title: RM2 macrophages

city: Jeongeup-Si

first: Hyoung-woo

last: Bai

address: 29 Geumgu-gil

institute: Korea Atomic Energy Research Institute (KAERI)

description: Library name: 6-1_1.fq.gz

data_processing:
Raw reads were trimmed using Trimmomatic v0.36 to remove adapter sequences and low-quality bases. Clean reads were aligned to the mm10 reference genome using HISAT2 v2.2.1. Read counts per gene were quantified using HTSeq-count v0.11.3 with GENCODE annotation.
Assembly: UCSC mm10
Supplementary files format and content: TXT/CSV files containing read count data for each gene across samples.
Supplementary files format and content: The read counts were generated using HTSeq-count (v0.11.3).

growth_protocol: RAW 264.7 cells were cultured in Dulbecco’s Modified Eagle’s Medium (DMEM) supplemented with 10% fetal bovine serum (FBS) and 1% penicillin-streptomycin (P/S). Cells were maintained at 37°C in a humidified atmosphere with 5% CO₂.

extract_protocol:
Total RNA was extracted from polarized and irradiated macrophages using WelPrep™ Total RNA Isolation Reagent (Welgene, Gyeongsan, Korea) according to the manufacturer’s instructions.
Total RNA was fragmented, mRNA was enriched or depleted, followed by reverse transcription and second strand synthesis. After adapter ligation and PCR amplification, ssCircs were converted into DNA nanoballs (DNBs) for PE100/PE150 sequencing.

treatment_protocol: Macrophages were polarized into M1 (LPS 100 ng/mL + IFN-γ 20 ng/mL) or M2 (IL-4 20 ng/mL) phenotypes for 24 h. Polarized cells were then irradiated with 10 Gy using a Gammacell 40 Exactor (¹³⁷Cs source) and incubated at 37°C for an additional 24 h.

value: Bone marrow

value: Macrophage

value: 10 Gy gamma radiation to M2 macrophages


title: HLF 3D Final DMSO Rep 1

status: Public on Apr 07 2025

type: SRA

city: Chapel Hill

first: Jesse

last: Raab

address: 120 Mason Farm Rd

department: Genetics

country: USA

institute: University of North Carolina Chapel Hill

description:
Library name: HLF_3D_d28_DMSO_1
Other: amplicon sequencing containing gRNA
Columns for processed data file; id = Gene ID; Score_HLF_2D_vs_t0_818 = RRA for 2D vs initial HLF; Score_HLF_3D_vs_t0_818 = RRA for 3D vs initial HLF; Score_PLCPRF5_2D_vs_t0 = RRA for 2D vs initial PLCPRF5 ; Score_PLCPRF5_3D_vs_t0_0042 = RRA for 3D vs initial PLCPRF5; Score_PLCPRF5_2D_vs_3D_8440042 = RRA for 2D vs 3D end for PLCPRF5; Score_HLF_2D_vs_3D_818 = RRA for 2D vs 3D HLF end point; Score_HLF_SNDX_vs_T0_885 = RRA for SNDX vs T0 in HLF; Score_HLF_DMSO_vs_t0_885 = RRA for DMSO vs T0 in HLF; Score_HLF_SNDX_vs_DMSO_885 = RRA SNDX vs DMSO in HLF at endpoint. FDR_HLF_2D_vs_t0_818 = FDR for 2D vs initial HLF; FDR_HLF_3D_vs_t0_818 = FDR for 3D vs initial HLF;FDR_PLCPRF5_2D_vs_t0 = FDR for 2D vs initial PLCPRF5 ;FDR_PLCPRF5_3D_vs_t0_0042 = FDR for 3D vs initial PLCPRF5; FDR_PLCPRF5_2D_vs_3D_8440042 = FDR for 2D vs 3D end for PLCPRF5; FDR_HLF_2D_vs_3D_818 = FDR for 2D vs 3D HLF end point; FDR_HLF_SNDX_vs_T0_885 = FDR for SNDX vs T0 in HLF; FDR_HLF_DMSO_vs_t0_885 = FDR for DMSO vs T0 in HLF; FDR_HLF_SNDX_vs_DMSO_885 =FDR SNDX vs DMSO in HLF at endpoint.

library_source: other

data_processing:
Data were processed using the MaGeck Pipeline.
mageck count --norm-method none
mageck test --control-sgrna --norm-method control
Pipeline implemented in Nextflow at github.com/raab-lab/crispr-screens
Supplementary files format and content: processed files contain RRA and FDR values for each gene in library for each comparison.
Library strategy: CRISPR Screen

molecule: other

organism: Homo sapiens

source_name: Liver cancer cells

growth_protocol: HLF cells were grown in DMEM + 10% FCS + penicillin and streptomycin. PLC/PRF/5 were grown in RPMI + 10% FCS + P/s. 2D growth was on normal tissue culture plastic dishes. 3D growth was media containin 0.75% methylcelluose and were grown on ultra-low attachment plasticware.

extract_protocol:
gDNA was harvested using
libraries were constructed using primers to amplify the gRNAs from genomic DNA and add indexes and illumina sequencing adapters as described in PMCID: PMC5526071

treatment_protocol: where indicated cells were treated with 5uM SNDX-5613

tag: tissue

value: Liver cancer cells

tag: cell line

value: HLF

tag: cell type

tag: treatment

value: DMSO 3D


title: RM0 macrophages

country: South Korea

description: Library name: 4-1_1.fq.gz

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

source_name: Bone marrow

value: 10 Gy gamma radiation to M0 macrophages


title: CD8 Donor 4 secretory lgA 4h

city: Silver Spring

first: Frederick

middle: Curtis

last: Mills

state: Maryland

address: 10903 New Hampshire Avenue

department: CDER/OPQR/OPQRIV

institute: FDA

description: 150 x 150 bp paired end reads

data_processing:
Sequencing reads were aligned to the Homo sapiens UCSC hg19 (RefSeq and Gencode gene annotations) using BaseSpace Onsite (Illumina). Gene level counts were determined using BaseSpace TopHat Alignment v1.0.1. Read mapping was done using TopHat 2 Aligner and FPKM estimation of reference genes and transcripts were performed using Cufflinks 2.
Assembly: hg19
Supplementary files format and content: Treg FPKM, CD8 FPKM  estimation of reference genes and transcripts were performed using Cufflinks 2.
Supplementary files format and content: Treg DGE TopGenes,CD8 DGE TopGenes .xlsx format, Genesretained if ≥1.5-fold induced by both stim AND p value ≤0.1 for both FCRL3 mAb Ab and secretory lgA stimulation

source_name: Peripheral blood

extract_protocol:
Cell pellets were stored at 4ºC with 50 μl of RNAlater (Invitrogen) until RNA purified using the RNAqueous-4PCR DNA-free RNA isolation kit following the provided protocol.  0.1-0.5 µg of total RNA pers sample was used after removal of ribosomal RNA using the Next rRNA depletion kit (New England Biolabs).
RNA samples passed quality control and proceeded to library preparation using TruSeq Stranded mRNA library prep kit (Illumina) with IDT for Illumina - TruSeq RNA UD indexes (Illumina, 20022371) following manufacturer’s protocol. Libraries were amplified using 12 cycles of PCR
RNA seq libraries were amplified using 12 cycles of PCR, pooled, and sequenced on Illumina NovaSeq 6000 with 150x150 bp paired-end reads

treatment_protocol: Sorted CD4+CD25hiCD127dim CD14- Treg cells or CD8+CCR7-CD45 RO- TTE cells  were incubated with 150 μg/mL biotinylated secretory lgA (Athens Research) or 20 µg/ml biotinylated FCRL3 mAb Ab clone 6F2 10 for 10 minutes at 4°C, then washed once.  secretory lgA and FCRL3 mAb Ab were biotinylated using EZ-Link Sulfo-NHS-LC-Biotin (Thermo Fisher).  Biotinylated reagents were crosslinked for 15 minutes at 37°C using 5 μg/mL streptavidin (Southern Biotech).  CD4+ Treg cells were cultured in X-Vivo 20 medium (Lonza), while CD8+ TTE cells were cultured in RPMI with 10% fetal calf serum, glutamine, nonessential amino acids, and sodium pyruvate for 4 hours or 20 hours at 37°C.

value: Peripheral blood

value: CD8 effector T

tag: individual

value: CD8 Donor 4

value: secretory lgA 4h


title: HLF 3D Final DMSO Rep 3

description:
Library name: HLF_3D_d28_DMSO_3
Other: amplicon sequencing containing gRNA
Columns for processed data file; id = Gene ID; Score_HLF_2D_vs_t0_818 = RRA for 2D vs initial HLF; Score_HLF_3D_vs_t0_818 = RRA for 3D vs initial HLF; Score_PLCPRF5_2D_vs_t0 = RRA for 2D vs initial PLCPRF5 ; Score_PLCPRF5_3D_vs_t0_0042 = RRA for 3D vs initial PLCPRF5; Score_PLCPRF5_2D_vs_3D_8440042 = RRA for 2D vs 3D end for PLCPRF5; Score_HLF_2D_vs_3D_818 = RRA for 2D vs 3D HLF end point; Score_HLF_SNDX_vs_T0_885 = RRA for SNDX vs T0 in HLF; Score_HLF_DMSO_vs_t0_885 = RRA for DMSO vs T0 in HLF; Score_HLF_SNDX_vs_DMSO_885 = RRA SNDX vs DMSO in HLF at endpoint. FDR_HLF_2D_vs_t0_818 = FDR for 2D vs initial HLF; FDR_HLF_3D_vs_t0_818 = FDR for 3D vs initial HLF;FDR_PLCPRF5_2D_vs_t0 = FDR for 2D vs initial PLCPRF5 ;FDR_PLCPRF5_3D_vs_t0_0042 = FDR for 3D vs initial PLCPRF5; FDR_PLCPRF5_2D_vs_3D_8440042 = FDR for 2D vs 3D end for PLCPRF5; FDR_HLF_2D_vs_3D_818 = FDR for 2D vs 3D HLF end point; FDR_HLF_SNDX_vs_T0_885 = FDR for SNDX vs T0 in HLF; FDR_HLF_DMSO_vs_t0_885 = FDR for DMSO vs T0 in HLF; FDR_HLF_SNDX_vs_DMSO_885 =FDR SNDX vs DMSO in HLF at endpoint.


title: M1 macrophages

description: Library name: 2-1_1.fq.gz

value: LPS (100 ng/mL) + IFN-γ (20 ng/mL), 24 h


title: CD8 Donor 3 SA control 20h

description: 150 x 150 bp paired end reads

value: CD8 Donor 3

value: SA control 20h


title: RM1 macrophages

description: Library name: 5-1_1.fq.gz

value: 10 Gy gamma radiation to M1 macrophages


title: CD8 Donor 3 secretory lgA 20h

description: 150 x 150 bp paired end reads

value: secretory lgA 20h


title: HLF 3D Final Rep 3

description:
Library name: HLF_CRISPR_3D_d28_DMSO_3
Other: amplicon sequencing containing gRNA
Columns for processed data file; id = Gene ID; Score_HLF_2D_vs_t0_818 = RRA for 2D vs initial HLF; Score_HLF_3D_vs_t0_818 = RRA for 3D vs initial HLF; Score_PLCPRF5_2D_vs_t0 = RRA for 2D vs initial PLCPRF5 ; Score_PLCPRF5_3D_vs_t0_0042 = RRA for 3D vs initial PLCPRF5; Score_PLCPRF5_2D_vs_3D_8440042 = RRA for 2D vs 3D end for PLCPRF5; Score_HLF_2D_vs_3D_818 = RRA for 2D vs 3D HLF end point; Score_HLF_SNDX_vs_T0_885 = RRA for SNDX vs T0 in HLF; Score_HLF_DMSO_vs_t0_885 = RRA for DMSO vs T0 in HLF; Score_HLF_SNDX_vs_DMSO_885 = RRA SNDX vs DMSO in HLF at endpoint. FDR_HLF_2D_vs_t0_818 = FDR for 2D vs initial HLF; FDR_HLF_3D_vs_t0_818 = FDR for 3D vs initial HLF;FDR_PLCPRF5_2D_vs_t0 = FDR for 2D vs initial PLCPRF5 ;FDR_PLCPRF5_3D_vs_t0_0042 = FDR for 3D vs initial PLCPRF5; FDR_PLCPRF5_2D_vs_3D_8440042 = FDR for 2D vs 3D end for PLCPRF5; FDR_HLF_2D_vs_3D_818 = FDR for 2D vs 3D HLF end point; FDR_HLF_SNDX_vs_T0_885 = FDR for SNDX vs T0 in HLF; FDR_HLF_DMSO_vs_t0_885 = FDR for DMSO vs T0 in HLF; FDR_HLF_SNDX_vs_DMSO_885 =FDR SNDX vs DMSO in HLF at endpoint.

value: None 3D


title: 3T3_H3K4me3_C3_rep1

city: Beijing

first: Jiacheng

last: Wang

address: No. 30 Shuangqing Road

country: China

institute: Tsinghua University

description: CUT&Tag for H3K4me3 on CBX7 overexpression stable cell line monoclone3 NIH3T3 cells

library_source: genomic

data_processing:
Paired-end RNA-seq reads were aligned to mm9 using HISAT2 v2.2.1 and FPKM value of each gene was calculated with StringTie v2.1.2.
The paired end ChIP-seq or CUT&Tag reads were mapped to mm9 using bowtie2 (version 2.2.5) with the parameters: -t -q -p 40 -N 1 -L 25 -X 2000 --no-mixed --no-discordant. The unmapped reads, not uniquely mapped, and duplicate reads were removed. Read coverages over the mm9 genome were calculated by bamCoverage from deepTools v3.3.1. The signal was then normalized by computing the number of reads per kilobase of bin per million reads sequenced (RPKM), followed by normalization using Z-score (whole genome 100bp bn with outliner regions excluded).
Hi-C data analysis was performed as previously described. Briefly, Hi-C libraries were aligned using HiCPro (version 2.10.0) with bowtie2 end-to-end algorithm and with the option ‘-very-sensitive’.
Assembly: mm9
Supplementary files format and content: Bigwig for ChIP-seq tracks, gene expression table for RNA-seq data, ValidPairs for Hi-C data
Library strategy: CUT&tag

molecule: genomic DNA

source_name: NIH 3T3

growth_protocol: NIH 3T3 cells were maintained in DMEM (SH30022.01, Hyclone) containing 5% FBS and 100 units/mL penicillin-100 ug/mL streptomycin solution (SV30010, HyClone).

