title: H3K14ub_clr3D_raf1-oe_FE_Exp19_Rep2

description:
Library name: Sample82
H3K14ub_clr3D_raf1-oe_FE_Exp19_Rep2

value: mat1Msmt0 leu1-32 ade6-210 ura4 mat2P(Bg-Bs)::ura4+ clr3D::KanMX6 lys1::Padh1-GFP-raf1-HphMX6


title: H3K9me3_ubc4-1_FE_Exp20_Rep1

status: Public on Oct 29 2025

type: SRA

city: Bethesda

first: Shiv

last: Grewal

state: MD

address: 9000 Rockville Pike

department: National Cancer Institute

country: USA

institute: National Institutes of Health

description:
Library name: Sample87
H3K9me3_ubc4-1_FE_Exp20_Rep1

library_source: genomic

data_processing:
Single ended fastq format sequences derived from ChIP-seq data were quality-trimmed using fastp (Chen et al. 2018).
Trimmed fastqs were aligned to the S. pombe reference (Wood et al. 2002) using the BWA aligner (Li H. and Durbin R. 2009) and fold enrichment bedgraphs were generated using Macs2 (Zhang Y et al, 2008).
Assembly: S. pombe V2 reference with the sequence of the full 40 kb mat region provided on a separate contig (MAT). Alignments of reads from strains lacking the REII element were to the standard genome as described but with the sequence of the REII element removed.
Supplementary files format and content: For ChIPseq, bedgraphs of Fold Enrichment of the IP over Input (FE) or raw pileups for the Inputs as generated by Macs2 (Zhang Y et al, 2008).

molecule: genomic DNA

organism: Schizosaccharomyces pombe

growth_protocol: Sample were grown in YEA medium at 30°C. For induction of gene under nmt1 promoter, cells were grown in PMG medium at 30°C.

extract_protocol:
For the H3K9me3 chromatin immunoprecipitation (ChIP) assay, 5x108 cells were crosslinked with 3% paraformaldehyde (PFA) for 30 minutes at room temperature, followed by quenching with 125 mM glycine. For Swi6 or Raf2 or H3K14ub ChIPs,1x109 cells were incubated for 2 hours at 18°C, fixed in 3% PFA, and washed in ice-cold PBS. Cells were treated with 10mM Dimethyl adipimidate (DMA) at room temperature for 45 minutes. Fixed cells were resuspended in ChIP lysis buffer (50 mM HEPES/KOH pH 7.5, 140 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate) supplemented with 1 mM PMSF and protease inhibitors (Roche cOmplete, Mini Protease Inhibitor Cocktail) and lysed by bead-beating ( Biospec Mini-Beadbeater-16). The lysates were sonicated with a Diagenode Bioruptor for 14-cycles on medium power setting (30 s ON, 30 s OFF) to shear DNA into 0.4–0.6 kb fragments. Cellular debris were removed by centrifugation and 2% supernatants was kept aside for whole cell extract input control. The remaining lysates were pre-cleared with agarose beads for 1 hour at 4°C. After bead removal, lysates were incubated with the appropriate antibody (2–10 μg) overnight at 4°C with slow rotation. Antibodies used includes anti-H3K9me3 (Abcam), anti-c-Myc (Santa Cruz), and home-made affinity-purified anti-Swi6. Pre-washed protein A and protein G agarose beads were added to the lysates and incubated for 4 hours at 4°C. The beads were sequentially washed, twice with Wash Buffer I (50 mM HEPES/KOH pH 7.5, 140 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate), twice with Wash Buffer II (50 mM HEPES/KOH pH 7.5, 500 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate), twice with Wash Buffer III (10 mM Tris/HCl pH 8.0, 250 mM LiCl, 0.5% IGEPAL, 0.5% sodium deoxycholate, 1 mM EDTA), and once with TE buffer (50 mM Tris/HCl pH 8.0, 10 mM EDTA). The chromatin was eluted from the beads twice with 50 μl of elution buffer (50 mM Tris/HCl pH 8.0, 10 mM EDTA, 1% SDS) at 65°C for 30 minutes each, with shaking (~1,200 rpm). Eluted chromatin and input control samples were reverse crosslinked overnight at 65°C. Samples were treated sequentially with RNase A (10 μg, 2 hours, 37°C) and Proteinase K (20 μg, 2 hours, 37°C), and subsequently purified using the Qiagen PCR purification kit.
Sequencing libraries were prepared using the NEBNext Ultra II DNA Library Prep Kit for Illumina according to the manufacturer’s protocol and analyzed using an Agilent 4200 TapeStation system (Agilent).

tag: strain

tag: genotype

value: mat1Msmt0 leu1-32 ade6 ura4 mat2P(Bg-Bs)::ura4+ ubc4-1

tag: chip antibody

value: Abcam anti-H3K9me3 (cat# ab8898)

tag: growth

value: Growth in YEA medium at 30°C

tag: fixation

value: 3% PFA


title: FigS4FG: Cas1/2 + 0.1mM IPTG

city: Ann Arbor

first: P. Lydia

last: Freddolino

state: MI

address: 1150 W. Medical Center Dr.

department: Biological Chemistry

institute: University of Michigan

library_source: other

data_processing:
*library strategy: Primer-amplified DNA sequencing
Read processing: Sequencing reads were assessed for quality with fastQC (version 0.11.8) and multiQC (version 0.92) to ensure the general quality of the datasets. For the newly acquired spacer sequences, the Read 1 sequences of the paired-end sequencing reads were trimmed to extract new spacer instances using Cutadapt (version 2.6) by identifying the flanking Repeat 26 sequences (attgtagcactgcgaaatgagaaagggagctacaac).
Deduplication: For samples with UMIs, the Read 2 sequences of the paired-end reads were processed with Cutadapt to extract the 8-nt UMI sequences by trimming known construct sequences. The newly spacer-UMI sequence combinations were paired with fastq-pair (version 0.4) and processed with UMI-tools (version 1.0.1) for deduplication after alignment. For samples with no UMIs during library construction, no UMI processing was performed (see the next step for an alternative approach to minimize PCR artifacts).
Spacer source identification: The preprocessed spacer sequences were aligned by bowtie2 (version 2.4.1) with the "very-sensitive" preset to the combined alignment reference containing the N.meningitidis 8013 genome sequence (RefSeq accession number NC_017501.1, assembly: GCF_000026965.1) and the MDA phage genome sequence. For samples with UMIs, aligned spacers were deduplicated using UMI-tools with the directional-adjacency method as noted above. For samples with no UMIs, to handle technical artifacts such as PCR jackpot sites that can over-amplify a subset of spacer sequences, a maximum cap of 5% of the total detected spacer counts on the corresponding Neisseria or phage genome was applied to each unique spacer sequence, i.e., for each unique spacer sequence, if its abundance among total spacers exceeded 5%, its abundance was set to 5% of the total detected spacer count of the given source genome.
Genomic context extraction: Any reads that mapped ambiguously were removed from further analysis using samtools (version 1.9). For each genomic location aligned with the 5' end of any new spacer, the genomic context was extracted as the reference genome sequences flanking the alignment location, including the sequence upstream 10 bp from the alignment sites.
Spacer counting: The numbers of spacers at each unique spacer-aligned location were counted using bedtools2 (version 2.26.0) and custom codes were used to format the genomic context sequences for sequence logo inputs.
Assembly: N.meningitidis 8013 genome sequence (RefSeq accession number NC_017501.1, assembly: GCF_000026965.1) MDA phage genome: J. Meyer et al., Characterization of MDAPhi, a temperate filamentous bacteriophage of Neisseria meningitidis. Microbiology (Reading) 162, 268-282 (2016).
Supplementary files format and content: For *.MDA.fa files: format: FASTA files, with each header formatted as ">MDA_kan:<start on genome>:<end on genome>(<strand>)[<spacer count>](rc)"; content: unique spacer sequences and their genomic contexts, with their source on MDA phage genome and counts listed in the headers
Supplementary files format and content: For *.all.fa files: format: FASTA files, with each header formatted as "><genome>:<start on genome>:<end on genome>(<strand>)[<spacer count>](rc)"; content: unique spacer sequences and their genomic contexts, with their source on either MDA phage genome or Nme genome and counts listed in the headers

molecule: other

organism: Neisseria meningitidis

growth_protocol: N. meningitidis (aka meningococcal) strains MC58, 8013, and 8013 mutant derivatives used in this study are listed in Supplemental Table 3. These strains were grown on GC Medium Base (GCB) (BD, 228950) plates with appropriate antibiotics and Kellogg’s supplements I and II (22.2 mM glucose [Fisher Scientific, D16-1], 0.68 mM glutamine [Sigma, G3126], 0.45 mM co-carboxylase [aka thiamine pyrophosphate, Sigma, C8754], 1.23 mM Fe(NO3)3 [Sigma, F8508]). Antibiotic concentrations used were 2.5 μg/mL for erythromycin (Erm), 100 μg/mL for kanamycin (Kan), 100 μg/mL for streptomycin (strp), 2.5 μg/mL for chloramphenicol (cm), and 100 μg/mL for spectinomycin (spc). All solid cultures were incubated at 37 ̊C in a 5% CO2 humidified atmosphere.  JM109 (Promega, L2005) and Mach1 (Invitrogen, C862003) chemically competent E. coli cells were used for plasmid cloning. E. coli BL21 (DE3) (Novagen, 69450-3) cells were used for protein purification. E. coli cells were grown at 37 ̊C in LB broth Lennox or on LB agar plates supplemented, when needed, with 50 μg/mL kanamycin, 50 μg/mL carbenicillin, 20 μg/mL for chloramphenicol or 100 μg/mL spectinomycin.

extract_protocol:
To detect spacer acquisition, 10 ng genomic DNA was used as template to PCR amplify CRISPR’s downstream end using Q5 DNA Polymerase with with primers described in Supplemental Table 1. The following PCR conditions were used: 98 ̊C for 30 s; 98 ̊C for 10 s, 60 ̊C for 10 s, 72 ̊C for 20 s (25 cycles); 72 ̊C for 2 min. PCR products were resolved on 2% agarose gel, stained by SYBR Safe (Invitrogen, S33102), and visualized using a Bio-Rad Chemidoc MP imager (12003154). The adapted “+1” “+2” bands are 66- and 132- nts larger than the un-adapted “0” product derived from parental CRISPR array, due to addition of repeat-spacer units (66-nt each). Adaptation efficiency was measured as the percentage of total CRISPR amplicons with new spacers. Quantification of PCR band intensity was done using Image Lab 6.0 software (Bio-Rad).
UMI library construction: Ligated products from above were used as template for 1st step Q5 PCR to amplify the leader-end of CRISPR array with primers OYZ3624+593 containing partial adaptor. Cycling conditions are 98 ̊C for 30 s; 98 ̊C for 10 s, 60 ̊C for 10 s, 72 ̊C for 25 s (25 cycles); 72 ̊C for 2 min. Following 2% agarose gel electrophoresis, the “+1” adapted band was gel extracted with QIAquick Gel Extraction Kit (Qiagen, 28706). Eluate is used as template for 2nd step Q5 PCR amplification using I5 and I7 index primers to add full Illumina adapter and indexes. 2nd PCR conditions are: 98 ̊C for 30 s; 98 ̊C for 10 s, 65 ̊C for 10 s, 72 ̊C for 25 s (15 cycles); 72 ̊C for 2 min.   Non-UMI library construction: For mutant strains carrying the Δcrispr::R26, Δcrispr::crispr(sp1), Δcrispr::crispr(sp1-2), Δcrispr::crispr(sp1-3), Δcrispr::crispr(sp1-5), Δcrispr::crispr(sp1-7), Δcrispr::crispr(sp1-8), Δcrispr::crispr(sp1-17), Δcrispr::crispr(sp1-25), Δcrispr::crispr(sp1-49) alleles, a non-UMI method was used due to the lack of unique restriction site (e.g., FatI) close enough to the newly acquired spacer. 10 ng of total genomic DNA from an adaptation experiment was used as template for 1st step PCR with primers are described in Supplemental Table 1. The following steps for “+1” adapted band gel extraction and 2nd step Q5 PCR were as described in the earlier paragraph.  All final libraries from 2nd step PCR were pooled together, cleaned up using QIAquick PCR Purification Kit, and then purified as one sample by agarose gel electrophoresis and gel extraction. This final pooled library was sequenced on an Illumina sequencing platform, NovaSeq (2x150 bp) at the Univ. of Michigan Advanced Genomics Core.

treatment_protocol: A phage transduction assay was initially performed. Rather than culturing cells on GCB plates with kanamycin, the cells were back-diluted to a concentration of 0.1 OD, and kanamycin was added at a concentration of 40 µg/mL to enrich for transductants. Adaptation assay was performed by incubating diluted culture with or without appropriate inducers, at 37 ̊C in a 5% CO2 humidified atmosphere. Inducer concentrations used were 0.1mM for IPTG (Fisher scientific, BP1755-10). After 24 hrs of induction, genomic DNA was isolated using QIAamp DNA Mini Kit (Qiagen, 51306) per manufacturer’s instructions with the following minor modification. After cell lysis at 56 ̊C for 40 min, RNase A (1mg/mL, Qiagen 19101) treatment was performed at RT for 2 min.

