title: NKL9_delta-hda1_H3K27me2/3_ChIPseq

description: Library name: NKL9_delta-hda1_H3K27me2/3_ChIPseq

data_processing:
Raw ChIP-seq data files, as fastq files, were mapped to version 14 of the Neurospora crassa genome (nc14) [Rodriguez et al., 2022 [Pubmed ID: ] with bowtie2 (version 2.4.2), and output sam files were converted to sorted bam files using samtools (version 1.14), which were used by Deeptools (version 3.5.0) to produce bigwig files with 25 basepair bin resolution, normalized by Reads per Kilobase Per Million Reads (RPKM), for display on the Integrative Genomics Viewer (IGV)
Assembly: Assembly: nc14_genome-seq-name.fasta (version 14; Rodriguez et al., [Pubmed ID: 35244156])
Supplementary files format and content: the bigwig files are generated by Deeptools; briefly, these files divide the genome into bins and the number (count) of sequencing reads per bin is reported for each bin; the bigwig file format is a single column with the enrichment per bin displayed, and the seven headers indicate the chromosome and bin size.

source_name: mycelia

growth_protocol: Cultures were grown in Vogels medium and 1.5% sucrose (standard minimal medium), shaking for 16 hours at 32oC.

extract_protocol:
Tissue was added to ChIP lysis buffer (50mM Hepes pH 7.5, 90mM NaCl, 1mM EDTA, 1% triton + proteinase inhibitors) and was disrupted by sonication, which simultaneously sheared chromatin, using a Bioruptor Pico (Diagenode) for 15 min with a cycle of 30 sec on followed by 30 sec off, at high power. Lysates were cleared by centrifugation, 1/20th Input was saved, and histone modification antibody was added (typically 1uL) and samples were nutated overnight at 4oC. The next day, equilibrated protein A/G magnetic agarose beads (Pierce/Thermo Scientific; cat # PI78609) was added to bind the antibody, incubated for 2 hours at 4oC, and washed twice in cold ChIP Lysis buffer, once with ChIP Lysis buffer + 0.5M NaCl, once with LiCl was buffer (10mM Tris pH 8.0, 250mM LiCl, 1mM EDTA, 0.5% NP40), and DNA/protein was eluted with TES buffer (50mM Tris pH 8.0, 10mM EDTA, 1% SDS) and incubated at 65oC. Samples (IP and input) were decrosslinked at 65oC overnight. The next day, samples were RNaseA treated for two hours at 50oC, then proteinase K treated for 2 hours at 50oC, the DNA was extracted with phenol:chloroform:IAA (25:24:1), and DNA was precipitated with ethanol, sodium acetate, and glycogen, and allowed to precipitate overnight at -80oC. The next day, samples were precipitated by centrifugation, washed, dried in a Speedvac and resuspended in 30uL TE. ChIP DNA was quantified with a Qubit 3.0 using the HS method.
Approximately 10 ng of DNA was used to generate ChIP-Seq libraries. Each library was prepared using the NEB Next Ultra II Library Preparation Kit (New England Biolabs, #E7645L) with the adapters from the NEBNext® Multiplex Oligos for Illumina®(Index Primers Set 1 [E7335L] or 2 [E7500L]) according to the manufacturer’s instructions, except that final libraries were PCR-amplified using only eight cycles for amplification. Libraries were sequenced on a NovaSeq 6000 at the University of Oregon Genomics and Cell Characterization Core Facility (UO GC3F).

treatment_protocol: Mycelia were washed in PBS prior to crosslinking. Mycelia were cross-linked for 15 min in 0.5% formaldehyde at room temperature, with shaking at 100 rpm, and then quenched with 0.125M glycine for histone modification ChIP.

value: mycelia

value: asexual fungal hyphae

value: overnight growth (16hrs) in 1xVogels+1.5% sucrose

tag: chip-seq antibody

value: Active Motif anti-H3K27me2me3 (cat# 39535)


title: TOV-112D cell line, BLU-222 (350nM), Biol Rep 2

status: Public on Jan 21 2025

type: SRA

city: Cambridge

first: Maxine

last: Chen

state: Massachusetts

address: 45 Sidney St.

country: USA

institute: Blueprint Medicines

library_source: transcriptomic

data_processing:
nf-core/rna-seq (Ewels et al. Nat Bioetechnol. 2020, doi: 10.5281/zenodo.1400710)
Read processing, alignment, and count were peformed using nf-core/rna-seq.
Briefly, adaptor sequence/low-quality reads were trimmed using Trim Galore! (--min-trimmed-reads 10000)
Read alignment was performed using STAR v2.7.11b (--min-mapped-reads 5)
Read count was performed using salmon 1.2
Assembly: hg38
Supplementary files format and content: count matrix csv

molecule: polyA RNA

organism: Homo sapiens

source_name: ovarian

extract_protocol:
Total RNA was extracted using Qiagen Rneasy Plus Mini kit, following manufacturer's instructions
RNA sequencing libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer’s instructions

tag: tissue

value: ovarian

tag: cell line

tag: treatment


title: NKL10_delta-hda1_H3K9me3_ChIPseq

city: Colorado Springs

first: Andrew

middle: David

last: Klocko

state: Colorado

address: 278 Centennial Hall, 1420 Austin Bluffs Pkwy

department: Chemistry and Biochemistry

institute: University of Colorado Colorado Springs

description: Library name: NKL10_delta-hda1_H3K9me3_ChIPseq

library_source: genomic

molecule: genomic DNA

organism: Neurospora crassa

tag: cell type

tag: genotype

value: mat ?; delta hda1::hph

value: Active Motif anti-H3K9me3 (cat# 39161)


title: NKL9_delta-hda1_H3K9me3_ChIPseq

description: Library name: NKL9_delta-hda1_H3K9me3_ChIPseq


title: TOV-112D cell line, BLU-222 (350nM), Biol Rep 1


title: TOV-112D cell line, DMSO, Biol Rep 3

value: DMSO


title: TOV-112D cell line, DMSO, Biol Rep 2


title: dual-V3, 4E+11, replicate4

city: Beijing

first: zhanzhao

last: liu

address: No. 38, Xueyuan Road

country: China

institute: peking university

data_processing:
The sequencing reads were analyzed by CRISPResso2
Experimentalparameter: FASTQ files for analysis(.fastq or .fastq.gz), Reference amplicon sequence, sgRNA used, quantification window size, quantification window center, Experiment name
code: CRISPResso \ --fastq_r1 base_editor.fastq.gz \ -a amplicon sequence \ -g sgRNA sequence \ -w 20 \ -wc -10 \ --base_editor_output \ --write_cleaned_report \ --place_report_in_output_folder
Assembly: mm10
Supplementary files format and content: Nucleotide_percentage_table_2.xlsx
Library strategy: Amplicon-seq

organism: Mus musculus

source_name: Heart

extract_protocol:
Genomic DNA was extracted from tissues using TIANamp Genomic DNA Kit (DP304, Tiangen, China)
The sgRNA-targeted loci were amplified using Taq PCR MasterMix (KT211, Tiangen, China) and purified by TIANgel Purification Kit (DP219, TIANGEN).

value: Heart

value: WT

value: AAV-MYL2-TadA8e-Sp N aa2-713-inteinN-U6-Camk2d sgRNA7 + AAV-MYL2-inteinC-Sp C aa714-1368-U6-Camk2d sgRNA7


title: TOV-112D cell line, DMSO, Biol Rep 1


title: dual-V3, 4E+11, replicate2


title: Shotgun sequencing of WT after O/N culture, rep 1

city: Paris

first: Axel

last: Cournac

address: 28 rue du docteur Roux

country: France

institute: Institut Pasteur

description:
Library name: FG0688
BY4741 without 2 micron transformed with plasmid pKanMX-REP1-STB-p (RSGB1057)

data_processing:
Reads were aligned using Bowtie2 (Langmead and Salzberg, 2012) in its most sensitive mode against the reference genomes.
Assembly: GCF_000146045.2 for S. cerevisiae , J01347.1 for the 2µ plasmid.
Supplementary files format and content: Reads from S. cerevisiae chromosomes and reads from 2µ plasmid were counted using bash commands.

organism: Saccharomyces cerevisiae

extract_protocol:
After the O/N incubation, a 1 mL aliquot from each culture was collected for subsequent shotgun sequencing. DNA was extracted using zymolyase, proteinase K and phenol and processed with Collibri kit.
Preparation of the samples for paired-end sequencing on an Illumina NextSeq500 (2x35 bp) was performed using Invitrogen TM Collibri TM PS DNA Library Prep Kit for Illumina and following manufacturer instructions.

tag: background

tag: strain


title: SK-OV-3 cell line, BLU-222 (770nM), Biol Rep 3


title: SK-OV-3 cell line, BLU-222 (770nM), Biol Rep 2


title: dual-V3, 4E+11, replicate1


title: dual-V3, 2E+11, replicate3


title: SK-OV-3 cell line, DMSO, Biol Rep 1


title: dual-V3, 2E+11, replicate1


title: NKL10_delta-hda1_H3K27me2/3_ChIPseq

description: Library name: NKL10_delta-hda1_H3K27me2/3_ChIPseq


title: SK-OV-3 cell line, DMSO, Biol Rep 2


title: RMUG-S cell line, BLU-222 (1500nM), Biol Rep 2

value: RMUGS


title: dual-V3, 1E+11, replicate3


title: dual-V3, 1E+11, replicate2


title: RMUG-S cell line, BLU-222 (1500nM), Biol Rep 1


title: dual-V3, 1E+11, replicate4


title: dual-V3, 1E+11, replicate1


title: dual-V3, 4E+11, replicate3


title: dual-V3, 5E+10, replicate2


title: RMG-I cell line, BLU-222 (850nM), Biol Rep 3

value: RMGI


title: RMUG-S cell line, DMSO, Biol Rep 2


title: dual-V3, 5E+10, replicate3


title: dual-V3, 5E+10, replicate1


title: RMUG-S cell line, DMSO, Biol Rep 3


title: RMG-I cell line, BLU-222 (850nM), Biol Rep 2


title: SK-OV-3 cell line, BLU-222 (770nM), Biol Rep 1


title: dual-V3, 2E+11, replicate4


title: dual-V3, 2E+11, replicate2


title: SK-OV-3 cell line, DMSO, Biol Rep 3


title: dual-V3, 2.5E+10, replicate4


title: RMG-I cell line, BLU-222 (850nM), Biol Rep 1


title: dual-V3, 2.5E+10, replicate3


title: RMG-I cell line, DMSO, Biol Rep 3


title: RMUG-S cell line, DMSO, Biol Rep 1


title: dual-V3, 2.5E+10, replicate2


title: dual-V3, 2.5E+10, replicate1


title: RMG-I cell line, DMSO, Biol Rep 2


title: dual-V2, 4E+11, replicate4

value: AAV-MYL2-HA-TadA8e-Sauri N aa1-438-inteinN-U6-Camk2d sgRNA7 + AAV-MYL2-inteinC-Sauri C aa439-1061-U6-Camk2d sgRNA7


title: RMG-I cell line, DMSO, Biol Rep 1


title: OVSAHO cell line, BLU-222 (120nM), Biol Rep 3

value: OVSAHO


title: OVSAHO cell line, BLU-222 (120nM), Biol Rep 2


title: dual-V2, 4E+11, replicate2


title: dual-V2, 4E+11, replicate1


title: OVSAHO cell line, DMSO, Biol Rep 3


title: dual-V2, 2E+11, replicate4


title: RMUG-S cell line, BLU-222 (1500nM), Biol Rep 3


title: OVSAHO cell line, DMSO, Biol Rep 2


title: dual-V2, 2E+11, replicate3


title: dual-V2, 2E+11, replicate1


title: dual-V2, 1E+11, replicate4


title: OVMANA cell line, BLU-222 (290nM), Biol Rep 2

value: OVMANA


title: OVMANA cell line, BLU-222 (290nM), Biol Rep 3


title: OVMANA cell line, BLU-222 (290nM), Biol Rep 1


title: OVSAHO cell line, DMSO, Biol Rep 1


title: dual-V2, 1E+11, replicate3


title: OVMANA cell line, DMSO, Biol Rep 3


title: OVMANA cell line, DMSO, Biol Rep 2


title: dual-V2, 1E+11, replicate1


title: dual-V2, 5E+10, replicate4


title: dual-V2, 4E+11, replicate3


title: OVISE cell line, BLU-222 (380nM), Biol Rep 3

value: OVISE


title: OVMANA cell line, DMSO, Biol Rep 1


title: dual-V2, 1E+11, replicate2


title: OVSAHO cell line, BLU-222 (120nM), Biol Rep 1


title: OVISE cell line, BLU-222 (380nM), Biol Rep 2


title: dual-V2, 5E+10, replicate2


title: dual-V3, 5E+10, replicate4


title: OVISE cell line, BLU-222 (380nM), Biol Rep 1


title: dual-V2, 5E+10, replicate3


title: dual-V2, 5E+10, replicate1


title: dual-V2, 2E+11, replicate2


title: OVISE cell line, DMSO, Biol Rep 3


title: dual-V2, 2.5E+10, replicate4


title: OVISE cell line, DMSO, Biol Rep 1


title: dual-V2, 2.5E+10, replicate3


title: dual-V2, 2.5E+10, replicate2


title: OVISE cell line, DMSO, Biol Rep 2


title: NIH:OVCAR-3 cell line, BLU-222 (100nM), Biol Rep 3


title: dual-V2, 2.5E+10, replicate1


title: NIH:OVCAR-3 cell line, BLU-222 (100nM), Biol Rep 2


title: N2a, Sauri-ABE, sgRNA10, replicate2 [amplicon]

value: mouse neural crest-derived cell line

value: pAAV-EFS-TadA8e-Sauri-U6-Camk2d sgRNA10


title: N2a, Sauri-ABE, sgRNA10, replicate3 [amplicon]


