title: gpnmb+/+ cryoinjured ventricle  (injury and borderzone region-BZI) , 96 hpci r3

city: Bad Nauheim

first: Mario

last: Looso

address: Ludwigstrasse 43

institute: Max Planck Institute for Heart and Lung Research

data_processing:
Trimmomatic version 0.39 was employed to trim reads after a quality drop below a mean of Q15 in a window of 5 nucleotides and keeping only filtered reads longer than 15 nucleotides (Bolger et al., Trimmomatic: a flexible trimmer for Illumina sequence data).
Reads were aligned versus Ensembl zebrafish genome version danRer11 (Ensembl release 109) with STAR 2.7.10a (Dobin et al., STAR: ultrafast universal RNA-seq aligner).
Alignments were filtered to remove: duplicates with Picard 3.0.0 (Picard: A set of tools (in Java) for working with next generation sequencing data in the BAM format), multi-mapping, ribosomal, or mitochondrial reads.
Gene counts were established with featureCounts 2.0.4 by aggregating reads overlapping exons excluding those overlapping multiple genes (Liao et al., featureCounts: an efficient general purpose program for assigning sequence reads to genomic features).
The raw count matrix was normalized with DESeq2 version 1.36.0 (Love et al., Moderated estimation of fold change and dispersion for RNA-Seq data with DESeq2).
Assembly: danRer11
Supplementary files format and content: The file indicates genome coverage at gene loci per sample

organism: Danio rerio

source_name: cardiac tissue (ventricle)

extract_protocol:
RNA was extracted using miRNeasy micro Kit (Qiagen) combined with on-column DNase digestion (RNase-free DNase set, Qiagen) to avoid contamination by genomic DANN
Library Preparation (non-strand specific, PolyA)

value: cardiac tissue (ventricle)

value: gpnmb+/+ (WT sibling)

value: cryoinjured


title: MC38-MHC-II, Replicate3

status: Public on Aug 03 2025

type: SRA

city: Beijing

first: Zexian (Davis)

last: Zeng

state: Beijing

address: No.5 Yiheyuan Road, Haidian District

country: China

institute: Peking University

library_source: genomic

data_processing:
The fastq files were processed using the ENCODE ATAC-seq pipeline to generate bam files, bigwig files, and peaks called by Genrich.
Deeptools is used for the heatmap plots. ATAC-seq peaks from all study samples were merged to create a union set of sites. Read densities were calculated for each peak for each sample, differential peaks between treatment group and control group were identified by DiffBind.
Assembly: mm10
Supplementary files format and content: BigWig files generated by merging the replicates.

molecule: genomic DNA

organism: Mus musculus

source_name: Tumor

extract_protocol:
Cells were lysed in 50 μL of RS buffer supplemented with 0.1% NP40, 0.01% Digitonin and 0.1% Tween 20 for 5 min on ice. Nuclei were isolated by centrifugation at 500 x g for 10min then resuspended in 50 mL of transposition mix (16.5 μL TW buffer, 10 μL 5× TTBL, 4 μL TTE Mix V50, 0.5 μL 1% Digitonin, 0.5 μL 10% Tween 20, 18.5 μL ddH2O) at 37 degrees for 30min.
Libraries were constructed by Hyperactive ATAC-Seq Library Prep Kit for Illumina (Vazyme#TD711) as manufacturer’s instructions.

tag: tissue

value: Tumor

tag: cell line

value: Primary cells

tag: cell type

value: Tumor-infiltrating immune cells

tag: genotype

value: WT


title: Dissociated tumor-bearing lung, mixed age and genotype (all samples represented), sublibrary 1