extract_protocol:
CUT&Tag experiments were performed as previously described with modifications (H. S. Kaya-Okur et al., 2019.). Briefly, cells suspended in washing buffer were Concanavalin A coated magnetic beads (Polyscience, 86057) for 10 min at room temperature. Cells were then incubated with primary antibody (H3K4me3, Active motif #39160; H3K27me3, Cell Signaling Technology 9733 C36B11; H2AK119ub, Cell Signaling Technology 8240s; H3K9me3, active motif #39161) at a ratio of 1:100 at 4°C for 2 h on a thermomixer at 400 rpm. After the removal of primary antibody, secondary antibody (Invitrogen, #SA5-10228) were added at a ratio of 1:100, and incubation was performed for 1 h at 4°C. After washing two times, beads were incubated with protein A-Tn5 (Vazyme, S603) at 4°C for 1 h. Tagmentation was performed at 37°C for 30 min after washing. SDS was then added to stripe Tn5 and tagmented DNA was purified with 3 × VAHTS DNA Clean Beads (Vazyme, N411).
PCR was performed to amplify the library for 16 cycles using the following PCR conditions: 72 °C for 3 min; 98 °C for 30s; and thermocycling at 98°C for 15s, 60°C for 30s and 72°C for 3min; followed by 72 °C 5 min. After the PCR reaction, libraries were purified with the 0.4x-1.7x AMPure (Beckman) beads size selection and were subjected to next generation sequencing.

value: NIH 3T3

value: fibroblast

tag: genotype

value: CBX7 OE


title: CD8 Donor 3 FCRL3 mAb 20h

description: 150 x 150 bp paired end reads

value: FCRL3 mAb 20h


title: 3T3_H3K4me3_C4_rep1

description: CUT&Tag for H3K4me3 on CBX7 overexpression stable cell line monoclone4 NIH3T3 cells


title: M0 macrophages

description: Library name: 1-1_1.fq.gz

value: Bone marrow

value: Macrophage


title: CD8 Donor 3 SA control 4h

description: 150 x 150 bp paired end reads

value: SA control 4h


title: HLF 2D Initial rep 3

description:
Library name: HLF_CRISPR_2D_d0_3
Other: amplicon sequencing containing gRNA
Columns for processed data file; id = Gene ID; Score_HLF_2D_vs_t0_818 = RRA for 2D vs initial HLF; Score_HLF_3D_vs_t0_818 = RRA for 3D vs initial HLF; Score_PLCPRF5_2D_vs_t0 = RRA for 2D vs initial PLCPRF5 ; Score_PLCPRF5_3D_vs_t0_0042 = RRA for 3D vs initial PLCPRF5; Score_PLCPRF5_2D_vs_3D_8440042 = RRA for 2D vs 3D end for PLCPRF5; Score_HLF_2D_vs_3D_818 = RRA for 2D vs 3D HLF end point; Score_HLF_SNDX_vs_T0_885 = RRA for SNDX vs T0 in HLF; Score_HLF_DMSO_vs_t0_885 = RRA for DMSO vs T0 in HLF; Score_HLF_SNDX_vs_DMSO_885 = RRA SNDX vs DMSO in HLF at endpoint. FDR_HLF_2D_vs_t0_818 = FDR for 2D vs initial HLF; FDR_HLF_3D_vs_t0_818 = FDR for 3D vs initial HLF;FDR_PLCPRF5_2D_vs_t0 = FDR for 2D vs initial PLCPRF5 ;FDR_PLCPRF5_3D_vs_t0_0042 = FDR for 3D vs initial PLCPRF5; FDR_PLCPRF5_2D_vs_3D_8440042 = FDR for 2D vs 3D end for PLCPRF5; FDR_HLF_2D_vs_3D_818 = FDR for 2D vs 3D HLF end point; FDR_HLF_SNDX_vs_T0_885 = FDR for SNDX vs T0 in HLF; FDR_HLF_DMSO_vs_t0_885 = FDR for DMSO vs T0 in HLF; FDR_HLF_SNDX_vs_DMSO_885 =FDR SNDX vs DMSO in HLF at endpoint.

value: Liver cancer cells

value: HLF

value: None 2D


title: 3T3_H3K4me3_WT_rep1

description: CUT&Tag for H3K4me3 on WT NIH3T3 cells

value: WT


title: HLF 3D Final Rep 2

description:
Library name: HLF_CRISPR_3D_d28_DMSO_2
Other: amplicon sequencing containing gRNA
Columns for processed data file; id = Gene ID; Score_HLF_2D_vs_t0_818 = RRA for 2D vs initial HLF; Score_HLF_3D_vs_t0_818 = RRA for 3D vs initial HLF; Score_PLCPRF5_2D_vs_t0 = RRA for 2D vs initial PLCPRF5 ; Score_PLCPRF5_3D_vs_t0_0042 = RRA for 3D vs initial PLCPRF5; Score_PLCPRF5_2D_vs_3D_8440042 = RRA for 2D vs 3D end for PLCPRF5; Score_HLF_2D_vs_3D_818 = RRA for 2D vs 3D HLF end point; Score_HLF_SNDX_vs_T0_885 = RRA for SNDX vs T0 in HLF; Score_HLF_DMSO_vs_t0_885 = RRA for DMSO vs T0 in HLF; Score_HLF_SNDX_vs_DMSO_885 = RRA SNDX vs DMSO in HLF at endpoint. FDR_HLF_2D_vs_t0_818 = FDR for 2D vs initial HLF; FDR_HLF_3D_vs_t0_818 = FDR for 3D vs initial HLF;FDR_PLCPRF5_2D_vs_t0 = FDR for 2D vs initial PLCPRF5 ;FDR_PLCPRF5_3D_vs_t0_0042 = FDR for 3D vs initial PLCPRF5; FDR_PLCPRF5_2D_vs_3D_8440042 = FDR for 2D vs 3D end for PLCPRF5; FDR_HLF_2D_vs_3D_818 = FDR for 2D vs 3D HLF end point; FDR_HLF_SNDX_vs_T0_885 = FDR for SNDX vs T0 in HLF; FDR_HLF_DMSO_vs_t0_885 = FDR for DMSO vs T0 in HLF; FDR_HLF_SNDX_vs_DMSO_885 =FDR SNDX vs DMSO in HLF at endpoint.


title: HLF 3D Final Rep 1

description:
Library name: HLF_CRISPR_3D_d28_DMSO_1
Other: amplicon sequencing containing gRNA
Columns for processed data file; id = Gene ID; Score_HLF_2D_vs_t0_818 = RRA for 2D vs initial HLF; Score_HLF_3D_vs_t0_818 = RRA for 3D vs initial HLF; Score_PLCPRF5_2D_vs_t0 = RRA for 2D vs initial PLCPRF5 ; Score_PLCPRF5_3D_vs_t0_0042 = RRA for 3D vs initial PLCPRF5; Score_PLCPRF5_2D_vs_3D_8440042 = RRA for 2D vs 3D end for PLCPRF5; Score_HLF_2D_vs_3D_818 = RRA for 2D vs 3D HLF end point; Score_HLF_SNDX_vs_T0_885 = RRA for SNDX vs T0 in HLF; Score_HLF_DMSO_vs_t0_885 = RRA for DMSO vs T0 in HLF; Score_HLF_SNDX_vs_DMSO_885 = RRA SNDX vs DMSO in HLF at endpoint. FDR_HLF_2D_vs_t0_818 = FDR for 2D vs initial HLF; FDR_HLF_3D_vs_t0_818 = FDR for 3D vs initial HLF;FDR_PLCPRF5_2D_vs_t0 = FDR for 2D vs initial PLCPRF5 ;FDR_PLCPRF5_3D_vs_t0_0042 = FDR for 3D vs initial PLCPRF5; FDR_PLCPRF5_2D_vs_3D_8440042 = FDR for 2D vs 3D end for PLCPRF5; FDR_HLF_2D_vs_3D_818 = FDR for 2D vs 3D HLF end point; FDR_HLF_SNDX_vs_T0_885 = FDR for SNDX vs T0 in HLF; FDR_HLF_DMSO_vs_t0_885 = FDR for DMSO vs T0 in HLF; FDR_HLF_SNDX_vs_DMSO_885 =FDR SNDX vs DMSO in HLF at endpoint.


title: HTR8-shMYBL2-2

city: Chongqing

first: Zhihong

last: Wu

state: Chongqing

address: No.1 Yixueyuan Rd, Yuzhong District, Chongqing

institute: Chongqing Medical University

description: Library name: Sample 11

data_processing:
FastQC was used to assess the quality of the raw sequencing data in FASTQ format.
The cleaned reads were then aligned to the reference genome (hg38) using Bowtie2.
Differentially expressed genes (DEGs) were identified using DESeq2.
Volcano plots and heatmaps were used to visualize the DEGs
GO and KEGG enrichment analyses were performed to explore the functional significance of the identified DEGs.
Assembly: hg38
Supplementary files format and content: The TXT files provide raw counts for all samples

source_name: placenta

extract_protocol:
Total RNA was extracted using Trizol reagent (Takara). 1.3μg of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were using NEBNext® Ultra™ RNA Library Prep Kit according to the manufacturer's instructions.

value: placenta

value: HTR-8/SVneo cells

value: Trophoblast cell line

value: MYBL2 knockdown

value: Lentiviral transfection


title: 3T3_H2AK119Ub_C5_rep1

description: CUT&Tag for H2AK119Ub on CBX7 overexpression stable cell line monoclone5 NIH3T3 cells


title: 3T3_H2AK119Ub_C4_rep1

description: CUT&Tag for H2AK119Ub on CBX7 overexpression stable cell line monoclone4 NIH3T3 cells


title: HTR8-shMYBL2-1

description: Library name: Sample 10


title: CD8 Donor 3 secretory lgA 4h

description: 150 x 150 bp paired end reads

value: Peripheral blood

value: CD8 effector T

value: CD8 Donor 3

value: secretory lgA 4h


title: HLF 2D Initial rep 2

description:
Library name: HLF_CRISPR_2D_d0_2
Other: amplicon sequencing containing gRNA
Columns for processed data file; id = Gene ID; Score_HLF_2D_vs_t0_818 = RRA for 2D vs initial HLF; Score_HLF_3D_vs_t0_818 = RRA for 3D vs initial HLF; Score_PLCPRF5_2D_vs_t0 = RRA for 2D vs initial PLCPRF5 ; Score_PLCPRF5_3D_vs_t0_0042 = RRA for 3D vs initial PLCPRF5; Score_PLCPRF5_2D_vs_3D_8440042 = RRA for 2D vs 3D end for PLCPRF5; Score_HLF_2D_vs_3D_818 = RRA for 2D vs 3D HLF end point; Score_HLF_SNDX_vs_T0_885 = RRA for SNDX vs T0 in HLF; Score_HLF_DMSO_vs_t0_885 = RRA for DMSO vs T0 in HLF; Score_HLF_SNDX_vs_DMSO_885 = RRA SNDX vs DMSO in HLF at endpoint. FDR_HLF_2D_vs_t0_818 = FDR for 2D vs initial HLF; FDR_HLF_3D_vs_t0_818 = FDR for 3D vs initial HLF;FDR_PLCPRF5_2D_vs_t0 = FDR for 2D vs initial PLCPRF5 ;FDR_PLCPRF5_3D_vs_t0_0042 = FDR for 3D vs initial PLCPRF5; FDR_PLCPRF5_2D_vs_3D_8440042 = FDR for 2D vs 3D end for PLCPRF5; FDR_HLF_2D_vs_3D_818 = FDR for 2D vs 3D HLF end point; FDR_HLF_SNDX_vs_T0_885 = FDR for SNDX vs T0 in HLF; FDR_HLF_DMSO_vs_t0_885 = FDR for DMSO vs T0 in HLF; FDR_HLF_SNDX_vs_DMSO_885 =FDR SNDX vs DMSO in HLF at endpoint.


title: CD8 Donor 3 FCRL3 mAb 4h

description: 150 x 150 bp paired end reads

value: FCRL3 mAb 4h


title: HTR8-shNC-3

description: Library name: Sample 9


title: CD8 Donor 2 SA control 20h

description: 150 x 150 bp paired end reads

value: CD8 Donor 2

value: SA control 20h


title: HTR8-shNC-2

description: Library name: Sample 8


title: HLF 2D Final rep 2

description:
Library name: HLF_CRISPR_2D_d28_DMSO_2
Other: amplicon sequencing containing gRNA
Columns for processed data file; id = Gene ID; Score_HLF_2D_vs_t0_818 = RRA for 2D vs initial HLF; Score_HLF_3D_vs_t0_818 = RRA for 3D vs initial HLF; Score_PLCPRF5_2D_vs_t0 = RRA for 2D vs initial PLCPRF5 ; Score_PLCPRF5_3D_vs_t0_0042 = RRA for 3D vs initial PLCPRF5; Score_PLCPRF5_2D_vs_3D_8440042 = RRA for 2D vs 3D end for PLCPRF5; Score_HLF_2D_vs_3D_818 = RRA for 2D vs 3D HLF end point; Score_HLF_SNDX_vs_T0_885 = RRA for SNDX vs T0 in HLF; Score_HLF_DMSO_vs_t0_885 = RRA for DMSO vs T0 in HLF; Score_HLF_SNDX_vs_DMSO_885 = RRA SNDX vs DMSO in HLF at endpoint. FDR_HLF_2D_vs_t0_818 = FDR for 2D vs initial HLF; FDR_HLF_3D_vs_t0_818 = FDR for 3D vs initial HLF;FDR_PLCPRF5_2D_vs_t0 = FDR for 2D vs initial PLCPRF5 ;FDR_PLCPRF5_3D_vs_t0_0042 = FDR for 3D vs initial PLCPRF5; FDR_PLCPRF5_2D_vs_3D_8440042 = FDR for 2D vs 3D end for PLCPRF5; FDR_HLF_2D_vs_3D_818 = FDR for 2D vs 3D HLF end point; FDR_HLF_SNDX_vs_T0_885 = FDR for SNDX vs T0 in HLF; FDR_HLF_DMSO_vs_t0_885 = FDR for DMSO vs T0 in HLF; FDR_HLF_SNDX_vs_DMSO_885 =FDR SNDX vs DMSO in HLF at endpoint.