value: strain 8013 (NCBI:txid604162)

tag: cell type

value: bacteria

tag: treatment -_phage

value: MDAΦ 3+21 hr

tag: treatment -_iptg

value: 0.1 mM IPTG

tag: umi availability

value: UMI-1 (FatI)

tag: molecule subtype

value: primer-amplified DNA


title: Wildtype_R3_1B, RNAseq

city: Boston

first: Jon

last: Seidman

state: Massachusetts

address: 77 Avenue Louis Pasteur

department: Genetics

institute: Harvard Medical School

library_source: transcriptomic

data_processing:
Libraries were sequenced (Illumina HiSeq 2000 or Illumina HiSeq 2500, 50-base paired-end reads).
All data was combined into a single fastq file
Reads were aligned to the hg38 reference genome using STAR.
Mitochondrial and duplicate reads were discarded using Samtools and Picard’s MarkDuplicates, respectively
The aligned reads were quantitated by Feature counts and counts were normalized.
Assembly: hg38
Supplementary files format and content: bam files and raw counts document for each sample

molecule: polyA RNA

organism: Homo sapiens

growth_protocol: Induced pluripotent stem cells (iPSCs) were routinely generated by re-plating 6 non-adherent cell line cultures (typically 5 x 106 cells) on a matrigel coated plate in MTESR medium (Stemcell Technologies)

extract_protocol:
RNA was purified from iPSCs using Trizol (Life Technologies) methods. Purified poly-A RNA that had gone through two rounds of oligo-dT selection was converted into cDNA for construction of libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: 4 undifferentiated IPS samples were differentiated into cardiomyocytes using published cardiac differentiation protocols  (Mummery et al. 2012, Lian et al. 2012)

tag: cell line

value: Induced pluripotent stem cells

value: Wildtype

tag: treatment

value: untreated


title: Wildtype_R2_1A, RNAseq


title: Fig5C, S6A: endo dcas9, ΔCRISPR::CRISPR(sp1-25), Cas1/2 + 0.1mM IPTG

source_name: endo dcas9, ΔCRISPR::CRISPR(sp1-25), iga-trpB::pLacNmecas1-cas2

value: endo dcas9, {delta}CRISPR::CRISPR(sp1-25), iga-trpB::pLacNmecas1-cas2

value: Non-UMI


title: H3K14ub_raf1-oe_FE_Exp19_Rep2

description:
Library name: Sample80
H3K14ub_raf1-oe_FE_Exp19_Rep2

value: mat1Msmt0 leu1-32 ade6-210 ura4-D18 mat2P(Bg-Bs)::ura4+ lys1::Padh1-GFP-raf1-HphMX6

value: anti-H3K14ub (provided by Dr. Jiemin Wong)

value: Growth in YEA medium at 30°C + 2hr at 18°C before fixation

value: 3% PFA + 10mM DMA


title: Wildtype_R1_05, RNAseq


title: H3K14ub_ubc4-1_raf1-oe_FE_Exp19_Rep1

description:
Library name: Sample85
H3K14ub_ubc4-1_raf1-oe_FE_Exp19_Rep1

value: mat1Msmt0 leu1-32 ade6 ura4 mat2P(Bg-Bs)::ura4+ ubc4-1 lys1::Padh1-GFP-raf1-HphMX6


title: Fig5C, S6A: endo dcas9, ΔCRISPR::CRISPR(sp1-17), Cas1/2 + 0.1mM IPTG

source_name: endo dcas9, ΔCRISPR::CRISPR(sp1-17), iga-trpB::pLacNmecas1-cas2

value: endo dcas9, {delta}CRISPR::CRISPR(sp1-17), iga-trpB::pLacNmecas1-cas2


title: 31-42D-Input_ENZ

city: sacramento

first: Xiong

last: Zhang

state: CA

address: 4645 2nd Ave

institute: University of California, Davis

description:
Library name: 42D-Input-ENZwithdrawal
paired-end

data_processing:
ChIP-seq validated antibodies against REV-ERBα (Proteintech, cat. #14506-1-AP, 5 μg; Cell signaling technology, cat. #13418, 5 μg), BRN2 (Genetex, cat. #GTX114650, 5 μg), BRD4 (Abcam, cat. #ab272042, 5 μg), p300 (Abcam, cat. #ab14984, 5 μg), ASCL1 (Abcam, cat. #556604, 5 μg), FOXA1 (Abcam, cat. #ab23738, 5 μg) and H3K27ac (Diagenode, cat. #C15410196, 2 μg), were used as indicated in Table S1.    Single-end or paired-end ChIP-seq fastq files were trimmed using Trim Galore v0.6.10 (https://anaconda.org/bioconda/trim-galore) and reads were aligned to the hg19 human genome with Bowtie2 v 2.5.1 (https://anaconda.org/bioconda/bowtie2). PCR duplicates in BAM files were removed with samtools mardup function. Significant ChIP-seq peaks were called using MACS2 (v 2.2.7.1) using a ChIP input file as a control with P-value < 0.05 in narrow peak mode (for REV-ERBα, BRN2, ASCL1, p300 and FOXA1) or broad peak mode (for BRD4 and H3K27ac).
Assembly: hg19
Supplementary files format and content: bigwig, peak files (except for Input)

extract_protocol:
Cells were fixed with 1% formaldehyde at room temperature for 8 min, and subsequently quenched with 0.125 mol/L glycine for another 8 min. Cells were washed with cold PBS and suspended with lysis buffer (50 mmol/L HEPES, pH 8.0, 140 mmol/L NaCl, 1 mmol/L EDTA, 10% glycerol, 0.5% NP-40, and 0.25% Triton X-100). Cell pellets were then resuspended in washing buffer (10 mmol/L Tris, pH 8.0, 1 mmol/L EDTA, 0.5 mmol/L EGTA, and 200 mmol/L NaCl), washed, and resuspended in shearing buffer (0.1% SDS, 1 mmol/L EDTA, pH 8, and10 mmol/L Tris-HCl, pH 8) before sonication. Sonication was performed using Covaris E220 following the manufacturer’s instruction. Soluble fractions of sheared chromatin were immunoprecipitated by magnetic protein G beads coated with specific antibodies at 4 °C overnight.  Chromatin-captured beads were washed five times with LiCl wash buffer (100 mmol/L Tris, pH 7.5, 500 mmol/L LiCl, 1% NP-40, and 1% sodium deoxycholate), and one time with TE buffer (10 mmol/L Tris, pH 7.5 and 0.1 mmol/L EDTA) before the chromatins were eluted by elution buffer (1% SDS and 100 mmol/L NaHCO3). The eluted DNA was incubated with RNase A for 30 min at 37 °C, followed by overnight incubation at 65 °C for reverse crosslinking. After proteinase K treatment, ChIP DNA was purified using PCR purification kit (Qiagen, #28104).
Libraries were prepared, analyzed with the Bioanalyzer 2100 (Agilent) and sequenced in either single-end (BGI, Hong Kong, China) or paired-end (Novogene, USA) 50-bp mode on Illumina Sequencers.

value: t-NEPC cell line

value: WT

value: 42D, maintained in 10 uM enzalutamide


title: 32-42D-Input_ENZwithdrawal

description:
Library name: 42D-Input-ENZ
paired-end

value: 42D,  enzalutamide withdrawal for 7 days


title: H3K14ub_WT_FE_Exp19_Rep3

description:
Library name: Sample79
H3K14ub_WT_FE_Exp19_Rep3

value: mat1Msmt0 ade6-210 ura4-D18 mat2P(Bg-Bs)::ura4+


title: Fig5C, S6A: endo dcas9, ΔCRISPR::CRISPR(sp1-8), Cas1/2 + 0.1mM IPTG

source_name: endo dcas9, ΔCRISPR::CRISPR(sp1-8), iga-trpB::pLacNmecas1-cas2

value: strain 8013 (NCBI:txid604162)

value: bacteria

value: endo dcas9, {delta}CRISPR::CRISPR(sp1-8), iga-trpB::pLacNmecas1-cas2

value: MDAΦ 3+21 hr

value: 0.1 mM IPTG

value: primer-amplified DNA


title: SMAD2+/P135*(RB9)_R3, RNAseq

value: Induced pluripotent stem cells

value: heterozygous

value: untreated


title: H3K14ub_clr3D_upf1D_FE_Exp18_Rep1

description:
Library name: Sample78
H3K14ub_clr3D_upf1D_FE_Exp18_Rep1

value: mat1Msmt0 leu1-32 ade6-210 ura4-D18 mat2P(Bg-Bs)::ura4+ clr3D::KanMX6 upf1D::KanMX6

value: anti-H3K14ub (provided by Dr. Jiemin Wong)

value: Growth in YEA medium at 30°C + 2hr at 18°C before fixation

value: 3% PFA + 10mM DMA


title: Fig5C, S6A: endo dcas9, ΔCRISPR::CRISPR(sp1-7), Cas1/2 + 0.1mM IPTG

source_name: endo dcas9, ΔCRISPR::CRISPR(sp1-7), iga-trpB::pLacNmecas1-cas2

value: endo dcas9, {delta}CRISPR::CRISPR(sp1-7), iga-trpB::pLacNmecas1-cas2

value: Non-UMI


title: human TET2-MUT HSCs 7

city: London

first: Hector

last: Huerga Encabo

address: The Francis Crick Institute, 1 Midland Rd

country: United Kingdom

institute: The Francis Crick Institute

description: Library name: HUE959A38

data_processing:
Each sample was sequenced to achieve 30 million Pair-end 100 bp reads/sample.
For the analysis of percentage of fragmented DNA and differentially annotated peaks we use the nf-core pipeline within the nextflow bioinformatics workflow framework (version 19.10.0).
Assembly: FASTQ files were aligned to the GRCh38 human genome
Supplementary files format and content: bigwig and narrow peak files

source_name: Bone marrow

extract_protocol:
25,000 control and 25,000 TET2Mut HSCs were sorted from the same humanized mouse engrafted with a mix of wild-type and TET2Mut hHSPCs. DNA was isolated using ZYMO DNA Clean kit (cat#D4014)
HiSeq4000 Sequencing System (Illumina) with a loading molarity of 200pM plus 10% Phix (illumine). Each samples was sequenced to achieve  40 million Pair-end 100 bp reads/sample.

tag: tissue

value: Bone marrow

value: Human HSCs


title: Fig5C, S6A: endo dcas9, ΔCRISPR::CRISPR(sp1-49), Cas1/2 + 0.1mM IPTG

source_name: endo dcas9, ΔCRISPR::CRISPR(sp1-49), iga-trpB::pLacNmecas1-cas2

value: strain 8013 (NCBI:txid604162)

value: endo dcas9, {delta}CRISPR::CRISPR(sp1-49), iga-trpB::pLacNmecas1-cas2


title: 30-42D-NR1D1_ENZwithdrawal

description:
Library name: 42D-NR1D1-ENZwithdrawal
paired-end

value: t-NEPC cell line

value: WT

value: 42D,  enzalutamide withdrawal for 7 days

value: REV-ERBα


title: FigS3EF: endo dcas9, Cas1/2 + 0.1mM IPTG

source_name: endo dcas9, iga-trpB::pLacNmecas1-cas2

value: bacteria

value: endo dcas9, iga-trpB::pLacNmecas1-cas2

value: MDAΦ 3+21 hr

value: 0.1 mM IPTG

value: UMI-1 (FatI)

value: primer-amplified DNA


title: SMAD2P135*/K157*_R1, RNAseq

value: Induced pluripotent stem cells

value: homozygous

value: untreated


title: H3K14ub_clr3D_upf1D_FE_Exp19_Rep2

description:
Library name: Sample83
H3K14ub_clr3D_upf1D_FE_Exp19_Rep2

value: mat1Msmt0 leu1-32 ade6-210 ura4-D18 mat2P(Bg-Bs)::ura4+ clr3D::KanMX6 upf1D::KanMX6

value: anti-H3K14ub (provided by Dr. Jiemin Wong)

value: Growth in YEA medium at 30°C + 2hr at 18°C before fixation

value: 3% PFA + 10mM DMA


title: H3K14ub_clr3D_FE_Exp19_Rep2

description:
Library name: Sample81
H3K14ub_clr3D_FE_Exp19_Rep2

value: mat1Msmt0 leu1-32 ade6-210 ura4 mat2P(Bg-Bs)::ura4+ clr3D::KanMX6


title: 31-42D-NR1D1_ENZ

description:
Library name: 42D-NR1D1-ENZ
paired-end

value: t-NEPC cell line

value: WT

value: 42D, maintained in 10 uM enzalutamide


title: Fig5C, S6A: endo dcas9, ΔCRISPR::CRISPR(sp1-3), Cas1/2 + 0.1mM IPTG

source_name: endo dcas9, ΔCRISPR::CRISPR(sp1-3), iga-trpB::pLacNmecas1-cas2

value: strain 8013 (NCBI:txid604162)

value: bacteria

value: endo dcas9, {delta}CRISPR::CRISPR(sp1-3), iga-trpB::pLacNmecas1-cas2

value: Non-UMI


title: H3K14ub_raf1-oe_FE_Exp18_Rep1

description:
Library name: Sample75
H3K14ub_raf1-oe_FE_Exp18_Rep1

value: mat1Msmt0 leu1-32 ade6-210 ura4-D18 mat2P(Bg-Bs)::ura4+ lys1::Padh1-GFP-raf1-HphMX6


title: 28-42D-Input_Vehicle

description:
Library name: 42D-Input-Vehicle
paired-end

value: 42D, DMSO treated, 24 h


title: H3K14ub_clr3D_raf1-oe_FE_Exp18_Rep1

description:
Library name: Sample77
H3K14ub_clr3D_raf1-oe_FE_Exp18_Rep1

value: mat1Msmt0 leu1-32 ade6-210 ura4 mat2P(Bg-Bs)::ura4+ clr3D::KanMX6 lys1::Padh1-GFP-raf1-HphMX6


title: human TET2-MUT HSCs 5

description: Library name: HUE959A36

value: Bone marrow

value: Human HSCs


title: Fig5C, S6A: endo dcas9, ΔCRISPR::CRISPR(sp1-5), Cas1/2 + 0.1mM IPTG

source_name: endo dcas9, ΔCRISPR::CRISPR(sp1-5), iga-trpB::pLacNmecas1-cas2

value: endo dcas9, {delta}CRISPR::CRISPR(sp1-5), iga-trpB::pLacNmecas1-cas2

value: MDAΦ 3+21 hr

value: 0.1 mM IPTG

value: primer-amplified DNA


title: human TET2-MUT HSCs 6

description: Library name: HUE959A37


title: 29-42D-Input_SR8278

description:
Library name: 42D-Input-SR8278
paired-end


title: human TET2-MUT HSCs 3

description: Library name: HUE959A34


title: H3K14ub_WT_FE_Exp18_Rep2

description:
Library name: Sample74
H3K14ub_WT_FE_Exp18_Rep2

value: mat1Msmt0 ade6-210 ura4-D18 mat2P(Bg-Bs)::ura4+

value: anti-H3K14ub (provided by Dr. Jiemin Wong)

value: Growth in YEA medium at 30°C + 2hr at 18°C before fixation

value: 3% PFA + 10mM DMA


title: human TET2-MUT HSCs 4

description: Library name: HUE959A35


title: 27-42D-FOXA1_SR8278

description:
Library name: 42D-FOXA1-SR8278
paired-end

value: t-NEPC cell line

value: WT


title: human TET2-MUT HSCs 2

description: Library name: HUE959A5


title: Fig5C, S6A: endo dcas9, ΔCRISPR::CRISPR(sp1), Cas1/2 + 0.1mM IPTG

source_name: endo dcas9, ΔCRISPR::CRISPR(sp1), iga-trpB::pLacNmecas1-cas2

value: strain 8013 (NCBI:txid604162)

value: bacteria

value: endo dcas9, {delta}CRISPR::CRISPR(sp1), iga-trpB::pLacNmecas1-cas2


title: H3K14ub_h3.2G13D_upf1D_FE_Exp17_Rep1

description:
Library name: Sample73
H3K14ub_h3.2G13D_upf1D_FE_Exp17_Rep1

value: mat1Msmt0 leu1-32 ade6-210 ura4-D18 mat2P(Bg-Bs)::ura4+ h3.2G13D::NatM6 upf1D::KanMX6