city: Stanford

first: Emily

last: Shuldiner

state: CA

address: 279 Campus Drive

department: Genetics

country: USA

institute: Stanford University

description:
Library name: Parse library 1
Parse Biosciences WT Mega v2

library_source: transcriptomic single cell

data_processing:
The processing pipeline provided by Parse Biosciences (split-pipe v1.1.1) was used with default settings to align sequencing reads to the GRCm38 mouse reference genome. Each of the 16 sublibraries was first processed individually using the command split-pipe –mode all, and the output of the 16 sublibraries was combined using split-pipe –mode combine.
Cell barcodes were filtered to include only cells meeting the following criteria: (1) expressing between 200 and 10,000 genes, (2) having between 500 and 100,000 read counts, and (3) having less than 10% of reads map to mitochondrial genes. Scrublet was used to simulate doublets and assign doublet scores to cells based on a k-nearest-neighbor classifier.  Cells with doublet scores >0.12 were removed from the dataset. Read counts were normalized per cell using the scanpy function ‘normalize_total’ with default parameters and scaled for variance stabilization using a shifted logarithm transformation (log X+1,  where X is the normalized counts). Cell types were annotated using SCINA as described in the manuscript.
Assembly: GRCm38
Supplementary files format and content: h5ad file containing raw and normalized count data from all 16 sublibraries, annotated by sublibrary, cell type, sample and sample characteristics including type (bulk or cancer cell fraction), age (young or old) and tumor genotype.

molecule: total RNA

source_name: Tumor-bearing lung

extract_protocol:
Whole tumor-bearing lungs were finely minced immediately after harvesting and enzymatically dissociated using collagenase IV, dispase, and trypsin at 37°C for 30 minutes. Bulk cell suspensions were viably frozen in Bambanker cryopreservation media (Wako Chemicals, 302-14681) at -80°C before transfer to liquid nitrogen. Cells were thawed and stained with antibodies against CD45, CD31, F4/80, and Ter119 (all from BioLegend) to identify hematopoietic and endothelial cells. Each sample was sorted for viability (DAPI-negative) and divided into two compartments: (1) “cancer cell” samples containing Tomatopos, CD45neg, CD3 neg , F4/80 neg  and Ter119 neg  cells which are presumed to be cancer cells, and (2) “bulk” samples containing all other viable cells. FACSAria™ sorters (BD Biosciences) were used for all cell sorting. Samples were fixed immediately after sorting using Parse Biosciences Cell Fixation kits (v2, May 2023) and stored at -20°C. To maximize recovery for cancer cell samples where we had limited input material, we used a modified version of the Parse fixation protocol. Specifically, all volumes were scaled down to ¼ of the recommended amount so that the entirety of the final suspension of fixed cells could be loaded into the plate used for barcoding and library preparation.
Samples were processed for multiplexed single-cell RNA-sequencing using the Parse Biosciences WT Mega v2 kit according to the manufacturer’s instructions. This kit uses a combinatorial barcoding approach, allowed multiplexing of all samples into 16 sublibraries, each containing a mixture of cells from all samples. Samples for this experiment were loaded into the kit and processed alongside and sequenced with samples from another experiment.

value: Tumor-bearing lung

value: Multiple

value: Kras(L/+); Tom (T/T); Cas9 (C/C)


title: MC38-MHC-II, Replicate2


title: gpnmb+/+ cryoinjured ventricle  (injury and borderzone region-BZI) , 96 hpci r2

country: Germany

library_source: transcriptomic

tag: treatment


title: gpnmb+/+ cryoinjured ventricle  (injury and borderzone region-BZI) , 96 hpci r1


title: MC38-Angio, Replicate3


title: MC38-MHC-II, Replicate1


title: Dissociated tumor-bearing lung, mixed age and genotype (all samples represented), sublibrary 8

description:
Library name: Parse library 8
Parse Biosciences WT Mega v2


title: liver-E13-7h-Ctl-rep1

type: RNA

city: Mont de Marsan

first: Marianne

last: Houssier

address: 371 rue du ruisseau

department: GB

country: France

institute: INRA NUMEA/IUT UPPA

data_processing:
Real time quantitative PCR results were analyzed using the Fluidigm real-time PCR analysis software v.4.1.3.   The relative expression was normalized with four reference genes (ActB, Luciferase, STAB1 and USP9X for for the hour kinetic, and HPRT1, Luciferase, STAB1 and UPS9X for the daily kinetic), selected according to the function GeNorm from the package CtrlGene of R (v.3.6.2).
Tests have been adapted to compare the relative expression between groups for the two trials (n=6 minimum) for each timing (2 ways analysis was excluded due to the flattening of the TM effects)