title: CD8 Donor 2 secretory lgA 20h

description: 150 x 150 bp paired end reads

value: secretory lgA 20h


title: HTR8-shNC-1

description: Library name: Sample 7


title: 3T3_H2AK119Ub_WT_rep1

description: CUT&Tag for H2AK119Ub on WT NIH3T3 cells

value: NIH 3T3

value: fibroblast


title: HLF 2D Initial rep 1

description:
Library name: HLF_CRISPR_2D_d0_1
Other: amplicon sequencing containing gRNA
Columns for processed data file; id = Gene ID; Score_HLF_2D_vs_t0_818 = RRA for 2D vs initial HLF; Score_HLF_3D_vs_t0_818 = RRA for 3D vs initial HLF; Score_PLCPRF5_2D_vs_t0 = RRA for 2D vs initial PLCPRF5 ; Score_PLCPRF5_3D_vs_t0_0042 = RRA for 3D vs initial PLCPRF5; Score_PLCPRF5_2D_vs_3D_8440042 = RRA for 2D vs 3D end for PLCPRF5; Score_HLF_2D_vs_3D_818 = RRA for 2D vs 3D HLF end point; Score_HLF_SNDX_vs_T0_885 = RRA for SNDX vs T0 in HLF; Score_HLF_DMSO_vs_t0_885 = RRA for DMSO vs T0 in HLF; Score_HLF_SNDX_vs_DMSO_885 = RRA SNDX vs DMSO in HLF at endpoint. FDR_HLF_2D_vs_t0_818 = FDR for 2D vs initial HLF; FDR_HLF_3D_vs_t0_818 = FDR for 3D vs initial HLF;FDR_PLCPRF5_2D_vs_t0 = FDR for 2D vs initial PLCPRF5 ;FDR_PLCPRF5_3D_vs_t0_0042 = FDR for 3D vs initial PLCPRF5; FDR_PLCPRF5_2D_vs_3D_8440042 = FDR for 2D vs 3D end for PLCPRF5; FDR_HLF_2D_vs_3D_818 = FDR for 2D vs 3D HLF end point; FDR_HLF_SNDX_vs_T0_885 = FDR for SNDX vs T0 in HLF; FDR_HLF_DMSO_vs_t0_885 = FDR for DMSO vs T0 in HLF; FDR_HLF_SNDX_vs_DMSO_885 =FDR SNDX vs DMSO in HLF at endpoint.

value: Liver cancer cells

value: HLF

value: None 2D


title: CD8 Donor 2 FCRL3 mAb 20h

description: 150 x 150 bp paired end reads

value: FCRL3 mAb 20h


title: hTSCs-shMYBL2-3

description: Library name: Sample 6

value: placenta

value: hTSCs

value: Human trophoblast stem cells


title: 3T3_H2AK119Ub_C3_rep1

description: CUT&Tag for H2AK119Ub on CBX7 overexpression stable cell line monoclone3 NIH3T3 cells

value: CBX7 OE


title: 3T3_H3K27me3_C4_rep1

description: CUT&Tag for H3K27me3 on CBX7 overexpression stable cell line monoclone4 NIH3T3 cells


title: HLF 2D Final rep 1

description:
Library name: HLF_CRISPR_2D_d28_DMSO_1
Other: amplicon sequencing containing gRNA
Columns for processed data file; id = Gene ID; Score_HLF_2D_vs_t0_818 = RRA for 2D vs initial HLF; Score_HLF_3D_vs_t0_818 = RRA for 3D vs initial HLF; Score_PLCPRF5_2D_vs_t0 = RRA for 2D vs initial PLCPRF5 ; Score_PLCPRF5_3D_vs_t0_0042 = RRA for 3D vs initial PLCPRF5; Score_PLCPRF5_2D_vs_3D_8440042 = RRA for 2D vs 3D end for PLCPRF5; Score_HLF_2D_vs_3D_818 = RRA for 2D vs 3D HLF end point; Score_HLF_SNDX_vs_T0_885 = RRA for SNDX vs T0 in HLF; Score_HLF_DMSO_vs_t0_885 = RRA for DMSO vs T0 in HLF; Score_HLF_SNDX_vs_DMSO_885 = RRA SNDX vs DMSO in HLF at endpoint. FDR_HLF_2D_vs_t0_818 = FDR for 2D vs initial HLF; FDR_HLF_3D_vs_t0_818 = FDR for 3D vs initial HLF;FDR_PLCPRF5_2D_vs_t0 = FDR for 2D vs initial PLCPRF5 ;FDR_PLCPRF5_3D_vs_t0_0042 = FDR for 3D vs initial PLCPRF5; FDR_PLCPRF5_2D_vs_3D_8440042 = FDR for 2D vs 3D end for PLCPRF5; FDR_HLF_2D_vs_3D_818 = FDR for 2D vs 3D HLF end point; FDR_HLF_SNDX_vs_T0_885 = FDR for SNDX vs T0 in HLF; FDR_HLF_DMSO_vs_t0_885 = FDR for DMSO vs T0 in HLF; FDR_HLF_SNDX_vs_DMSO_885 =FDR SNDX vs DMSO in HLF at endpoint.


title: 3T3_H3K27me3_C5_rep1

description: CUT&Tag for H3K27me3 on CBX7 overexpression stable cell line monoclone5 NIH3T3 cells


title: CD8 Donor 2 SA control 4h

description: 150 x 150 bp paired end reads

value: Peripheral blood

value: CD8 effector T

value: SA control 4h


title: HTR8-shMYBL2-3

description: Library name: Sample 12

value: HTR-8/SVneo cells

value: Trophoblast cell line

value: MYBL2 knockdown

value: Lentiviral transfection


title: CD8 Donor 2 secretory lgA 4h

description: 150 x 150 bp paired end reads

value: CD8 Donor 2

value: secretory lgA 4h


title: 3T3_H3K27me3_C3_rep1

description: CUT&Tag for H3K27me3 on CBX7 overexpression stable cell line monoclone3 NIH3T3 cells

value: NIH 3T3

value: fibroblast


title: hTSCs-shMYBL2-1

description: Library name: Sample 4


title: CD8 Donor 2 FCRL3 mAb 4h

description: 150 x 150 bp paired end reads

value: FCRL3 mAb 4h


title: hTSCs-shMYBL2-2

description: Library name: Sample 5


title: blueX42b

city: Lübeck

first: Leonardo

last: de Assis

address: Marie Curie

country: Germany

institute: University of Lübeck

description: Library name: BSR657

data_processing:
Sequencing was performed on the NextSeq 500 platform at the NGS core facility  SELA. The sequencing data was aligned to the GRCh38 version of the human genome using STAR and the bam sort tool from biobambam2 for downstream processing of the BAM file, including merging, sorting, and marking duplicates. To count the number of reads that overlap each gene, we used featureCounts.
Assembly: GRCh38
Supplementary files format and content: raw count files are provided

source_name: HaCaT

growth_protocol: Human skin immortalized keratinocyte cells (HaCaT) were cultivated in Dulbecco modified Eagle medium (DMEM), supplemented with 10% fetal bovine serum (FBS), 4 mM L-glutamine, 100 U/mL penicillin and 100 pg/mL of streptomycin, in 5% CO2 at 37oC. All reagents were acquired from ThermoFisher Scientific (USA).

extract_protocol:
Total RNA was extracted using TRIzol (Thermo Fisher, USA) according to the manufacturer’s instructions. The extraction process included the use of molecular-grade chloroform and isopropanol, and the RNA was subsequently washed with molecular-grade ethanol (all reagents were from Sigma-Aldrich, USA). Subsequent analysis used high-quality RNA (280/260 and 260/230 indexes > 1.8).
RNASeq Libraries were prepared using a QuantSeq 3’ mRNA-Seq Library Prep Kit-FWD (Lexogen, Vienna, Austria) with 1μg RNA. The library concentration was measured by Qubit Fluorometer and Qubit dsDNA HS Assay Kit (Applied Biosystems), and the size distribution was determined using an Agilent D1000 ScreenTape System (Agilent Technologies).

treatment_protocol: HaCaT cells (5 x 10⁵ cells per 100 mm plate) were exposed to a blue light LED source (λ = 408 nm, irradiance = 4.6 mW.cm-2) developed by the Optics and Photonics Research Center at the Institute of Physics, University of São Paulo. The cells were irradiated in phosphate-buffered saline at an irradiation of 50 J/cm² three times a week for up to 14 weeks. Light dose was constant through the experiment and chosen to provide 50% cell death in HaCaT cells. After each irradiation, the culture medium was reintroduced until the next session.

value: HaCaT

value: wild-type

value: 42X blue light stimulation


title: blueX42a

description: Library name: BSR655


title: CD8 Donor 1 SA control 20h

description: 150 x 150 bp paired end reads

value: CD8 Donor 1

value: SA control 20h


title: 3T3_H3K9me3_C5_rep1

description: CUT&Tag for H3K9me3 on CBX7 overexpression stable cell line monoclone5 NIH3T3 cells

value: CBX7 OE


title: hTSCs-shNC-3

description: Library name: Sample 3

value: placenta

value: hTSCs

value: Human trophoblast stem cells

value: WT


title: hTSCs-shNC-2

description: Library name: Sample 2


title: darkX42b

description: Library name: BSR653

value: control 42X blue light stimulation


title: HLF 2D Final rep 3

description:
Library name: HLF_CRISPR_2D_d28_DMSO_3
Other: amplicon sequencing containing gRNA
Columns for processed data file; id = Gene ID; Score_HLF_2D_vs_t0_818 = RRA for 2D vs initial HLF; Score_HLF_3D_vs_t0_818 = RRA for 3D vs initial HLF; Score_PLCPRF5_2D_vs_t0 = RRA for 2D vs initial PLCPRF5 ; Score_PLCPRF5_3D_vs_t0_0042 = RRA for 3D vs initial PLCPRF5; Score_PLCPRF5_2D_vs_3D_8440042 = RRA for 2D vs 3D end for PLCPRF5; Score_HLF_2D_vs_3D_818 = RRA for 2D vs 3D HLF end point; Score_HLF_SNDX_vs_T0_885 = RRA for SNDX vs T0 in HLF; Score_HLF_DMSO_vs_t0_885 = RRA for DMSO vs T0 in HLF; Score_HLF_SNDX_vs_DMSO_885 = RRA SNDX vs DMSO in HLF at endpoint. FDR_HLF_2D_vs_t0_818 = FDR for 2D vs initial HLF; FDR_HLF_3D_vs_t0_818 = FDR for 3D vs initial HLF;FDR_PLCPRF5_2D_vs_t0 = FDR for 2D vs initial PLCPRF5 ;FDR_PLCPRF5_3D_vs_t0_0042 = FDR for 3D vs initial PLCPRF5; FDR_PLCPRF5_2D_vs_3D_8440042 = FDR for 2D vs 3D end for PLCPRF5; FDR_HLF_2D_vs_3D_818 = FDR for 2D vs 3D HLF end point; FDR_HLF_SNDX_vs_T0_885 = FDR for SNDX vs T0 in HLF; FDR_HLF_DMSO_vs_t0_885 = FDR for DMSO vs T0 in HLF; FDR_HLF_SNDX_vs_DMSO_885 =FDR SNDX vs DMSO in HLF at endpoint.

value: Liver cancer cells

value: HLF

value: None 2D


title: 3T3_H3K9me3_C4_rep1

description: CUT&Tag for H3K9me3 on CBX7 overexpression stable cell line monoclone4 NIH3T3 cells

value: NIH 3T3


title: hTSCs-shNC-1

description: Library name: Sample 1

value: Lentiviral transfection


title: 3T3_H3K9me3_WT_rep1

description: CUT&Tag for H3K9me3 on WT NIH3T3 cells

value: fibroblast


title: CD8 Donor 1 FCRL3 mAb 20h

description: 150 x 150 bp paired end reads

value: Peripheral blood

value: CD8 effector T

value: FCRL3 mAb 20h


title: MCF10A_OSMTGFBEGF_Replicate3

city: Portland

first: Laura

middle: M

last: Heiser

state: OR

address: 2730 S Moody Ave

department: Biomedical Engineering

institute: Oregon Health and Science University

description:
Library name: Sample27
RNA200630LH_3_OSM_TGFB_EGF_S27

data_processing:
RNAseq data was preprocessed and aligned using a pipeline adapted from Tatlow, et al (Tatlow & Piccolo, 2016).
TrimGalore (v. 0.4.3) was used to trim adapter sequences and low-quality bases using CutAdapt (v. 1.10) and to generate FASTQ quality reports using FastQC (v. 0.11.5).
After adapter trimming, reads were filtered to have a minimum length of 30 bp. Trimmed reads were pseudo-aligned to the GENCODE V24 transcriptome (GRCh38.p5) using Kallisto (v. 0.46.2).
Gene-level quantifications were obtained from transcript-level abundance estimates using the R package tximport (v. 1.8.0) in R (v. 3.5.0).
Assembly: hg38
Supplementary files format and content: MDD_ligandCombination_RNAseq_counts_allGene.csv: comma-separated value table of per-sample transcript abundance estimates output by Kallisto, in units of estimaed counts

molecule: polyA RNA

growth_protocol: Cells were cultured in growth media containing DMEM/F12, 5% horse serum, 20 ng/ml EGF, 0.5 µg/ml hydrocortisone, 100 ng/ml cholera toxin, 10 µg/ml insulin, and 1% Pen/Strep.

extract_protocol:
Total RNA was extracted from flash-frozen samples using a Qiagen Rneasy Mini kit.
Libraries were prepared using an Illumina TruSeq Stranded mRNA library preparation kit.

treatment_protocol: Cells were cultured to 50-80% and detached using 0.05% trypsin-EDTA. Post-detachment, 520,000 cells were seeded into collagen-1 coated 8-well plates in growth media. Six hours after seeding, cells were washed with PBS and growth factor-free media was added. After an 18-hour incubation in the new media, cells were treated with single ligand or combinations of ligands in fresh growth factor-free media: 10 ng/ml EGF (R&D Systems #236-EG), 10 ng/ml OSM (R&D Systems #8475-OM), and 10 ng/ml TGFβ (R&D Systems #240-B).