title: NIH:OVCAR-3 cell line, BLU-222 (100nM), Biol Rep 1


title: NIH:OVCAR-3 cell line, DMSO, Biol Rep 3


title: NIH:OVCAR-3 cell line, DMSO, Biol Rep 2


title: NIH:OVCAR-3 cell line, DMSO, Biol Rep 1


title: N2a, Sauri-ABE, sgRNA7, replicate3 [amplicon]

value: pAAV-EFS-TadA8e-Sauri-U6-Camk2d sgRNA7


title: OV-90 cell line, BLU-222 (420nM), Biol Rep 3


title: OV-90 cell line, BLU-222 (420nM), Biol Rep 1


title: N2a, Sauri-ABE, sgRNA10, replicate1 [amplicon]


title: OV-90 cell line, DMSO, Biol Rep 3


title: N2a, Sauri-ABE, sgRNA7, replicate1 [amplicon]


title: N2a, Sauri-ABE, sgRNA9, replicate2 [amplicon]

value: pAAV-EFS-TadA8e-Sauri-U6-Camk2d sgRNA9


title: OV-90 cell line, BLU-222 (420nM), Biol Rep 2

value: ovarian


title: N2a, Sauri-ABE, sgRNA9, replicate3 [amplicon]


title: N2a, Sauri-ABE, sgRNA6, replicate3 [amplicon]

value: pAAV-EFS-TadA8e-Sauri-U6-Camk2d sgRNA6


title: N2a, Sauri-ABE, sgRNA7, replicate2 [amplicon]


title: OV-90 cell line, DMSO, Biol Rep 2


title: OV-90 cell line, DMSO, Biol Rep 1


title: OAW42 cell line, BLU-222 (260nM), Biol Rep 3


title: N2a, Sauri-ABE, sgRNA6, replicate2 [amplicon]


title: OAW42 cell line, BLU-222 (260nM), Biol Rep 2


title: N2a, Sauri-ABE, sgRNA3, replicate3 [amplicon]

value: pAAV-EFS-TadA8e-Sauri-U6-Camk2d sgRNA3


title: OAW42 cell line, BLU-222 (260nM), Biol Rep 1


title: N2a, Sauri-ABE, sgRNA3, replicate2 [amplicon]


title: N2a, Sauri-ABE, sgRNA9, replicate1 [amplicon]


title: OAW42 cell line, DMSO, Biol Rep 3

value: DMSO


title: OAW42 cell line, DMSO, Biol Rep 2


title: N2a, Sauri-ABE, sgRNA3, replicate1 [amplicon]


title: N2a, Sauri-ABE, sgRNA1, replicate3 [amplicon]

value: pAAV-EFS-TadA8e-Sauri-U6-Camk2d sgRNA1


title: OAW42 cell line, DMSO, Biol Rep 1


title: N2a, Sauri-ABE, sgRNA1, replicate2 [amplicon]

value: WT


title: Kuramochi cell line, BLU-222 (50nM), Biol Rep 3

value: Kuramochi


title: N2a, Sauri-ABE, sgRNA1, replicate1 [amplicon]


title: Kuramochi cell line, BLU-222 (50nM), Biol Rep 2


title: N2a, SaKKH-ABE, sgRNA9, replicate2 [amplicon]

value: pAAV-EFS-TadA8e-SaKKH-U6-Camk2d sgRNA9


title: Kuramochi cell line, BLU-222 (50nM), Biol Rep 1


title: N2a, SaKKH-ABE, sgRNA9, replicate1 [amplicon]


title: Kuramochi cell line, DMSO, Biol Rep 2


title: N2a, SaKKH-ABE, sgRNA8, replicate3 [amplicon]

value: pAAV-EFS-TadA8e-SaKKH-U6-Camk2d sgRNA8


title: N2a, SaKKH-ABE, sgRNA9, replicate3 [amplicon]


title: Kuramochi cell line, DMSO, Biol Rep 1


title: N2a, SaKKH-ABE, sgRNA8, replicate2 [amplicon]


title: FU-OV-1 cell line, BLU-222 (120nM), Biol Rep 3


title: N2a, SaKKH-ABE, sgRNA7, replicate3 [amplicon]

value: pAAV-EFS-TadA8e-SaKKH-U6-Camk2d sgRNA7


title: N2a, Sauri-ABE, sgRNA6, replicate1 [amplicon]


title: Kuramochi cell line, DMSO, Biol Rep 3


title: N2a, SaKKH-ABE, sgRNA8, replicate1 [amplicon]


title: FU-OV-1 cell line, BLU-222 (120nM), Biol Rep 1


title: FU-OV-1 cell line, BLU-222 (120nM), Biol Rep 2


title: N2a, SaKKH-ABE, sgRNA7, replicate2 [amplicon]


title: N2a, SaKKH-ABE, sgRNA7, replicate1 [amplicon]


title: FU-OV-1 cell line, DMSO, Biol Rep 3


title: N2a, SaKKH-ABE, sgRNA5, replicate1 [amplicon]

value: pAAV-EFS-TadA8e-SaKKH-U6-Camk2d sgRNA5


title: N2a, SaKKH-ABE, sgRNA5, replicate3 [amplicon]


title: N2a, SaKKH-ABE, sgRNA5, replicate2 [amplicon]


title: FU-OV-1 cell line, DMSO, Biol Rep 1


title: COV644 cell line, BLU-222 (1600nM), Biol Rep 3


title: N2a, SaKKH-ABE, sgRNA4, replicate3 [amplicon]

value: pAAV-EFS-TadA8e-SaKKH-U6-Camk2d sgRNA4


title: COV644 cell line, BLU-222 (1600nM), Biol Rep 2


title: N2a, SaKKH-ABE, sgRNA4, replicate2 [amplicon]


title: N2a, SaKKH-ABE, sgRNA4, replicate1 [amplicon]


title: COV644 cell line, DMSO, Biol Rep 2


title: COV644 cell line, DMSO, Biol Rep 1


title: COV644 cell line, BLU-222 (1600nM), Biol Rep 1


title: COV644 cell line, DMSO, Biol Rep 3


title: N2a, SaKKH-ABE, sgRNA2, replicate2 [amplicon]

value: pAAV-EFS-TadA8e-SaKKH-U6-Camk2d sgRNA2


title: COV434 cell line, BLU-222 (650nM), Biol Rep 3


title: N2a, SaKKH-ABE, sgRNA2, replicate3 [amplicon]

value: mouse neural crest-derived cell line


title: N2a, SaKKH-ABE, sgRNA1, replicate3 [amplicon]

value: pAAV-EFS-TadA8e-SaKKH-U6-Camk2d sgRNA1


title: N2a, SaKKH-ABE, sgRNA2, replicate1 [amplicon]


title: N2a, SaKKH-ABE, sgRNA1, replicate1 [amplicon]


title: FU-OV-1 cell line, DMSO, Biol Rep 2


title: COV434 cell line, BLU-222 (650nM), Biol Rep 2


title: N2a, Nme2-ABE, sgRNA9, replicate3 [amplicon]

value: pAAV-EFS-TadA8e-Nme2-U6-Camk2d sgRNA9


title: COV434 cell line, DMSO, Biol Rep 2


title: COV434 cell line, DMSO, Biol Rep 3


title: N2a, SaKKH-ABE, sgRNA1, replicate2 [amplicon]


title: COV318 cell line, BLU-222 (50nM), Biol Rep 3


title: N2a, Nme2-ABE, sgRNA8, replicate3 [amplicon]

value: pAAV-EFS-TadA8e-Nme2-U6-Camk2d sgRNA8


title: N2a, Nme2-ABE, sgRNA9, replicate1 [amplicon]


title: COV318 cell line, BLU-222 (50nM), Biol Rep 1

value: ovarian


title: COV318 cell line, BLU-222 (50nM), Biol Rep 2


title: N2a, Nme2-ABE, sgRNA8, replicate2 [amplicon]


title: COV434 cell line, BLU-222 (650nM), Biol Rep 1


title: COV318 cell line, DMSO, Biol Rep 3


title: COV318 cell line, DMSO, Biol Rep 2


title: N2a, Nme2-ABE, sgRNA8, replicate1 [amplicon]


title: COV318 cell line, DMSO, Biol Rep 1


title: N2a, Nme2-ABE, sgRNA7, replicate3 [amplicon]

value: pAAV-EFS-TadA8e-Nme2-U6-Camk2d sgRNA7


title: COV434 cell line, DMSO, Biol Rep 1


title: CaOV-3 cell line, BLU-222 (120nM), Biol Rep 3


title: N2a, Nme2-ABE, sgRNA9, replicate2 [amplicon]


title: CaOV-3 cell line, BLU-222 (120nM), Biol Rep 1


title: CaOV-3 cell line, BLU-222 (120nM), Biol Rep 2


title: N2a, Nme2-ABE, sgRNA4, replicate2 [amplicon]

value: pAAV-EFS-TadA8e-Nme2-U6-Camk2d sgRNA4


title: N2a, Nme2-ABE, sgRNA7, replicate1 [amplicon]


title: CaOV-3 cell line, DMSO, Biol Rep 2

value: DMSO


title: N2a, Nme2-ABE, sgRNA4, replicate1 [amplicon]


title: N2a, Nme2-ABE, sgRNA1, replicate3 [amplicon]

value: pAAV-EFS-TadA8e-Nme2-U6-Camk2d sgRNA1


title: N2a, Nme2-ABE, sgRNA1, replicate2 [amplicon]

value: WT


title: CaOV-3 cell line, DMSO, Biol Rep 3


title: N2a, Nme2-ABE, sgRNA1, replicate1 [amplicon]


title: A2780 cell line, DMSO, Biol Rep 3


title: dual-AAV, 4E+11, replicate2 [amplicon]

data_processing:
The sequencing reads were analyzed by CRISPResso2
Experimentalparameter: FASTQ files for analysis(.fastq or .fastq.gz), Reference amplicon sequence, sgRNA used, quantification window size, quantification window center, Experiment name
code: CRISPResso \ --fastq_r1 base_editor.fastq.gz \ -a amplicon sequence \ -g sgRNA sequence \ -w 20 \ -wc -10 \ --base_editor_output \ --write_cleaned_report \ --place_report_in_output_folder
Assembly: mm10
Supplementary files format and content: Nucleotide_percentage_table
Library strategy: Amplicon-seq

value: Heart

value: AAV-MYL2-HA-TadA8e-Sauri N aa1-438-inteinN + AAV-MYL2-inteinC-Sauri C aa439-1061-U6-Camk2d sgRNA7


title: dual-AAV, 4E+11, replicate4 [amplicon]


title: A2780 cell line, BLU-222 (200nM), Biol Rep 1


title: A2780 cell line, DMSO, Biol Rep 1


title: dual-AAV, 4E+11, replicate1 [amplicon]


title: A2780 cell line, DMSO, Biol Rep 2


title: CaOV-3 cell line, DMSO, Biol Rep 1


title: N2a, Nme2-ABE, sgRNA7, replicate2 [amplicon]


title: dual-AAV, 4E+11, replicate3 [amplicon]


title: A2780 cell line, BLU-222 (200nM), Biol Rep 2


title: N2a, Nme2-ABE, sgRNA4, replicate3 [amplicon]


title: WDR26 KO HeLa biol rep 2 RNA

city: London

first: Caroline

last: Schild-Poulter

address: 1151 Richmond Street North

country: Canada

institute: Western University

description: rRNA depleted RNA

data_processing:
Trim galore v.0.6.6 with the following parameters (‘–phred33 -length 36 -q 5 -stringency 1 -e 0.1‘) was used to trim the raw data, and HISAT2 v2.0.4 mapped the paired-end reads against the Homo sapiens GRCh38 (primary assembly downloaded from Ensembl)
SAMtools was then used to sort and convert SAM files.
StringTie v.2.1.5 was used to obtain gene and transcript abundance for each sample by providing read alignments and Homo sapiens GRCh38 genome annotation as input.
Tximport R/Bioconductor package was used to import transcript coverage and abundance into R, and the DESeq2 R/Bioconductor package conducted a differential analysis of transcript count data.
The independent hypothesis weighting (IHW) method was used to weigh P values and adjust for multiple testing using the procedure of Benjamini Hochberg (BH). Finally, the Lancaster method was used to aggregate transcripts' p-values.
Assembly: GRCh38
Supplementary files format and content: csv file containing normalized TPM counts for each sample

molecule: total RNA

source_name: HeLa

growth_protocol: All cells were cultured in high glucose (4.5 g/L) Dulbecco’s modified Eagle’s medium (Wisent Bioproducts, St. Bruno, Quebec, Canada) supplemented with 10% fetal bovine serum, 1% sodium pyruvate, and 1% L-glutamine (609-065-EL, Wisent Bioproducts) at 37˚C and 5% CO2

extract_protocol:
RNA from three individual plates of WT and WDR26 KO HeLa cells was isolated using the RNeasy Mini Kit (74104, Qiagen). 20 µL at 4 nM of RNA was sent to Canada’s Michael Smith Genome Sciences Centre – BC Cancer for sequencing.
Sequencing faciltity constructed libraries using Ribodepletion 3.2 protocol

value: HeLa

value: WDR26 KO


title: dual-AAV, 2E+11, replicate4 [amplicon]


title: A2780 cell line, BLU-222 (200nM), Biol Rep 3


title: WDR26 KO HeLa biol rep 3 RNA

description: rRNA depleted RNA


title: dual-AAV, 2E+11, replicate2 [amplicon]