label: EVAGREEN

organism: Anas platyrhynchos x Cairina moschata

source_name: liver at embryonic day 13, 7h after the increase of temperature

label_protocol: The sample amplifications were realized in two steps by using the Fluidigm method. A first pre-amplification with Preamp Master Mix (Fluidigm) was done following program: 95°C/10 min and 14 cycles of 95°C/15 sec and 60°C/4 min. Pre-amplified samples were treated by exonuclease (NEB) before a low EDTA buffer (10mM Tris-HCL, 0.1 mM EDTA) dilution and before moving samples to a 96x96 chip for Fluidigm Gene Expression Array. The reaction was made using 20× EvaGreen (Interchim) dye following the program:70°C/2400 sec, 60°C/30 sec, 30 cycles of 96°C/5 sec and 60°C/20 sec.

extract_protocol: In the first trial whole livers (8 per condition) were collected 30 minutes, 1h, 2h, 3h, 4h, 5h and 7h after the first day of temperature increase (E13). In the second trial, whole livers (8 per condition) were collected 1 hour after the daily temperature increase (5 p.m.), 3, 7 and 11 days after the temperature increase (E16, E20 and E24) and three days after the end of the temperature increase, at hatching (E30). Similar samples were taken at the same times for the control group, not exposed to the temperature increase. The livers were immediately immersed in liquid nitrogen before being stored at -80°C.

value: liver

tag: developmental stage

value: embryonic day 13

tag: time

value: 7h after the increase of temperature

tag: group

value: Ctl group


title: gpnmb-/- cryoinjured ventricle (injury and borderzone region-BZI), 96 hpci r2

value: gpnmb-/- (mutant)


title: MC38-Angio, Replicate2


title: gpnmb-/- cryoinjured ventricle (injury and borderzone region-BZI), 96 hpci r3


title: MC38-Angio, Replicate1


title: 4T1-MHCII, Replicate4

data_processing:
We applied the RNA-Seq immune analysis pipeline (RIMA) to analyze bulk RNA-Seq data. In brief, sequencing reads were aligned to the mouse reference genome (GRCm38/mm10) using STAR v2.6.1d. Salmon v0.13.1 was utilized to map transcripts to genes and generate a gene count matrix.
Differentially expressed genes were identified using DESeq2 v1.34.0, with an adjusted P-value (FDR) threshold of <0.05 for determining significance. The replicates of RNA-Seq from each condition were considered as a covariate in DESeq2.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include raw counts for each Sample
Supplementary files format and content: csv file includes TPM values for each Sample

extract_protocol:
RNA was lysis by TCL buffer(QIAGEN) and extracted by VAHTS RNA Clean Beads (Vazyme).
RNA was reverse transcribed by Maxima™ H Minus cDNA synthesis kit(Invitrogen) into cDNA, then cDNA was amplified by KAPA PCR mix(TOYOBO).  Libraries for RNA-seq were prepared using TruePrep DNA Library Prep Kit V2 for Illumina kit(Vazyme) following manufacturer's protocols.

value: Primary macrophages

value: Tumor infiltrating immune cells


title: gpnmb-/- cryoinjured ventricle (injury and borderzone region-BZI), 96 hpci r1

value: cardiac tissue (ventricle)


title: Day 27 PB Kidney Organoid snRNA-seq

city: Los Angeles

first: Nils

last: Lindström

address: 1425 San Pablo Street Lab 409

department: Stem Cell Biology and Regenerative Medicine

institute: University of Southern California (USC) -

description: Library name: Day 27 PB snRNA-seq

data_processing:
Raw fastq files were processed using Cell Ranger (v9.0.0), as described in the text.
Feature-barcode matricies were read into Seurat 5.2 using Read10X, as described in the text.
Assembly: Homo sapiens, GRCh38-2024-A
Supplementary files format and content: The processed .rds file contains the merged snRNA-sequencing data for day 21 proximal-biased and day 27 proximal-biased samples. The file includes the merged processed single-nucleus RNA-sequencing object.