value: normal breast epithelium

value: 10ng/mL OSM+10ng/mL TGFB+10ng/mL EGF


title: CD8 Donor 1 SA control 4h

description: 150 x 150 bp paired end reads

value: CD8 Donor 1

value: SA control 4h


title: blueX14b

description: Library name: BSR680

value: HaCaT

value: wild-type

value: 14X blue light stimulation


title: 3T3_RNA_C5_batch4

description: Smart-seq2 on CBX7 overexpression stable cell line monoclone5 NIH3T3 cells

data_processing:
Paired-end RNA-seq reads were aligned to mm9 using HISAT2 v2.2.1 and FPKM value of each gene was calculated with StringTie v2.1.2.
The paired end ChIP-seq or CUT&Tag reads were mapped to mm9 using bowtie2 (version 2.2.5) with the parameters: -t -q -p 40 -N 1 -L 25 -X 2000 --no-mixed --no-discordant. The unmapped reads, not uniquely mapped, and duplicate reads were removed. Read coverages over the mm9 genome were calculated by bamCoverage from deepTools v3.3.1. The signal was then normalized by computing the number of reads per kilobase of bin per million reads sequenced (RPKM), followed by normalization using Z-score (whole genome 100bp bn with outliner regions excluded).
Hi-C data analysis was performed as previously described. Briefly, Hi-C libraries were aligned using HiCPro (version 2.10.0) with bowtie2 end-to-end algorithm and with the option ‘-very-sensitive’.
Assembly: mm9
Supplementary files format and content: Bigwig for ChIP-seq tracks, gene expression table for RNA-seq data, ValidPairs for Hi-C data

extract_protocol:
RNA-Seq libraries were prepared using Smart-Seq2 protocol (S. Picelli et al., 2014.).
1ng cDNA was fragmented by Tn5 and PCR was performed to amplify the library for 16 cycles using the following PCR conditions: 72 °C for 3 min; 98 °C for 30s; and thermocycling at 98°C for 15s, 60°C for 30s and 72°C for 3min; followed by 72 °C 5 min. After the PCR reaction, libraries were purified with the 0.4x-1.7x AMPure (Beckman) beads size selection and were subjected to next generation sequencing.

value: CBX7 OE


title: 3T3_H3K9me3_C3_rep1

description: CUT&Tag for H3K9me3 on CBX7 overexpression stable cell line monoclone3 NIH3T3 cells


title: 3T3_H3K27me3_WT_rep1

description: CUT&Tag for H3K27me3 on WT NIH3T3 cells

value: WT


title: MCF10A_OSMTGFB_Replicate3

description:
Library name: Sample25
RNA200630LH_3_OSM_TGFB_S25

value: 10ng/mL OSM+10ng/mL TGFB


title: darkX14b

description: Library name: BSR674

value: control 14X blue light stimulation


title: 3T3_RNA_C4_batch4

description: Smart-seq2 on CBX7 overexpression stable cell line monoclone4 NIH3T3 cells

value: NIH 3T3


title: CD8 Donor 1 FCRL3 mAb 4h

description: 150 x 150 bp paired end reads

value: FCRL3 mAb 4h


title: CD8 Donor 1 secretory lgA 4h

description: 150 x 150 bp paired end reads

value: secretory lgA 4h


title: MCF10A_TGFB_Replicate3

description:
Library name: Sample24
RNA200630LH_3_TGFB_S24

value: 10ng/mL TGFB


title: 3T3_RNA_C3_batch4

description: Smart-seq2 on CBX7 overexpression stable cell line monoclone3 NIH3T3 cells

value: fibroblast


title: blueX3b

description: Library name: BSR668

value: 3X blue light stimulation


title: Treg Donor 6 secretory lgA 20h

description: 150 x 150 bp paired end reads

value: Peripheral blood

value: CD4 regulatory T

value: Treg Donor 6

value: secretory lgA 20h


title: MCF10A_OSM_Replicate3

description:
Library name: Sample23
RNA200630LH_3_OSM_S23

value: normal breast epithelium

value: 10ng/mL OSM


title: 3T3_RNA_WT_batch4

description: Smart-seq2 on WT NIH3T3 cells


title: Treg Donor 6 FCRL3 mAb 20h

description: 150 x 150 bp paired end reads

value: FCRL3 mAb 20h


title: blueX3a

description: Library name: BSR665

value: HaCaT

value: wild-type


title: MCF10A_EGFTGFB_Replicate3

description:
Library name: Sample22
RNA200630LH_3_EGF_TGFB_S22

value: 10ng/mL EGF+10ng/mL TGFB


title: darkX42a

description: Library name: BSR651

value: control 42X blue light stimulation


title: CD8 Donor 1 secretory lgA 20h

description: 150 x 150 bp paired end reads

value: CD8 effector T

value: CD8 Donor 1


title: 3T3_RNA_C4_batch3

value: NIH 3T3

value: CBX7 OE


title: blueX14a

description: Library name: BSR677

value: 14X blue light stimulation


title: darkX3b

description: Library name: BSR662

value: control 3X blue light stimulation


title: Treg Donor 6 SA control 20h

description: 150 x 150 bp paired end reads

value: Peripheral blood

value: SA control 20h


title: 3T3_RNA_C3_batch3

value: fibroblast


title: MCF10A_EGFOSM_Replicate3

description:
Library name: Sample26
RNA200630LH_3_EGF_OSM_S26

value: 10ng/mL EGF+10ng/mL OSM


title: Treg Donor 6 secretory lgA 4h

description: 150 x 150 bp paired end reads

value: CD4 regulatory T

value: Treg Donor 6

value: secretory lgA 4h


title: darkX3a

description: Library name: BSR659

value: HaCaT


title: 3T3_RNA_WT_batch3

description: Smart-seq2 on WT NIH3T3 cells

value: WT


title: MCF10A_EGF_Replicate3

description:
Library name: Sample21
RNA200630LH_3_EGF_S21

value: normal breast epithelium

value: 10ng/mL EGF


title: FS_101_UCS_PPS_M

city: Jerusalem

first: Shani

last: Vaknine Treidel

state: Israel

address: The Safra Campus, Givat Ram

department: Biological Chemistry

country: Israel

institute: The Hebrew University of Jerusalem

description:
N_FS_101_S8
N_rawcounts_miRs.csv

data_processing:
Quality control was re-assessed using FastQC version 0.11.8, with Cutadapt for removing the adaptor sequences.
Flexbar for further quality screening and cleaning.
Assembly: Alignment to tRFs was done using MINTmap to MINTbase v2.0 and to microRNA using miRDeep2 to miRbase 22.1.
Supplementary files format and content: Tab-delimited csv files containing DESeq2 normalized counts for all samples.

source_name: Umbilical cord serum

extract_protocol:
RNA from serum was extracted with the miRNeasy Serum/Plasma Advanced Kit (Qiagen, 217204) according to the manufacturer’s instructions.
Libraries were constructed using the D-Plex Small RNA-seq Kit from Illumina (Diagenode, C05030001), using 1600 pg/sample in the newborn cohort and 400 pg/sample in the maternal one.

value: Umbilical cord serum

tag: Sex

value: Male

tag: age

value: newborn

tag: condition

value: stress


title: 3T3_RNA_C5_batch2

value: NIH 3T3

value: CBX7 OE


title: MCF10A_T0Ctrl_Replicate3

description:
Library name: Sample19
RNA200630LH_3_CTRL_S19


title: MCF10A_PBS_Replicate3

description:
Library name: Sample20
RNA200630LH_3_PBS_S20

value: PBS


title: Treg Donor 6 FCRL3 mAb 4h

description: 150 x 150 bp paired end reads

value: Peripheral blood

value: FCRL3 mAb 4h


title: MCF10A_OSMTGFBEGF_Replicate2

description:
Library name: Sample18
RNA200630LH_2_OSM_TGFB_EGF_S18

value: 10ng/mL OSM+10ng/mL TGFB+10ng/mL EGF


title: 3T3_RNA_WT_batch2

description: Smart-seq2 on WT NIH3T3 cells

value: fibroblast


title: darkX14a

description: Library name: BSR671

value: wild-type

value: control 14X blue light stimulation


title: Treg Donor 5 secretory lgA 20h

description: 150 x 150 bp paired end reads

value: CD4 regulatory T

value: Treg Donor 5

value: secretory lgA 20h


title: MCF10A_EGFOSM_Replicate2

description:
Library name: Sample17
RNA200630LH_2_EGF_OSM_S17

value: normal breast epithelium

value: 10ng/mL EGF+10ng/mL OSM


title: FS_97_UCS_PPS_M

description:
N_FS_97_S19
N_rawcounts_miRs.csv

value: Umbilical cord serum

value: Male


title: FS_76_UCS_PPS_M

description:
N_FS_76_S3
N_rawcounts_miRs.csv

value: newborn

value: stress


title: Treg Donor5 FCRL3 mAb 20h

description: 150 x 150 bp paired end reads

value: Treg Donor5

value: FCRL3 mAb 20h


title: FS_75_UCS_PPS_M

description:
N_FS_75_S8
N_rawcounts_miRs.csv


title: MCF10A_TGFB_Replicate2

description:
Library name: Sample15
RNA200630LH_2_TGFB_S15

value: 10ng/mL TGFB


title: Treg Donor 5 SA control 20h

description: 150 x 150 bp paired end reads

value: Peripheral blood

value: SA control 20h


title: PM10

city: Piscataway

first: Shuo

last: Xiao

state: NJ

address: 170 Frelinghuysen Rd

department: Pharmacology and Toxicology

institute: Rutgers University

description: Mouse ovarian follicle maturation window,PFNA treated

data_processing:
Partek flow software
Remove rDNA and mtDNA contaminants using Bowtie2
Alignment by HISAT2
Quantification by Partek EM algorithm
Assembly: Ensembl Transcripts release 99
Supplementary files format and content: Raw count

source_name: Ovary

extract_protocol:
RNA was harvested using Arcturus™ PicoPure™ RNA Isolation Kit from Applied Biosystem
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: Ovary

value: Ovarian follicle from CD-1 mouse

value: Tissue

value: WT

value: PFNA


title: FS_69_UCS_PPS_M

description:
N_FS_69_S7
N_rawcounts_miRs.csv


title: MCF10A_OSM_Replicate2

description:
Library name: Sample14
RNA200630LH_2_OSM_S14

value: 10ng/mL OSM


title: PM9


title: Treg Donor 5 secretory lgA 4h

description: 150 x 150 bp paired end reads

value: CD4 regulatory T

value: Treg Donor 5

value: secretory lgA 4h


title: 3T3_RNA_C5_batch1

description: Smart-seq2 on CBX7 overexpression stable cell line monoclone5 NIH3T3 cells