title: HK2 cells Control rep4

city: Wuhan

first: Tao

last: Qiu

address: No. 238 Jiefang Road, Wuchang District, Wuhan, China

institute: Renmin Hospital of Wuhan University

description: Library name: V76-4

data_processing:
Data filtering The sequencing data was filtered with SOAPnuke  by (1) Removing reads containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base quality less than or equal to 15) is more than 20%; (3) Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format. The subsequent analysis and data mining were performed on Dr. Tom Multi-omics Data mining system (https://biosys.bgi.com).
RNA identification Bowtie2 was applied to align the clean reads to the gene set, in which known and novel, coding and noncoding transcripts were included.
Gene Quantification Differential Expression Analysis Expression level of gene was calculated by RSEM (v1.3.1) . The heatmap was drawn by pheatmap (v1.0.8)  according to the gene expression difference in different samples. Essentially, differential expression analysis was performed using the DESeq2(v1.4.5)  (or DEGseq or PoissonDis)with Q value ≤ 0.05 (or FDR ≤ 0.001).
Gene Annotation To take insight to the change of phenotype, GO (http://www.geneontology.org/) and KEGG (https://www.kegg.jp/) enrichment analysis of annotated different expression gene was performed by Phyper based on Hypergeometric test. The significant levels of terms and pathways were corrected by Q value with a rigorous threshold (Q value ≤ 0.05) .
Assembly: hg38
Supplementary files format and content: tab-delimited text files include FPKM and normalized counts values for each Sample

source_name: HK2 cells

extract_protocol:
1. Experimental Procedures 1.1 Sample Lysis 1.1.1 Transfer appropriate tissue sample into corresponding tissue grinding tube (tissue≤30 mg, cell≤1×107). 1.1.2 Add 600 μL Buffer RLT Plus. Homogenize the lysate for using a rotor–stator homogenizer, stay at room temperature for 5 min. 1.1.3 Centrifuge at 12,000×g for 3 min in room temperature, transfer the supernatant to AllPrep DNA spin column. 1.1.4 Centrifuge 12,000×g for 30 s in room temperature, transfer the solution from the collection tube for the RNA purification. 1.1.5 Transfer the DNA spin column to the new collection tube for DNA purification. 1.2 DNA Purification 1.2.1 Add 500μL Buffer AW1 to AllPrep DNA spin column, centrifuge at 10,000×g for 30 s and discard the filtrate. 1.2.2 Add 500μL Buffer AW2 to AllPrep DNA spin column, centrifuge at 10,000×g for 30 s and discard the filtrate. 1.2.3 Centrifuge at 16,000×g for 2 min, transfer the AllPrep DNA spin column to 1.5mL centrifuge tube. 1.2.4 Add 50μL Buffer EB to AllPrep DNA spin column, stay at room temperature for 1 min. 1.2.5 Centrifuge at 16,000×g for 2 min and collect the DNA. 1.3 RNA Purification 1.3.1 Add the equal volume of 70% ethanol to the collection tube, mix by pipetting. 1.3.2 Transfer 700 μL mixed solution, to a RNeasy spin column placed in a 2 mL collection tube. 2.3.3 Centrifuge at 10,000×g for 30 s and allow it to empty by gravity flow. 1.3.4 Add 700 μL Buffer RW1 to RNeasy spin column. Centrifuge at 10,000×g for 30 s and discard the filtrate. 1.3.5 Add 500 μL Buffer RPE to RNeasy spin column. Centrifuge at 10,000×g for 30 s and discard the filtrate. 1.3.6 Add 500 μL Buffer RPE to RNeasy spin column. Centrifuge at 10,000×g for 30 s and discard the filtrate. 1.3.7 Centrifuge at 16,000×g for 2 min and transfer the RNeasy spin column to the 1.5 mL centrifuge tube. 1.3.8 Add 35 μL RNase-free water to RNeasy spin column. Stay at room temperature for 1min. 1.3.9 Centrifuge at 16,000×g for 2 min at room temperature to collect RNA.
After total RNA was extracted, mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase, which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I, RNase H and dUTP Solution. An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys were 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina Novaseq™ 6000 (LC-Bio Technology CO., Ltd., Hangzhou, China) following the vendor's recommended protocol.

value: HK2 cells

value: human renal tubular epithelial cells

value: hypoxia 24h/reoxygenation 4h


title: dual-AAV, 1E+11, replicate4 [amplicon]


title: dual-AAV, 1E+11, replicate3 [amplicon]


title: dual-AAV, 2E+11, replicate3 [amplicon]


title: dual-AAV, 1E+11, replicate2 [amplicon]


title: WT HeLa biol rep 3 RNA

description: rRNA depleted RNA


title: WDR26 KO HeLa biol rep 1 RNA

description: rRNA depleted RNA


title: HK2 cells Control rep3

description: Library name: V76-3


title: dual-AAV, 5E+10, replicate2 [amplicon]


title: dual-AAV, 2.5E+10, replicate4 [amplicon]


title: WDR26 KO HeLa_biol rep 3 [ATAC]

description:
KOs.bw
anno_KO_vs_WT_sig_logfc1_df.csv

data_processing:
Raw reads were trimmed with Trim Galore (v.0.6.6) with the following parameters (‘–phred33 -length 36 -q 5 -stringency 1 -e 0.1‘) and mapped to Homo sapiens GRCh38 using Bowtie2 v2.4.4 with the default parameters.
SAMtools v1.12 was then used to create and sort BAM files from the aligned reads recorded in SAM format.
The duplicated reads were then marked with the MarkDuplicates function from Picard (v.2.26.3).
The mitochondrial DNA reads, and blacklist regions of the genome were filtered out using Bedtools intersect (v.2.30.0).
MACS2 v2.2.7.1 (with parameters --nomodel -f BAMPE) was used to call the peaks for each sample. The peaks from all samples were merged into a set of non-redundant open regions with Bioconductor package soGGi v1.24.1. The peaks that were present in at least two samples were kept for downstream analysis.
Assembly: GRCh38
Supplementary files format and content: bigWig
Supplementary files format and content: annotated csv file of genomic regions that are differentially accessible in WDR26 KO vs WT HeLa cells

extract_protocol:
the cells were washed with ice-cold PBS, scraped, and transferred to a fresh microcentrifuge tube. The viability of the cells was then determined using Trypan blue and the TC20 Automatic Cell Counter; if > 95%, 2x105-cell aliquots were prepared and centrifuged at 500 x g for 5 minutes at 4°C. The supernatant was carefully removed and the resulting pellet was resuspended in 200 µL of ATAC Resuspension Buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2) supplemented with digitonin (100 units/mL [final]), Tween-20 (0.1% [final]), and NP-40 (0.1% [final]) and incubated on ice for 3 minutes. The reaction was then quenched by transferring the sample to 15 mL Falcon tubes containing 4 mL ATAC Resuspension Buffer supplemented only with Tween-20 (0.1% [final]) and centrifuged at 500 x g for 10 minutes at 4°C. The supernatant was removed, leaving behind a nuclei-containing pellet. The pellet was resuspended in 500 µL of 1X TD Buffer (10 mM Tris-HCl pH 7.5, 5 mM MgCl2, 10 mM DMF, 35% PBS) supplemented with digitonin (100 u/mL [final]) and Tween-20 (0.1% [final]); afterwards, viability and nuclei concentration was determined using Trypan blue and the TC20 Automatic Cell Counter. If 0%, 2x105-cell aliquots were prepared in 190 µL of 1X TD Buffer. After 10 µL of 100 nM Tn5 enzyme is added to the sample, the tagmentation is performed at 37°C for 30 minutes, with shaking at 700 rpm. The DNA was then immediately isolated using the Zymo DNA clean and concentrator-5 (D4014).
PCR was performed using the Illumina i5 and i7 indexing primers containing adaptors for 8 cycles (75°C, 5 min; 98°C, 30 s; 8 cycles of (98°C,10 s; 63°C, 30 s; 72°C, 60 s); 4°C indefinitely. The PCR amplified DNA was cleaned using the Zymo DNA clean and concentrator-5, double size selected using Ampure XP beads (Cat#: A63880) and quantitated using Collibri library quantitation kit (Cat#: A38524100).

treatment_protocol: Cells were washed with pre-warmed, sterile PBS and incubated in DMEM containing 200 u/mL of DNaseI (LS002006, Worthington) for 30 minutes to remove free-floating DNA.


title: HK2 cells Control rep2

description: Library name: V76-2


title: dual-AAV, 5E+10, replicate4 [amplicon]


title: HK2 cells DEF6-OE rep4

description: Library name: OE_2225-4


title: HK2 cells DEF6-OE rep2

description: Library name: OE_2225-2


title: HK2 cells Control rep1

description: Library name: V76-1


title: dual-AAV, 5E+10, replicate1 [amplicon]


title: WT HeLa biol rep 2 RNA

description: rRNA depleted RNA


title: WDR26 KO HeLa_biol rep 2 [ATAC]

description:
KOs.bw
anno_KO_vs_WT_sig_logfc1_df.csv


title: dual-AAV, 2.5E+10, replicate2 [amplicon]


title: WDR26 KO HeLa_biol rep 1 [ATAC]

description:
KOs.bw
anno_KO_vs_WT_sig_logfc1_df.csv


title: WT HeLa biol rep 1 RNA

description: rRNA depleted RNA


title: HK2 cells DEF6-OE rep3

description: Library name: OE_2225-3


title: HK2 cells DEF6-OE rep1

description: Library name: OE_2225-1


title: single-AAV, 4E+11, replicate3 [amplicon]


title: dual-AAV, 2.5E+10, replicate3 [amplicon]


title: single-AAV, 4E+11, replicate4 [amplicon]


title: dual-AAV, 5E+10, replicate3 [amplicon]


title: dual-AAV, 2.5E+10, replicate1 [amplicon]


title: single-AAV, 4E+11, replicate2 [amplicon]


title: WT HeLa biol rep 1 [ATAC]

description:
WTs.bw
anno_KO_vs_WT_sig_logfc1_df.csv


title: single-AAV, 2E+11, replicate1 [amplicon]


title: 293T, Sauri-ABE, sgRNA7, replicate3 [amplicon]

value: human kidney epithelial-like cell line

value: pAAV-EFS-TadA8e-Sauri-U6-Camk2d sgRNA7


title: single-AAV, 2E+11, replicate4 [amplicon]


title: 293T, Sauri-ABE, sgRNA6, replicate3 [amplicon]

value: pAAV-EFS-TadA8e-Sauri-U6-Camk2d sgRNA6


title: single-AAV, 1E+11, replicate4 [amplicon]


title: single-AAV, 1E+11, replicate2 [amplicon]


title: 293T, Sauri-ABE, sgRNA7, replicate2 [amplicon]


title: single-AAV, 5E+10, replicate3 [amplicon]


title: WT HeLa_biol rep 2 [ATAC]

description:
WTs.bw
anno_KO_vs_WT_sig_logfc1_df.csv


title: WT HeLa biol rep 3 [ATAC]

description:
WTs.bw
anno_KO_vs_WT_sig_logfc1_df.csv


title: A549 ZNF252P ASO repeat3

city: Nanjing

first: Erbao

last: Zhang

state: Jiangsu

address: longmian da dao

department: Department of Epidemiology

institute: Nanjing Medical University

data_processing:
We applied the reads filtering towards the raw reads after sequencing to achieve the clean data following the criteria: a)10% base quality <15 b) 13% base quality <20.
Hisat2 2.0.4 mapping to reference genome
count counting
Assembly: GRCh_38
Supplementary files format and content: TXT file contain counts for each sample

extract_protocol:
lung cancer cells RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: lung cancer cells

value: ZNF252P knockdown


title: single-AAV, 2E+11, replicate2 [amplicon]


title: A549 ZNF252P ASO repeat1


title: 293T, Sauri-ABE, sgRNA7, replicate1 [amplicon]


title: 293T, Sauri-ABE, sgRNA6, replicate2 [amplicon]


title: single-AAV, 2E+11, replicate3 [amplicon]


title: A549 ASO-NC repeat3

value: Control


title: single-AAV, 1E+11, replicate3 [amplicon]


title: single-AAV, 1E+11, replicate1 [amplicon]


title: 293T, Sauri-ABE, sgRNA6, replicate1 [amplicon]


title: single-AAV, 5E+10, replicate4 [amplicon]


title: single-AAV, 4E+11, replicate1 [amplicon]


title: A549 ZNF252P ASO repeat2


title: 293T, Sauri-ABE, sgRNA1, replicate3 [amplicon]

value: pAAV-EFS-TadA8e-Sauri-U6-Camk2d sgRNA1


title: single-AAV, 5E+10, replicate2 [amplicon]


title: single-AAV, 5E+10, replicate1 [amplicon]


title: single-AAV, 2.5E+10, replicate4 [amplicon]


title: 293T, Sauri-ABE, sgRNA1, replicate2 [amplicon]


title: single-AAV, 2.5E+10, replicate1 [amplicon]


title: single-AAV, 2.5E+10, replicate3 [amplicon]