title: 26-42D-FOXA1_Vehicle

description:
Library name: 42D-FOXA1-Vehicle
paired-end

value: 42D, DMSO treated, 24 h


title: human TET2-MUT HSCs 1

description: Library name: HUE959A4

value: Bone marrow


title: Fig5C, S6A: endo dcas9, ΔCRISPR::R26, Cas1/2 + 0.1mM IPTG

source_name: endo dcas9, ΔCRISPR::R26, iga-trpB::pLacNmecas1-cas2

value: endo dcas9, {delta}CRISPR::R26, iga-trpB::pLacNmecas1-cas2

value: Non-UMI


title: H3K14ub_clr3D_FE_Exp18_Rep1

description:
Library name: Sample76
H3K14ub_clr3D_FE_Exp18_Rep1

value: mat1Msmt0 leu1-32 ade6-210 ura4 mat2P(Bg-Bs)::ura4+ clr3D::KanMX6


title: H3K14ub_h3.2G13D_FE_Exp17_Rep1

description:
Library name: Sample72
H3K14ub_h3.2G13D_FE_Exp17_Rep1

value: mat1Msmt0 leu1-32 ade6-210 ura4-D18 mat2P(Bg-Bs)::ura4+ h3.2G13D::NatMX6


title: human TET2-WT HSCs 4

description: Library name: HUE959A40

value: Human HSCs


title: 25-42D-ASCL1_SR8278

description:
Library name: 42D-ASCL1-SR8278
paired-end


title: Fig4DE: ΔtracrΔcas9, ΔCRISPR::R26, Cas1/2, Nmecas9ΔBHΔREC1/2-FLAG+sgRNA + 0.1mM IPTG

source_name: ΔtracrΔcas9, ΔCRISPR::R26, NICS::pLacNmecas1-cas2, iga-trpB::pTet Nmecas9ΔBHΔREC1/2-FLAG+pTR sgRNA

value: {delta}tracr{delta}cas9, {delta}CRISPR::R26, NICS::pLacNmecas1-cas2, iga-trpB::pTet Nmecas9{delta}BH{delta}REC1/2-FLAG+pTR sgRNA

value: MDAΦ 3+21 hr

value: 0.1 mM IPTG

value: primer-amplified DNA


title: H3K14ub_raf1D_FE_Exp17_Rep1

description:
Library name: Sample71
H3K14ub_raf1D_FE_Exp17_Rep1

value: mat1Msmt0 leu1-32 ade6-210 ura4-D18 mat2P(Bg-Bs)::ura4+ raf1D::KanMX

value: anti-H3K14ub (provided by Dr. Jiemin Wong)

value: Growth in YEA medium at 30°C + 2hr at 18°C before fixation

value: 3% PFA + 10mM DMA


title: Fig5C, S6A: endo dcas9, Cas1/2 + 0.1mM IPTG

value: strain 8013 (NCBI:txid604162)

value: bacteria

value: endo dcas9, iga-trpB::pLacNmecas1-cas2


title: 23-42D-BRD4_SR8278

description:
Library name: 42D-BRD4-SR8278
paired-end

value: t-NEPC cell line

value: WT


title: 24-42D-ASCL1_Vehicle

description:
Library name: 42D-ASCL1-Vehicle
paired-end

value: 42D, DMSO treated, 24 h


title: human TET2-WT HSCs 3

description: Library name: HUE959A39

value: Bone marrow


title: Fig4DE: ΔtracrΔcas9, ΔCRISPR::R26, Cas1/2, Nmecas9ΔREC1/2-FLAG+sgRNA + 0.1mM IPTG

source_name: ΔtracrΔcas9, ΔCRISPR::R26, NICS::pLacNmecas1-cas2, iga-trpB::pTet Nmecas9ΔREC1/2-FLAG+pTR sgRNA

value: {delta}tracr{delta}cas9, {delta}CRISPR::R26, NICS::pLacNmecas1-cas2, iga-trpB::pTet Nmecas9{delta}REC1/2-FLAG+pTR sgRNA

value: Non-UMI


title: Fig5C, S6A: endo dcas9, ΔCRISPR::CRISPR(sp1-2), Cas1/2 + 0.1mM IPTG

source_name: endo dcas9, ΔCRISPR::CRISPR(sp1-2), iga-trpB::pLacNmecas1-cas2

value: endo dcas9, {delta}CRISPR::CRISPR(sp1-2), iga-trpB::pLacNmecas1-cas2


title: H3K14ub_WT_FE_Exp17_Rep1

description:
Library name: Sample70
H3K14ub_WT_FE_Exp17_Rep1

value: mat1Msmt0 ade6-210 ura4-D18 mat2P(Bg-Bs)::ura4+


title: human TET2-WT HSCs 1

description: Library name: HUE959A1

value: Human HSCs


title: Input_P

data_processing:
Single ended fastq format sequences derived from ChIP-seq data were quality-trimmed using fastp (Chen et al. 2018).
Trimmed fastqs were aligned to the S. pombe reference (Wood et al. 2002) using the BWA aligner (Li H. and Durbin R. 2009) and fold enrichment bedgraphs were generated using Macs2 (Zhang Y et al, 2008).
Assembly: S. pombe V2 reference with the sequence of the full 40 kb mat region provided on a separate contig (MAT). Alignments of reads from strains lacking the REII element  were to the standard genome as described but with the sequence of the REII element removed.
Supplementary files format and content: For ChIPseq, bedgraphs of Fold Enrichment of the IP over Input  (FE) or  raw pileups for the Inputs as generated by Macs2  (Zhang Y et al, 2008).

source_name: mat1Msmt0 ade6-210 ura4-D18 mat2P(Bg-Bs)::ura4+

extract_protocol:
For the H3K9me3 chromatin immunoprecipitation (ChIP) assay, 5x108 cells were crosslinked with 3% paraformaldehyde (PFA) for 30 minutes at room temperature, followed by quenching with 125 mM glycine. For Swi6 or Raf2 ChIPs,1x109 cells were incubated for 2 hours at 18°C, fixed in 3% PFA, and washed in ice-cold PBS. Cells were treated with 10mM Dimethyl adipimidate (DMA) at room temperature for 45 minutes. Fixed cells were resuspended in ChIP lysis buffer (50 mM HEPES/KOH pH 7.5, 140 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate) supplemented with 1 mM PMSF and protease inhibitors (Roche cOmplete, Mini Protease Inhibitor Cocktail) and lysed by bead-beating ( Biospec Mini-Beadbeater-16). The lysates were sonicated with a Diagenode Bioruptor for 14-cycles on medium power setting (30 s ON, 30 s OFF) to shear DNA into 0.4–0.6 kb fragments. Cellular debris were removed by centrifugation and 2% supernatants was kept aside for whole cell extract input control. The remaining lysates were pre-cleared with agarose beads for 1 hour at 4°C. After bead removal, lysates were incubated with the appropriate antibody (2–10 μg) overnight at 4°C with slow rotation. Antibodies used includes anti-H3K9me3 (Abcam), anti-c-Myc (Santa Cruz), and home-made affinity-purified anti-Swi6. Pre-washed protein A and protein G agarose beads were added to the lysates and incubated for 4 hours at 4°C. The beads were sequentially washed, twice with Wash Buffer I (50 mM HEPES/KOH pH 7.5, 140 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate), twice with Wash Buffer II (50 mM HEPES/KOH pH 7.5, 500 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate), twice with Wash Buffer III (10 mM Tris/HCl pH 8.0, 250 mM LiCl, 0.5% IGEPAL, 0.5% sodium deoxycholate, 1 mM EDTA), and once with TE buffer (50 mM Tris/HCl pH 8.0, 10 mM EDTA). The chromatin was eluted from the beads twice with 50 μl of elution buffer (50 mM Tris/HCl pH 8.0, 10 mM EDTA, 1% SDS) at 65°C for 30 minutes each, with shaking (~1,200 rpm). Eluted chromatin and input control samples were reverse crosslinked overnight at 65°C. Samples were treated sequentially with RNase A (10 μg, 2 hours, 37°C) and Proteinase K (20 μg, 2 hours, 37°C), and subsequently purified using the Qiagen PCR purification kit.
Sequencing libraries were prepared using the NEBNext Ultra II DNA Library Prep Kit for Illumina according to the manufacturer’s protocol and analyzed using an Agilent 4200 TapeStation system (Agilent).

value: Growth in YEA medium at 30°C

value: 3% PFA


title: 22-42D-BRD4_Vehicle

description:
Library name: 42D-BRD4-Vehicle
paired-end


title: human TET2-WT HSCs 2

description: Library name: HUE959A2


title: 21-42D-p300_Vehicle

description:
Library name: 42D-p300-Vehicle
paired-end


title: CD34_T3

description: Library name: HUE638A9

data_processing:
FASTQ files were trimmed using Trimmomatic (v 0.36). Read alignment and gene quantification was performed using RSEM(v1.2.31)/STAR(v2.5.2a)
Obtained counts were then uploaded and analyzed using Deseq2(v1.20.0) on R (3.5.1)
Assembly: Ensembl GRCh38 release 89
Supplementary files format and content: tab separated gene counts per gene per sample

source_name: Human HSPCs

extract_protocol:
RNA was isolated using RNAeasy microkit (Qiagen)
Libraries were prepared using KAPA Stranded with RiboErase RNA-seq kit (according to the manufacturer’s instructions). Briefly, 17–25 ng of starting RNA were subjected first to cytoplasmic and mitochondrial ribosomal RNA (rRNA) depletion by hybridization of complementary DNA oligonucleotides, followed by treatment with RNase H and DNase to remove rRNA duplexed to DNA and original DNA oligonucleotides. Samples depleted of rRNA were then subjected to 94 °C for 6 min in the 2×Fragment, Prime, and Elute Buffer in order to obtain 200–300 bp fragments. cDNA synthesis was run in two steps following the manufacturer’s instructions. The ligation step consisted of a final volume of 110 μl of the adaptor ligation reaction mixture with 60 μl of input cDNA, 5μl of diluted adaptor, and 45 μl of ligation mix (50 μl of ligation buffer + 10 μl of DNA ligase). The Kapa Dual- Indexed Adaptors stock concentration was diluted to 1.5mM to get the best adaptor concentration for library construction. The ligation cycle was run according to the manufacturer’s instructions. To remove short fragments such as adaptor dimers, 2X AMPure XP bead clean-ups were done (0.63 SPRI and 0.7 SPRI).

value: Human HSPCs


title: Fig4BC, Fig4DE: ΔtracrΔcas9, ΔCRISPR::R26, Cas1/2, Nmecas9ΔBHΔREC1/2-FLAG + 0.1mM IPTG

source_name: ΔtracrΔcas9, ΔCRISPR::R26, NICS::pLacNmecas1-cas2, iga-trpB::pTet Nmecas9ΔBHΔREC1/2-FLAG

value: {delta}tracr{delta}cas9, {delta}CRISPR::R26, NICS::pLacNmecas1-cas2, iga-trpB::pTet Nmecas9{delta}BH{delta}REC1/2-FLAG

value: MDAΦ 3+21 hr

value: 0.1 mM IPTG

value: primer-amplified DNA


title: 20-42D-P300_SR8278

description:
Library name: 42D-p300-SR8278
paired-end


title: Fig4BC: ΔtracrΔcas9, ΔCRISPR::R26, Cas1/2, Nmecas9ΔPI-FLAG + 0.1mM IPTG

source_name: ΔtracrΔcas9, ΔCRISPR::R26, NICS::pLacNmecas1-cas2, iga-trpB::pTet Nmecas9ΔPI-FLAG

value: strain 8013 (NCBI:txid604162)

value: bacteria

value: {delta}tracr{delta}cas9, {delta}CRISPR::R26, NICS::pLacNmecas1-cas2, iga-trpB::pTet Nmecas9{delta}PI-FLAG


title: Input_O

source_name: mat1Msmt0 ade6-210 ura4-D18 mat2P(Bg-Bs)::ura4+ h3.2G13D::NatMX6 leu1+::Pnmt1-GFP-raf1

value: Growth in PMG medium at 30°C


title: 19-42D-NR1D1_Vehicle

description:
Library name: 42D-NR1D1-Vehicle2
paired-end

value: t-NEPC cell line

value: WT

value: 42D, DMSO treated, 24 h

value: REV-ERBα


title: Fig4BC: ΔtracrΔcas9, ΔCRISPR::R26, Cas1/2, Nmecas9ΔRuvCIII-FLAG + 0.1mM IPTG

source_name: ΔtracrΔcas9, ΔCRISPR::R26, NICS::pLacNmecas1-cas2, iga-trpB::pTet Nmecas9ΔRuvCIII-FLAG

value: {delta}tracr{delta}cas9, {delta}CRISPR::R26, NICS::pLacNmecas1-cas2, iga-trpB::pTet Nmecas9{delta}RuvCIII-FLAG

value: Non-UMI


title: Input_M

source_name: mat1Msmt0 leu1-32 ade6-210 ura4-D18 mat2P(Bg-Bs)::ura4+ lys1::Padh1-GFP-HphMX6

value: Growth in YEA medium at 30°C


title: CD34_W2_LPS

description: Library name: HUE638A6


title: Input_L

source_name: mat1Msmt0 ade6-210 ura4-DS/E mat2P(Bg-Bs)::ura4+ raf1R576H::KanMX6 leu1+::Pnmt1-GFP-raf1R576H

value: 3% PFA


title: Fig4BC: ΔtracrΔcas9, ΔCRISPR::R26, Cas1/2, Nmecas9ΔHNH-FLAG + 0.1mM IPTG

source_name: ΔtracrΔcas9, ΔCRISPR::R26, NICS::pLacNmecas1-cas2, iga-trpB::pTet Nmecas9ΔHNH-FLAG

value: {delta}tracr{delta}cas9, {delta}CRISPR::R26, NICS::pLacNmecas1-cas2, iga-trpB::pTet Nmecas9{delta}HNH-FLAG


title: 17-42D-NR1D1_AZD5153

description:
Library name: 42D-NR1D1-AZD5153
paired-end


title: CD34_W2_

description: Library name: HUE638A5

value: Human HSPCs


title: Fig4DE: ΔtracrΔcas9, ΔCRISPR::R26, Cas1/2, Nmecas9-FLAG+sgRNA + 0.1mM IPTG

source_name: ΔtracrΔcas9, ΔCRISPR::R26, NICS::pLacNmecas1-cas2, iga-trpB::pTet Nmecas9-FLAG+pTR sgRNA