value: NIH 3T3

value: fibroblast

value: CBX7 OE


title: FS_32_UCS_PPS_M

description:
N_FS_32_S12
N_rawcounts_miRs.csv

value: Umbilical cord serum

value: Male

value: newborn

value: stress


title: Treg Donor 5 FCRL3 mAb 4h

description: 150 x 150 bp paired end reads

value: Peripheral blood

value: FCRL3 mAb 4h


title: Treg Donor 6 SA control 4h

description: 150 x 150 bp paired end reads

value: Treg Donor 6

value: SA control 4h


title: FS_28_UCS_PPS_M

description:
N_FS_28_S4
N_rawcounts_miRs.csv


title: MCF10A_EGF_Replicate2

description:
Library name: Sample12
RNA200630LH_2_EGF_S12

value: normal breast epithelium

value: 10ng/mL EGF


title: MCF10A_EGFTGFB_Replicate2

description:
Library name: Sample13
RNA200630LH_2_EGF_TGFB_S13

value: 10ng/mL EGF+10ng/mL TGFB


title: PM7

value: Ovary

value: Ovarian follicle from CD-1 mouse

value: Tissue

value: WT

value: PFNA


title: Treg Donor 4 secretory lgA 20h

description: 150 x 150 bp paired end reads

value: CD4 regulatory T

value: Treg Donor 4

value: secretory lgA 20h


title: PM6


title: MCF10A_OSMTGFB_Replicate2

description:
Library name: Sample16
RNA200630LH_2_OSM_TGFB_S16

value: 10ng/mL OSM+10ng/mL TGFB


title: FS_85_UCS_PPS_M

description:
N_FS_85_S5
N_rawcounts_miRs.csv

value: Umbilical cord serum

value: Male

value: newborn

value: stress


title: FS_135_UCS_PPS_F

description:
N_FS_135_S13
N_rawcounts_miRs.csv

value: Female


title: Treg Donor 4 FCRL3 mAb 20h

description: 150 x 150 bp paired end reads

value: Peripheral blood

value: FCRL3 mAb 20h


title: 3T3_RNA_WT_batch1

description: Smart-seq2 on WT NIH3T3 cells

value: NIH 3T3

value: fibroblast


title: PM5

value: Ovary

value: Ovarian follicle from CD-1 mouse


title: FS_98_UCS_PPS_F

description:
N_FS_98_S7
N_rawcounts_miRs.csv


title: MCF10A_T0Ctrl_Replicate2

description:
Library name: Sample10
RNA200630LH_2_CTRL_S10

value: normal breast epithelium


title: FS_94_UCS_PPS_F

description:
N_FS_94_S23
N_rawcounts_miRs.csv


title: Treg Donor 4 SA control 20h

description: 150 x 150 bp paired end reads

value: SA control 20h


title: MCF10A_OSMTGFBEGF_Replicate1

description:
Library name: Sample9
RNA200630LH_1_OSM_TGFB_EGF_S9

value: 10ng/mL OSM+10ng/mL TGFB+10ng/mL EGF


title: Treg Donor 4 secretory lgA 4h

description: 150 x 150 bp paired end reads

value: CD4 regulatory T

value: Treg Donor 4

value: secretory lgA 4h


title: MCF10A_EGFOSM_Replicate1

description:
Library name: Sample8
RNA200630LH_1_EGF_OSM_S8

value: 10ng/mL EGF+10ng/mL OSM


title: FS_91_UCS_PPS_F

description:
N_FS_91_S22
N_rawcounts_miRs.csv

value: Umbilical cord serum


title: PM4

value: Tissue

value: WT

value: PFNA


title: PM3


title: PM8


title: Treg Donor 5 SA control 4h

description: 150 x 150 bp paired end reads

value: Peripheral blood

value: Treg Donor 5

value: SA control 4h


title: PM2


title: Treg Donor 4 FCRL3 mAb 4h

description: 150 x 150 bp paired end reads

value: FCRL3 mAb 4h


title: MCF10A_TGFB_Replicate1

description:
Library name: Sample6
RNA200630LH_1_TGFB_S6

value: 10ng/mL TGFB


title: MCF10A_OSMTGFB_Replicate1

description:
Library name: Sample7
RNA200630LH_1_OSM_TGFB_S7

value: 10ng/mL OSM+10ng/mL TGFB


title: FS_27_UCS_PPS_F

description:
N_FS_27_S9
N_rawcounts_miRs.csv

value: Female

value: newborn

value: stress


title: Treg Donor 4 SA control 4h

description: 150 x 150 bp paired end reads

value: CD4 regulatory T


title: MCF10A_PBS_Replicate2

description:
Library name: Sample11
RNA200630LH_2_PBS_S11

value: normal breast epithelium

value: PBS


title: Treg Donor 3 secretory lgA 20h

description: 150 x 150 bp paired end reads

value: Treg Donor 3

value: secretory lgA 20h


title: PM1

value: Ovary

value: Ovarian follicle from CD-1 mouse

value: Tissue


title: MCF10A_OSM_Replicate1

description:
Library name: Sample5
RNA200630LH_1_OSM_S5

value: 10ng/mL OSM


title: FS_145_UCS_CTL_M

description:
N_FS_145_S14
N_rawcounts_miRs.csv

value: Umbilical cord serum

value: Male

value: control


title: Treg Donor 3 FCRL3 mAb 20h

description: 150 x 150 bp paired end reads

value: Peripheral blood

value: FCRL3 mAb 20h


title: CM12

description: Mouse ovarian follicle maturation window, control

value: WT

value: DMSO


title: MCF10A_EGFTGFB_Replicate1

description:
Library name: Sample4
RNA200630LH_1_EGF_TGFB_S4

value: 10ng/mL EGF+10ng/mL TGFB


title: Treg Donor 3 SA control 20h

description: 150 x 150 bp paired end reads

value: CD4 regulatory T

value: SA control 20h


title: MCF10A_EGF_Replicate1

description:
Library name: Sample3
RNA200630LH_1_EGF_S3

value: normal breast epithelium

value: 10ng/mL EGF


title: CM10


title: FS_168_UCS_CTL_M

description:
N_FS_168_S26
N_rawcounts_miRs.csv

value: newborn


title: FS_119_UCS_CTL_M

description:
N_FS_119_S10
N_rawcounts_miRs.csv


title: FS_31_UCS_PPS_F

description:
N_FS_31_S11
N_rawcounts_miRs.csv

value: Female

value: stress


title: Treg Donor 3 secretory lgA 4h

description: 150 x 150 bp paired end reads

value: Treg Donor 3

value: secretory lgA 4h


title: CM11

value: Ovary

value: Ovarian follicle from CD-1 mouse

value: Tissue


title: MCF10A_T0Ctrl_Replicate1

description:
Library name: Sample1
RNA200630LH_1_CTRL_S1


title: CM9


title: FS_117_UCS_CTL_M

description:
N_FS_117_S21
N_rawcounts_miRs.csv

value: Umbilical cord serum

value: Male

value: control


title: Treg Donor 3 FCRL3 mAb 4h

description: 150 x 150 bp paired end reads

value: Peripheral blood

value: FCRL3 mAb 4h


title: FS_72_UCS_CTL_M

description:
N_FS_72_S20
N_rawcounts_miRs.csv


title: MCF10A_PBS_Replicate1

description:
Library name: Sample2
RNA200630LH_1_PBS_S2

value: PBS


title: CM8

value: WT

value: DMSO


title: CM7


title: Treg Donor 2 secretory lgA 20h

description: 150 x 150 bp paired end reads

value: CD4 regulatory T

value: Treg Donor 2

value: secretory lgA 20h


title: E5-AP2-G-DD, input

city: Barcelona

first: Alba

last: Pérez-Cantero

state: Barcelona

address: Rosselló, 153

country: Spain

institute: Barcelona Institute for Global Health (ISGlobal)

description: Library name: chip_E5-AP2G-DD_input

data_processing:
ChIP-seq reads were trimmed using the bbduk command from BBmap software (version July, 26 2018). 3' end was trimmed when quality score < 6. Reads shorter than 10 bp after trimming were discarded
Quality control of the reads was performed using FastQC (v0.11.9) checking reads contamination with FastqScreen (v0.14.0)
Reads were mapped using Bowtie2 (v2.4.5) using the following parameters different from the default ones --very-sensitive --local -5 4 -3 4 -I 50 -X 2000
SAMtools (v1.15) was used for compressing, sorting and filtering-out < 5 mapping quality reads from the alignment files
PCR duplicates were removed using GATK (v4.4.0.0) MarkDuplicates command
Tracks were generated using deepTools (v3.5.1). To generate individual coverage tracks the command bamCompare was used with a bin size of 10 bp and a smoothing length of 200 bp. To obtain the tracks normalized by input, the bamCompare command was used with this parameters: --outFileFormat bedgraph --scaleFactorsMethod None --normalizeUsing RPKM -bs 10 --smoothLength 200 --pseudocount 10 -of bedgraph
Assembly: Reference Plasmodium falciparum (3D7) genome retrieved from PlasmoDB (VEuPathDB). Manually edited for analysis of transgenic parasite lines.
Supplementary files format and content: bedgraph (tracks normalized by input)

organism: Plasmodium falciparum

source_name: Plasmodium falciparum

extract_protocol:
Chromatin extraction from cultures at the late trophozoite/schizont was carried out using the MAGnify chromatin immunoprecipitation system (Life Technologies) after saponin lysis and formaldehyde crosslinking. Samples were then sonicated using an M220 sonicator (Covaris) at 10% duty factor, 200 cycles per burst, 140 W of peak incident power for 10min. Immunoprecipitation was performed overnight at 4ºC with 2µg of chromatin and 4µg of antibodies against H3K9me3 or H3K9ac (Diagenode). Washing, de-crosslinking and elution were performed following the manufacturer instructions, but to avoid high temperatures that may result in denaturation of extremely AT-rich intergenic regions, steps were performed at 45ºC instead of 65ºC.
Libraries for Illumina sequencing were prepared from 5 ng of immunoprecipitated DNA using a protocol adapted for extremely AT-rich genomes.After end-repair and addition of 3′ A-overhangs, NEBNext Multiplex Oligos for Illumina (NEB, E7500) were ligated. Purification steps were performed with Agencourt AMPure XP beads (Beckman Coulter, A63880). Libraries were amplified using the KAPA HiFi PCR Kit (KAPA Biosystems, KK2103) in KAPA HiFi Fidelity Buffer with the following conditions: 95°C for 3 min; 9 cycles at 98°C for 20 s and 62°C for 2 min 30 s; and 62 °C for 5 min. Amplified libraries were purified using 0.9X AMPure XP beads to remove adapter dimers. The library size was analysed in a 4200 TapeStation System (Agilent Technologies) and 125 bp paired-end reads were obtained using the HiSeq2500 or the NextSeq 500 System (Illumina).

tag: Stage

tag: chip antibody

tag: genetic modification

value: FKBP destabilization domain fused to PfAP2-G

value: Plasmodium falciparum


title: E5-AP2-G-DD, H3K9me3 IP

description: Library name: chip_E5-AP2G-DD_me3


title: FS_53_UCS_CTL_M

description:
N_FS_53_S16
N_rawcounts_miRs.csv

value: newborn


title: FS_47_UCS_CTL_M

description:
N_FS_47_S5
N_rawcounts_miRs.csv


title: CM6

value: Ovary


title: FS_143_UCS_CTL_M

description:
N_FS_143_S23
N_rawcounts_miRs.csv


title: FS_29_UCS_CTL_M

description:
N_FS_29_S10
N_rawcounts_miRs.csv


title: Treg Donor 2 SA control 20h

description: 150 x 150 bp paired end reads

value: SA control 20h


title: CM5

value: Ovarian follicle from CD-1 mouse

value: Tissue


title: E5-Δap2-g, input

description: Library name: chip_E5del_input

value: pfap2-g deletion (+366 to +6945 bp from ATG)


title: Treg Donor 2 FCRL3 mAb 20h

description: 150 x 150 bp paired end reads

value: FCRL3 mAb 20h


title: E5-Δap2-g, H3K9me3 IP

description: Library name: chip_E5del_me3


title: CM3


title: FS_2_UCS_CTL_M

description:
N_FS_2_S1
N_rawcounts_miRs.csv

value: Umbilical cord serum

value: Male

value: control


title: Treg Donor 2 secretory lgA 4h

description: 150 x 150 bp paired end reads

value: Peripheral blood

value: secretory lgA 4h


title: 1.2B, input

description: Library name: chip_1.2B_input

value: none (wt)


title: FS_167_UCS_CTL_F

description:
N_FS_167_S18
N_rawcounts_miRs.csv

value: Female


title: CM2

value: WT

value: DMSO


title: Treg Donor 3 SA control 4h

description: 150 x 150 bp paired end reads

value: CD4 regulatory T

value: Treg Donor 3

value: SA control 4h


title: Treg Donor 2 FCRL3 mAb 4h

description: 150 x 150 bp paired end reads

value: Treg Donor 2

value: FCRL3 mAb 4h


title: CM1

value: Ovary

value: Ovarian follicle from CD-1 mouse

value: Tissue


title: Treg Donor 2 SA control 4h

description: 150 x 150 bp paired end reads


title: Subclone 3E (ap2-g F1), input

description: Library name: chip_3E_F1_input

value: pfap2-g deletion (-3522 to +992 bp from ATG) + integration of pfap2-g F1 at PF3D7_1144400

value: Plasmodium falciparum


title: FS_161_UCS_CTL_F

description:
N_FS_161_S16
N_rawcounts_miRs.csv

value: Umbilical cord serum

value: newborn

value: control


title: PO11

description: Mouse ovarian follicle ovulation window,PFNA treated

value: hCG+PFNA


title: 1.2B, H3K9me3 IP

description: Library name: chip_1.2B_me3

value: none (wt)


title: Treg Donor 1 secretory lgA 20h

description: 150 x 150 bp paired end reads

value: Peripheral blood

value: Treg Donor 1

value: secretory lgA 20h


title: FS_153_UCS_CTL_F

description:
N_FS_153_S25
N_rawcounts_miRs.csv

value: Female


title: PO10

value: WT


title: Subclone 3E (ap2-g F1), H3K9ac IP

description: Library name: chip_3E_F1_ac


title: Treg Donor 1 FCRL3 mAb 20h

description: 150 x 150 bp paired end reads

value: CD4 regulatory T

value: FCRL3 mAb 20h


title: FS_148_UCS_CTL_F

description:
N_FS_148_S24
N_rawcounts_miRs.csv


title: Treg Donor 1 SA control 20h

description: 150 x 150 bp paired end reads

value: SA control 20h


title: Dnuc-3 0mM phosphate 12h Experiment 3 Replicate 3

city: Ithaca

first: Lori

middle: B

last: Huberman

state: NY

address: 236 Tower Rd.

department: Plant Pathology and Plant-Microbe Biology, School of Integrative Plant Science

institute: Cornell University

description: Library name: Dnuc-3_0mM_Phosphate_12h_Exp3_Rep3

data_processing:
Illumina Casava1.8 software used for base calling
Sequenced reads were trimmed for adaptor sequence and aligned to the predicted transcripts from the N. crassa OR74A genome (v12) and TPMs were quantified with Salmon v. 1.4.0 with the --validateMappings setting.
Assembly: Neurospora crassa OR74A NC12
Supplementary files format and content: tab-deliminated text file with TPM values for each sample

organism: Neurospora crassa

source_name: Mycelia

growth_protocol: N. crassa conidia were inoculated into 3ml of Vogel's minimal media + 2% sucrose and incubated at 25C in constant light with constant shaking at 200rpm for 24h.

extract_protocol:
Mycelia were filtered using Whatman paper #1 and flash frozen using liquid nitrogen. RNA was isolated by beading beating in Trizol reagent and then cleaned up using the Qiagen RNeasy kit.
RNA were prepared for sequencing using poly-A enrichment and standard Illumina protocols

treatment_protocol: Mycelia were washed in 3ml Fries minimal media with 7mM phosphate (for 7mM phosphate) or Fries minimal media with 0mM phosphate (for 0mM phosphate) three times and then transferred to 3ml Fries minimal media with 7mM phosphate or 0mM phosphate as indicated and incubated at 25C in constant light with constant shaking at 200rpm for either 4h or 12h as indicated prior to harvesting for RNAseq.

value: Mycelia

tag: strain

value: nuc-3::HygR mat a

value: 12h Fries minimal medium 0mM phosphate

tag: batch


title: Treg Donor 1 secretory lgA 4h

description: 150 x 150 bp paired end reads

value: secretory lgA 4h


title: PO8

value: Ovary

value: Ovarian follicle from CD-1 mouse

value: Tissue


title: Dnuc-3 0mM phosphate 12h Experiment 3 Replicate 2

description: Library name: Dnuc-3_0mM_Phosphate_12h_Exp3_Rep2


title: FS_118_UCS_CTL_F

description:
N_FS_118_S9
N_rawcounts_miRs.csv

value: Umbilical cord serum

value: newborn

value: control


title: Treg Donor 1 FCRL3 mAb 4h

description: 150 x 150 bp paired end reads

value: Peripheral blood

value: Treg Donor 1

value: FCRL3 mAb 4h


title: Treg Donor 1 SA control 4h

description: 150 x 150 bp paired end reads

value: SA control 4h


title: FS_68_UCS_CTL_F

description:
N_FS_68_S18
N_rawcounts_miRs.csv

value: Female


title: FS_166_UCS_CTL_F

description:
N_FS_166_S17
N_rawcounts_miRs.csv


title: FS_146_UCS_CTL_F

description:
N_FS_146_S15
N_rawcounts_miRs.csv


title: PO6

value: WT

value: hCG+PFNA


title: Wild type 0mM phosphate 12h Experiment 3 Replicate 3

description: Library name: WT_0mM_Phosphate_12h_Exp3_Rep3

value: Mycelia

value: FGSC 4200

value: Wild type mat a


title: PO5


title: FS_52_UCS_CTL_F

description:
N_FS_52_S15
N_rawcounts_miRs.csv


title: PO4


title: FS_44_UCS_CTL_F

description:
N_FS_44_S13
N_rawcounts_miRs.csv


title: SMC co-cultured with IPAHAdFb 10

city: Giessen

first: Marek

last: Bartkuhn

state: Hessen

address: Aulweg 132

department: Biomedical Informatics and Systems Medicine

institute: Justus-Liebig-University Giessen

data_processing:
Demutliplexing and FASTQ extraction was performed using bcl2fastq v2.20.0.422.
Primary processing of FASTQ data including quality control, filtering, trimming,alignment of reads and counting of gene-sprecific genes was done using nf-core RNA-seq pipeline v3.7
Analysis of differentially expressed genes was performed using DESeq2.
Assembly: HG38
Supplementary files format and content: Supplementary files format and content: Supplementary files format and content: RNA-seq read counts per gene (csv)

source_name: pulmonary artery

growth_protocol: PASMC and PAAF were grown in SMC medium.