title: DU145, GEX

city: South San Francisco

first: Tomasz

last: Włodarczyk

state: California

address: 1 DNA Way

institute: Genentech

description:
scRNA-seq
LIB5463782_SAM24425416

data_processing:
scMultiome data processing of sequencing reads was performed using our Single Cell Multiome ATAC + Gene Expression (ARCSeq) - 10X Cellranger bioinformatics pipeline (martian v4.0.5)which implements the CellRanger ARC seq (cellranger-arc count ) workflow (cellranger-arc_2.0.0) using the GRCh38 genome reference. ATAC-seq (atac_fragments.tsv.gz) and scRNA-seq (raw_feature_bc_matrix.h5) matrices were generated from fastq files.
The cell hashing (hashed-tag oligonucleotide (HTO)) (*.hashing.tsv) feature count matrices were generated with  cumulus_feature_barcoding (https://github.com/lilab-bcb/cumulus_feature_barcoding) (v0.11.1). This  barcode count matrix was then used to demultiplex the scRNAseq data using a DropleUtils (v1.21.0)-based  workflow with the emptyDrops(test.ambient = TRUE, by.rank=30000) and hashedDrops(  doublet.nmads=3, doublet.min=2, confident.nmads=1, confident.min=1) key steps and parameters. ATAC-seq data was processed with ArchR v1.0.3. Briefly, low quality cells were removed (minTSS>=4 and  minFrags>=1000) and arrow files were generated followed by generation of Tile and Gene Score matrices  using a tile size of 500 bp. Doublets were identified and filtered out using ArchR’s addDoubletScores()  function with default parameters.  Filtered ATACSeq data was merged with the libary-size normalized scRNAseq using the function addGeneIntegrationMatrix. For both modalities we used addIterativeLSI to reduce dimensionality. The results were combined into single space in which cell clusters were identified. Peaks were generated using addReproduciblePeakSet() with macs2. Peaks were annotated with addPeakAnnotations()(using public cisBP database) followed by  addDeviationsMatrix().  The peaks.mtx.gz and gex.mtx.gz files contains processed peaks and normalized gene expression data.
Assembly: GRCh38-2020-A
Supplementary files format and content: matrix.mtx.gz, features.tsv.gz, barcodes.tsv.gz - output of Cellranger
Supplementary files format and content: gex.mtx.gz, peaks.mtx.gz, gex_peaks_barcodes.tsv, peaks_features.tsv, gex_features.tsv - files representing ArchR GeneExpressionMatrix (normalized counts) and PeakMatrix assays, row names (genes or peaks) and column names (barcodes)
Supplementary files format and content: <library name>.hashing.csv cell hashing count matrix generated by cumulus_feature_barcoding with the first column storing HTO ID and other column names being barcodes
Library strategy: Single cell multiome (scMultiome)

source_name: prostate adenocarcinoma

growth_protocol: LNCap Clone FGC, VCAP and DU145 cells were obtained from ATCC and cultured with RPMI-1640 media with 10% FBS and 2mM L-Glutamine; NCI-H660 cells were obtained from ATCC and cultured with DMEM/F12 with 0.005 mg/ml insulin,0.01 mg/ml Transferrin, 30nM Sodium selenite,10nM Hydrocortisone,10nM beta-estradiol, 4mM L-Glutamine. The cells were split every 4-5 days to maintain the appropriate density. For the drug response assay, cells were seeded in 6 well format.The cells were split every 4-5 days to maintain the appropriate density.

extract_protocol:
After 24 hours from treatment, the cells were harvested for the single-cell RNA-ATAC Co-assay.
The library construction was following the standard 10X protocol with the following modifications to the protocol:  1) 1µl of 10µM HTO additive primer was spiked in during the pre-AMP and cDNA PCR steps; 2) during the 0.6X cDNA cleanup, the supernatant was saved to amplify the HTO library. Along with the transcriptome library, the HTO library was amplified from the supernatant using the HTO-specific primer. The detailed protocol can be found on the cell hashing website (https://cite-seq.com/cell-hashing/).

treatment_protocol: 1.5E5 DU145 cells were seeded into each well of a 6 well plate and 5E3 DU145 cells were seeded into each well of a 96 well plate; 1.5-2E6 LNCAP or VCAP cells were seeded into T75 flasks; 5E5 cells NCI-H660 cells were seeded into each well of a 6 well plate. After 48 hours, the media was removed and cells were treated with DMSO, 1uM Enzalutamide, 0.1 uM SMARCA2.4_1 or 1 uM ARV-110 in complete media.

value: prostate adenocarcinoma


title: Sk.Mus, sgRNA7, replicate5 [amplicon]

source_name: Muscle

value: Muscle

value: AAV-MYL2-TadA8e-Sauri-U6-Camk2d sgRNA7


title: Sk.Mus, sgRNA7, replicate4 [amplicon]

value: WT


title: Sk.Mus, sgRNA7, replicate3 [amplicon]


title: H660, ATAC

description:
ATAC-seq
LIB5467654_SAM24427130


title: isolated islet, ATG7 knockout, rep 3

city: Indianapolis

first: Matthew

middle: C

last: Austin

state: Indiana

address: 1210 Waterway Blvd., Suite 4000

institute: Indiana University School of Medicine

description: Library name: 3586_Female-ATG7KO_S50_L001

data_processing:
Reads were mapped to reference genome using STAR v2.5
Quality of RNA-seq data was evaluated by NGSUtils,bamutils v0.5.9
Low quality mapped reads were excluded and featureCounts v1.5.1 was used to quantify gene level expression
Differential gene expression analysis was performed using edgeR v3.30.3
Assembly: UCSC mm10
Supplementary files format and content: excel file with raw counts, log2 FPKM, and fold change

source_name: islet

extract_protocol:
Qiagen RNAeasy mini kit with on-column DNAse treatment
cDNA libraries were prepped using SMART-seq ultra-low input RNA kit: Clontech SMART-Seq v4 Ultra Low Input RNA Kit; Illumina Nextera XT DNA Lib Kit

value: islet

value: ATG7 beta-cell KO


title: isolated islet, ATG7 knockout, rep 2

description: Library name: 3581_Male-ATG7KO_S48_L001


title: H660, GEX

description:
scRNA-seq
LIB5467655_SAM24427130


title: DU145, ATAC

description:
ATAC-seq
LIB5463780_SAM24425416


title: Sk.Mus, sgRNA7, replicate2 [amplicon]


title: isolated islet, ATG7 knockout, rep 1

description: Library name: 3509_Male-ATG7KO_S46_L001


title: H660, HTO

description:
DNA-seq
LIB5467656_SAM24427130


title: Sk.Mus, sgRNA7, replicate1 [amplicon]


title: isolated islet, control, rep 3

description: Library name: 3585_Female-Control_S49_L001

value: littermate control


title: LNCaP, ATAC, 1

description:
ATAC-seq
LIB5458336_SAM24418231_1

value: LNCaP clone FGC


title: LNCaP, ATAC, 2

description:
ATAC-seq
LIB5458336_SAM24418231_2


title: dual-AAV, 2E+11, replicate1 [amplicon]

value: Heart

value: AAV-MYL2-HA-TadA8e-Sauri N aa1-438-inteinN + AAV-MYL2-inteinC-Sauri C aa439-1061-U6-Camk2d sgRNA7


title: VCaP, ATAC, 1

description:
ATAC-seq
LIB5458335_SAM24418230_1

value: VCaP


title: A549 ASO-NC repeat2


title: dual-AAV, 1E+11, replicate1 [amplicon]


title: isolated islet, control, rep 2

description: Library name: 3448_Male-Control_S47_L001


title: A549 ASO-NC repeat1


title: 293T, Sauri-ABE, sgRNA1, replicate1 [amplicon]

value: human kidney epithelial-like cell line


title: VCaP, ATAC, 2

description:
ATAC-seq
LIB5458335_SAM24418230_2


title: Brain, sgRNA7, replicate5 [amplicon]

source_name: Brain

value: Brain


title: single-AAV, 2.5E+10, replicate2 [amplicon]


title: Brain, sgRNA7, replicate4 [amplicon]


title: LNCaP, GEX

description:
scRNA-seq
LIB5458338_SAM24418231


title: LNCaP, HTO

description:
DNA-seq
cells_x_features.mtx.gz
cells_x_features.genes.txt
cells_x_features.barcodes.txt

data_processing:
Cellranger + ArchR
scMultiome data processing of sequencing reads was performed using our Single Cell Multiome ATAC + Gene Expression (ARCSeq) - 10X Cellranger bioinformatics pipeline (martian v4.0.5)which implements the CellRanger ARC seq (cellranger-arc count ) workflow (cellranger-arc_2.0.0) using the GRCh38 genome reference. ATAC-seq (atac_fragments.tsv.gz) and scRNA-seq (raw_feature_bc_matrix.h5) matrices were generated from fastq files.
HTO sequencing reads were processed using kb-python 0.27.0 to produce cells_x_features.mtx.gz count matrix file. The cell hashing (hashed-tag oligonucleotide (HTO)) was then used to demultiplex the scRNAseq data with the demuxEM v0.1.5  ATAC-seq data was processed with ArchR v1.0.3. Briefly, low quality cells were removed (minFrags>=500) and arrow files were generated followed by generation of Tile and Gene Score matrices  using a tile size of 500 bp. Doublets were identified and filtered out using ArchR’s addDoubletScores()  function with default parameters.  Filtered ATACSeq data was merged with the libary-size normalized scRNAseq using the function addGeneIntegrationMatrix. For both modalities we used addIterativeLSI to reduce dimensionality. The results were combined into single space in which cell clusters were identified. Peaks were generated using addReproduciblePeakSet() with macs2. Peaks were annotated with addPeakAnnotations()(using public cisBP database) followed by  addDeviationsMatrix().  The peaks.mtx.gz and gex.mtx.gz files contains processed peaks and normalized gene expression data.
Assembly: GRCh38-2020-A
Supplementary files format and content: matrix.mtx.gz, features.tsv.gz, barcodes.tsv.gz - output of Cellranger
Supplementary files format and content: gex.mtx.gz, peaks.mtx.gz, gex_peaks_barcodes.tsv, peaks_features.tsv, gex_features.tsv - files representing ArchR GeneExpressionMatrix (normalized counts) and PeakMatrix assays, row names (genes or peaks) and column names (barcodes)
Supplementary files format and content: cells_x_features.mtx.gz, cells_x_features.genes.txt, cells_x_features.barcodes.txt - HTO cout matrix, row names (HTO) and column names (barcodes)
Library strategy: Single cell multiome (scMultiome)

growth_protocol: LNCaP Clone FGC cells were obtained from ATCC and cultured with RPMI-1640 media with 10% FBS and 2mM L-Glutamine. The cells were split every 4-5 days to maintain the appropriate density.

extract_protocol:
The single-cell RNA-seq was performed using the Chromium Single Cell 3' kit (V3.1) from 10X Genomics with cell hashing. The single-cell RNA-ATAC co-assay was performed using the 10X Genomics Single Cell Multiome ATAC + Gene Expression kit.
The library construction was following the standard 10X protocol with the following modifications to the protocol:  1) 1µl of 10µM HTO additive primer was spiked in during the pre-AMP and cDNA PCR steps; 2) during the 0.6X cDNA cleanup, the supernatant was saved to amplify the HTO library. Along with the transcriptome library, the HTO library was amplified from the supernatant using the HTO-specific primer. The detailed protocol can be found on the cell hashing website (https://cite-seq.com/cell-hashing/).

treatment_protocol: The cells were cultured in DMEM with 10% FBS, 100μM NEAA, 2mM Glutamine. They were split every 2-3 days. One day before transfection, the cell culture dish was treated with 5mL 1% gelatin in PBS, incubated for 10 minutes, then aspirated. 3.5x10^6 293T cells were seeded into each 10 cm dish to reach ~80% confluence. On the day of transfection, 20 µl Lipofectamine 2000 was added to 480 µl OptiMEM. In a new tube, the plasmid was mixed in 500µl Opti-MEM at the following ratio: carrier plasmid, 5 µg; delta8.9, 16 µg; VSVG, 1 µg. Both mixes were combined and incubated for 20 minutes before adding to the dish. The dish was incubated at 37˚C for 6 hours and then 6 ml of complete media was added. Virus was then harvested 48 hours after transfection. Briefly, all supernatants were harvested and filtered through a 0.45 µm filter bottle. The virus was concentrated by using the Lenti-X concentrator (TAKARA Bio.) following the manufacturer’s instructions and resuspended in 1 ml 1% BSA in PBS per dish. The concentrated virus was divided into 200µl aliquots and stored in -80˚C until infection. Two days before infection, 4X10 5 LNCaP cells were seeded into each well of a 6-well plate. On the day of infection, aspirate the media and change to 0.5mL RPMI + 10% FBS + 1X Glutamax with 8 µg/ml Polybrene. A total of 200 µl concentrated lentivirus was added to each well to achieve high MOI, and then the plate was centrifuged at 1800 rpm for 45 minutes at room temperature. After that the plate was put into the incubator for another 3 hours before 2 ml of the full media was added to each well. Two days after infection, the media was refreshed with 1µg / ml puromycin. The cells were then grown for another 7 days before harvesting for the single-cell analysis, during which the cells were split accordingly when the confluence reached 100%. The cells from different wells were stained with human TotalSeq-A cell hashing antibodies (BioLegend) containing distinct barcodes following the manufacturer’s protocol. The detailed protocol can be found on the cell hashing website (https://cite-seq.com/cell-hashing/).

value: LNCaP


title: VCaP,  GEX

description:
scRNA-seq
LIB5458337_SAM24418230


title: isolated islet, control, rep 1

description: Library name: 3508_Male-Control_S45_L001


title: Mettl3 KO MTL3 eclip-2

city: Ann Arbor

first: Zhaowei

last: Han

state: Michigan

address: 1000 Wall St

department: Gilbert S. Omenn Department of Computational Medicine & Bioinformatics

institute: University of Michigan

description:
Library name: 11646-JX-6
PE150 on a 300 cycle S4 flow cell

library_source: other

data_processing:
eCLIP-seq data were processed using the CLIP Tool Kit (CTK). Reads were preprocessed with FASTX-Toolkit and cutadapt, mapped to the mm10 genome with Bowtie, and duplicates were removed with tag2collapse.pl. Peaks were identified using tag2peak.pl, and visualization-ready bigwig files were generated with bed2wig.pl, ensuring high-resolution data analysis.
Assembly: mm10
Supplementary files format and content: Bam files
Library strategy: iCLIP

molecule: other

source_name: organoids

growth_protocol: Rx:GFP and Mettl3 KO harboring Dox-inducible HA-METTL3 were differentiatied with GMEM supplemented with 5% KSR, 1% NEAA, 1% β-ME, 1% Sodium Pyruvate) and AGN (0.1µM) at 37°C.