value: {delta}tracr{delta}cas9, {delta}CRISPR::R26, NICS::pLacNmecas1-cas2, iga-trpB::pTet Nmecas9-FLAG+pTR sgRNA

value: MDAΦ 3+21 hr


title: Fig4BC: ΔtracrΔcas9, ΔCRISPR::R26, Cas1/2, Nmecas9ΔRuvCII-FLAG + 0.1mM IPTG

source_name: ΔtracrΔcas9, ΔCRISPR::R26, NICS::pLacNmecas1-cas2, iga-trpB::pTet Nmecas9ΔRuvCII-FLAG

value: {delta}tracr{delta}cas9, {delta}CRISPR::R26, NICS::pLacNmecas1-cas2, iga-trpB::pTet Nmecas9{delta}RuvCII-FLAG

value: 0.1 mM IPTG

value: primer-amplified DNA


title: Input_Q

source_name: mat1Msmt0 leu1-32 ade6-216 his2 ura4-DS/E otr1R(Sph1)::ura4+


title: Input_K

source_name: mat1Msmt0 ade6-210 ura4-DS/E mat2P(Bg-Bs)::ura4+ raf1R576H::KanMX6 leu1+::Pnmt1-GFP-raf1


title: Fig4BC, Fig4DE: ΔtracrΔcas9, ΔCRISPR::R26, Cas1/2, Nmecas9ΔREC1/2-FLAG + 0.1mM IPTG

source_name: ΔtracrΔcas9, ΔCRISPR::R26, NICS::pLacNmecas1-cas2, iga-trpB::pTet Nmecas9ΔREC1/2-FLAG

value: strain 8013 (NCBI:txid604162)

value: bacteria

value: {delta}tracr{delta}cas9, {delta}CRISPR::R26, NICS::pLacNmecas1-cas2, iga-trpB::pTet Nmecas9{delta}REC1/2-FLAG


title: Input_J

source_name: mat1Msmt0 ade6-210 ura4-DS/E mat2P(Bg-Bs)::ura4+ raf1R576H::KanMX6 leu1+::Pnmt1-GFP

value: Growth in PMG medium at 30°C


title: 16-LuCaP173-BRN2_SR8278

description: Library name: LuCaP173-BRN2-SR8278

source_name: LuCaP173.1 PDX

value: LuCaP173.1 PDX

value: de novo NEPC

value: WT


title: Input_I

source_name: mat1Msmt0 leu1-32 ade6-210 ura4-D18 mat2P(Bg-Bs)::ura4+


title: CD34_T1_LPS

description: Library name: HUE638A4


title: CD34_T2_LPS

description: Library name: HUE638A8


title: 13-LuCaP173-SR8278

description: Library name: LuCaP173-Input-SR8278(NR1D1/BRN2)


title: Input_N

source_name: mat1Msmt0 ade6-216 his2 ura4-DS/E otr1R(Sph1)::ura4+ raf2-myc::KanMX6 leu1+::Pnmt1-GFP

value: Growth in PMG medium at 30°C + 2hr at 18°C before fixation

value: 3% PFA + 10mM DMA


title: Input_H

source_name: mat1Msmt0 ade6-210 ura4-D18 mat2P(Bg-Bs)::ura4+

value: Growth in YEA medium at 30°C

value: 3% PFA


title: CD34_T2

description: Library name: HUE638A7

source_name: Human HSPCs

value: Human HSPCs


title: 18-42D-NR1D1_A485

description:
Library name: 42D-NR1D1-A485
paired-end

value: t-NEPC cell line

value: REV-ERBα


title: CD14_T3

description: Library name: HUE638A23

source_name: Human Monocytes

value: Human Monocytes


title: Input_G

value: Growth in YEA medium at 30°C + 2hr at 18°C before fixation


title: CD14_W3_LPS

description: Library name: HUE638A22


title: 12-LuCaP173-NR1D1

description: Library name: LuCaP173-NR1D1-Vehicle

value: Vehicle, daily, 10 days


title: CD14_T3_LPS

description: Library name: HUE638A24


title: Input_F

source_name: mat1Msmt0 leu1-32 ade6-216 ura4-DS/E mat2P(Bg-Bs)::ura4+ raf1R576H::KanMX6 ebs1∆::KanMX6


title: CD34_T1_

description: Library name: HUE638A3


title: Fig4BC, Fig4DE: ΔtracrΔcas9, ΔCRISPR::R26, Cas1/2, Nmecas9-FLAG + 0.1mM IPTG

source_name: ΔtracrΔcas9, ΔCRISPR::R26, NICS::pLacNmecas1-cas2, iga-trpB::pTet Nmecas9-FLAG

value: strain 8013 (NCBI:txid604162)

value: {delta}tracr{delta}cas9, {delta}CRISPR::R26, NICS::pLacNmecas1-cas2, iga-trpB::pTet Nmecas9-FLAG

value: MDAΦ 3+21 hr

value: 0.1 mM IPTG

value: Non-UMI

value: primer-amplified DNA


title: Fig3BC: ΔtracrΔcas9, ΔCRISPR::R26, Cas1/2, Nme dcas9+CRISPRΔ40nt leader+tracr + 0.1mM IPTG

source_name: ΔtracrΔcas9, ΔCRISPR::R26, NICS::pLacNmecas1-cas2, iga-trpB::pTet Nme dcas9+CRISPRΔ40nt leader+pTR tracr

value: bacteria

value: {delta}tracr{delta}cas9, {delta}CRISPR::R26, NICS::pLacNmecas1-cas2, iga-trpB::pTet Nme dcas9+CRISPR{delta}40nt leader+pTR tracr


title: 14-LuCaP173-NR1D1_SR8278

description: Library name: LuCaP173-NR1D1-SR8278

value: LuCaP173.1 PDX

value: de novo NEPC

value: WT


title: 11-LuCaP173-Vehicle

description: Library name: LuCaP173-Input-Vehicle(NR1D1/BRN2)


title: Fig3BC: ΔtracrΔcas9, ΔCRISPR::R26, Cas1/2, Nme dcas9+CRISPRΔ40nt Leader + 0.1mM IPTG

source_name: ΔtracrΔcas9, ΔCRISPR::R26, NICS::pLacNmecas1-cas2, iga-trpB::pTet Nme dcas9+CRISPRΔ40nt Leader

value: {delta}tracr{delta}cas9, {delta}CRISPR::R26, NICS::pLacNmecas1-cas2, iga-trpB::pTet Nme dcas9+CRISPR{delta}40nt Leader


title: CD14_W3

description: Library name: HUE638A21


title: Fig4BC: ΔtracrΔcas9, ΔCRISPR::R26, Cas1/2, Nmecas9ΔRuvCIΔBH-FLAG + 0.1mM IPTG

source_name: ΔtracrΔcas9, ΔCRISPR::R26, NICS::pLacNmecas1-cas2, iga-trpB::pTet Nmecas9ΔRuvCIΔBH-FLAG

value: {delta}tracr{delta}cas9, {delta}CRISPR::R26, NICS::pLacNmecas1-cas2, iga-trpB::pTet Nmecas9{delta}RuvCI{delta}BH-FLAG


title: Input_E

source_name: mat1Msmt0 leu1-32 ade6-210 ura4-DS/E mat2P(Bg-Bs)::ura4+ raf1R576H::KanMX6 upf1∆::KanMX6

value: Growth in YEA medium at 30°C

value: 3% PFA


title: 10-42D-H3K27acSR8278

description: Library name: 42D-H3K27ac-SR8278(H3K27ac)

value: t-NEPC cell line


title: Fig3BC: ΔtracrΔcas9, ΔCRISPR::R26, Cas1/2, Nme dcas9+sgRNA + 0.1mM IPTG

source_name: ΔtracrΔcas9, ΔCRISPR::R26, NICS::pLacNmecas1-cas2, iga-trpB::pTet Nme dcas9+pTR sgRNA

value: {delta}tracr{delta}cas9, {delta}CRISPR::R26, NICS::pLacNmecas1-cas2, iga-trpB::pTet Nme dcas9+pTR sgRNA


title: CD14_T2_LPS

description: Library name: HUE638A20

value: Human Monocytes


title: Input_D

source_name: mat1Msmt0 leu1-32 ade6-210 ura4-DS/E mat2P(Bg-Bs)::ura4+ raf1R576H::KanMX6


title: 8-Input-SR8278

description: Library name: 42D-Input-SR8278(H3K27ac)


title: Input_C


title: CD34_W1_LPS

description: Library name: HUE638A2

value: Human HSPCs


title: Fig3BC: ΔtracrΔcas9, ΔCRISPR::R26, Cas1/2, Nme dcas9+tracr + 0.1mM IPTG

source_name: ΔtracrΔcas9, ΔCRISPR::R26, NICS::pLacNmecas1-cas2, iga-trpB::pTet Nme dcas9+pTR tracr

value: strain 8013 (NCBI:txid604162)

value: {delta}tracr{delta}cas9, {delta}CRISPR::R26, NICS::pLacNmecas1-cas2, iga-trpB::pTet Nme dcas9+pTR tracr

value: MDAΦ 3+21 hr


title: Fig3BC: ΔtracrΔcas9, ΔCRISPR::R26, Cas1/2, Nme dcas9 + 0.1mM IPTG

source_name: ΔtracrΔcas9, ΔCRISPR::R26, NICS::pLacNmecas1-cas2, iga-trpB::pTet Nme dcas9

value: {delta}tracr{delta}cas9, {delta}CRISPR::R26, NICS::pLacNmecas1-cas2, iga-trpB::pTet Nme dcas9

value: 0.1 mM IPTG

value: Non-UMI

value: primer-amplified DNA


title: 9-42D-H3K27acVehicle

description: Library name: 42D-H3K27ac-Vehicle(H3K27ac)

value: DMSO, 24 h


title: CD14_T2

description: Library name: HUE638A19


title: 15-LuCaP173-BRN2

description: Library name: LuCaP173-BRN2-Vehicle

value: LuCaP173.1 PDX

value: de novo NEPC

value: WT

value: Vehicle, daily, 10 days


title: 7-Input-Veh

description: Library name: 42D-Input-Vehicle(H3K27ac)


title: Fig3BC: ΔtracrΔcas9, ΔCRISPR::R26, Cas1/2, empty + 0.1mM IPTG

source_name: ΔtracrΔcas9, ΔCRISPR::R26, NICS::pLacNmecas1-cas2, iga-trpB::empty

value: bacteria

value: {delta}tracr{delta}cas9, {delta}CRISPR::R26, NICS::pLacNmecas1-cas2, iga-trpB::empty


title: CD14_W2_LPS

description: Library name: HUE638A18


title: Input_B

source_name: mat1Msmt0 leu1-32 ade6-210 ura4-D18 mat2P(Bg-Bs)::ura4+ lys1::Padh1-GFP-raf1-HphMX6

value: Growth in YEA medium at 30°C

value: 3% PFA


title: 6-42D-InputSR8278

description: Library name: 42D-Input-SR8278(NR1D1/BRN2)

value: t-NEPC cell line


title: Input_A

description: Input_for_samples_1:2:3:26:28:29:32:33:36:37:43

source_name: mat1Msmt0 leu1-32 ade6-210 ura4-D18 mat2P(Bg-Bs)::ura4+ lys1::Padh1-GFP-HphMX6


title: CD14_W2_

description: Library name: HUE638A17

value: Human Monocytes


title: Fig2EF, FigS4FG: Δcas9, ΔCRISPR::R26, Cas1/2 + 0.1mM IPTG

value: strain 8013 (NCBI:txid604162)


title: H3K9me3_raf1-OE+Caffeine_Exp16_Rep2

value: Abcam anti-H3K9me3 (cat# ab8898)

value: Growth in YEA medium supplemented with 16mM Caffeine at 30°C for 2 weeks


title: 5-42D-InputVeh

description: Library name: 42D-Input-Vehicle(NR1D1/BRN2)


title: 4-42D-BRN2SR8278

description: Library name: 42D-BRN2-SR8278


title: CD14_T1_LPS

description: Library name: HUE638A16


title: Fig2EF: endo dcas9, ΔCRISPR::R26, Cas1/2 + 0.1mM IPTG

source_name: endo dcas9, ΔCRISPR::R26, iga-trpB::pLacNmecas1-cas2

value: endo dcas9, {delta}CRISPR::R26, iga-trpB::pLacNmecas1-cas2

value: MDAΦ 3+21 hr

value: 0.1 mM IPTG

value: UMI-2 (BsmAI)


title: 3-42D-BRN2Veh

description: Library name: 42D-BRN2-Vehicle

value: DMSO, 24 h


title: CD14_T1_

description: Library name: HUE638A15


title: 2-42D-NR1D1SR8278.

description: Library name: 42D-NR1D1-SR8278

value: REV-ERBα


title: Fig2BC, FigS3EF: ΔtracrΔcas9, Cas1/2, empty + 0.1mM IPTG

value: UMI-1 (FatI)

value: primer-amplified DNA


title: H3K9me3_Caffeine_Exp16_Rep2


title: H3K9me3_raf1R518H_FE_Exp13_Rep2

source_name: mat1Msmt0 leu1-32 ade6-216 his2 ura4-DS/E otr1R(Sph1)::ura4+ raf1R518H::KanMX6


title: Fig2EF: endo dcas9, Cas1/2 + 0.1mM IPTG

source_name: endo dcas9, iga-trpB::pLacNmecas1-cas2

value: bacteria

value: endo dcas9, iga-trpB::pLacNmecas1-cas2


title: H3K9me3_GFP-OE_FE_Exp14_Rep2

value: Growth in YEA medium at 30°C


title: CD14_W1_LPS

description: Library name: HUE638A14

source_name: Human Monocytes

value: WT


title: Fig2EF: endo dcas9, ΔCRISPR::R26, Cas1/2


title: Fig2BC: Δtracr, Cas1/2, tracr + 0.1mM IPTG


title: H3K9me3_raf1-OE_FE_Exp14_Rep2

value: 3% PFA


title: CD34_T3_LPS

description: Library name: HUE638A12

source_name: Human HSPCs

value: Human HSPCs


title: CD14_W1_

description: Library name: HUE638A13

value: Human Monocytes


title: 42D, NR1D1/REV-ERBα, 24 h

description: Library name: 42D-siNR1D1/REV-ERBα

data_processing:
ATAC-seq data analysis was performed using nf-core ATAC-seq pipeline with default parameters. Deeptools, bedtools, IGV and Manorm were used for the downstream analysis
Assembly: hg19
Supplementary files format and content: txt files include raw counts for each sample

extract_protocol:
ATAC-seq experiments were performed using 42D cells. 50,000 variable cells were used for transposase-accessible chromatin experiments following.
Library constructions were performed using  50 bp paired-end (50PE) sequencing  to obtain >50 million genomic reads.