extract_protocol:
RNeasy Micro (Qiagen)
NEB Next® Ultra ™II RNA Library Prep Kit for Illumina with rRNA Depletion kit v2

treatment_protocol: 24h co-culture followed by FACS and RNA extraction

value: pulmonary artery

value: smooth muscle cells

value: donor PASMC #1 direct co-culture with IPAH PAAF #4


title: PO9

value: Ovary

value: Ovarian follicle from CD-1 mouse

value: Tissue


title: Wild type 0mM phosphate 12h Experiment 3 Replicate 2

description: Library name: WT_0mM_Phosphate_12h_Exp3_Rep2

value: 12h Fries minimal medium 0mM phosphate


title: Wild type 0mM phosphate 12h Experiment 3 Replicate 1

description: Library name: WT_0mM_Phosphate_12h_Exp3_Rep1


title: SMC co-cultured with IPAHAdFb 11

value: donor PASMC #1 direct co-culture with IPAH PAAF #3


title: FS_15_UCS_CTL_F

description:
N_FS_15_S2
N_rawcounts_miRs.csv

value: Umbilical cord serum

value: newborn

value: control


title: PO7


title: Subclone 3E (ap2-g F1), H3K9me3 IP

description: Library name: chip_3E_F1_me3

value: pfap2-g deletion (-3522 to +992 bp from ATG) + integration of pfap2-g F1 at PF3D7_1144400

value: Plasmodium falciparum


title: FS_101_Maternal_PPS_M

description:
M_FS_101_S23
M_rawcounts_miRs.csv

source_name: Serum

value: Serum

value: Male

value: stress


title: SMC co-cultured with IPAHAdFb 1

value: donor PASMC #3 direct co-culture with IPAH PAAF #1


title: PO2

value: WT

value: hCG+PFNA


title: SMC co-cultured with IPAHAdFb 12

value: pulmonary artery

value: smooth muscle cells

value: donor PASMC #1 direct co-culture with IPAH PAAF #2


title: PO1

value: Ovary

value: Ovarian follicle from CD-1 mouse

value: Tissue


title: ChIP-Seq SAMD1 delPA

city: Marburg

first: Robert

last: Liefke

address: Hans-Meerwein-Str. 2

department: Institute of Molecular Biology and Tumor Research (IMT)

institute: Philipps University of Marburg

data_processing:
ChIP-Seq data were aligned to mouse Genome mm39 using bowtie2 allowing one mismatch.
Bigwig files were obtained using deepTools/bamCoverage normalized via RPKM.
Assembly: mm39
Supplementary files format and content: bigwig

source_name: SAMD1KO + FLAG-SAMD1 delPA

growth_protocol: E14 mouse ES cells (E14TG2a) were cultured in DMEM, 15% FCS, 1 x L-Glutamine, 1 x Non-essential amino acids, 1 x Sodium pyruvate, 1 x Penicillin/Streptomycin , 0.15% β-mercaptoethanol and 100 Units/ml of LIF on gelatin-coated plates.

extract_protocol:
ChIP experiments were performed in accordance to the One Day ChIP kit protocol (Diagenode).
For ChIP-Seq library five nanograms of precipitated DNA were used for indexed sequencing library preparation using the Microplex library preparation kit v2 (Diagenode).

treatment_protocol: SAMD1 mES KO cells were created as described in Stielow et al., 2021. SAMD1 KO mES cells were transiently transfected using jetPRIME transfection kit (Polyplus, 101000046) with various FLAG-SAMD1 expression constructs, or empty vector control.

value: mouse ES cell

value: FLAG-SAMD1 delPA

value: FLAG (Sigma-Aldrich, F3165)


title: Dnuc-3 0mM phosphate 12h Experiment 3 Replicate 1

description: Library name: Dnuc-3_0mM_Phosphate_12h_Exp3_Rep1

value: Mycelia

value: nuc-3::HygR mat a

value: 12h Fries minimal medium 0mM phosphate


title: SMC co-cultured with IPAHAdFb 2

value: donor PASMC #3 direct co-culture with IPAH PAAF #4


title: FS_97_Maternal_PPS_M

description:
M_FS_097_S15
M_rawcounts_miRs.csv

value: Serum

value: Male

value: newborn

value: stress


title: ChIP-Seq SAMD1 delSAM

source_name: SAMD1KO + FLAG-SAMD1 delSAM

value: FLAG-SAMD1 delSAM


title: CO12

description: Mouse ovarian follicle ovulation window,control

value: WT

value: hCG


title: FS_75_Maternal_PPS_M

description:
M_FS_075_S16
M_rawcounts_miRs.csv


title: SMC co-cultured with IPAHAdFb 3

value: pulmonary artery

value: smooth muscle cells

value: donor PASMC #3 direct co-culture with IPAH PAAF #3


title: CO11

value: Ovary

value: Ovarian follicle from CD-1 mouse

value: Tissue


title: ChIP-Seq SAMD1 WHmut

source_name: SAMD1KO + FLAG-SAMD1 WHmut

value: mouse ES cell

value: FLAG-SAMD1 WHmut

value: FLAG (Sigma-Aldrich, F3165)


title: FS_32_Maternal_PPS_M

description:
M_FS_032_S8
M_rawcounts_miRs.csv


title: FS_69_Maternal_PPS_M

description:
M_FS_069_S7
M_rawcounts_miRs.csv


title: SMC co-cultured with IPAHAdFb 5

value: donor PASMC #2 direct co-culture with IPAH PAAF #1


title: ChIP-Seq SAMD1 del1-26

source_name: SAMD1KO + FLAG-SAMD1 del1-26

value: FLAG-SAMD1 del1-26


title: PO3

value: hCG+PFNA


title: ChIP-Seq SAMD1 WT

source_name: SAMD1KO + FLAG-SAMD1 WT

value: FLAG-SAMD1 WT


title: ChIP-Seq empty

source_name: SAMD1KO + empty

value: empty


title: SMC co-cultured with IPAHAdFb 4

value: donor PASMC #3 direct co-culture with IPAH PAAF #2


title: CO9

value: WT


title: FS_28_Maternal_PPS_M

description:
M_FS_028_S24
M_rawcounts_miRs.csv

value: Serum

value: Male

value: newborn

value: stress


title: CO8

value: Ovary

value: hCG


title: FS_135_Maternal_PPS_F

description:
M_FS_135_S4
M_rawcounts_miRs.csv

value: Female


title: FDB_dHT_TMP269-5Aza_4

type: genomic

city: Basel

first: Faiza

last: Noreen

address: Mattenstrasse 28

department: Department of Biomedicine

country: Switzerland

institute: University of Basel

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridized to Infinium MouseMethylation array (Illumina) using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader (HiScan) and standard recommended Illumina scanner setting

data_processing:
Sesame package in R environment (v4.3.2)
Raw IDAT files from the mouse model MM285k arrays were pre-processed with the sesame package (v4.3.2) with the default "TQCDPB" preprocessing steps. Noob normalization was applied to all samples to derive beta values.  Noob normalized beta values

label: Cy5 and Cy3

source_name: muscle

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was extracted from muscle fiber samples using DNeasy Blood & Tissue Kit (Qiagen) according to standard instructions

value: muscle

tag: disease state

value: dHT

value: male


title: SMC co-cultured with IPAHAdFb 6

value: pulmonary artery

value: smooth muscle cells

value: donor PASMC #2 direct co-culture with IPAH PAAF #4


title: FDB_dHT_TMP269-5Aza_5


title: SMC co-cultured with IPAHAdFb 7

value: donor PASMC #2 direct co-culture with IPAH PAAF #3


title: FS_98_Maternal_PPS_F

description:
M_FS_098_S11
M_rawcounts_miRs.csv


title: CO7

value: Ovarian follicle from CD-1 mouse

value: Tissue


title: FDB_dHT_TMP269-5Aza_3


title: CO6

value: WT


title: SMC co-cultured with IPAHAdFb 8

value: donor PASMC #2 direct co-culture with IPAH PAAF #2


title: FDB_dHT_TMP269-5Aza_2


title: CO5


title: FS_91_Maternal_PPS_F

description:
M_FS_091_S12
M_rawcounts_miRs.csv

value: Serum


title: CO10


title: SMC control 1

value: donor PASMC #3 direct co-culture with donor PAAF #3


title: FS_31_Maternal_PPS_F

description:
M_FS_031_S19
M_rawcounts_miRs.csv

value: newborn

value: stress


title: FDB_dHT_TMP269-5Aza_1


title: SMC control 2

value: donor PASMC #2 direct co-culture with donor PAAF #2


title: FDB_dHT_Vehicle_4

value: Vehicle


title: SMC control 3

value: donor PASMC #1 direct co-culture with donor PAAF #4


title: FS_168_Maternal_CTL_M

description:
M_FS_168_S6
M_rawcounts_miRs.csv

value: Male

value: control


title: CO3

value: Ovary

value: hCG


title: CO4


title: FS_27_Maternal_PPS_F

description:
M_FS_027_S3
M_rawcounts_miRs.csv

value: Female


title: FDB_dHT_Vehicle_3

value: muscle

value: dHT

value: male


title: FDB_dHT_Vehicle_5


title: CO1

value: Ovarian follicle from CD-1 mouse

value: Tissue

value: WT


title: FDB_dHT_Vehicle_2


title: FS_145_Maternal_CTL_M

description:
M_FS_145_S13
M_rawcounts_miRs.csv

value: Serum


title: SMC control 4

value: pulmonary artery

value: smooth muscle cells

value: donor PASMC #1 direct co-culture with donor PAAF #1


title: CO2


title: NSC+Met-d30-r2

city: New York

first: Jianlong

state: New York

department: Department of Medicine

institute: Columbia University Irving Medical Center

data_processing:
For RNA-seq data processing, FastQC (v0.10.1) was used to check the sequencing quality and reads were aligned to the human genome hg38 using STAR (v2.7.6a) with the default settings.
Transcript assembly and differential expression analyses were performed using Cufflinks (v2.2.1). Assembly of novel transcripts was not allowed (-G). Other parameters of Cufflinks were the default setting.
The summed FPKM (fragments per kilobase per million mapped reads) of transcripts sharing each gene_id was calculated and exported by the Cuffdiff program.
Downstream analysis was performed using iDEP (v1.1) and R packages.
Assembly: hg38
Supplementary files format and content: tab-delimited text file

source_name: FUCCI-hNSCs differentiated from WA09 FUCCI-ESCs

growth_protocol: WA09 or H9 FUCCI-hESCs were differentiated into FUCCI-hNSCs using commercially available PSC neural induction medium (Cat. no. A1647801, Gibco) following the manufacturer’s details.  Briefly, 250 x 103 FUCCI-hESCs were seeded in a 6-well plate in PluriSTEM medium supplemented with rock inhibitor. The next day, PluriStem medium was replaced with 2 ml of neural induction medium (49 ml of neurobasal medium + 1 ml of neural induction supplement) and cultured for 7 days with medium replacement every alternate day. After neural induction, cells were cultured and maintained in a neural expansion medium (49 ml neurobasal + 49 ml advanced DMEM + 2 ml neural induction supplement) with a medium change every alternate day and passaged using accutase (5-8 minutes) without rock inhibitor.  All cells were cultured at 37°C in an environment with 5% CO2.

extract_protocol:
Total RNA from cultured cells was extracted using a GeneJET RNA purification kit (Cat No. K0732) according to the manufacturer’s protocol. RNA quality was evaluated by Agilent 2100 BioAnalyzer.
The preparation and sequencing of RNA-seq libraries were outsourced to BGI. Libraries were sequenced on the NovaSeq 6000 platform with 150 bp paired-end read length.

treatment_protocol: To test the effect of metabolites on neuronal cells, FUCCI-hNSCs were seeded (2 x 103/well in a 96-well plate for short-term treatment or 10 x 103 in a 24-well plate for long-term treatment) with a neural expansion medium supplemented with 200 µM glutamic acid (Cat No. G5667-100G, Sigma) or 35 µM methionine (Cat No. M9625-25G, Sigma). Both metabolites at these concentrations were not toxic to cells (Fig. S4B). Metabolites were replenished along with fresh medium every other day. Long-term treatment was carried out until day 30 with passaging every 4-6 days.

value: Neuronal stem cells

value: WA09 hESC FUCCI reporter

value: Methionine


title: Hi-C, i8, recombined, clone 62, replicate 2

city: Amsterdam

first: Bas

last: van Steensel

address: Plesmanlaan 121

country: Netherlands

institute: Netherlands Cancer Institute

description: Library name: HiC_Sample_6

data_processing:
Mouse strain-specific variants were obtained from the Mouse Genomes Project (Keane et al. 2011) and homozygous SNPs were filtered using SnpSift (Cingolani et al. 2021) version 4.3p. bcftools (Danecek et al. 2021) version 1.9 was used to insert single-nucleotide variants into the GRCm38/mm10 mouse genome and the resulting fasta files were concatenated to produce one diploid hybrid genome.
Sequencing reads were aligned to the hybrid genome using bwa-mem (Li et al. 2009) version 0.7.17-r1188 with the “-SP” options and bam files were created using samtools (Li et al. 2009) version 1.19.2.
pairtools (Abdennur et al. 2023) version 1.1.2 was used to perform parsing of the alignments into contact pairs, duplicate removal and phasing. cooler (Abdennur et al. 2020) version 0.10.3 was used to create normalized contact matrices from the phased read pairs. The matrices were loaded into R using GENOVA (van der Weide et al. 2021) for subsequent analysis.
Assembly: 129S1/CAST hybrid
Supplementary files format and content: Phased and normalized contact matrices at multiple resolutions stored in mcool format

source_name: F1 hybrid 129/Sv:CAST/EiJ

extract_protocol:
Hi-C was performed as in (Haarhuis et al. 2017). Cells were crosslinked using 2% formaldehyde. DNA was digested with MboI, followed by the incorporation of biotin-labeled nucleotides at the overhangs and subsequent blunt-end ligation. Streptavidin pull-down was used to enrich the ligated DNA.
Hi-C sequencing libraries were constructed with the standard end-repair and A-tailing protocols.