extract_protocol:
UV crosslinked WT and Mettl3 KO Rx:GFP RPCs were collected and resuspended in 600µl of RIPA lysis buffer with freshly added Protease Inhibitor Cocktail (Roche, 11873580001) and 1 μl of Superase-In RNase inhibitor (Thermo Fisher, AM2694)) for 15 min on ice and then sonicated with Qsonica 800R (30 s, on; 30 s off; 20 minutes, 30% amplitude). Sonicated lysates were centrifuged at 13,000 × g for 15 min at 4 °C. Clarified lysates were incubated with 15µl METTL3 antibody (Abcam, Ab195352) at 4 °C overnight. Two percent of lysate was saved as size-matched input. 30µl of Protein A Dynabeads (Thermo Fisher, 10001D) were added into IP tubes and incubated at 4 °C for 2 hrs. The immunoprecipitated (IP) samples were washed with low salt buffer (20 mM Tris-HCl pH 8, 150mM NaCl, 2 mM EDTA, 1% Triton X-100, 0.1% SDS, freshly added RNase Inhibitor at 1:1000 dilution) twice and then washed with LiCl wash buffer (10 mM Tris-HCl pH 8, 0.25 M LiCl, 1 mM EDTA, 1% NP-40, 0.25% sodium deoxycholate, freshly added RNase Inhibitor at 1:1000 dilution) twice. The IP samples underwent final washes twice with TE buffer (10 mM Tris-HCl pH 80 and 1mM EDTA, freshly added RNase Inhibitor at 1:1000 dilution). IP samples were eluted from beads with 300 µl elution buffer (50 mM Tris-HCl pH 8, 150mM NaCl, 1 mM EDTA, 1% SDS, 50mM NaHCO3 and freshly added RNase Inhibitor at 1:1000 dilution and 7µl of Proteinase K) at 37 °C for 30 minutes. 500µl Trizol was added to extract RNA and then digested with DNase (Thermo Fisher, NC1424104) at 37 °C for 30 minutes. The Isopropanol precipitated RNA was resuspended in 17.5 µl of RNase/DNase free water at 55 °C for 5 minutes.
Libraries were amplified using standard RNA library prep kit by UM AGC. The quantity and quality of the final libraries were assessed using a Bioanalyzer (Agilent Technology Inc). All samples were sequenced by PE150 on the Illumina NovaSeq shared flow cell sequencer. Two biological replicates were conducted for each experiment

treatment_protocol: 6 days of differentiation of Rx:GFP and Mettl3 KO RPCs.

value: organoids

value: Mettl3 KO Rx:GFP

value: Mettl3 KO

value: AGN treated

tag: batch

value: METTL3 (Abcam, Ab195352)


title: LNCaP, ATAC

description:
ATAC-seq
matrix.mtx.gz
barcodes.tsv.gz
features.tsv.gz
peaks.mtx.gz
gex_peaks_barcodes.tsv
gex_features.tsv

value: prostate adenocarcinoma


title: CS-B

city: Boston

first: Sarah

middle: J.

last: Hill

state: MA

address: 450 Brookline Ave., Dana Building, Room 1410C

department: Medical Oncology

institute: Dana-Farber Cancer Institute

data_processing:
Raw fastq data were aligned and preprocessed using the GATK Best processes for SNV and indel discovery
Reads were aligned to hg19 using BWA mem. The aligned files were then marked for duplicates using the Picard implementation of MarkDuplicates
The de-duplicated file was then recalibrated using the gatk-4.1.4.1 BaseRecalibrator and ApplyBQSR tools.
Mutect2 was used to call SNV's and indels, and generated a filtered variant call file using GATK FilterMutectCalls.
Assembly: hg19 was used for ARK1, ARK2, CS-A, UPSC-A, EMCA-A, and CS-B.
Supplementary files format and content: Variant call files (VCF) which contain SNV's and Indels
Library strategy: Whole-exome sequencing

source_name: Endometrial Cancer

growth_protocol: ARK1 and ARK2 cells were grown in Roswell Park Memorial Institute (RPMI) 1640 (Gibco Cat. #11875-093), 10% FBS (Sigma Cat. #F2442), and 1% penicillin/streptomycin (P/S) (Gibco Cat. #15140-122). Organoids were grown in advanced DMEM/F12 (Gibco Cat. #12634-028), supplemented with 1% P/S, 1% HEPES (Gibco Cat. # 15630080), 1X Glutamax (Gibco Cat. # 35050061), 500nM A83-01 (BioGems Cat. #9094360), 10µM SB202190 (BioGems Cat. #1523072), 10mM Nicotinamide (Sigma Aldrich Cat. #N0636), 1X B-27 (Gibco Cat. #17504044), 1.25mM N-acetylcysteine (Sigma Aldrich Cat. #A9165), 1µM Prostaglandin E2 (BioGems Cat. # 3632464), 10% Noggin and 10% R-Spondin1 conditioned media, 10ng/mL FGF-10 (Peprotech Cat. #100-26), 50ng/mL EGF (Peprotech Cat. #100-15), and 10ng/mL FGF2 (Peprotech Cat. #100-18B).

extract_protocol:
Cell lines were trypsinized and organoids were scraped, and the pellets were stored at -80°C until DNA was prepared. DNA was prepared using Qiagen's DNA Mini kit (Qiagen Cat. # 51304) according to the manufacturer's protocol. DNA was snap frozen and sent to Novogene (Sacramento, CA) for standard whole exome sequencing according to their protocol.
WES libraries were prepared by Novogene.

treatment_protocol: Cells were untreated.

value: Endometrial Cancer


title: Mettl3 KO MTL3 eclip-1

description:
Library name: 11646-JX-5
PE150 on a 300 cycle S4 flow cell


title: LNCaP, GEX

description:
scRNA-seq
matrix.mtx.gz
barcodes.tsv.gz
features.tsv.gz
gex.mtx.gz
gex_peaks_barcodes.tsv
peaks_features.tsv


title: EMCA-A


title: Mettl3 KO 1/10 Input

description:
Library name: 11646-JX-4
PE150 on a 300 cycle S4 flow cell

value: NO


title: Kindey, sgRNA7, replicate5 [amplicon]

source_name: Kindey

value: Kindey

value: WT

value: AAV-MYL2-TadA8e-Sauri-U6-Camk2d sgRNA7


title: Rx-GFP MTL3 eclip-2

description:
Library name: 11646-JX-3
PE150 on a 300 cycle S4 flow cell


title: UPSC-A


title: 16HBE14o- -35kbHDR cl33 -80.1kb

city: Cleveland

first: Ann

last: Harris

state: Ohio

address: 2109 Adelbert Rd Building

department: Genetics and Genome Sciences

institute: Case Western Reserve University

description: 4C-seq library with the CFTR -80.1 kb region as the viewpoint

data_processing:
Libraries were sequenced on the Nextseq550 machine and demultiplexed using the primer sequences.
4C-seq was quantified and mapped using the pipe4C v1.1 (https://github.com/deLaatLab/pipe4C) processing pipeline using default parameters, aligned to the hg19 genome.
Genome_build: hg19
Supplementary_files_format_and_content: Aligned 4C-seq of each clone and viewpoint in bigWig format

source_name: Human airway epithelium

growth_protocol: Cells were grown in indicated media using standard methods

extract_protocol:
Nuclei from 1e7 cells grown to confluency were made as per Krijger, P et al, 2020, Methods (PMID: 31351925) with corresponding samples as listed in the treatment protocol section.
All libraries were constructed as per PMID: 31351925 with the samples corresponding to the Methods papers as listed in the treatment protocol section.
4C-seq Barcoded libraries with Illumina sequencing adapters were made as per PMID: 31351925 for corresponding samples as listed in the treatment protocol section.

treatment_protocol: KLF5 depletion and CRISPR KLF5-null cell generation was performed as per Paranjapye, A et al, 2021, (PMID: 34217701).

value: CRISPR/Cas9 mediated HDR of KLF5 site -35kb from CFTR Promoter

tag: growth media

value: DMEM + 10% FBS


title: Kindey, sgRNA7, replicate4 [amplicon]


title: Brain, sgRNA7, replicate1 [amplicon]


title: 16HBE14o- -35kbHDR cl4 -80.1kb


title: CS-A


title: Brain, sgRNA7, replicate2 [amplicon]


title: Rx-GFP MTL3 eclip-1

description:
Library name: 11646-JX-2
PE150 on a 300 cycle S4 flow cell


title: Kindey, sgRNA7, replicate3 [amplicon]


title: Rx-GFP 1/10 Input

description:
Library name: 11646-JX-1
PE150 on a 300 cycle S4 flow cell


title: ARK1


title: Calu-3 KLF5si APIP I4

description: 4C-seq library with the chromosome 11p13 APIP Intron 4 DHS as the viewpoint

value: Wild type


title: 16HBE14o- WT -80.1kb


title: Kindey, sgRNA7, replicate2 [amplicon]


title: dTAGMTL3-24hr-2

description:
Library name: 11904-JX-8
PE150 on a 300 cycle S4 flow cell

data_processing:
Bulk RNA-seq data is analyzed with Cufflinks v2.2.1 for transcript assembly, Cuffmerge for merging annotations, and Cuffdiff for identifying differentially expressed genes (DEGs).
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: csv files include FPKM values for each Sample

growth_protocol: The Rx:GFP harboring FKBP12F36V-HA knocked into c-terminal of Mettl3 were differentiatied with GMEM supplemented with 5% KSR, 1% NEAA, 1% β-ME, 1% Sodium Pyruvate) and AGN (0.1µM) at 37°C.

extract_protocol:
RNA extraction for RNA-seq was performed by combination of Trizol reagent (ThermoFisher Scientific) and RNeasy mini kit (QIAGEN)
RNAs were sent to University of Michigan DNA Sequencing Core for RNA quality analysis, PolyA+ mRNA selection and library construction, and sequencing using Illumina NovaSeq S4 Libraries platform. Duplicate samples for each group were subjected to two round of independent library preparation and sequencing to avoid sample and batch effect of mRNA-seq.

treatment_protocol: At day 5 and day 6 treated the differentiatied RPCs with or without dTAG13 (125nM) for 1 hr, 2 hr, 8 hr and 24 hr. Collecting the cells at the same time.

value: Rx:GFP FKBP12F36V-HA KI

value: FKBP12F36V-HA knocked into the C-terminal end of the two endogenous Mettl3 alleles

value: dTAG13 treated


title: Brain, sgRNA7, replicate3 [amplicon]

value: Brain


title: Calu-3 KLF5si 11.2516

description: 4C-seq library with the chromosome 11p13 11.2516 DHS as the viewpoint


title: ARK2


title: Kindey, sgRNA7, replicate1 [amplicon]


title: dTAGMTL3-24hr-1

description:
Library name: 11904-JX-7
PE150 on a 300 cycle S4 flow cell

value: organoids


title: Calu-3 NC APIP I4


title: Lung, sgRNA7, replicate4 [amplicon]

source_name: Lung

value: Lung


title: dTAGMTL3-8hr-2

description:
Library name: 11904-JX-6
PE150 on a 300 cycle S4 flow cell


title: dTAGMTL3-8hr-1

description:
Library name: 11904-JX-5
PE150 on a 300 cycle S4 flow cell


title: 16HBE14o- KLF5null cl15 +48.9 kb

description: 4C-seq library with the CFTR +48.9 kb region as the viewpoint

value: CRISPR/Cas9 mediated KLF5-null


title: Lung, sgRNA7, replicate3 [amplicon]


title: dTAGMTL3-1hr-2

description:
Library name: 11904-JX-4
PE150 on a 300 cycle S4 flow cell


title: 16HBE14o- KLF5null cl15 -20.9 kb

description: 4C-seq library with the CFTR -20.9 kb region as the viewpoint


title: dTAGMTL3-1hr-1

description:
Library name: 11904-JX-3
PE150 on a 300 cycle S4 flow cell


title: Lung, sgRNA7, replicate2 [amplicon]


title: 16HBE14o- KLF5null cl15 CFTR promoter

description: 4C-seq library with the CFTR promoter as the viewpoint


title: Spleen, sgRNA7, replicate5 [amplicon]

source_name: Spleen

value: Spleen


title: dTAGMTL3-0hr-1

description:
Library name: 11904-JX-1
PE150 on a 300 cycle S4 flow cell

value: No


title: 16HBE14o- KLF5null cl8 -20.9 kb


title: dTAGMTL3-0hr-2

description:
Library name: 11904-JX-2
PE150 on a 300 cycle S4 flow cell


title: 16HBE14o- KLF5null cl8 +48.9 kb


title: Spleen, sgRNA7, replicate4 [amplicon]


title: Spleen, sgRNA7, replicate3 [amplicon]


title: GV oocytes from Rpa1 OcKO mouse 3

city: Amherst

first: Wei

last: Cui

address: 240 Thatcher Road

institute: University of Massachusetts Amherst

description:
Library name: Sample 18
x18 in raw_counts.csv

data_processing:
RNA-seq was undertaken by Azenta Life Sciences (NJ, USA) under ultra-low input RNA-seq workflow. Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36. The trimmed reads were mapped to the Mus musculus GRCm38 reference genome available on ENSEMBL using the STAR aligner v.2.5.2b.
Unique gene hit counts were calculated by using featureCounts from the Subread package v.1.5.2 and only unique reads that fell within exon regions were counted.
Assembly: Mus musculus GRCm38
Supplementary files format and content: sample.counts.txt: unique hit counts for each sample
Supplementary files format and content: raw_counts.csv: raw gene hit counts of all samples

source_name: germinal vesicle (GV) oocytes

extract_protocol:
Total RNA was isolated from the GV oocytes without any cumulus cells using the RNeasy Plus Micro Kit (QIAGEN), followed by Agilent 2100 Bioanalyzer RNA 6000 Pico Assay (Agilent Technologies Inc).
RNA-seq libraries were prepared using the NEBNext Single Cell/Low Input RNA Library Prep Kit (New England Biolabs) following the manufacturer’s protocols. The quantity of library was evaluated by Qubit dsDNA HS Assay (Thermo Fisher Scientific) and the quality was analyzed by the Bioanalyzer (Agilent).