value: t-NEPC


title: H3K9me3_tor1D_upf1D_Exp12_Rep1

source_name: mat1Msmt0 leu1-32 ade6-210 ura4-D18 mat2P(Bg-Bs)::ura4+ tor1∆::NatMX6 upf1∆::KanMX6

value: Abcam anti-H3K9me3 (cat# ab8898)


title: CD34_W3

description: Library name: HUE638A11


title: 1-42D-NR1D1Veh

description: Library name: 42D-NR1D1-Vehicle

value: t-NEPC cell line


title: 42D, siCtrl, 24 h

description: Library name: 42D-siCtrl


title: H3K9me3_tor1D_Exp12_Rep1

source_name: mat1Msmt0 leu1-32 ade6-210 ura4-D18 mat2P(Bg-Bs)::ura4+ tor1∆::NatMX6


title: Fig2BC: Δtracr, Cas1/2, empty

value: strain 8013 (NCBI:txid604162)

value: MDAΦ 3+21 hr


title: CD34_W3_LPS

description: Library name: HUE638A10


title: H3K9me3_WT_Exp12_Rep6

source_name: mat1Msmt0 ade6-210 ura4-D18 mat2P(Bg-Bs)::ura4+


title: 42D, SR8278 7.5 uM, 24 h

description: Library name: 42D-SR8278


title: CD34_W1_

description: Library name: HUE638A1


title: Fig2BC: Cas1/2 + 0.1mM IPTG

value: 0.1 mM IPTG


title: 42D, DMSO treated, 24 h

description: Library name: 42D-DMSO


title: HSPC_WT_LPS

city: LONDON

first: Giuseppe

middle: Alessandro

last: D'Agostino

state: ENGLAND

address: 1 Midland Road

description:
Library name: HSPC_WT_LPS
10X 3' GEX

library_source: transcriptomic single cell

data_processing:
For the HSPC single cell RNA-seq data, FASTQ files from different lanes were merged and STAR v. 2.7.10b was used to align each of them to the Ensembl h38 genome, release 108, using the following parameters: --runMode alignReads, --soloType CB_UMI_Simple, --soloUMIlen 12, --runRNGseed 1. For the myeloid progeny single cell RNA-seq data, cellranger v. 7.1.0 was used using pre-computed references (“refdata-cellranger-GRCh38-3.0.0”) and chemistry=ARC-v1.
Assembly: Ensembl h38 genome, release 108
Supplementary files format and content: tar.gz archives of the filtered gene counts from STARSolo and HDF5 files from the CellRanger v. 7.0 output (multiome gene expression)

molecule: cytoplasmic RNA

source_name: Bone Marrow

extract_protocol:
HSPCs samples were prepared using 10X 3’ V3.1 and sequenced using the HiSeq4000, for immune progeny samples we used the 10X multiome kit and were sequenced in NovaSeq6000.
The concentration and viability of the single cell suspension was measured using trypan blue using Eve Automatic Cell Counter. Approximately 3,000-10,000 cells were loaded on Chromium Chip and partitioned in nanolitre scale droplets using the Chromium Controller and Chromium Next GEM Single Cell Reagents (Chromium Single Cell 3' Reagent Kits User Guide (v3.1)). Within each droplet the cells were lysed, and the RNA was reverse transcribed. All the resulting cDNA within a droplet shared the same cell barcode. Illumina compatible libraries were generated from the cDNA using Chromium Next GEM Single Cell library reagents in accordance with the manufacturer’s instructions (10x Genomics, CG000315 Chromium Single Cell 3' Reagent Kits User Guide (v3.1 - Dual Index)). For QC of libraries, we used the Agilent TapeStation and sequenced using the Illumina HiSeq4000. Sequencing read configuration: 28-10-10-90. For the immune progeny, we sorted human hematopoietic cell subsets from humanized mice reconstituted with either TET2WT or TET2Mut HSCs as described in Figure S5A. The concentration and viability of the single nuclei suspension was measured using acridine orange (AO) and propidium iodide (PI) and the Luna-FX7 Automatic Cell Counter. Approximately 15,000-20,000 nuclei were transposed, then loaded on Chromium Chip and partitioned in nanolitre scale droplets using the Chromium Controller and Chromium Next GEM Single Cell Reagents (Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Reagent Kits User Guide, User Guide, CG000338). Sequencing read configuration: 28-10-10-90 (GEX). The 10x Barcodes in each library type are used to associate individual reads back to the individual partitions, and thereby, to each individual nucleus.
scRNA-Seq 10X  3' Gene Expression and 10X Multiome Gene Expression

value: Bone Marrow

value: LPS

tag: library type

value: mRNA


title: H3K9me3_raf1-OE_37C_Exp11_Rep1

value: Growth in YEA medium at 37°C for 4 days


title: Fig1F: Δcas9, Cas1/2, Nmecas9 PID swap + 0.1mM IPTG

source_name: Δcas9, iga-trpB::pLacNmecas1-cas2, NICS::Nmecas9 PID swap

value: bacteria

value: {delta}cas9, iga-trpB::pLacNmecas1-cas2, NICS::Nmecas9 PID swap

value: UMI-1 (FatI)

value: primer-amplified DNA


title: H3K9me3_WT_37C_Exp11_Rep1

value: 3% PFA


title: Fig4BC: ΔtracrΔcas9, ΔCRISPR::R26, Cas1/2, empty + 0.1mM IPTG

value: {delta}tracr{delta}cas9, {delta}CRISPR::R26, NICS::pLacNmecas1-cas2, iga-trpB::empty

value: Non-UMI


title: Fig2BC: Δtracr, Cas1/2, empty + 0.1mM IPTG


title: HSPC_WT_CTRL

description:
Library name: HSPC_WT_CTRL
10X 3' GEX

value: Human HSPCs

value: WT

value: UNTREATED


title: 16D, NR1D1/REV-ERBα overexpression

description: Library name: 6-LN16DNR1D1OE

data_processing:
Data were trimmed using trim-glare and the resultant read sequences were aligned to the hg19 human reference genome using bowtie2 aligner. Aligned reads in Bam format were counted using HTSeq and transformed into FPKM in R software.
Assembly: hg19
Supplementary files format and content: txt files include raw counts for each sample

molecule: total RNA

extract_protocol:
RNA was harvest using TRIzol® reagent and 1.3 ug of total RNA was used for sequencing library constructions.
Library constructions were performed using the NEBnext Ultra ii Straned RNA Library Prep Kit, and sequencing was performed on an Illumina NextSeq 500 system (50 x 50 bp paired end reads).

value: adenocarcinoma

value: NR1D1/REV-ERBα OE, stable transfection


title: LuCaP35ENZR PDX tumor, Vehicle treated, Day 10, rep2

description: Library name: 9-LuCaP35ENZR-Vehicle-2

source_name: LuCaP35 PDX tumor

value: LuCaP35 PDX tumor

value: enzalutamide resistant PDX

value: Vehicle,daily, p.o.


title: H3K9me3_WT_Exp11_Rep5

value: Abcam anti-H3K9me3 (cat# ab8898)

value: Growth in YEA medium at 30°C


title: Fig1F: Δcas9, Cas1/2, empty + 0.1mM IPTG

value: strain 8013 (NCBI:txid604162)

value: bacteria

value: MDAΦ 3+21 hr

value: 0.1 mM IPTG


title: Fig1F: Δcas9, Cas1/2, Nmecas9 H1024A + 0.1mM IPTG

source_name: Δcas9, iga-trpB::pLacNmecas1-cas2, NICS::Nmecas9 H1024A

value: {delta}cas9, iga-trpB::pLacNmecas1-cas2, NICS::Nmecas9 H1024A

value: UMI-1 (FatI)

value: primer-amplified DNA


title: LuCaP35ENZR PDX tumor, Vehicle treated, Day 10

description: Library name: 7-LuCaP35CR


title: Fig1F: Δcas9, Cas1/2, Nme dcas9 + 0.1mM IPTG

source_name: Δcas9, iga-trpB::pLacNmecas1-cas2, NICS::Nme dcas9

value: {delta}cas9, iga-trpB::pLacNmecas1-cas2, NICS::Nme dcas9


title: LuCaP35ENZR PDX tumor, Vehicle treated, Day 10, rep1

description: Library name: 8-LuCaP35ENZR-Vehicle-1

value: WT


title: HSPC_TET2_CTRL

description:
Library name: HSPC_KO_CTRL
10X 3' GEX

value: Bone Marrow

value: Human HSPCs

value: UNTREATED

value: mRNA


title: HSPC_TET2_LPS

description:
Library name: HSPC_KO_LPS
10X 3' GEX

value: LPS


title: H3K9me3_Caffeine_Exp10_Rep1

value: Growth in YEA medium supplemented with 16mM Caffeine at 30°C for 2 weeks

value: 3% PFA


title: H3K9me3_raf1-OE+Caffeine_Exp10_Rep1

value: Abcam anti-H3K9me3 (cat# ab8898)


title: WT, M, 24 wk, rep 3

first: Hayley

middle: S

last: McLoughlin

address: 109 Zina Pitcher Pl

department: Neurology, Human Genetics

description: Library name: 13015-JE-12

data_processing:
Reads were mapped to the GRCm39 mouse genome using STAR 2.7.10b
Kallisto 0.46.2 was used to generate TPM data
Assembly: GRCm39
Supplementary files format and content: TPM data provided in a separate .csv file for each sample

organism: Mus musculus

source_name: spinal cord

extract_protocol:
RNA was extracted using TRIzol, Qiagen qiashredder, and Qiagen RNEasy Plus Kit. Library prepared from 200ng RNA.
Library was prepared by the University of Michigan Advanced Genomics core using a polyA-dependent method. Kits used include NEBNext Poly(A) mRNA magnetic isolation modules and NEBNext ultraexpress RNA library prep kit.

value: spinal cord

tag: Sex

value: M

tag: time

value: 24 wk


title: Fig1F: Δcas9, Cas1/2, Nmecas9 + 0.1mM IPTG

value: strain 8013 (NCBI:txid604162)

value: bacteria

value: MDAΦ 3+21 hr

value: 0.1 mM IPTG


title: H3K9me3_h3.2G13D_FE_Exp9_Rep2

source_name: mat1Msmt0 leu1-32 ade6-210 ura4-D18 mat2P(Bg-Bs)::ura4+ h3.2G13D::NatMX6

value: Growth in YEA medium at 30°C


title: 42D, siNR1D1/REV-ERBα, Day 3

description: Library name: 4-42D-siNR1D1

value: t-NEPC cell line

value: siNR1D1/REV-ERBα, 3 days


title: 16D, Empty vector

description: Library name: 5-LN16DEmpty

value: adenocarcinoma

value: WT

value: Empty vector, stable transfection


title: H3K9me3_h3.2G13D_upf1D_FE_Exp9_Rep1

source_name: mat1Msmt0 leu1-32 ade6-210 ura4-D18 mat2P(Bg-Bs)::ura4+ h3.2G13D::NatM6 upf1∆::KanMX6


title: WT, M, 24 wk, rep 1

description: Library name: 13015-JE-10


title: WT, M, 24 wk, rep 2

description: Library name: 13015-JE-11


title: Fig1F: Cas1/2 + 0.1mM IPTG

value: UMI-1 (FatI)

value: primer-amplified DNA


title: 42D, siCtrl, Day 3

description: Library name: 3-42D-siCtrl

value: siCtrl, 3 days


title: WT, F, 24 wk, rep 3

description: Library name: 13015-JE-9

value: F


title: Fig1E, FigS2BCD: Cas1/2 + 0.1mM IPTG

value: Non-UMI


title: Fig1E: Cas1/2, no phage


title: H3K9me3_h3.2G13D_raf1-OE_FE_Exp9_Rep1

source_name: mat1Msmt0 ade6-210 ura4-D18 mat2P(Bg-Bs)::ura4+ h3.2G13D::NatMX6 leu1+::Pnmt1-GFP-raf1

value: Abcam anti-H3K9me3 (cat# ab8898)

value: Growth in PMG medium at 30°C

value: 3% PFA


title: 42D, SR8278 7.5 uM, Day 2

description: Library name: 2-42D-SR8278-7.5uM


title: Fig1E: 8013 WT + 0.1mM IPTG

value: strain 8013 (NCBI:txid604162)

value: bacteria


title: H3K9me3_h3.2G13D_FE_Exp9_Rep1

source_name: mat1Msmt0 ade6-210 ura4-D18 mat2P(Bg-Bs)::ura4+ h3.2G13D::NatMX6 leu1+::Pnmt1-GFP


title: WT, F, 24 wk, rep 2

description: Library name: 13015-JE-8

value: spinal cord

value: 24 wk


title: H3K9me3_clr3D_upf1D_FE_Exp8_Rep1

source_name: mat1Msmt0 leu1-32 ade6-210 ura4-D18 mat2P(Bg-Bs)::ura4+ clr3∆::KanMX6 upf1∆::KanMX6

value: Growth in YEA medium at 30°C


title: WT, F, 24 wk, rep 1

description: Library name: 13015-JE-7


title: H3K9me3_clr3D_FE_Exp8_Rep2

source_name: mat1Msmt0 leu1-32 ade6-210 ura4 mat2P(Bg-Bs)::ura4+ clr3∆::KanMX6


title: LuCaP173.1 PDX tumor, SR8278 20 mg/kg, Day 10, rep2

description: Library name: 18-LuCaP173-SR8278-2

source_name: LuCaP173.1 PDX tumor

value: LuCaP173.1 PDX tumor

value: enzalutamide resistant PDX

value: SR8278 20 mg/kg, daily, p.o.


title: Fig1E: 8013 WT, no phage


title: LuCaP173.1 PDX tumor, SR8278 20 mg/kg, Day 10, rep1

description: Library name: 17-LuCaP173-SR8278-1

value: WT


title: KO, M, 24 wk, rep 3

description: Library name: 13015-JE-6

value: M

value: Atxn3 KO


title: LuCaP173.1 PDX tumor, Vehicle treated, Day 10, rep3

description: Library name: 16-LuCaP173-Vehicle-3

value: Vehicle,daily, p.o.


title: CTRL, M, Ventral, Rep 2

description: Library name: 12659-JE-14

data_processing:
Reads were mapped to the GRCh38 human genome using STAR 2.7.10b
Kallisto 0.46.2 was used to generate TPM data
Assembly: GRCh38
Supplementary files format and content: TPM data provided in a separate .csv file for each sample

extract_protocol:
RNA was extracted using TRIzol, Qiagen qiashredder, and Qiagen RNEasy Plus Kit. Library prepared from 200ng RNA.
Library was prepared by the University of Michigan Advanced Genomics core using a ribo depletion method.