value: F1 hybrid 129/Sv:CAST/EiJ

value: mESC

value: recombined + CRISPR/Cas9 edited


title: FS_72_Maternal_CTL_M

description:
M_FS_072_S22
M_rawcounts_miRs.csv

value: Male

value: newborn

value: control


title: NSC+Met-d30-r1

value: FUCCI-hNSCs differentiated from WA09 FUCCI-ESCs


title: FDB_dHT_Vehicle_1

value: muscle

value: dHT

value: male

value: Vehicle


title: FS_94_Maternal_PPS_F

description:
M_FS_094_S20
M_rawcounts_miRs.csv

value: Serum

value: Female

value: stress


title: SMC co-cultured with IPAHAdFb 9

value: pulmonary artery

value: smooth muscle cells

value: donor PASMC #1 direct co-culture with IPAH PAAF #1


title: FS_53_Maternal_CTL_M

description:
M_FS_053_S21
M_rawcounts_miRs.csv


title: Hi-C, i8, recombined, clone 62, replicate 1

description: Library name: HiC_Sample_5

value: F1 hybrid 129/Sv:CAST/EiJ


title: Sol_dHT_TMP269-5Aza_5


title: Hi-C, i8, recombined, clone 58, replicate 2

description: Library name: HiC_Sample_4

value: mESC


title: NSC+Glu-d30-r1

value: Neuronal stem cells

value: WA09 hESC FUCCI reporter

value: Glutamic acid


title: FS_47_Maternal_CTL_M

description:
M_FS_047_S5
M_rawcounts_miRs.csv

value: Male

value: newborn

value: control


title: Sol_dHT_TMP269-5Aza_4

value: muscle

value: dHT


title: FS_2_Maternal_CTL_M

description:
M_FS_002_S14
M_rawcounts_miRs.csv


title: NSC-p11-r2

value: FUCCI-hNSCs differentiated from WA09 FUCCI-ESCs


title: NSC-p11-r1


title: Sol_dHT_TMP269-5Aza_3

value: male


title: FS_166_Maternal_CTL_F

description:
M_FS_166_S9
M_rawcounts_miRs.csv

value: Serum

value: Female


title: Sol_dHT_TMP269-5Aza_2


title: FS_153_Maternal_CTL_F

description:
M_FS_153_S10
M_rawcounts_miRs.csv


title: NSC+SR-d13-r2

value: Plasma from Restricted sleep


title: Hi-C, i8, parental, replicate 2

description: Library name: HiC_Sample_2

value: recombined + CRISPR/Cas9 edited


title: Sol_dHT_TMP269-5Aza_1


title: NSC+SR-d13-r1


title: NSC+Ad-d13-r2

value: Plasma from Adequate sleep


title: FS_52_Maternal_CTL_F

description:
M_FS_052_S18
M_rawcounts_miRs.csv


title: KPC treated with RMC-7977 + Palbociclib + FGK4.5 for 14 days, Batch 3431, unsorted, Replicate 1

city: Redwood City

first: Ximo

last: Pechuan-Jorge

state: CA

address: 700 Saginaw Drive

institute: Revolution Medicines

description:
Library name: CB-3431_PDAC_123_RM42PalboCD40_D14_1_IGO_12437_HF_14_S7
10X Genomics

library_source: transcriptomic single cell

data_processing:
Count matrices were generated by aligning sequencing reads using Cell Ranger (version 8.0.1) (90) with default settings and the mouse reference transcriptome, GRCm39-2024-A. To remove potential ambient RNA contamination, CellBender's `removebackground` function was applied (version 1.0) (91). The resulting ambient-corrected count matrices were then analyzed using Seurat (version 5.1.0) (92). Quality control was performed for each sample with custom thresholds, selected based on the distribution of quality control metrics. Key metrics included the percentage of mitochondrial and ribosomal reads, the number of features detected, and the per-cell library size. Since neutrophils exhibited overall lower library sizes compared to other cell types, quality control filters were adjusted accordingly.  For downstream analysis, Seurat’s standard procedures for normalization, dimensionality reduction, and clustering were followed. The number of principal components was determined using the Talus plot method (93). Cell counts were normalized using SCTransform, with cell cycle scores regressed out using the gene list from Kowalczyk et al. (94), along with the percentage of mitochondrial and ribosomal reads. Optimal clustering resolution was selected using the clustree R package (version 0.5.0) (95), and clusters were assigned cell types based on the expression of known marker genes from the literature. Cluster identities were further validated by comparing them with annotations from ImmGen (96) using SingleR (version 2.6.0) (97). This clustering approach was applied to each sample independently, allowing for the removal of sample-specific artifacts.  For immune cell analysis, batch effects were addressed by integrating cells across all samples using the fastMNN algorithm (98). To refine the cell population structure, subclustering was performed independently for major cell types (tumor cells, lymphoid cells, myeloid cells, vasculature, and fibroblasts). This approach enabled the identification of finer cell population structures and facilitated the removal of doublets and low-quality cells through inspection of population marker gene expression and quality control metrics.  Clusters were scored for the Mouse Hallmark Gene Set signatures of the Molecular Signatures Database (MSigDB) using Seurat’s AddModuleScore function in combination with the msigdbr R package (R package version 2023.1.1, https://igordot.github.io/msigdbr/) to retrieve the pathway databases. The clusters were also scored for common cancer-related pathways using PROGENy (99).   Gene signatures for senescence and antigen presentation were compiled from various published signatures (100,101) or manually curated (Sup Table 2). Specifically, senescent-like “Sen-High” tumor cells were defined as high for three signatures: a Cancer SENESCopedia signature (100), the SenMayo signature (101), and genes encoding SASP factors (Sup Table 2). Thresholding of Sen-high cells for each signature was determined by performing Gaussian Mixture Modeling. The thresholds were picked by modeling each senescence signature score as a mixture of two Gaussians, and the thresholds were set at the decision boundary of the two components of the Gaussian mixture model.  Plots were generated using R (v.4.4.1; 14 June 2024) and R visualization packages such as ComplexHeatmap (102) and scCustomize (https://doi.org/10.5281/zenodo.5706430).  data processing step  Count matrices were generated by aligning sequencing reads using Cell Ranger (version 8.0.1) (90) with default settings and the mouse reference transcriptome, GRCm39-2024-A. To remove potential ambient RNA contamination, CellBender's `removebackground` function was applied (version 1.0) (91). The resulting ambient-corrected count matrices were then analyzed using Seurat (version 5.1.0) (92). Quality control was performed for each sample with custom thresholds, selected based on the distribution of quality control metrics. Key metrics included the percentage of mitochondrial and ribosomal reads, the number of features detected, and the per-cell library size. Since neutrophils exhibited overall lower library sizes compared to other cell types, quality control filters were adjusted accordingly. For downstream analysis, Seurat’s standard procedures for normalization, dimensionality reduction, and clustering were followed. The number of principal components was determined using the Talus plot method (93). Cell counts were normalized using SCTransform, with cell cycle scores regressed out using the gene list from Kowalczyk et al. (94), along with the percentage of mitochondrial and ribosomal reads. Optimal clustering resolution was selected using the clustree R package (version 0.5.0) (95), and clusters were assigned cell types based on the expression of known marker genes from the literature. Cluster identities were further validated by comparing them with annotations from ImmGen (96) using SingleR (version 2.6.0) (97). This clustering approach was applied to each sample independently, allowing for the removal of sample-specific artifacts. For immune cell analysis, batch effects were addressed by integrating cells across all samples using the fastMNN algorithm (98). To refine the cell population structure, subclustering was performed independently for major cell types (tumor cells, lymphoid cells, myeloid cells, vasculature, and fibroblasts). This approach enabled the identification of finer cell population structures and facilitated the removal of doublets and low-quality cells through inspection of population marker gene expression and quality control metrics. Clusters were scored for the Mouse Hallmark Gene Set signatures of the Molecular Signatures Database (MSigDB) using Seurat’s AddModuleScore function in combination with the msigdbr R package (R package version 2023.1.1, https://igordot.github.io/msigdbr/) to retrieve the pathway databases. The clusters were also scored for common cancer-related pathways using PROGENy (99).  Gene signatures for senescence and antigen presentation were compiled from various published signatures (100,101) or manually curated (Sup Table 2). Specifically, senescent-like “Sen-High” tumor cells were defined as high for three signatures: a Cancer SENESCopedia signature (100), the SenMayo signature (101), and genes encoding SASP factors (Sup Table 2). Thresholding of Sen-high cells for each signature was determined by performing Gaussian Mixture Modeling. The thresholds were picked by modeling each senescence signature score as a mixture of two Gaussians, and the thresholds were set at the decision boundary of the two components of the Gaussian mixture model. Plots were generated using R (v.4.4.1; 14 June 2024) and R visualization packages such as ComplexHeatmap (102) and scCustomize (https://doi.org/10.5281/zenodo.5706430).
Assembly: GRCm39-2024-A
Supplementary files format and content: Cellbender output h5 files, cell by gene matrix with ambient RNA removed
Supplementary files format and content: R rds files, Seurat objects of CD45+ or tumor cells

source_name: Pancreas

extract_protocol:
Pancreatic tumors were dissected from mice and normal pancreas and splenic tissue was trimmed away. Tumors were placed into Miltenyi gentleMACS C tubes containing 1.5 mL solution of 1 mg/mL Collagenase V (Sigma-Aldrich, C5138) and 0.1 mg/mL DNase I (Sigma-Aldrich, DN25) in HBSS. Tumors were chopped with scissors into small pieces (1-2 mm), and an additional 3 mL of Collagenase V/DNase solution was added. Tumors were incubated at 37ºC on a gentleMACS Dissociator using the mTDK1 program. Tubes were then centrifuged and pellets were resuspended in 2 mL ACK Lysing Buffer (Quality Biological, 118-156-101) and incubated at room temperature for 5 mins to lyse red blood cells, then quenched with PBS.  Single cell suspensions were then transferred through a 100 um Nylon Cell Strainer (Falcon, 352360).
Tumor or CD45+ cells from 2-3 mice treated with the same treatment group were pooled into a single sample (see Sup Table 1), and cells were encapsulated and processed following the 10x Genomics user manual (Reagent Kit 5’ v2).

value: Pancreas

value: KPC

value: Batch 3431 unsorted


title: KPC treated with RMC-7977 + Palbociclib + FGK4.5 for 14 days, Batch 3431, unsorted, Replicate 3

description:
Library name: CB-3431_PDAC_123_RM42PalboCD40_D14_3_IGO_12437_HF_15_S61
10X Genomics


title: FS_118_Maternal_CTL_F

description:
M_FS_118_S2
M_rawcounts_miRs.csv


title: Sol_dHT_Vehicle_5

value: Vehicle


title: KPC treated with RMC-7977 + Palbociclib + FGK4.5 for 7 days, Batch 3413, unsorted, Replicate 3

description:
Library name: CB-3413_PDAC_123_RM42PalboCD40_D7_3_IGO_12437_HD_8_S15
10X Genomics

value: Batch 3413 unsorted


title: Sol_dHT_Vehicle_4


title: FS_44_Maternal_CTL_F

description:
M_FS_044_S1
M_rawcounts_miRs.csv


title: NSC+Glu-d30-r2

value: Neuronal stem cells

value: WA09 hESC FUCCI reporter

value: Glutamic acid


title: Sol_dHT_Vehicle_3

value: muscle


title: NSC+Ad-d13-r1


title: FS_15_Maternal_CTL_F

description:
M_FS_015_S17
M_rawcounts_miRs.csv

value: newborn

value: control


title: Hi-C, i8, recombined, clone 58, replicate 1

description: Library name: HiC_Sample_3

value: F1 hybrid 129/Sv:CAST/EiJ

value: mESC


title: Sol_dHT_Vehicle_2

value: dHT

value: male


title: NSC-p13-r2

value: FUCCI-hNSCs differentiated from WA09 FUCCI-ESCs


title: Hi-C, i8, parental, replicate 1

description: Library name: HiC_Sample_1

value: recombined + CRISPR/Cas9 edited


title: KPC treated with RMC-7977 + Palbociclib + FGK4.5 for 7 days, Batch 3036, sorted, CD45 compartment, Replicate 2

description:
Library name: CB-3036_KPC1-RM42PalboCD40_D7_CD45_2_IGO_12437_FM_2_S103
10X Genomics

value: Pancreas

value: Batch 3036 sorted


title: Colorectal cancer tissue, Sensitive4

city: Shanghai

first: Xi

last: Cheng

state: State...

address: Ruijin er lu 197

institute: Shanghai Institute of Digestive Surgery

data_processing:
Reads filtering under criteria removing reads with 20% of the base quality lower than 13
Mapsplice v2.1.8 mapping to reference genome
count counting
Assembly: GRCh38
Supplementary files format and content: TXT file contain counts for each sample

source_name: Human colorectal cancer tissue

extract_protocol:
Human colorectal cancer tissues were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent.
RNA library using standard Ion proton RNA-Seq Kit v2.0 protocol
Life Technologies Ion Proton Analyzer

value: colorectal cancer (CRC)

value: colorectal cancer tissue

tag: phenotype

value: Sensitive


title: KPC treated with RMC-7977 + Palbociclib + FGK4.5 for 7 days, Batch 3413, unsorted, Replicate 1

description:
Library name: CB-3413_PDAC_123_RM42PalboCD40_D7_1_IGO_12437_HD_7_S14
10X Genomics

value: KPC

value: Batch 3413 unsorted


title: Sol_dHT_Vehicle_1

value: Vehicle


title: NSC-p13-r1

value: Neuronal stem cells

value: WA09 hESC FUCCI reporter


title: Colorectal cancer tissue, Sensitive9


title: KPC treated with RMC-7977 + Palbociclib + FGK4.5 for 7 days, Batch 3036, sorted, CD45 compartment, Replicate 1

description:
Library name: CB-3036_KPC1-RM42PalboCD40_D7_CD45_1_IGO_12437_FM_1_S40
10X Genomics


title: Colorectal cancer tissue, Sensitive5


title: HEK293T cells, SARS-CoV-2 NSP13 D374A mutant 3

city: Wuhan

first: Aixin

last: Li

state: Hubei Province

address: No.299, Bayi Road, Wuchang District, Wuhan City, Hubei Province

department: School of Basic Medical Sciences

institute: Wuhan University

data_processing:
Alignments were processed with HISAT2. The resulting reads were normalized to the total reads used for alignment (reads per million, r.p.m) for each strand. The read counts across each gene were counted with HT-seq with the union mode, and DESeq2 were used to perform the differentially gene expression analysis.
Assembly: hg38
Supplementary files format and content: Processed data files include bw data for each Sample

source_name: kidney

growth_protocol: HEK293T cells were maintained in Dulbecco’s modified Eagle’s medium (DMEM) (C11995500BT, Gibco, USA) supplemented with 10% FBS, 100 U/ml penicillin, and 100 μg/ml streptomycin sulfate, and cultured at 37℃ with 5% CO2.

