (PCR) primers, or fragments thereof, and quality of bases lower than 20, pass filter data of fastq format were processed by Cutadapt (V1.9.1, phred cutoff: 20, error rate: 0.1, adapter overlap: 1bp, min. length: 75, proportion of N: 0.1) to be high quality clean data. Alignment: Firstly, reference genome sequences and gene model annotation files of relative species were downloaded from genome website. Secondly, Hisat2 (v2.2.1) was used to index reference genome sequence. Finally, clean data were aligned to reference genome via software Hisat2 (v2.2.1). Expression analysis: In the beginning transcripts in fasta format are converted from known gff annotation file and indexed properly. Then, with the file as a reference gene file, HTSeq (v0.6.1) estimated gene and isoform expression levels from the pair-end clean data.
Assembly: GRCm38.p5
Supplementary files format and content: xls file includes RPKM values for each Sample.

source_name: Stomach

growth_protocol: Stomach tissues of adult Mist1CreERT2;RFPLSL mice were dissociated into single cells and isolated RFP+ cells via fluorescence-activated cell sorting (FACS). And organoids were suspended with 50 μl Matrigel and maintained in proliferating medium at 37 °C with 5% CO2 in a humidified incubator.

extract_protocol:
Total mRNA was extracted using TRIZOL Reagent following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent technologies).
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: Stomach

value: Gpx4 KO Mist1+ derived organoid

value: Gastric epithelia

value: Gpx4 KO

value: Organoid proliferative culture


title: Gpx4 KO_Mist1+ organoids_ P15_2

description:
Library name: Sample 26
all.fpkm_anno_1.txt
G-2-15-2


title: 29523-NPC-1

description: Library name: R18001291LR01


title: HUDEP-2 Guide 3 Rep1

description: Library name: HUDEP-2 Guide 3 Rep1

value: WT


title: Gpx4 KO_Mist1+ organoids_ P15_1

description:
Library name: Sample 25
all.fpkm_anno_1.txt
G-2-15-1


title: 29523-MND50-3

description: Library name: R17029208LR01


title: HUDEP-2 Guide 2 Rep3

description: Library name: HUDEP-2 Guide 2 Rep3

value: transfected with TETv4 plasmid and plasmid containing sgRNA2


title: 29523-MND28-3

description: Library name: R17029205LR01


title: 29523-MND50-1

description: Library name: R17029206LR01


title: HUDEP-2 Guide 2 Rep2

description: Library name: HUDEP-2 Guide 2 Rep2


title: Mist1+ organoids_P15_3

description:
Library name: Sample 24
all.fpkm_anno_1.txt
M-2-15-3

value: Mist1+ derived organoid


title: 29523-MND28-2

description: Library name: R17029204LR01


title: 29523-MND28-1

description: Library name: R17029203LR01


title: 29523-IPS-3

description: Library name: R17030705LR01


title: HUDEP-2 Guide 2 Rep1

description: Library name: HUDEP-2 Guide 2 Rep1


title: HUDEP-2 Guide 1 Rep3

description: Library name: HUDEP-2 Guide 1 Rep3

value: transfected with TETv4 plasmid and plasmid containing sgRNA1


title: Mist1+ organoids_P15_1

description:
Library name: Sample 22
all.fpkm_anno_1.txt
M-2-15-1


title: 29523-IPS-2

description: Library name: R17030704LR01


title: 29523-IPS-1

description: Library name: R18007936LR01


title: Gpx4 KO_Mist1+ organoids_ P10_3

description:
Library name: Sample 21
all.fpkm_anno_1.txt
G-2-10-3


title: 29422-NPC-1

description: Library name: R17030718LR01


title: 29422-NPC-2

description: Library name: R17030719LR01


title: Gpx4 KO_Mist1+ organoids_ P10_2

description:
Library name: Sample 20
all.fpkm_anno_1.txt
G-2-10-2


title: HUDEP-2 Guide 1 Rep2

description: Library name: HUDEP-2 Guide 1 Rep2


title: 29422-MND50-3

description: Library name: R17030572LR01


title: HUDEP-2 Guide 1 Rep1

description: Library name: HUDEP-2 Guide 1 Rep1