tag: tissue type

value: ventral

value: CTRL

tag: pmi

value: 22 hr


title: H3K9me3_clr3D_raf1-OE_FE_Exp8_Rep1

source_name: mat1Msmt0 leu1-32 ade6-210 ura4 mat2P(Bg-Bs)::ura4+ clr3∆::KanMX6 lys1::Padh1-GFP-raf1-HphMX6

tag: strain

value: Abcam anti-H3K9me3 (cat# ab8898)


title: CTRL, M, Dorsal, Rep 2

description: Library name: 12659-JE-13

value: dorsal

tag: genotype


title: H3K9me3_clr3D_FE_Exp8_Rep1

source_name: mat1Msmt0 leu1-32 ade6-210 ura4 mat2P(Bg-Bs)::ura4+ clr3∆::KanMX6 lys1::Padh1-GFP-HphMX6

tag: chip antibody

tag: growth

value: 3% PFA


title: KO, M, 24 wk, rep 1

description: Library name: 13015-JE-4


title: LuCaP173.1 PDX tumor, Vehicle treated, Day 10, rep2

description: Library name: 15-LuCaP173-Vehicle-2

tag: cell type


title: KO, M, 24 wk, rep 2

description: Library name: 13015-JE-5


title: KO, F, 24 wk, rep 3

description: Library name: 13015-JE-3

value: F


title: Raf2-myc_WT_FE_Exp7_Rep1

source_name: mat1Msmt0 ade6-216 his2 ura4-DS/E otr1R(Sph1)::ura4+ raf2-myc::KanMX6 leu1+::Pnmt1-GFP

value: Santa Cruz anti-Myc (9E10) (cat# sc-40)

value: Growth in PMG medium at 30°C + 2hr at 18°C before fixation

tag: fixation

value: 3% PFA + 10mM DMA


title: Raf2-myc_raf1-OE_FE_Exp7_Rep1

source_name: mat1Msmt0 ade6-216 his2 ura4-DS/E otr1R(Sph1)::ura4+ raf2-myc::KanMX6 leu1+::Pnmt1-GFP-raf1


title: CTRL, F, Ventral, Rep 2

description: Library name: 12659-JE-10

value: spinal cord

value: 26 hr


title: LuCaP173.1 PDX tumor, Vehicle treated, Day 10, rep1

description: Library name: 14-LuCaP173-Vehicle-1

value: LuCaP173.1 PDX tumor

value: enzalutamide resistant PDX


title: 42D, DMSO treated, Day 2

description: Library name: 1-42D-DMSO

value: t-NEPC cell line

value: WT

value: DMSO


title: H3K9me3_raf1-OE_FE_Exp6_Rep1

source_name: mat1Msmt0 leu1-32 ade6-210 ura4-D18 mat2P(Bg-Bs)::ura4+ lys1::Padh1-GFP-raf1-HphMX6

value: Growth in YEA medium at 30°C


title: KO, F, 24 wk, rep 2

description: Library name: 13015-JE-2

value: Atxn3 KO

value: 24 wk


title: LuCaP35ENZR PDX tumor, SR8278 20 mg/kg, Day 10, rep3

description: Library name: 13-LuCaP35ENZR-SR8278-3

value: LuCaP35 PDX tumor

value: SR8278 20 mg/kg, daily, p.o.


title: CTRL, F, Dorsal, Rep 2

description: Library name: 12659-JE-9

value: dorsal

value: CTRL


title: KO, F, 24 wk, rep 1

description: Library name: 13015-JE-1

value: F


title: LuCaP35ENZR PDX tumor, SR8278 20 mg/kg, Day 10, rep2

description: Library name: 12-LuCaP35ENZR-SR8278-2


title: CTRL, F, Ventral, Rep 1

description: Library name: 12659-JE-8

value: ventral

value: 21 hr


title: CTRL, M, Ventral, Rep 1

description: Library name: 12659-JE-12

value: spinal cord

value: M

value: 27 hr


title: KI, F, 56 wk, rep3

description: Library name: 11514-JE-18

value: Female

value: KI

value: 56 wk


title: LuCaP35ENZR PDX tumor, SR8278 20 mg/kg, Day 10, rep1

description: Library name: 11-LuCaP35ENZR-SR8278-1

value: enzalutamide resistant PDX

value: WT


title: CTRL, M, Dorsal, Rep 1

description: Library name: 12659-JE-11


title: H3K9me3_raf1R576H_raf1R576H-OE_FE_Exp5_Rep1

source_name: mat1Msmt0 ade6-210 ura4-DS/E mat2P(Bg-Bs)::ura4+ raf1R576H::KanMX6 leu1+::Pnmt1-GFP-raf1R576H

value: Abcam anti-H3K9me3 (cat# ab8898)

value: Growth in PMG medium at 30°C

value: 3% PFA


title: CTRL, F, Dorsal, Rep 1

description: Library name: 12659-JE-7


title: WT, F, 56 wk, rep3

description: Library name: 11514-JE-14


title: H3K9me3_raf1R576H_raf1-OE_FE_Exp5_Rep1

source_name: mat1Msmt0 ade6-210 ura4-DS/E mat2P(Bg-Bs)::ura4+ raf1R576H::KanMX6 leu1+::Pnmt1-GFP-raf1


title: SCA3, F, Dorsal

description: Library name: 12659-JE-5

value: 5 hr


title: KI, M, 56 wk, rep3

description: Library name: 11514-JE-12

value: Male


title: WT, F, 56 wk, rep2

description: Library name: 11514-JE-13


title: H3K9me3_raf1R576H_FE_Exp5_Rep4

source_name: mat1Msmt0 ade6-210 ura4-DS/E mat2P(Bg-Bs)::ura4+ raf1R576H::KanMX6 leu1+::Pnmt1-GFP


title: TPP, Full Riboswitch, No Ligand, unmodified

city: Chapel Hill

first: David

last: Qiu

state: NC

address: 104 Airport Dr

department: Chemistry

institute: UNC Chapel Hill

description: Library name: TPP_FullRiboswitch_NoLigand_Control

data_processing:
ShapeMapper 2.1.5
DanceMapper
Supplementary files format and content: Files with format _profile.txt are from ShapeMapper v2.1.5. Each row in these tables describes per-nucleotide mutation rates and normalized reactivity profiles
Supplementary files format and content: Files with format_DanceMap.txt are reactivity files from DanceMapper. Each row in these tables describes the modelled per-nucleotide reactivity for each population in an ensemble.

organism: Escherichia coli

source_name: bacteria

extract_protocol:
RNA was generated by in vitro transcription with T7 polymerase
MaP-RT was performed using targeted primers. Two rounds of PCR were performed to add Illumina adapter sequences and barcodes.

value: bacteria

value: Full Native Riboswitch

value: No chemical probe (Control), No Ligand


title: SCA3, F, Ventral

description: Library name: 12659-JE-6

source_name: spinal cord

value: ventral

value: F


title: KI, M, 56 wk, rep2

description: Library name: 11514-JE-11

value: spinal cord


title: SCA3, M, Ventral

description: Library name: 12659-JE-4

value: M

value: 28 hr


title: H3K9me3_raf1R576H_upf1∆_ago1∆_FE_Exp4_Rep1

source_name: mat1Msmt0 leu1-32 ade6-210 ura4-DS/E mat2P(Bg-Bs)::ura4+ raf1R576H::KanMX6 upf1∆::KanMX6 ago1∆::HphMX6

value: Growth in YEA medium at 30°C


title: TPP, Full Riboswitch, No Ligand, TMO modified

description: Library name: TPP_FullRiboswitch_NoLigand_TMO

value: TMO, No Ligand


title: TPP, Full Riboswitch, No Ligand, DMS modified

description: Library name: TPP_FullRiboswitch_NoLigand_DMS

value: DMS, No Ligand


title: H3K9me3_raf1R576H_upf1∆_FE_Exp4_Rep2

source_name: mat1Msmt0 leu1-32 ade6-210 ura4-DS/E mat2P(Bg-Bs)::ura4+ raf1R576H::KanMX6 upf1∆::KanMX6


title: SCA3, M, Dorsal

description: Library name: 12659-JE-3

value: dorsal


title: KI, F, 56 wk, rep2

description: Library name: 11514-JE-10

value: Female

value: KI

value: 56 wk


title: SCA3, F, Dorsal, Ventral, rep 2

description: Library name: 12659-JE-2

value: punch


title: H3K9me3_GFP-OE_FE_Exp6_Rep1

source_name: mat1Msmt0 leu1-32 ade6-210 ura4-D18 mat2P(Bg-Bs)::ura4+ lys1::Padh1-GFP-HphMX6

value: Abcam anti-H3K9me3 (cat# ab8898)

value: 3% PFA


title: WT, M, 56 wk, rep3

description: Library name: 11514-JE-9

value: Male

value: WT


title: H3K9me3_raf1R576H_FE_Exp4_Rep3

source_name: mat1Msmt0 leu1-32 ade6-210 ura4-DS/E mat2P(Bg-Bs)::ura4+ raf1R576H::KanMX6


title: TPP, Full Riboswitch, 50 uM TPP, TMO modified

description: Library name: TPP_FullRiboswitch_TMO

value: bacteria

value: Full Native Riboswitch

value: TMO, 50 uM TPP


title: LuCaP35ENZR PDX tumor, Vehicle treated, Day 10, rep3

description: Library name: 10-LuCaP35ENZR-Vehicle-3

source_name: LuCaP35 PDX tumor

value: LuCaP35 PDX tumor

value: enzalutamide resistant PDX

value: Vehicle,daily, p.o.


title: SCA3, F, Dorsal, Ventral, rep 1

description: Library name: 12659-JE-1

value: spinal cord

value: F


title: WT, M, 56 wk, rep2

description: Library name: 11514-JE-8


title: H3K9me3_WT_FE_Exp4_Rep3

source_name: mat1Msmt0 ade6-210 ura4-D18 mat2P(Bg-Bs)::ura4+

value: Growth in YEA medium at 30°C


title: TPP, 1 Nucleotide Deletion, unmodified

description: Library name: TPP_1NtDel_Control

value: 1 Nucleotide Deletion

value: No chemical probe (Control), 50 uM TPP


title: KI, M, 56 wk, rep1

description: Library name: 11514-JE-7

value: KI

value: 56 wk


title: reflected amnion tissue (AM174) biol rep 4

city: Wien

first: Andreas

middle: B

last: Diendorfer

address: Leberstraße 20

country: Austria

institute: TAmiRNA GmbH

description: Library name: AM174_RA_tissue

data_processing:
Next-generation sequencing (NGS) data was analyzed using the miND® analysis pipeline (Diendorfer et al., 2022) and evaluated with fastQC v0.11.9 (Andrews, 2010) and multiQC v1.14 (Ewels et al., 2016). Reads were adapter trimmed and quality filtered using cutadapt v3.3 (Martin, 2011). Mapping steps were performed with Bowtie v1.3.0 (Langmead et al., 2009) and miRDeep2 v2.0.1.2 (Friedländer et al. 2012). Reads were initially mapped against the genomic reference GRCh38.p12 by Ensembl (Zerbino et al., 2018) allowing two mismatches and subsequently against miRBase v22.1 (Griffiths-Jones 2004), filtered for microRNAs of hsa, allowing one mismatch. For a general RNA composition, non-microRNA mapped reads were mapped against RNAcentral v19.0 (Sweeney et al., 2019) and assigned to RNA species of interest.
Assembly: GRCh38.p12
Supplementary files format and content: CSV with raw miRNA reads for all samples

source_name: amniotic membrane

growth_protocol: Biopsy punches of reflected and placental amnion were incubated ex vivo for 72 hours in Dulbecco Modified Eagle’s medium (high glucose, 1 % v/v L-glutamine, 1 % v/v penicillin/streptomycin) at 37 °C, 5 % CO2, humidified atmosphere. Supernatant were subjected to size exclusion chromatography to separate extracellular vesicle and protein fractions.

extract_protocol:
Total RNA was extracted from 200 µL EV or protein fraction, or tissue, using the miRNeasy Mini Kit. RNA was eluted in 30 µL nuclease-free water and stored at -80 °C until further analysis.
For both the EV and protein fraction, 8.5 µL total RNA were used as input for the generation of small RNA sequencing libraries, while for the tissue, 100 ng total RNA were used. Libraries were generated with the RealSeq Biofluids library preparation kit (RealSeq Biosciences). To each sample, 1 µL miND spike-in standards were added during the first step. Adapter-ligated libraries were amplified (20 cycles for EV & protein fractions; 19 cycles for tissue) using barcoded Illumina reverse primers in combination with the Illumina forward primer. Sequencing was performed on an Illumina NovaSeq SP SR100 (Illumina, USA).