value: germinal vesicle (GV) oocytes


title: Spleen, sgRNA7, replicate2 [amplicon]


title: 16HBE14o- KLF5null cl4 +48.9 kb


title: GV oocytes from Rpa1 OcKO mouse 2

description:
Library name: Sample 17
x17 in raw_counts.csv


title: Spleen, sgRNA7, replicate1 [amplicon]


title: Lung, sgRNA7, replicate5 [amplicon]


title: 16HBE14o- KLF5null cl4 CFTR promoter


title: GV oocytes from Control mouse 3

description:
Library name: Sample 15
x15 in raw_counts.csv


title: Calu-3 NC 11.2516


title: Liver, sgRNA7, replicate4 [amplicon]

source_name: Liver

value: Liver


title: Liver, sgRNA7, replicate5 [amplicon]


title: 16HBE14o- cl42 +48.9 kb


title: GV oocytes from Control mouse 2

description:
Library name: Sample 14
x14 in raw_counts.csv


title: GV oocytes from Control mouse 1

description:
Library name: Sample 13
x13 in raw_counts.csv


title: EV+Dox-2 d6

city: ANN ARBOR

first: Yuanhao

last: Huang

state: MI

address: 1418 McIntyre st

description:
Library name: 3912-JX-24
PE150 on a 300 cycle S4 flow cell

data_processing:
data is mapped to reference genome using STAR and processed using cuffdiff toolkit
Assembly: mm10
Supplementary files format and content: FPKM tsv file

growth_protocol: Rx:GFP Mettl3 KO cells harboring Dox-inducible HA-METTL3 were differentiatied with GMEM supplemented with 5% KSR, 1% NEAA, 1% β-ME, 1% Sodium Pyruvate) and AGN (0.1µM) at 37°C.

treatment_protocol: RPCs of Mettl3 KO were treated with or without Dox(2µg/ml) for 6 days

value: Rx:GFP Mettl3 KO line

value: Mettl3 KO, Dox-inducible HA-METTL3

value: Dox treated


title: Liver, sgRNA7, replicate2 [amplicon]

value: WT

value: AAV-MYL2-TadA8e-Sauri-U6-Camk2d sgRNA7


title: 16HBE14o- cl42 -20.9 kb

value: Wild type

value: DMEM + 10% FBS


title: Lung, sgRNA7, replicate1 [amplicon]


title: 16HBE14o- cl35 +48.9 kb


title: Liver, sgRNA7, replicate3 [amplicon]


title: EV-2 d6

description:
Library name: 3912-JX-16
PE150 on a 300 cycle S4 flow cell


title: 16HBE14o- cl35 -20.9 kb


title: 16HBE14o- KLF5null cl4 -20.9 kb


title: 16HBE14o- cl42 CFTR promoter


title: 16HBE14o- cl35 CFTR promoter


title: Liver, sgRNA7, replicate1 [amplicon]


title: Eu replaced with EF1a reverse D345 cells, wapl, ChIP, rep2

city: Baltimore

first: Fei

last: Ma

state: MD

address: 251 Bayview Blvd

institute: NIA

data_processing:
ChIP-seq reads were aligned to the mm10 genome using bwa-mem26. Aligned reads were converted to bigWig format using deepTools7 bamCoverage with the flags “—normalizeUsing CPM –ignoreDuplicates –minMappingQuality 30 –binSize 1”. ChIP-seq reads were aligned to mm10 using bwa-mem2 version 2.2.1 Aligned reads were processed using bamCoverage from deepTools version 3.5.1 (parameters --normalizeUsing CPM --ignoreDuplicates --minMappingQuality 30 --binSize 1) to generate bigWig files
Assembly: mm10
Supplementary files format and content: bigwig files

source_name: Bone marrow

growth_protocol: Pro-B cell lines were grown with complete 1640 RPMI medium (10% fetal bovine serum and 0.05mM 2-Mercaptoethanol)

extract_protocol:
Two million pro-B cells were initially crosslinked with 1.5 mM EGS at room temperature for 15 minutes with continuous rotation. This was followed by fixation with 1% formaldehyde for 15 minutes at room temperature, also with rotation, and quenched using 200 mM glycine. After washing twice with PBS, cells were then resuspended in a buffer containing 1% SDS and incubated for 10 min on ice before sonication. Chromatin was sonicated with Bioruptor (Diagenode, 30s on/ 30s off, 20 min on time) and diluted 10X with dilution buffer (0.01% SDS, 1.1% Triton X-100, 1.2 mM EDTA, 16.7 mM Tris-HCl, PH8.0, 167 mM NaCl), and followed by immunoprecipitation with specific antibodies overnight at 4 °C
The ChIP-seq libraries were prepared using the TruSeq Nano DNA Low Throughput Library Prep Kit (Illumina, Cat#20015964) according to the manufacturer's protocol. Samples were indexed using the TruSeq DNA Single Indexes Set A (Illumina, Cat#20015960) and pooled for sequencing.

treatment_protocol: No treatment

value: Bone marrow

value: pro-B cell


title: Calu-3 KLF5si +48.9 kb


title: Heart, sgRNA7, replicate3 [amplicon]

value: Heart


title: 16HBE14o- KLF5null cl8 CFTR promoter


title: Heart, sgRNA7, replicate5 [amplicon]


title: GV oocytes from Rpa1 OcKO mouse 1

description:
Library name: Sample 16
x16 in raw_counts.csv


title: EV-1 d6

description:
Library name: 3912-JX-15
PE150 on a 300 cycle S4 flow cell

value: organoids


title: Eu replaced with EF1a reverse D345 cells, Nipbl, ChIP, rep2


title: Heart, sgRNA7, replicate4 [amplicon]


title: Eu replaced with EF1a reverse D345 cells, wapl, ChIP, rep1


title: Calu-3 KLF5si -80.1 kb

description: 4C-seq library with the CFTR -80.1 kb region as the viewpoint


title: Calu-3 KLF5si -20.9 kb


title: Heart, sgRNA7, replicate1 [amplicon]


title: Calu-3 KLF5si CFTR promoter

description: 4C-seq library with the CFTR promoter region as the viewpoint


title: Eu replaced with EF1a reverse D345 cells, Nipbl, ChIP, rep1


title: Sk.Mus, sgRNA6, replicate4 [amplicon]

value: Muscle

value: AAV-MYL2-TadA8e-Sauri-U6-Camk2d sgRNA6


title: Sk.Mus, sgRNA6, replicate3 [amplicon]


title: Eu replaced with EF1a forward D345 cells, wapl, ChIP, rep2


title: Calu-3 NC +48.9 kb

description: 4C-seq library with the CFTR +48.9 kb region as the viewpoint


title: EV+Dox-1 d6

description:
Library name: 3912-JX-23
PE150 on a 300 cycle S4 flow cell


title: Eu replaced with EF1a forward D345 cells, wapl, ChIP, rep1


title: Sk.Mus, sgRNA6, replicate2 [amplicon]


title: Calu-3 NC -80.1 kb


title: Eu replaced with EF1a forward D345 cells, Nipbl, ChIP, rep1


title: Sk.Mus, sgRNA6, replicate1 [amplicon]


title: Calu-3 NC -20.9 kb

description: 4C-seq library with the CFTR -20.9 kb region as the viewpoint


title: Eu replaced with EF1a forward D345 cells, Nipbl, ChIP, rep2


title: Brain, sgRNA6, replicate4 [amplicon]

value: Brain


title: Heart, sgRNA7, replicate2 [amplicon]


title: Brain, sgRNA6, replicate3 [amplicon]


title: 22015MPB; hPB; NGS-2712

city: Heraklion

first: Matthieu

last: Lavigne

address: Nikolaou Plastira 100

country: Greece

institute: IMBB-FORTH

description:
Library name: 2712
22015MPB

data_processing:
The quality of the FASTQ files was assessed with the FastQC software. Reads were aligned to the human (hg38) genomewith the Hisat2 aligner (hisat2 -p32 -x $REFERENCE_GENOME -q fastq/$FILE_ID.fastq -S $FILE_ID.sam --score-min L,0,-0.5 -k 2). Htseq-counts was utilized to summarize reads at the gene level (htseq-count -f bam -s yes -i gene_id bam/$FILE_ID.bam data/refs/Homo_sapiens/UCSC/hg38/Annotation/Genes/genes.gtf> $COUNTS_DIR/NGS$FILE_ID).
For downstream analysis presented in the paper, differential expression analysis (DEA) was conducted by running EdgeR via SARTools 1.5.0. For each comparison (dPB (peripheral M-MDSCs from DLBCL patients) vs hPB (peripheral M-MDSCs from healthy individuals)  and  M-MDSCs from blood dPB) vs M-MDSCs from BM (dBM)  of DLBCL patients, DEGs in either group of the comparison) were defined by applying the following threshold p-value <0.05, which was considered statistically significant. Heatmaps and GO Bubbleplots were created in R with an in-house   developed script which is based on the complex heatmap R package. GO analysis was run on the webtool Metascape using default parameters.
Assembly: hg38
Supplementary files format and content: The processed data consists of a count table of the number of raw reads per gene for all samples.

source_name: Peripheral blood

growth_protocol: The DLBCL cohort consisted of 33 newly diagnosed patients recruited through the Haematology Clinic at the University General Hospital of Heraklion, Greece and an age-matched group of 12 healthy individuals. Diagnosis was based on the 5th WHO criteria. Eligible healthy donors had no history of autoimmune disease or immunosuppression due to a known disease or medication. Bone marrow was obtained from healthy volunteers during total hip arthroplasty at the Orthopedic Clinic of the University General Hospital of Heraklion, Greece.

extract_protocol:
Flow cytometry analysis in whole blood and bone marrow samples: Peripheral blood (PB) and BM samples were collected into tubes containing EDTA, and mononuclear cells (PBMCs and BMMCs) were isolated over a density gradient using Ficoll-Paque Plus (GE Healthcare) within 24 hours of sample collection. Following density gradient centrifugation, at least one million single cells per sample were stained with fluorochrome-coupled antibodies. The monoclonal antibodies used for labelling of samples were: ECD-labelled anti-HLA-DR (Immu-357), PC7-labeled anti-CD33 (D3HL60.251), APC-labeled anti-CD14 (RM052), FITC-labeled anti-CD11b (94), PE-labeled anti-CD15 (80H5), all antibodies from Beckman Coulter-Immunotech. Total MDSCs, monocytic MDSCs (M-MDSCs) and granulocytic myeloid derived suppressor cells (PMN-MDSCs) were measured by flow cytometry using the NAVIOS cytometry system (Beckmann Coulter) and analysed using KALUZA software (Beckmann Coulter).  Gating strategy is shown in Figure 1. Briefly, total MDSCs were assessed as CD11b+CD33+ HLADRlow/−, while M-MDSCs were gated as CD11b+CD33+ HLADRlow/−CD14+ CD15− and PMN-MDSCs as CD11b+ CD33+ HLA-DRlow/−CD14− CD15+. Cell sorting of MDSCs was performed under aseptic conditions using 70-micron nozzle with a BD FACS Aria III (BD Biosciences). RNA Isolation and 3′ RNA sequencing. RNA from FACS-sorted M-MDSCs was isolated using Nucleospin RNA XS kit (Macherey-Nagel), according to the manufacturer’s instructions. The quality and quantity of isolated RNA were measured using 2100 Bioanalyser  (Agilent)  and RNA 6000 Pico Kit reagents (Agilent).
RNA samples with RNA integrity number (RIN)>7 were used for library construction using the 3′ mRNA-Seq Library Prep Kit FWD for Illumina (QuantSeq-LEXOGEN) as per the manufacturer’s instructions. Amplification was controlled to obtain optimal unbiased libraries across samples by assessing the number of cycles (ranging from 20-24) required by qPCR. DNA High Sensitivity Kit for bioanalyzer was used to assess the quantity and quality of libraries, according to the manufacturer’s instructions (Agilent). Libraries were multiplexed and sequenced on an Illumina Nextseq 500 at the genomics facility of IMBB FORTH according to the manufacturer’s instructions.

treatment_protocol: All DLBCL patients were treated homogeneously with the RCHOP immunochemotherapy combination. Exclusion criteria were infections, autoimmune diseases, or prior steroid treatment. Demographics, disease characteristics, and outcomes were collected from the patients’ medical files after signing informed consent.