extract_protocol:
Total cellular RNA was extracted by the RNApure Tissue & Cell Kit (Cowin Biotech, China)
A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase(RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 370~420 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

treatment_protocol: HEK293T cells were co-transfected with pEF1α-Luc and pHA-NSP13, pHA-NSP13 D374A mutant or empty vector for 24 h

value: kidney

value: Human embryonic kidney cells

value: SARS-CoV-2 NSP13 D374A mutant Over expression

value: co-transfected with pEF1α-Luc plasmid and pHA-NSP13 D374A mutant plasmid


title: HEK293T cells, SARS-CoV-2 NSP13 D374A mutant 2


title: KPC treated with Vehicle for 14 days, Batch 2718, sorted, tumor compartment

description:
Library name: CB-2718_KPC1_VehD14_Tumor_IGO_12437_EM_7_S24
10X Genomics

value: Batch 2718 sorted


title: KPC treated with Vehicle for 14 days, Batch 2718, sorted, CD45 compartment

description:
Library name: CB-2718_KPC1_VehD14_CD45_IGO_12437_EM_8_S25
10X Genomics


title: EDL_dHT_TMP269-5Aza_4

value: muscle

value: dHT

value: male


title: Colorectal cancer tissue, Sensitive6


title: HEK293T cells, SARS-CoV-2 NSP13 D374A mutant 1


title: EDL_dHT_TMP269-5Aza_2


title: Colorectal cancer tissue, Sensitive2


title: KPC treated with RMC-7977 + Palbociclib for 14 days, Batch 2718, sorted, CD45 compartment

description:
Library name: CB-2718_KPC1_RM42PalboD14_CD45_IGO_12437_EM_14_S13
10X Genomics

value: Pancreas


title: EDL_dHT_TMP269-5Aza_3


title: HEK293T cells, SARS-CoV-2 NSP13 3

value: SARS-CoV-2 NSP13 Over expression

value: co-transfected with pEF1α-Luc plasmid and pHA-NSP13 plasmid


title: EDL_dHT_TMP269-5Aza_1


title: HEK293T cells, SARS-CoV-2 NSP13 1


title: KPC treated with RMC-7977 + Palbociclib for 14 days, Batch 2718, sorted, tumor compartment

description:
Library name: CB-2718_KPC1_RM42PalboD14_Tumor_IGO_12437_EM_13_S12
10X Genomics


title: EDL_dHT_Vehicle_5


title: HEK293T cells, Vector 3

value: WT

value: co-transfected with pEF1α-Luc plasmid and Vector plasmid


title: Colorectal cancer tissue, Sensitive8

value: colorectal cancer (CRC)

value: colorectal cancer tissue

value: Sensitive


title: KPC treated with Palbociclib for 14 days, Batch 2718, sorted, tumor compartment

description:
Library name: CB-2718_KPC1_PalboD14_Tumor_IGO_12437_EM_9_S26
10X Genomics

value: KPC


title: EDL_dHT_Vehicle_4

value: Vehicle


title: Colorectal cancer tissue, Sensitive1


title: EDL_dHT_TMP269-5Aza_5


title: KPC treated with RMC-7977 for 14 days, Batch 2718, sorted, CD45 compartment

description:
Library name: CB-2718_KPC1_RM42D14_CD45_IGO_12437_EM_12_S11
10X Genomics


title: HEK293T cells, Vector 2

value: kidney

value: Human embryonic kidney cells


title: KPC treated with RMC-7977 for 14 days, Batch 2718, sorted, tumor compartment

description:
Library name: CB-2718_KPC1_RM42D14_Tumor_IGO_12437_EM_11_S10
10X Genomics


title: Colorectal cancer tissue, Insensitive5

value: Insensitive


title: KPC treated with Palbociclib for 14 days, Batch 2718, sorted, CD45 compartment

description:
Library name: CB-2718_KPC1_PalboD14_CD45_IGO_12437_EM_10_S9
10X Genomics

value: Batch 2718 sorted


title: EDL_dHT_Vehicle_3

value: muscle


title: EDL_dHT_Vehicle_1

value: dHT


title: HLF treated with SNDX IP for TEAD4 replicate 2

city: Chapel Hill

first: Jesse

last: Raab

address: 120 Mason Farm Rd

institute: University of North Carolina Chapel Hill

description: Library name: 1181_MD0076_HLF_TEAD4_SNDX_2

data_processing:
trim_galore version 0.6.7 --paired
bowtie2 version 2.3.4.1 --very-sensitive-local -X 800
picard version 2.20.0 MarkDuplicates
samtools view -b -q 30
deeptools version 3.5.4  bamCoverage --binSize 30 --smoothLength 60 --extendReads --ignoreDuplicates --efectiveGenomeSize 2701495761
macs version 2.2.7.1 macs2 callpeak -g 2701495761 --call-summits -q .05
individual bigwig files were averaged using wiggle tools from ucsc tools wiggletools mean ${bws} |\\   awk '\$1 ~ /^chr[XY0-9]+\$/' |\\   wigToBigWig stdin ${chrom_sizes} group${group_avg}_mean.bw
individual narrowPeak files were used to generate consensus peaks using RMSPC  version 1.8
all data processing steps are implemented as  Nextflow pipeline at github.com/raab-lab/cut-n-run using the --mode cnr
Assembly: hg38
Supplementary files format and content: peak files produced from Macs2, consensus peak files across all samples generated using RMSPC, and bigwig files for individual replicates as well as average bigwig tracks for each treatment condition.
Library strategy: CUT&RUN

source_name: liver cancer

growth_protocol: HLF cells were grown in DMEM + 10% FBS + penicillin and streptomycin

extract_protocol:
CUT&RUN was performed adapted from PMID: PMC6598765
Kapa Hyperprep DNA kit

treatment_protocol: 5uM SNDX-5613 for 24 hours

value: liver cancer

value: HLF

tag: antibody

value: SNDX


title: EDL_dHT_Vehicle_2

tag: tissue

value: male


title: KPC treated with Vehicle for 7 days, Batch 2706, sorted, tumor compartment

description:
Library name: CB-2706_KPC1_Veh_D7_CD45_IGO_12437_EI_24_S21
10X Genomics

value: Pancreas

tag: cell line

value: Batch 2706 sorted


title: Colorectal cancer tissue, Insensitive8

value: colorectal cancer (CRC)


title: Colorectal cancer tissue, Sensitive7

value: colorectal cancer tissue


title: FDB_WT_Vehicle_5

value: wt

value: wild type RyR1

value: no


title: Colorectal cancer tissue, Sensitive3

value: Sensitive


title: Colorectal cancer tissue, Insensitive2


title: KPC treated with RMC-7977 + Palbociclib for 7 days, Batch 2706, sorted, tumor compartment

description:
Library name: CB-2706_KPC1_RM42PalboD7_Tumor_IGO_12437_EI_28_S17
10X Genomics

value: KPC


title: KPC treated with Vehicle for 7 days, Batch 2706, sorted, CD45 compartment

description:
Library name: CB-2706_KPC1_VehD7_Tumor_IGO_12437_EI_23_S20
10X Genomics


title: HLF treated with SNDX IP for IgG replicate 8

description: Library name: 1174_JR961_HLF_IgG_SNDX_1

tag: cell type

value: IgG


title: FDB_WT_Vehicle_4

tag: treatment


title: HLF treated with DMSO IP for TEAD4 replicate 2

description: Library name: 1177_MD0072_HLF_TEAD4_DMSO_2

value: DMSO


title: HLF treated with SNDX IP for IgG replicate 9

description: Library name: 1182_MD0077_HLF_IgG_SNDX_2


title: FDB_WT_Vehicle_3

value: muscle


title: KPC treated with RMC-7977 + Palbociclib for 7 days, Batch 2706, sorted, CD45 compartment

description:
Library name: CB-2706_KPC1_RM42PalboD7_CD45_IGO_12437_EI_29_S18
10X Genomics


title: HLF treated with DMSO IP for IgG replicate 9

description: Library name: 1178_MD0073_HLF_IgG_DMSO_2


title: Colorectal cancer tissue, Insensitive9

value: Insensitive


title: FDB_WT_Vehicle_2


title: Colorectal cancer tissue, Insensitive1


title: Sol_WT_Vehicle_5


title: HLF treated with DMSO IP for IgG replicate 8

description: Library name: 1170_JR957_HLF_IgG_DMSO_1

value: liver cancer


title: Colorectal cancer tissue, Insensitive12


title: Colorectal cancer tissue, Insensitive13


title: HLF treated with DMSO IP for NFYB replicate 1

description: Library name: 1168_JR955_HLF_NFYB_DMSO_1

value: HLF

value: NFYB


title: HLF treated with DMSO IP for TEAD4 replicate 1

description: Library name: 1169_JR956_HLF_TEAD4_DMSO_1


title: KPC treated with Palbociclib for 7 days, Batch 2706, sorted, CD45 compartment

description:
Library name: CB-2706_KPC1_PalboD7_CD45_IGO_12437_EI_25_S14
10X Genomics


title: HLF treated with DMSO IP for H3K27ac replicate 1

description: Library name: 1167_JR954_HLF_H3K27ac_DMSO_1


title: Colorectal cancer tissue, Insensitive4


title: KPC treated with RMC-7977 + Palbociclib for 7 days, Batch 2493, sorted, CD45 compartment

description:
Library name: 5191_CB-2493_KPC1_RM42Palbo_CD45_IGO_12437_DO_18_S21
10X Genomics

value: Batch 2493 sorted


title: Colorectal cancer tissue, Insensitive10


title: HLF treated with SNDX IP for NFYB replicate 1

description: Library name: 1172_JR959_HLF_NFYB_SNDX_1

value: SNDX


title: HLF treated with SNDX IP for TEAD4 replicate 1

description: Library name: 1173_JR960_HLF_TEAD4_SNDX_1


title: KPC treated with RMC-7977 + Palbociclib for 7 days, Batch 2493, sorted, tumor compartment

description:
Library name: 5190_CB-2493_KPC1_RM42Palbo_Tumor_IGO_12437_DO_17_S20
10X Genomics

value: Pancreas


title: HLF treated with SNDX IP for H3K4me3 replicate 8

description: Library name: 1066_JR941_HLF_H3K4me3_SNDX_4


title: Colorectal cancer tissue, Insensitive11

value: colorectal cancer (CRC)


title: Colorectal cancer tissue, Insensitive6

value: colorectal cancer tissue


title: Sol_WT_Vehicle_2

value: wt

value: male


title: KPC treated with RMC-7977 for 7 days, Batch 2706, sorted, tumor compartment

description:
Library name: CB-2706_KPC1_RM42D7_Tumor_IGO_12437_EI_26_S15
10X Genomics

value: Batch 2706 sorted


title: KPC treated with RMC-7977 for 7 days, Batch 2706, sorted, CD45 compartment

description:
Library name: CB-2706_KPC1_RM42D7_CD45_IGO_12437_EI_27_S16
10X Genomics


title: FDB_WT_Vehicle_1

value: wild type RyR1

value: no


title: KPC treated with RMC-7977 for 7 days, Batch 2493, sorted, CD45 compartment

description:
Library name: 5189_CB-2493_KPC1_RM42_CD45_IGO_12437_DO_16_S19
10X Genomics

value: KPC


title: KPC treated with Palbociclib for 7 days, Batch 2706, sorted, tumor compartment

description:
Library name: CB-2706_KPC1_PalboD7_Tumor_IGO_12437_EI_30_S19
10X Genomics


title: Colorectal cancer tissue, Insensitive7


title: HLF treated with SNDX IP for H3K4me3 replicate 7

description: Library name: 1065_JR940_HLF_H3K4me3_SNDX_3


title: Sol_WT_Vehicle_4


title: Colorectal cancer tissue, Insensitive3


title: KPC treated with RMC-7977 for 7 days, Batch 2493, sorted, tumor compartment

description:
Library name: 5188_CB-2493_KPC1_RM42_Tumor_IGO_12437_DO_15_S18
10X Genomics


title: Sol_WT_Vehicle_3


title: KPC treated with Palbociclib for 7 days, Batch 2493, sorted, CD45 compartment

description:
Library name: 5187_CB-2493_KPC1_Palbo_CD45_IGO_12437_DO_14_S4
10X Genomics


title: Sol_WT_Vehicle_1


title: HLF treated with SNDX IP for H3K4me3 replicate 6

description: Library name: 1064_JR939_HLF_H3K4me3_SNDX_2


title: EDL_WT_Vehicle_5


title: Subclone D7 (E5-AP2-G-DD), H3K9me3 IP

description: Library name: chip_D7_DD_me3

source_name: Plasmodium falciparum

value: FKBP destabilization domain fused to PfAP2-G

value: Plasmodium falciparum


title: HLF treated with DMSO IP for H3K4me3 replicate 7

description: Library name: 1063_JR938_HLF_H3K4me3_DMSO_4

value: DMSO


title: KPC treated with Palbociclib for 7 days, Batch 2493, sorted, tumor compartment

description:
Library name: 5186_CB-2493_KPC1_Palbo_Tumor_IGO_12437_DO_13_S2
10X Genomics


title: HLF treated with SNDX IP for H3K4me3 replicate 5

description: Library name: 1060_JR935_HLF_H3K4me3_SNDX_1

value: liver cancer


title: HLF treated with DMSO IP for H3K4me3 replicate 6

description: Library name: 1061_JR936_HLF_H3K4me3_DMSO_2

value: HLF


title: EDL_WT_Vehicle_3

value: muscle


title: EDL_WT_Vehicle_2


title: Subclone B11 (E5-AP2-G-DD), input

description: Library name: chip_B11_DD_input


title: KPC treated with Vehicle for 7 days, Batch 2493, sorted, CD45 compartment

description:
Library name: 5185_CB-2493_KPC1_Ctrl_CD45_IGO_12437_DO_12_S1
10X Genomics

value: Batch 2493 sorted


title: KPC treated with Vehicle for 7 days, Batch 2493, sorted, tumor compartment

description:
Library name: 5184_CB-2493_KPC1_Ctrl_Tumor_IGO_12437_DO_11_S17
10X Genomics


title: Subclone D3 (ap2-g F1+F0), input

description: Library name: chip_D3_F1F0_input

value: pfap2-g deletion (-3522 to +992 bp from ATG) + integration of pfap2-g F1+F0 at PF3D7_1144400


title: EDL_WT_Vehicle_1