value: amniotic membrane

tag: region

value: reflected amnion

tag: sample type/fraction

value: tissue

tag: donor


title: KI, F, 56 wk, rep1

description: Library name: 11514-JE-6

value: Female


title: Swi6_raf1R576H_ebs1∆_FE_Exp3_Rep1

source_name: mat1Msmt0 leu1-32 ade6-216 ura4-DS/E mat2P(Bg-Bs)::ura4+ raf1R576H::KanMX6 ebs1∆::KanMX6

value: anti-Swi6 (affinity purified)

value: Growth in YEA medium at 30°C + 2hr at 18°C before fixation

value: 3% PFA + 10mM DMA


title: TPP, 3 Nucleotide Deletion, unmodified

description: Library name: TPP_3NtDel_Control

value: bacteria

value: 3 Nucleotide Deletion

value: TMO, 50 uM TPP


title: TPP, 1 Nucleotide Deletion, TMO modified

description: Library name: TPP_1NtDel_TMO

value: DMS, 50 uM TPP


title: H3K9me3_WT_FE_Exp5_Rep4

source_name: mat1Msmt0 leu1-32 ade6-210 ura4-D18 mat2P(Bg-Bs)::ura4+

value: Abcam anti-H3K9me3 (cat# ab8898)

value: Growth in PMG medium at 30°C

value: 3% PFA


title: placental amnion tissue (AM173) biol rep 3

description: Library name: AM173_PA_tissue

value: placental amnion


title: placental amnion tissue (AM174) biol rep 4

description: Library name: AM174_PA_tissue


title: WT, F, 56 wk, rep1

description: Library name: 11514-JE-5

value: spinal cord

value: WT


title: WT, M, 56 wk, rep1

description: Library name: 11514-JE-4

value: Male

value: 56 wk


title: TPP, 3 Nucleotide Deletion, TMO modified

description: Library name: TPP_3NtDel_TMO

value: No chemical probe (Control), 50 uM TPP


title: reflected amnion tissue (AM173) biol rep 3

description: Library name: AM173_RA_tissue

value: amniotic membrane

value: reflected amnion

value: tissue


title: Swi6_raf1R576H_FE_Exp3_Rep1

value: anti-Swi6 (affinity purified)

value: Growth in YEA medium at 30°C + 2hr at 18°C before fixation

value: 3% PFA + 10mM DMA


title: Swi6_raf1R576H_upf1∆_FE_Exp3_Rep1


title: reflected amnion tissue (AM172) biol rep 2

description: Library name: AM172_RA_tissue


title: TPP, Full Riboswitch, 50 uM TPP, DMS modified

description: Library name: TPP_FullRiboswitch_DMS

value: bacteria

value: Full Native Riboswitch


title: H3K9me3_raf1R576H_ebs1∆_FE_Exp2_Rep1

value: Abcam anti-H3K9me3 (cat# ab8898)

value: Growth in YEA medium at 30°C


title: KI, F, 24 wk, rep3

description: Library name: 11910-JE-12

value: Female

value: KI

value: 24 wk


title: TPP, U Substitution, unmodified

description: Library name: TPP_USub_Control

value: U Substitution

value: DMS, 50 uM TPP


title: Swi6_WT_FE_Exp3_Rep1


title: TPP, U Substitution, TMO modified

description: Library name: TPP_USub_TMO

value: TMO, 50 uM TPP


title: placental amnion tissue (AM172) biol rep 2

description: Library name: AM172_PA_tissue

value: placental amnion


title: KI, F, 24 wk, rep2

description: Library name: 11910-JE-11

value: spinal cord


title: H3K9me3_raf1R576H_upf1∆_FE_Exp2_Rep1

value: 3% PFA


title: reflected amnion tissue (AM171) biol rep 1

description: Library name: AM171_RA_tissue

value: amniotic membrane

value: reflected amnion

value: tissue


title: TPP, native, unmodified

description: Library name: TPP_Native_Control

value: Native

value: No chemical probe (Control), 50 uM TPP


title: KI, F, 24 wk, rep1

description: Library name: 11910-JE-10


title: TPP, native, DMS modified

description: Library name: TPP_Native_DMS

value: bacteria


title: placental amnion tissue (AM171) biol rep 1

description: Library name: AM171_PA_tissue


title: H3K9me3_raf1R576H_FE_Exp2_Rep2

value: Abcam anti-H3K9me3 (cat# ab8898)


title: WT, M, 24 wk, rep3

description: Library name: 11910-JE-9

value: Male

value: WT


title: WT, M, 24 wk, rep2

description: Library name: 11910-JE-8


title: H3K9me3_WT_FE_Exp2_Rep2

value: Growth in YEA medium at 30°C


title: H3K9me3_raf1R576H_FE_Exp1_Rep1

source_name: mat1Msmt0 leu1-32 ade6-216 ura4-DS/E mat2P(Bg-Bs)::ura4+ raf1R576H::KanMX6


title: reflected amnion protein fraction (AM174) biol rep 4

description: Library name: S8 Protein (AM174_RA_SUP)

value: protein fraction


title: Myc_Cap_MOCK_rep3

city: Rochester

first: LIGUO

last: WANG

state: MN

address: 200 1st St SW

department: Division of Computational Biology

institute: Mayo Clinic

data_processing:
Image data were processed using the Illumina Standard Pipeline.
Base-calling and data filtering processed by the Mayo Clinic Genome Analysis Core (GAC) using the pipeline Cassava 1.7.
Raw sequences were mapped to the mouse reference genome (GRCm38) using STAR (2.5.2b) with the following parameters:  --limitBAMsortRAM 31532137230 --outSAMtype BAM   Unsorted      --outSAMstrandField intronMotif   --outSAMunmapped Within      --outSAMheaderCommentFile /tmp/7795325.1.ngs-pri/tmp.jiuaN3DG28   --alignIntronMax 200000   --alignMatesGapMax 200000   --alignSJDBoverhangMin 10   --chimSegmentMin 12   --chimJunctionOverhangMin 12 --twopass1readsN 18446744073709551615   --twopassMode Basic.
RseQC ("FPKM_count.py" command) was used to calculate raw fragment count, FPM (fragments per million) and FPKM (fragments per kilobase of exon per million).
DESeq2 was used to identify differentially expressed genes (adjusted pvalue < 0.05).
Assembly: GRCm38/mm10.
Supplementary files format and content: The processed file contains the following columns: chrom, gene_start, gene_end, gene_symbol, gene_size, gene_strand, Frag_count, FPM, and FPKM.

source_name: MyC-CaP

extract_protocol:
Myc-CaP cells treated with irradiation (6 Gy), enzalutamide (10 μM, 48 h) or combination.Then we used RNA seq data from different treatments for gene expression analysis
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols. The SMART-seq Stranded Kit for total RNA generates strand-specific RNA-seq libraries using Takara Bio’s SMART technology which uses reverse transcription with random priming rather than oligo(dT) priming, thus capturing the full transcriptome instead of poly-A fractions

tag: cell line

value: MyC-CaP

value: MOCK


title: WT, M, 24 wk, rep1

description: Library name: 11910-JE-7

value: 24 wk


title: placental amnion protein fraction (AM174) biol rep 4

description: Library name: S7 Protein (AM174_PA_SUP)

value: placental amnion


title: reflected amnion EV fraction (AM174) biol rep 4

description: Library name: S8 EV (AM174_RA_SUP)

value: EV fraction


title: Myc_Cap_MOCK_rep1

tag: treatment


title: H3K9me3_raf1R518H_FE_Exp1_Rep1

source_name: mat1Msmt0 leu1-32 ade6-210 ura4-DS/E mat2P(Bg-Bs)::ura4+ raf1R518H::KanMX6

value: 3% PFA


title: Myc_Cap_MOCK_rep2


title: H3K9me3_WT_FE_Exp1_Rep1


title: WT, F, 24 wk, rep3

description: Library name: 11910-JE-6

tag: tissue

value: spinal cord

value: Female


title: placental amnion EV fraction (AM174) biol rep 4

description: Library name: S7 EV (AM174_PA_SUP)

value: amniotic membrane


title: WT, F, 24 wk, rep2

description: Library name: 11910-JE-5


title: WT, F, 24 wk, rep1

description: Library name: 11910-JE-4


title: Myc_Cap_IR_rep3

value: IR


title: RNA-seq of larval brain and appendages (ctrl, 90AEL, rep3)

city: Gwangju

first: Il-Ju

last: Kim

address: 123, Cheomdangwagi-ro, Buk-gu, Gwangju, Republic of Korea

country: South Korea

institute: GIST

description: Library name: Ctrl90_3_Lib

data_processing:
Adapter trimming and quality filtering were performed according to the QuantSeq 3’ mRNA pipeline.
Transcript abundances were quantified using kallisto (v0.50.0) with default single-end parameters.
Assembly: Drosophila melanogaster transcriptome r6.54 from FlyBase.
Supplementary files format and content: Processed data files include gene-level transcript abundance in tab-delimited TSV format, reporting estimated counts and TPM values for each gene.

organism: Drosophila melanogaster

source_name: brain and appendages

growth_protocol: Flies were maintained at 25°C and 60% humidity under a 12h:12h light:dark cycle on standard fly medium.

extract_protocol:
Total RNA was extracted from dissected larval tissues (brains, imaginal discs, salivary glands, fat bodies) using Trizol (Takara) according to the manufacturer’s instructions.
Libraries were generated using the QuantSeq 3’ mRNA-Seq Library Prep Kit and sequenced on an Illumina NextSeq 500 platform by EBIOGEN.

treatment_protocol: After hatching, larvae were reared at 25°C until 60 AEL, then shifted to 30°C. Dissections were performed at either 90 or 108 AEL.

value: brain and appendages


title: Myc_Cap_IR_rep2


title: RNA-seq of larval brain and appendages (ctrl, 90AEL, rep2)

description: Library name: Ctrl90_2_Lib


title: placental amnion protein fraction (AM173) biol rep 3

description: Library name: S5 Protein (AM173_PA_SUP)


title: placental amnion EV fraction (AM173) biol rep 3

description: Library name: S5 EV (AM173_PA_SUP)


title: RNA-seq of larval brain and appendages (ctrl, 90AEL, rep1)

description: Library name: Ctrl90_1_Lib


title: KI, M, 24 wk, rep3

description: Library name: 11910-JE-3

value: KI


title: reflected amnion protein fraction (AM172) biol rep 2

description: Library name: S4 Protein (AM172_RA_SUP)

value: reflected amnion


title: TPP, native, TMO modified

description: Library name: TPP_Native_TMO

value: bacteria

value: Native

value: TMO, 50 uM TPP


title: RNA-seq of larval brain and appendages (Nplp1, 90AEL, rep3)

description: Library name: Nplp90_3_Lib


title: reflected amnion EV fraction (AM172) biol rep 2

description: Library name: S4 EV (AM172_RA_SUP)


title: placental amnion protein fraction (AM172) biol rep 2

description: Library name: S3 Protein (AM172_PA_SUP)

value: protein fraction


title: RNA-seq of larval brain and appendages (Nplp1, 90AEL, rep2)

description: Library name: Nplp90_2_Lib


title: Myc_Cap_ENZ_rep2

value: MyC-CaP

value: ENZ


title: Myc_Cap_ENZ_rep1


title: placental amnion EV fraction (AM172) biol rep 2

description: Library name: S3 EV (AM172_PA_SUP)


title: M#1-iPSC

city: New York

first: Prokopios Alexandros

last: Polyzos

address: 413 E 69th St

institute: Weill Cornell Medicine

description: Library name: LS_R6

data_processing:
Alignment with STAR aligner (version 2.7.10a)
fliter and assign reads to genes mm10 – (GRCm38.95) with featureCounts (v2.0.6)
Differential analysis was performed with DESeq2 in R4.2.2
Assembly: mm10 and mm10.GRCm38.95.gtf
Supplementary files format and content: tab-delimited text file with raw counts for all genes

source_name: iPSC

growth_protocol: Cells were maintained in Embryonic Stem cell media (KO-DMEM) with FBS + LIF in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA-seq libraries were prepared and sequenced by Novogene Bioinformatics Technology Co. Ltd.
Sequencing libraries were prepared using the NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® (New England Biolabs) following the manufacturer’s instructions. High-throughput sequencing was performed on an Illumina NovaSeq 6000 platform.

value: iPSC

value: induced pluripotent cell


title: RNA-seq of larval brain and appendages (ctrl, 108AEL, rep2)

description: Library name: Ctrl108_2_Lib


title: RNA-seq of larval brain and appendages (Nplp1, 90AEL, rep1)

description: Library name: Nplp90_1_Lib


title: Myc_Cap_ENZ_IR_rep3


title: Myc_Cap_ENZ_IR_rep2


title: M#2-iPSC

description: Library name: LS_R7


title: GC#3-iPSC

description: Library name: LS_R4


title: RNA-seq of larval brain and appendages (ctrl, 108AEL, rep1)

description: Library name: Ctrl108_1_Lib


title: reflected amnion protein fraction (AM171) biol rep 1

description: Library name: S2 Protein (AM171_RA_SUP)


title: Myc_Cap_IR_rep1


title: Myc_Cap_ENZ_IR_rep1


title: Myc_Cap_ENZ_rep3


title: KI, M, 24 wk, rep2

description: Library name: 11910-JE-2

value: Male

value: 24 wk


title: reflected amnion EV fraction (AM173) biol rep 3

description: Library name: S6 EV (AM173_RA_SUP)

value: EV fraction


title: GC#2-iPSC

description: Library name: LS_R3


title: GC#1-iPSC

description: Library name: LS_R2


title: RNA-seq of larval brain and appendages (Nplp1, 108AEL, rep3)

description: Library name: Nplp108_3_Lib


title: M#3-iPSC

description: Library name: LS_R8


title: CD4_repeat_3

city: Zurich

first: Francesc

last: Castro-Giner

address: Otto-Stern-Weg 7

country: Switzerland

institute: ETH Zurich

description: CD4_repeat_3 dCas9 (i.e. no knockout) - SgRNAs as barcodes for studying loss of clonality - whole lungs using 4T1 into BALB (Imm.competent) mouse, with vector lentiGuide-Puro plus stable dCas9 transduction, IgG treatment, Replicate 4

data_processing:
Mapping using bowtie2 (v2.3.5.1; parameters: -L 11 -N 1 -I S,1,0.75 --norc), allowing for one mismatch.
Normalized abundance of individual sgRNAs were obtained using MAGeCK (v0.5.9.4).
Assembly: lentiviral libraries encompassing 2215 sgRNAs against mouse immune interactome genes  or 2180 sgRNAs against the homologue human genes
Supplementary files format and content: counts.txt.gz are tab-delimited files containing raw counts for each library
Library strategy: CRISPR-seq

source_name: No Cas9 (i.e. no knockout) - SgRNAs as barcodes for studying loss of clonality

extract_protocol:
All tissue samples were processed through a common DNA extraction protocol, as described (Scheidmann et al., 2022). Briefly, tumor and metastasis-carrying organs were lysed in a FastPrep tissue homogenizer (MP) using dedicated matrix beads-containing disposable tubes (MP) in presence of a DNA extraction buffer (50 mM Tris-Cl pH 8.0, 50 mM EDTA, 1% SDS). The lysate was then digested for at least 16 hours at 65 °C in presence of Proteinase K (Qiagen) and then for 30 minutes at 37 °C in presence of RNAase A (Qiagen). Separation of genomic DNA was carried out by first adding pre-chilled 7.5 M ammonium acetate, followed by isopropanol addition to the resulting supernatant, leading the DNA to precipitate. The pellet was then washed with 70% ethanol and the genomic DNA was resuspended in Tris-EDTA buffer (Ambion) and frozen at -20 °C. Finally, DNA extraction from cultivated cells was carried out using the Dneasy kit (Qiagen). For CRISPR genomics applications, DNA samples were quantified using NanoDrop ND-1000 UV-Vis Spectrophotometer (Thermo Fisher).
Samples were processed to reach a theoretical coverage of 500–1,000× per target. For mouse samples, 10-15 µg of genomic DNA were amplified in a one-step PCR with barcoded primers targeting the pLentiGuide vector backbone (P5 and P7). The primer sequences in the table below highlight an 8 bp barcode position in blue and vector binding site in bold, mapping between the sgRNA scaffold and the U6 promoter. All pPrimers were ordered as desalted Oligos oligos at IDT (Integrated DNA Technologies)(at Integrated DNA Technologies or at Microsynth) Microsynth and resuspended in nuclease-free water. For human samples, 10 µg of gDNA were pre-amplified in a nested PCR with the external primers targeting the huTHY1insert and the upstream portion of the U6 promoter (primer sequences in table below). In the second PCR step, barcoded primers targeting the pLentiguide vector backbone (P5 and P7) were used as internal primers (primer sequences in table above). For mouse samples, PCR conditions were as follows: 100 µl as reaction volume, KAPA HiFi Hot Start Ready Mix (2X; Roche)0.02 U/µl of Q5 polymerase (New England Biosciences), and 25-31 cycles of amplification. For human samples, only 23-27 cycles of amplification were applied in the first step using KAPA HiFi Hot Start Ready Mix (2X; Roche). Since some samples did not yield any clearly detectable product after the first PCR, all products were purified with AMPure XP Beads (Beckman Coulter) or Sera-Mag Select Beads (2X, Cytiva Europa GmbH) and used as input for a second PCR (23-27 cycles) with the same primers that were used for the first PCR. When loading a second PCR, pre-amplified fragments were re-quantified using NanoDrop. To reach the theoretical coverage after sequencing, 200 ng of pre-amplified product were re-amplified using nested barcoded primers (P5 and P7). PCR conditions for the second PCR were as follows: 200 ng of pre-amplified fragments per 25 µl reaction, 0.02 U/µl of Q5 polymerase (New England Biosciences), and 27 cycles of amplification. The amplified product containing the spacer sequence with a size of 202 bp was purified by SPRI bead cleanup and a right-sided size selection to remove the genomic DNA input. Using a dual barcoding system, the final NGS amplicons were multiplexed and sequenced on an Illumina platform with 21 dark cycles (DC) in Read 1 to skip the invariable region of the primer binding side (U6 promoter).