value: Peripheral blood

value: Myeloid derived suppressor cells (MDSCs)


title: Eu deleted D345 cells,Wapl, ChIP, rep1


title: 3M; hPB; NGS-3099

description:
Library name: 3099
3M


title: Eu deleted D345 cells,Wapl, ChIP, rep2


title: 22052P3PB; hPB; NGS-2711

description:
Library name: 2711
22052P3PB


title: Calu-3 NC CFTR promoter

description: 4C-seq library with the CFTR promoter as the viewpoint


title: Brain, sgRNA6, replicate1 [amplicon]


title: Eu deleted D345 cells, Nipbl, ChIP, rep1


title: Brain, sgRNA6, replicate2 [amplicon]


title: Eu deleted D345 cells, Nipbl, ChIP, rep2


title: 25M; dPB; NGS-3106

description:
Library name: 3106
25M

value: RCHOP immunochemotherapy


title: atac_A42B42 female and male

city: Montreal

first: Gustavo

last: Turecki

state: Quebec

address: 6875 Boulevard LaSalle

department: Psychiatry

institute: McGill University

description: Case Male

data_processing:
FASTQ files were produced with 10x cellranger-atac mkfastq.
Alignments were generated with refdata-cellranger-arc-GRCh38-2020-A-2.0.0 and cellranger-atac count with default paramters. 10x fragment files were converted to peak count matrices using ArchR [release_1.0.1]. The open chromatin peaks were first identified in ArchR using MACS2 (cutOff=0.1) in each of the four pseudobulk replicates generated from each broad cell-type (n=7) and cluster (n=38). Open chromatin peaks identified in atleast two pseudobulk replicates were retained for each cell-type and cluster. We separately merged peaks across cell-types and across clusters using ArchR iterative overlap peak merging and removal (IPR) to generate reproducible, non-overlapping, fixed-with (501bp) chromatin cis-regulatory elements (cCREs). Per cell Tn5 insertion counts were computed using cCREs identified at broad cell-type and cluster levels. For cluster level peak count matrix, only cCREs present in atleast 0.5% of cells were retained.
Assembly: GRCh38

source_name: Brain BA9

extract_protocol:
Frozen brain tissue sections were dounced for 5mins in the lysis buffer. The lysis suspension was homogeneously mixed by pipetting up and down 10-15 times following which only 80% of the lysis solution was mixed with 5ml of wash buffer to make diluted nuclei suspensions. The samples were mixed and passed through a 30-um cell strainer to remove cellular debris and washed twice in 10ml wash buffer. Next, Optiprep cushion was created followed by gradient centrifugation for 30mins at 10,000g and resuspended in 1ml wash buffer. Nuclei were counted with Hoescht 33342 (1:2000) three times (average was used) with Cell countess (Olumpys). Nuclei were then spun down at 500g for 5mins and diluted in 1xNB (10x Genomics)_x005F_x000D_ to obtain a final concentration of 3080 nuclei/ul.
Equal volume of nuclei suspensions from a male and female subject (either from case or control) were pooled together to obtain a final concentration of 3080 nuclei/ul. The combined nuclei were loaded in one of the lanes of 10x microfluidic chip. Each microfluidic chip was loaded with at least four multiplexed libraries representing both cases and controls. Single-cell capture and library preparations were done using 10x Genomics Chromium Single Cell v1.1 reagents following the protocol outlined by the user guide [https://www.10xgenomics.com/support/single-cell-atac/documentation/steps/library-prep/chromium-single-cell-atac-reagent-kits-user-guide-v-1-1-chemistry]. Cell Ranger atac v2.0 was used for alignment against the GRCh38 reference available on the 10x Genomics website (refdata-cellranger-arc-GRCh38-2020-A-2.0.0).
10x snATAC-seq

value: Brain BA9

value: Case


title: atac_A28B28 female and male

description: Control Male

value: Control


title: D345 cells, Wapl, ChIP, rep2


title: 23M; dPB; NGS-3105

description:
Library name: 3105
23M


title: Kindey, sgRNA6, replicate3 [amplicon]

data_processing:
The sequencing reads were analyzed by CRISPResso2
Experimentalparameter: FASTQ files for analysis(.fastq or .fastq.gz), Reference amplicon sequence, sgRNA used, quantification window size, quantification window center, Experiment name
code: CRISPResso \ --fastq_r1 base_editor.fastq.gz \ -a amplicon sequence \ -g sgRNA sequence \ -w 20 \ -wc -10 \ --base_editor_output \ --write_cleaned_report \ --place_report_in_output_folder
Assembly: mm10
Supplementary files format and content: Nucleotide_percentage_table
Library strategy: Amplicon-seq

extract_protocol:
Genomic DNA was extracted from tissues using TIANamp Genomic DNA Kit (DP304, Tiangen, China)
The sgRNA-targeted loci were amplified using Taq PCR MasterMix (KT211, Tiangen, China) and purified by TIANgel Purification Kit (DP219, TIANGEN).

value: Kindey

value: WT


title: 19M; dPB; NGS-3103

description:
Library name: 3103
19M


title: atac_A7B7 female and male

description: Case Male


title: D345 cells, Wapl, ChIP, rep1


title: atac_A25B25 female and male

description: Control Male


title: Kindey, sgRNA6, replicate2 [amplicon]


title: atac_A19B19 female and male

description: Control Male


title: Kindey, sgRNA6, replicate1 [amplicon]


title: 12M; dPB; NGS-3101

description:
Library name: 3101
12M


title: D345 cells, Nipbl, ChIP, rep2


title: D345 cells, Nipbl, ChIP, rep1


title: atac_A29B29 female and male

description: Control Male


title: atac_A41B41 female and male

description: Control Male


title: Lung, sgRNA6, replicate4 [amplicon]

value: Lung


title: 22013MPB; dPB; NGS-2708

description:
Library name: 2708
22013MPB


title: 22066P3PB; dPB; NGS-2715

description:
Library name: 2715
22066P3PB


title: atac_A35B35 female and male

description: Case Male


title: Lung, sgRNA6, replicate2 [amplicon]


title: I_CRE_12

city: Zurich

first: Christoph

last: Schneider

address: Winterthurerstrasse 190, Y23 J12

department: Physiology

country: Switzerland

institute: University of Zurich

data_processing:
Taking raw fastqt files we estimated transcript counts using Kallisto v0.48.0 with mm10 reference genome and used tximport v1.28.0 to import them in R v4.3.2. Normalized counts were generated using DESeq2 v1.40.1 R Bioconductor package.
Assembly: mm10
Supplementary files format and content: tab-delimited text file including gene name and normalized counts per sample

source_name: small intestine

extract_protocol:
Single cells were isolated from the small intestine according to a published protocol (PMID: 33740294). In brief, duodenal tissue from 10-week-old mice was opened longitudinally and incubated for 15 minutes in Ca2+/Mg2+-free HBSS buffer supplemented with 2% FCS, 10 mM HEPES, and 5 mM DTT. The tissues were then transferred into a fresh Ca2+/Mg2+-free HBSS solution supplemented with 2% FCS, 10 mM HEPES, and 5 mM EDTA, and incubated for another 15 minutes. After vortexing, the tissue samples were moved to a Ca2+/Mg2+-containing HBSS solution supplemented with 2% FCS and 10 mM HEPES and incubated for an additional 5 minutes. The tissues were subsequently placed in Ca2+/Mg2+-containing HBSS media supplemented with 2% FCS, 10 mM HEPES, 100 mg/mL Liberase TM, and 30 mg/mL DNase I, where they were manually cut into small pieces. Following a 20-minute incubation, mechanical dissociation was performed using GentleMACS C tubes (Miltenyi Biotec) and the m_intestine_01 program on the gentleMACS dissociator (Miltenyi Biotec). The samples were then filtered (100 μm) and kept on ice for subsequent staining. All incubations were performed at 37 °C under gentle agitation.  Single-cell suspensions were incubated with an Fc-receptor blocking antibody diluted in FACS buffer (1x PBS supplemented with 5% FCS and 0.1% sodium azide). They were then resuspended in a cocktail of antibodies including CD45, CD3, CD4, CD8a, CD11c, CD19, NK1.1, Thy1.1Ter119, CD49b (DX5), CD11b, SiglecF, and Klrg1. Cells were incubated with DAPI dye to enable the exclusion of dead cells during live cell acquisition. Cells that were negative for all other markers but positive for CD45, Thy1.1 and Klrg1 were sorted using the FACSymphony S6. In total, approximately 10,000 ILC2s were sorted into RLT Lysis Buffer (Qiagen) and pooled (2x) prior to RNA extraction.
Library was constructed by Novogene following standard protocol

value: small intestine

value: Sorted lamina propria ILC2s


title: 6M; dPB; NGS-3100

description:
Library name: 3100
6M


title: I_CRE_10


title: I_CRE_11


title: I_CRE_9


title: Lung, sgRNA6, replicate1 [amplicon]


title: atac_A39B39 female and male

description: Control Male


title: 22M; dBM; NGS-3104

description:
Library name: 3104
22M

value: Bone marrow


title: 14M; dBM; NGS-3102

description:
Library name: 3102
14M


title: Spleen, sgRNA6, replicate4 [amplicon]

value: Spleen


title: I_CRE_8


title: atac_A17B17 female and male

description: Control Male


title: Kindey, sgRNA6, replicate4 [amplicon]


title: atac_A38B38 female and male

description: Case Male


title: 2M; dBM; NGS-3098

description:
Library name: 3098
2M


title: Spleen, sgRNA6, replicate3 [amplicon]


title: I_WT_7


title: L030MBM; dBM; NGS-2719

description:
Library name: 2719
L030MBM


title: atac_A5B5 female and male

description: Case Male


title: Lung, sgRNA6, replicate3 [amplicon]


title: Spleen, sgRNA6, replicate2 [amplicon]


title: 22013MBM; dBM; NGS-2716

description:
Library name: 2716
22013MBM


title: I_WT_6


title: Spleen, sgRNA6, replicate1 [amplicon]


title: atac_A6B6 female and male

description: Case Male


title: L009MBM; dBM; NGS-2714

description:
Library name: 2714
L009MBM


title: I_WT_4


title: 22020MBM; dBM; NGS-2713

description:
Library name: 2713
22020MBM


title: I_WT_3


title: I_WT_5


title: Liver, sgRNA6, replicate4 [amplicon]

value: Liver


title: atac_A40B40 female and male

description: Control Male


title: atac_A14B14 female and male

description: Control Male


title: 22048P3BM; dBM; NGS-2710

description:
Library name: 2710
22048P3BM


title: Liver, sgRNA6, replicate3 [amplicon]


title: atac_A34B34 female and male

description: Case Male


title: I_WT_1


title: exp2_A498_sgKDM5C_5_H3K27ac

city: Freiburg

first: Patrick

last: Metzger

address: Breisacher Str. 153

department: Institute for Medical Bioinformatics and Systems Medicine

country: Germany

institute: University Hospital Freiburg

description: Library name: exp2_A498_sgKDM5C_5_H3K27ac

data_processing:
Sequence reads were trimmed for adapter sequences and low-quality sequences using Trim Galore (v 0.6.6) with default settings.
Sequences were aligned to UCSC hg19 using Bowtie2 (v 2.4.5) (parameters: --dovetail, --local, --very-sensitive-local, --no-unal, --no-mixed, --no-discordant, -I 10, -X 700). Spike-in sequences were aligned to UCSC dm6 for exp1 and exp2 and to E. coli NCBI K12 MG1655 for exp3.
BigWig files were generated using bamCoverage from deepTools (v 3.5.0)
Tag directories were generated using makeTagDirectory with the option -totalReads from Homer (v 4.11)
Peaks were called using Homer's findPeaks with -style histone and -C 0 and experimental samples were compared to the corresponding IgG control. Peaks with 4-fold more tags in the experimental sample compared to the control and cumulative Poisson p-value ≤ 0.0001 were kept, while peaks within blacklisted regions from ENCODE were excluded using intersectBed from BEDTools.
Unique and overlapping peaks were determined using Homer's mergePeaks with -d given.
Assembly: hg19
Supplementary files format and content: bigWig of coverage, peaks (.Clean.bed) (except for IgG controls)
Library strategy: CUT&RUN

source_name: kidney

extract_protocol:
Samples were processed following the EpiCypher® CUTANATM CUT&RUN Protocol (for histone PTMs, transcription factors (TFs), and chromatin regulators).
RNA libraries were prepared using the NEBNext® UltraTM II DNA Library Prep Kit and NEBNext® Multiplex Oligos Set (New England Biolabs).

value: kidney

tag: antibody


title: atac_A16B16 female and male

description: Case Male


title: atac_A24B24 female and male

description: Case Male


title: I_WT_2


title: Heart, sgRNA6, replicate4 [amplicon]

city: Beijing

first: zhanzhao

last: liu

address: No. 38, Xueyuan Road

source_name: Heart

value: Heart

value: AAV-MYL2-TadA8e-Sauri-U6-Camk2d sgRNA6


title: exp2_A498_sgKDM5C_4_H3K27ac

description: Library name: exp2_A498_sgKDM5C_4_H3K27ac


title: tarsal plates, 21 months wildtype, replicate 2

city: New York

middle: E

last: Millar

state: NY

address: Icahn Building, Floor 13 Room 020C, 1425 Madison Ave

department: Developmental, Cell and Regenerative Biology

institute: Icahn School of Medicine at Mount Sinai

library_source: transcriptomic single cell

data_processing:
For data analysis, Cell Ranger Single-Cell Software Suite (v7.0.1, 10x Genomics) was used to align and quantify sequencing data against the mm10 mouse reference genome (refdata-gex-mm10-2020-A).
Assembly: GRCm38/mm10
Supplementary files format and content: Tab-separated values files adn matrix files

source_name: tarsal plates

extract_protocol:
The dorsal portion of the eyelids and the surrounding tissues near the tarsal plates were removed using a scalpel. The remaining tarsal plates containing Meibomian glands were digested with 0.2% collagenase A in PBS for 1 hour at 37 °C. The tarsal plates were then rinsed twice with PBS and tissues surrounding the Meibomian glands were removed with fine-tip forceps. Tissues from four littermate mice were pooled together in PBS for each replicate. The Meibomian gland tissue-containing solutions were then transferred into 1.5mL centrifuge tubes using Pasteur pipettes. The tissue solution was centrifuged at 300g/min for 5 minutes, the supernatant was carefully removed, and the tissue pellet was rinsed once with PBS. Isolation of nuclei was performed using the protocol (CG000375 Rev B) from 10X Genomics.
RNA-seq libraries were prepared based on the 10X Genomics protocol (CG000315 Rev E) using 10000 nuclei per replicate. Single-cell separation was performed using the Chromium Next GEM Chip G Single Cell Kit. The RNA-seq libraries were sequenced in paired-end mode on an Illumina Novaseq platform with the Novaseq S4 flowcell.