value: tumor

value: xenograft

value: BALBc

tag: crispr lib

value: Immuno Signalome (2215) sgRNA library

tag: sgrna library

tag: effect type

value: sgRNAs used as barcodes (no KO)

tag: vector

value: lentiGuide-Thy1 + EF1alpha_dCas9

tag: full library_complexity


title: KI, M, 24 wk, rep1

description: Library name: 11910-JE-1

value: spinal cord

tag: Sex

value: KI

tag: time


title: RNA-seq of larval brain and appendages (Nplp1, 108AEL, rep2)

description: Library name: Nplp108_2_Lib

value: brain and appendages

tag: genotype


title: RNA-seq of larval brain and appendages (ctrl, 108AEL, rep3)

description: Library name: Ctrl108_3_Lib


title: V6.5

description: Library name: LS_R1

source_name: mESC

value: mESC

value: Embryonic Stem Cell


title: placental amnion protein fraction (AM171) biol rep 1

description: Library name: S1 Protein (AM171_PA_SUP)

value: amniotic membrane

value: placental amnion

value: protein fraction


title: RNA-seq of larval brain and appendages (Nplp1, 108AEL, rep1)

description: Library name: Nplp108_1_Lib


title: placental amnion EV fraction (AM171) biol rep 1

description: Library name: S1 EV (AM171_PA_SUP)


title: reflected amnion EV fraction (AM171) biol rep 1

description: Library name: S2 EV (AM171_RA_SUP)

value: reflected amnion


title: CD4_repeat_1

description: CD4_repeat_1 dCas9 (i.e. no knockout) - SgRNAs as barcodes for studying loss of clonality - whole lungs using 4T1 into BALB (Imm.competent) mouse, with vector lentiGuide-Puro plus stable dCas9 transduction, CD4/CD8 treatment, Replicate 4


title: 35S::DXO1 (N194)/dxo1 MS replicate 2

status: Public on Oct 28 2025

city: Philadelphia

first: Diep

middle: R

last: Ganguly

state: PA

address: 433 S University Ave

department: Department of Biology

institute: University of Pennsylvania

description: Library name: 17539X10_191112_D00550_0579_BCE2E8ANXX_S10_L008_R1_001

data_processing:
*library strategy: genome-wide mapping of uncapped and cleaved transcripts (GMUCT)
Raw read quality was diagnosed using FastQC.
Trim Galore (Babraham Bioinformatics) and Cutadapt was used for adapter and low-quality read trimming with PHRED score < 20 (-q 20).
Reads were aligned to the TAIR10 genome assembly using STAR (Dobin et al 2014).
FeatureCounts (Liao et al 2014) was used for determine transcript abundance on gene-level features extracted from the TAIR10 annotation retrived from EnsemblPlants (Kersey et al 2016).
Bedtools (genomecov -bga -split -scale -5) was used to generate a bedGraph file from the BAM files. The flag -5 was included to only consider read depth at the first nucleotide of the read for GMUCT libraries. A per-million scaling factor was provided to the -scale flag, determined by 1,000,000/total reads (total reads = samtools view -F 260 -c).
bedGraphToBigWig (kentUtils) was used to generate bigWig files (using the .bed files) for visualizing read depth across TAIR10 features.
Assembly: TAIR10
Supplementary files format and content: .bed: bedgraph file of scaled counts (RPM) across TAIR10 genome coordinates for each sample.
Supplementary files format and content: .bigWig: files for visualizing read coverage (scaled to reads per million, RPM) in a genome browser (e.g. IGV) for each sample.

organism: Arabidopsis thaliana

source_name: Seedlings

growth_protocol: Arabidopsis seedlings were was grown on half-strength Murashige and Skoog medium (Phytotech Labs, Lenexa, KS, USA)  at 22 °C under a 16-h-light (100-150 µmol m-2 s-1)/8-h-dark photoperiod.

extract_protocol:
Tissue of 12-day-old seedlings was snap frozen in liquid N2 and homogenized with an autoclaved and chilled mortar and pestle. Cells were lysed using Qiazol lysis reagent (Qiagen, Valencia, CA, USA) and the lysate was homogenized using Qiashredders (Qiagen, Valencia, CA, USA). Total RNA was then isolated using Qiagen miRNEasy mini columns (Qiagen, Valencia, CA, USA) as per the manufacturer’s instructions. All RNA was then treated with RNase-free DNase (#79254, Qiagen, Valencia, CA, USA) at room temperature for 30 minutes followed by purification via ethanol precipitation.
GMUCT libraries were constructed using an estabilished protocol (Willmann et al., 2014).

value: Seedlings

tag: ecotype

value: MS


title: 35S::DXO1 (N194)/dxo1 MS replicate 1

description: Library name: 17539X9_191112_D00550_0579_BCE2E8ANXX_S9_L008_R1_001


title: 35S::DXO1 (E394A+D396A)/dxo1 MS replicate 2

description: Library name: 17539X6_191112_D00550_0579_BCE2E8ANXX_S6_L008_R1_001


title: reflected amnion protein fraction (AM173) biol rep 3

description: Library name: S6 Protein (AM173_RA_SUP)


title: 35S::DXO1 (E394A+D396A)/dxo1 MS replicate 1

description: Library name: 17539X5_191112_D00550_0579_BCE2E8ANXX_S5_L008_R1_001


title: normal breast organoid, sgMETTL3-4 (scRNA-seq)

first: Xintao

state: MA

address: 440 brookline ave

institute: Dana Faber Cancer Institute

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using Cell Ranger software v3.1.0
Assembly: hg19
Supplementary files format and content: Tab-separated values files and matrix files

source_name: breast

growth_protocol: Organoids were digested with TrypLE Express and resuspended in 10 mg/ml Cultrex growth factor-reduced BME type 2 (Trevigen, Cat. No. 3533-010-02). A 50 μl drop of the cell suspension was added to the center of a well of a 24-well suspension culture plate (Greiner, Cat. No. M9312) and incubated at 37 °C for 20 min. 500 μL of organoid culture medium was then added over the drop. The medium was changed every 3-4 days.

extract_protocol:
Normal breast organoids were digested to single cell suspension by TrypLE Express and processed according to the 10xGenomics scRNA-seq sample preparation protocol (Chromium Single Cell 3′ v2 Reagent Kit, 10xGenomics).
The 10xGenomics reaction mix and single cell suspension were loaded into a Single Cell A ChIP and processed by the Chromium™ Controller to generate Gel Bead-In-EMulsions (GEMs), followed by removal of leftover biochemical reagents. Barcoded cDNA is then amplified by PCR followed with illumina sequencing library preparing procedures.

treatment_protocol: Vector expressing CAS9 and sgRNAs targeting either AACS1 or METTL3 was lentivirally transduced into normal breast organoids.

value: breast

value: normal breast organoid

tag: cell type

value: mammary epithelial cells

value: METTL3 KO


title: normal breast organoid, sgMETTL3-2 (scRNA-seq)


title: 35S::DXO1 (WT)/dxo1 MS replicate 2

description: Library name: 17539X2_191112_D00550_0579_BCE2E8ANXX_S2_L008_R1_001

value: 35S::DXO1 (WT)/dxo1


title: MCF10A cells, sgMETTL3-4, rep3 (RNA-seq)

data_processing:
RNA-seq data were processed using VIPER pipeline (Cornwell et al., 2018).  Fastq files were aligned to the human reference GRCh37/hg19 genome using the STAR RNA-Seq aligner (version STAR_2.5.1b) (Dobin et al., 2013).
Genes with 0 counts across all samples were filtered out.
Assembly: hg19
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

growth_protocol: we performed RNA-seq in control or METTL3 depleted MCF10A cells to evaluate whether changes in chromatin state are associated with the transcription of mammary epithelial luminal genes.

extract_protocol:
RNA was extracted and purified with the Direct-zol RNA Kit (zymo research).
Library prep begins with Sample Quality Control (Sample QC), ensuring that the provided samples meet the stringent criteria of the RNA-Seq technique. Following this, tailored libraries are meticulously crafted based on the target organism and application, with the library’s quality assessed through Library QC. Subsequently, a 150 bp paired-end sequencing strategy, employing Illumina PE150 technology, captures the essence of the samples.


title: normal breast organoid, sgAAVS1 (scRNA-seq)

value: AAVS1 KO


title: MCF10A cells, sgMETTL3-2, rep2 (RNA-seq)


title: MCF10A cells, sgMETTL3-2, rep3 (RNA-seq)


title: MCF10A cells, sgMETTL3-4, rep1 (RNA-seq)


title: MCF10A cells, sgMETTL3-2, rep1 (RNA-seq)


title: CD4_repeat_2

description: CD4_repeat_2 dCas9 (i.e. no knockout) - SgRNAs as barcodes for studying loss of clonality - whole lungs using 4T1 into BALB (Imm.competent) mouse, with vector lentiGuide-Puro plus stable dCas9 transduction, CD4/CD8 treatment, Replicate 5

value: tumor

value: xenograft

value: BALBc

value: Immuno Signalome (2215) sgRNA library

value: sgRNAs used as barcodes (no KO)

value: lentiGuide-Thy1 + EF1alpha_dCas9


title: MCF10A cells, sg control, rep3 (RNA-seq)


title: BUC5254A12

first: Probir

last: Chakravarty

institute: Francis Crick Institute

description: Library name: BUC5254A12

data_processing:
The RSEM package (version 1.3.0) (Li and Dewey, 2011) was used in conjunction with the STAR alignment algorithm (version 2.5.2a) (Dobin et al., 2013) for the mapping and subsequent gene-level counting of the sequenced reads with respect to Ensembl mouse GRCm38 release 89  transcriptome
Normalisation of raw count data and differential expression analysis was performed with the DESeq2 package (version 1.16.1)  within the R programming environment (version 3.3.1)
Assembly: GRCm38 release 89
Supplementary files format and content: VST log2 normalised expression values. Rows = genes; Columns = samples.
Supplementary files format and content: raw_counts. Rows = genes; Columns = samples.

source_name: Dendritic Cells

growth_protocol: RPMI 1640 media with 10% FCS, PSG, NaPyruvate, NEAA, HEPES, 2-Me

extract_protocol:
Qiagen Rneasy Kit
NEBNext Ultra II Directional PolyA mRNA Kit

treatment_protocol: DNGR-1 ligand (F-actin plus myosin II)

value: Dendritic Cells

value: Stimulated


title: MCF10A cells, sgMETTL3-4, rep2 (RNA-seq)


title: MCF10A cells, sg control, rep1 (RNA-seq)


title: BUC5254A10

description: Library name: BUC5254A10


title: BUC5254A11

description: Library name: BUC5254A11


title: BUC5254A9

description: Library name: BUC5254A9

value: Unstimulated


title: MCF10A cells, sg control, rep2 (RNA-seq)


title: BUC5254A4

description: Library name: BUC5254A4

value: WT


title: BUC5254A2

description: Library name: BUC5254A2


title: BUC5254A6

description: Library name: BUC5254A6


title: BUC5254A3

description: Library name: BUC5254A3


title: BUC5254A5

description: Library name: BUC5254A5


title: 35S::DXO1 (WT)/dxo1 MS replicate 1

description: Library name: 17539X1_191112_D00550_0579_BCE2E8ANXX_S1_L008_R1_001

value: Seedlings

value: MS


title: NC Group,input,3

city: Jinan

first: Ke

last: Zou

address: No. 105, Jiefang Road, Jinan, Shandong 250013, China

country: China

institute: Shandong university

data_processing:
Libraries were qualified using BioAnalyzer 2100 system (Agilent Technologies, Inc., United States) bioanalyzer and then sequenced in a NovaSeq platform (Illumina) with 150 bp paired-end reads.
Paired-end reads were harvested from Illumina NovaSeq 6000 sequencer, and were quality controlled by Q30.
After 3’ adaptor-trimming and low quality reads removing by cutadapt software (v1.9.3).
Clean reads of all libraries were aligned to the reference genome (RN5)  by Hisat2 software (v2.0.4).
Methylated sites on RNAs (peaks) were identified by MACS software.
Differentially methylated sites were identified by diffReps.
These peaks identified by both softwares overlapping with exons of mRNA were figured out and chosen by home-made scripts.
Assembly: RN5
Supplementary files format and content: xlsx for each sample

organism: Rattus norvegicus

source_name: esophageal tissue

extract_protocol:
Total RNA was subjected to immunoprecipitation with the GenSeq® m6A-IP Kit (GenSeq Inc.) followed the manufacturer’s instructions.
RNA libraries for IP and input samples were then constructed with GenSeq® Low Input Whole RNA Library Prep Kit (GenSeq, Inc.) by following the manufacturer’s instructions.

value: esophageal tissue

tag: antibody

value: no treatment


title: NC Group,IP,3


title: NC Group,input,1


title: NC Group,input,2


title: BE Group,input,3

value: esophagoduodenostomy(EDA) surgery


title: BE Group,IP,3


title: BE Group,IP,2


title: BE Group,input,2


title: BE Group,IP,1