value: tarsal plates

tag: age

value: 21 months

tag: Sex

value: male


title: atac_A33B33 female and male

description: Case Male

value: Brain BA9


title: Heart, sgRNA6, replicate3 [amplicon]

institute: peking university


title: tarsal plates, 21 months wildtype, replicate 1


title: exp2_A498_sgCtrl_H3K27ac

description: Library name: exp2_A498_sgCtrl_H3K27ac

value: sgCtrl


title: Heart, sgRNA6, replicate2 [amplicon]


title: tarsal plates, 8 weeks wildtype, replicate 2


title: atac_A23B23 female and male

description: Control Male

value: Control


title: exp2_A498_sgKDM5C_5_H3K27me3

description: Library name: exp2_A498_sgKDM5C_5_H3K27me3


title: Liver, sgRNA6, replicate2 [amplicon]


title: Heart, sgRNA6, replicate1 [amplicon]


title: atac_A32B32 male

description: Control Male


title: Sk.Mus, sgRNA1, replicate4 [amplicon]

source_name: Muscle

value: Muscle

value: AAV-MYL2-TadA8e-Sauri-U6-Camk2d sgRNA1


title: exp2_A498_sgKDM5C_4_H3K27me3

description: Library name: exp2_A498_sgKDM5C_4_H3K27me3


title: Sk.Mus, sgRNA1, replicate3 [amplicon]

value: WT


title: mouse eyelid, 8 weeks wildtype [Spatial transcriptomics]

description: Fresh frozen spatial transcriptome sequencing

data_processing:
*library strategy: Spatial Transcriptomics
The sequencing data were aligned and quantified using Space Ranger Software Suite (v2.1.0, 10x Genomics) against the reference genome (mm10).
Assembly: GRCm38/mm10
Supplementary files format and content: aligned_fiducials.jpg: aligned fiducials of the tissue image
Supplementary files format and content: detected_tissue_image.jpg: image of tissue and spots
Supplementary files format and content: scalefactors_json.json:  scalefactors  in json format
Supplementary files format and content: tissue_hires_image.png: hi-res image of tissue
Supplementary files format and content: tissue_lowres_image.png: low-res image of tissue
Supplementary files format and content: tissue_positions_list.csv: list of spatial barcodes and the coordinates sepcifying spots
Supplementary files format and content: barcodes.tsv.gz: list of spatial barcodes
Supplementary files format and content: features.tsv.gz: list of gene IDs
Supplementary files format and content: matrix.mtx.gz: gene expression count data in Matrix Market Exchange Format

source_name: eyelid

extract_protocol:
Eyelids from an 8-week-old male C57BL/6J mouse  was dissected, OCT embedded, sectioned at 10 μM, and mounted onto the assay slide containing four capture areas (6.5mm x 6.5mm) with spatially barcoded poly T capture probes.
After permeabilization, the captured mRNAs underwent reverse transcription, followed by cleaving from the slide. cDNA amplification, fragmentation, end-repair, poly A-tailing, adapter ligation, and sample indexing were performed in accordance with the manufacturer’s protocol.

value: eyelid

value: 8 weeks

value: wild type


title: exp2_A498_sgCtrl_H3K27me3

description: Library name: exp2_A498_sgCtrl_H3K27me3


title: E13.5_PGC_Fem_IgG

city: Montpellier

first: Maud

last: Borensztein

address: 1919 route de Mende

department: IGMM

institute: CNRS, Univ of Montpellier

data_processing:
FastQC (v0.11.9) and MultiQC (v1.13) were used to control CUT&RUN data quality. UMIs were used to confirm the homogeneous yield of library amplification and sequencing for each sample. Paired-end reads with at least one undefined UMI were discarded using Cutadapt v4.1 and seqkit v2.3 . The reads were then trimmed using Trim Galore(v0.6.6) (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/7 ; options “--length 20 –illumina – 2colour 20”). Trimmed reads were mapped with Bowtie2 (v2.4.2) (options “--end-to-end –very-sensitive–reorder”) to the mm10 reference genome, modified as followed: autosomal, sexual and mitochondrial chromosomes are kept, and 20 668 274 SNPs positions (0.76% of genome size) related to Mus musculus Castaneus strain are N-masked using SNPsplit (v0.6) (https://ftp.ebi.ac.uk/pub/databases/mousegenomes/REL-1505- SNPs_Indels/strain_specific_vcfs/CAST_EiJ.mgp.v5.snps.dbSNP142.vcf). SAMtools (v1.11)  was used to sort and convert the data formats. PCR duplicates were removed using GATK MarkDuplicates, and reads were unmapped with or without primary alignment discarded (SAMtools options “-F 0x04 -F 0x100 -F 542 0x800”). The coverage for each developmental stage was calculated from the bam file using the deepTools bamCoverage tool (v3.5.1, normalization by scale factor, bin=10 nt). Peak calling of H3K27me3 histone marks was performed for E11.5 and E12.5 female samples using immunoglobulin G (IgG) as input for each stage (E11.5 IgG from male PGC, E12.5 IgG from female PGC) with MACS2 (v2.2.7.1, options “-f BAMPE –broad –broad-cutoff 0.1”). Allele-specific reads (i.e. reads from B6: Xa and Cast: Xi) were sorted using SNPsplit. The d-score parameter (reads Cast / reads B6 + reads Cast]) was calculated using featureCounts from the Rsubread R package(v2.12.3). H3K27me3 enrichment heatmaps show the log2 fold change in the coverage difference between the H3K27me3 mark and the IgG control for each developmental stage, normalized by the sequencing depth using deepTools bamCompare (bin= 10 nt). computeMatrix and plotHeatmap.
Assembly: mm10
Supplementary files format and content: BigWig, broad peak, except for IgG
Supplementary files format and content: CSV files including FeatureCount library
Library strategy: Cut&Run

source_name: Primordial Germ Cells

extract_protocol:
genomic DNA
DNA was isolated with antibody and PA-Mnase incubation. Library preparation was performed according to manufacturer’s instructions (NEBNext ® Ultra™ II DNA Library Prep Kit for Illumina) using the following modified library amplification program: 98 °C for 30 s (98 °C for 10 s, 65 °C for 15 s) × 15 cycles, 65 °C for 5 min), hold at 4 °C. Average library size and quality control were performed using a Fragment Analyzer (High Sensitivity NGS kit) and qPCR (Roche Light Cycler 480).

value: Primordial Germ Cells

tag: embryonic stage

value: B6 x Cast

value: Xist KO/+:Oct4-eGFP+/-

value: Female

value: IgG control


title: atac_A8B8 female and male

description: Control Male


title: Liver, sgRNA6, replicate1 [amplicon]

value: Liver

value: AAV-MYL2-TadA8e-Sauri-U6-Camk2d sgRNA6


title: atac_A22B22 female and male

description: Case Male

value: Case


title: Sk.Mus, sgRNA1, replicate2 [amplicon]


title: exp2_A498_sgKDM5C_5_H3K4me3

description: Library name: exp2_A498_sgKDM5C_5_H3K4me3

value: kidney


title: exp2_A498_sgKDM5C_4_H3K4me3

description: Library name: exp2_A498_sgKDM5C_4_H3K4me3


title: Sk.Mus, sgRNA1, replicate1 [amplicon]


title: E11.5_Rep2_PGC_Fem_H3K27me3-Part2

description: E11.5_Rep2_PGC_Fem_H3K27me3_peaks.broadPeak - Copy.bw


title: atac_A12B12 female and male

description: Case Male

value: Brain BA9


title: atac_A20B20 female and male

description: Case Male


title: Brain, sgRNA1, replicate4 [amplicon]

source_name: Brain

value: Brain


title: E11.5_Rep2_PGC_Fem_H3K27me3-Part1


title: atac_A37B37 female and male

description: Case Male


title: exp2_A498_sgKDM5C_5_H3K4me1

description: Library name: exp2_A498_sgKDM5C_5_H3K4me1


title: Brain, sgRNA1, replicate3 [amplicon]


title: tarsal plates, 8 weeks wildtype, replicate 1

value: tarsal plates

value: male


title: sample 3, 90 days post radiation

city: San Francisco

last: Knox

address: 513 Parnassus Ave

department: Cell Tissue Biology

institute: University of California San Francisco

data_processing:
Raw data (FASTQ) were processed through fastp to remove reads containing adapter and poly-N sequences and reads with low quality from raw data
Assembly: Paired-end clean reads were aligned to the Mus musculus mm10 reference genome using the Spliced Transcripts Alignment to a Reference (STAR) software. FeatureCounts was used to count the read numbers mapped to each gene.
Supplementary files format and content: Comma-separated Values file includes Raw Counts for each sample

source_name: salivary gland

extract_protocol:
Total RNA was isolated from four 50 μm tissue sections of Non-IR or 30-, 60- and 90-day post-IR submandibular glands (n=3) using the RNAqueous Micro Total RNA Isolation Kit (Thermo Fisher Scientific, AM1931), and treated with DNAse I (Thermo Fisher Scientific, AM1931) to remove genomic DNA
RNA libraries were prepared with SMARTER mRNA-seq Library Prep Kit following manufacturer's protocols

value: salivary gland

value: WT

value: 10 Gy radiation


title: atac_A3B3 female and male

description: Case Male


title: Brain, sgRNA1, replicate2 [amplicon]

value: AAV-MYL2-TadA8e-Sauri-U6-Camk2d sgRNA1


title: sample 2, 90 days post radiation


title: exp2_A498_sgKDM5C_4_H3K4me1

description: Library name: exp2_A498_sgKDM5C_4_H3K4me1


title: atac_A11B11 female and male

description: Control Male

value: Control


title: sample 1, 90 days post radiation


title: E12.5_Rep2_PGC_Fem_H3K27me3

value: Primordial Germ Cells

value: B6 x Cast


title: atac_A21B21 female and male

description: Case Male


title: exp2_A498_sgCtrl_IgG

description: Library name: exp2_A498_sgCtrl_IgG

value: sgCtrl


title: N5

city: PITTSBURGH

first: Uma

last: Chandran

state: PA

address: 5607 Baum Blvd

department: Biomedical Informatics

institute: University of Pittsburgh

description: UDI-P 115

data_processing:
Stranded reads were checked for quality using FastQC (v0.11.5) and they were trimmed for quality and adapters using Cutadapt (v1.12).
Each sample was mapped to the Homo Sapien Ensembl reference genome GRCh38  or Mus Musculus Ensembl reference genome GRCm39, the appropriate reference was used based on organism, using the fast alignment tool HISAT2 v2.1.0 with default settings
Genes in GRCh38  or GRCm39 were quantified used HTSeq v0.9.0 using default settings.  The appropriate reference was used based on organism
edgeR, an R Bioconductor package, with R version 4.2.1, was used for differential gene analysis comparing various sample groups
Assembly: GRCh38 and GRCm39
Supplementary files format and content: HT-Seq Raw Counts in tab-delimited text file

source_name: Non-lesion Skin

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 100ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared usingRoche Kapa RNA Hyper prep with Riboerase (HMR) for Illumina platforms, version KR1351 – v4.21 (Cat. #: 8098140702)

treatment_protocol: Tamoxifen ip injections induced GPX4 knockdown in select keratin-14 expressing epidermal keratinocytes.

value: Non-lesion Skin

tag: disease

value: Psoriasis

tag: patient

value: patient 3


title: Brain, sgRNA1, replicate1 [amplicon]


title: exp2_A498_sgCtrl_H3K4me3

description: Library name: exp2_A498_sgCtrl_H3K4me3


title: sample 3, 60 days post radiation


title: sample 2, 60 days post radiation


title: Kindey, sgRNA1, replicate4 [amplicon]

source_name: Kindey

value: Kindey


title: atac_A31B31 female and male

description: Control Male


title: P5

description: UDI-P 114

source_name: Lesion Skin

value: Lesion Skin


title: Kindey, sgRNA1, replicate2 [amplicon]


title: sample 1, 60 days post radiation


title: atac_A13B13 female and male

description: Control Male

value: Brain BA9


title: N2

description: UDI-P 113

value: patient 2


title: atac_A2B2 female and male

description: Control Male


title: sample 3, 30 days post radiation


title: Kindey, sgRNA1, replicate1 [amplicon]


title: P2

description: UDI-P 112


title: atac_A27B27 female and male

description: Case Male

value: Case


title: exp2_A498_sgCtrl_H3K4me1

description: Library name: exp2_A498_sgCtrl_H3K4me1

value: kidney


title: Lung, sgRNA1, replicate4 [amplicon]

source_name: Lung

value: Lung


title: sample 2, 30 days post radiation

value: salivary gland

value: WT


title: atac_A10B10 female and male

description: Case Male


title: Lung, sgRNA1, replicate3 [amplicon]

value: AAV-MYL2-TadA8e-Sauri-U6-Camk2d sgRNA1


title: sample 1, 30 days post radiation

value: 10 Gy radiation


title: atac_A15B15 female and male

description: Control Male

value: Control


title: Kindey, sgRNA1, replicate3 [amplicon]


title: atac_A36B36 female and male

description: Case Male


title: P1

description: UDI-P 110

value: patient 1


title: Lung, sgRNA1, replicate2 [amplicon]


title: atac_A18B18 female and male

description: Control Male


title: Lung, sgRNA1, replicate1 [amplicon]


title: atac_A30B30 female and male

description: Control Male


title: G9a-iKO-CFA1

city: Houston

first: Hui-Lin

last: Pan

state: TX

address: 1515 Holcombe Blvd

department: Anesthesiology and Perioperative Medicine

institute: University of Texas MD Anderson Cancer Center

data_processing:
Reads were mapped to mouse genome GRCm39 (mm39) using Hisat2 v2.2.1
The mapped files were converted and sorted into bam files using samtools v1.19.2
Then reads abundant of each gene were calculated using FeatureCounts v2.0.6
Estimation of fold change and differentially expressed genes (DEGs) were analyzed using DESeq2
Assembly: GRCm39
Supplementary files format and content: tab-delimited text files include FeatureCounts values for each Sample.

source_name: Dorsal root ganglion

extract_protocol:
Dorsal root ganglia (DRG) were removed, flash frozen on liquid nitrogen, and total RNA was extracted using RNeasy Plus Universal Mini Kit (Qiagen, #73404)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: WT and G9aiKO mice were treated with vehicle or CFA in the left paw, 14 days later tissues collected.

value: Dorsal root ganglion

value: G9a conditional knockout

value: CFA


title: G9a-iKO-CFA2