molecule: nuclear RNA

organism: Homo sapiens

source_name: Kidney organoid

growth_protocol: Takasato et al., 2016 Nature Protocols

extract_protocol:
6 individual organoids from multiple independent wells were snap-frozen in liquid nitrogen before nuclei isolation as described in Kim et al., 2024 Developmental Cell.
10X Genomics Chromium Next GEM Single Cell Multiome Reagents PN-1000283, following 10X Genomics CG000338 Rev E.

treatment_protocol: Organoids were treated with 10 uM LY294002 between days 10 and 12 of kidney organoid differentiation for proximal biasing.

value: Kidney organoid

value: Proximal-biased:10 µM LY294002 between differentiation days 10 and 12 (48 hours)


title: Day 21 PB Kidney Organoid snRNA-seq

description: Library name: Day 21 PB snRNA-seq


title: 4T1-MHCII, Replicate2

value: Tumor


title: Chd2KD_rep3_noab

city: Pittsburgh

first: Sarah

middle: J

last: Hainer

state: PA

address: 4249 Fifth Ave

department: Department of Biological Sciecnes

institute: University of Pittsburgh

description:
Library name: Chd2KD_rep3_noab
Protein A- MNase-digested DNA

data_processing:
Fastq files were trimmed to 25 bp using an awk command. Integrity of sequencing data was verified by fastqc version 0.11.9. Reads were aligned to the Mus musculus (mm10) and Drosophila melanogaster (dm6) genomes using bowtie2 version 2.4.5 with parameters -I 10 -X 1000 -N 1 --very-sensitive for paired end-sequencing. Low quality reads were filtered using Picard version 2.5.0 and filtered for mapping quality (MAPQ ≥ 10) using SAMtools version 1.14. Reads were counted with SAMtools version 1.14 flagstat. Datasets were computationally size selected using SAMtools, with 150-500 bp for H3K4me3 and 130-500 bp for CHD1. For H3K4me3, normalized bigwigs were generated using bamcoverage with parameters --centerReads --binSize 5 –scaleFactor x, where the scaling factor was determined for each sample using Drosophila reads. For CHD1 CUT&RUN, normalized bigwigs were generated using bamcoverage with parameters --centerReads --binSize 5 --normalizeUsing RPGC --effectiveGenomeSize 2308125349. Normalized bigwigs for three or four replicates were averaged using WiggleTools and the ‘mean’ function. Browser tracks were generated from merged bigwig files using IGV genome browser. To generate metaplots, the output of deepTools plotProfile containing binned data (10 bp) from TSS to 2 kb or -1 kb to +2 kb. Output from plotProfile was plotted in GraphPad Prism 10 to generate final metaplots. The mm10 Encode Blacklisted regions were also excluded from the normalized bigwigs.
Assembly: mm10, dm6
Supplementary files format and content: Bigwig files contain Drosophila spike in normalized fragment sizes corresponding to 150-500bp for H3K4me3 CUT&RUNs
Library strategy: CUT&Run

growth_protocol: ES-E14TG2a (E14) embryonic stem (ES) cells from male Mus musculus origin (RRID:CVCL9108) were cultured in Dulbecco’s Modified Eagle Medium (Sigma-Aldrich, D6546-500 mL), 10% Fetal Bovine Serum (Sigma-Aldrich, F2442), nonessential amino acids (Corning, 25-025-CI), 2mM L-glutamine (Corning, 25-005-CI), β-mercaptoethanol, and Leukemia Inhibitory Factor (LIF). Cells were cultured under naïve conditions (serum/LIF +2i), with 3 nM CHIR99021 GSK inhibitor (Med Chem Express, HY-10182/CS-0181) and 1 nM PD0325901 MEK inhibitor (Med Chem Express, HY-10254CS-0062). Cells were passaged every 48 hours using 0.02% trypsin (Corning, 25-052-CI) and quenching with fresh medium. ES cells were grown on plates precoated with 0.2% porcine skin gelatin type A (Sigma Aldrich, G1890) at 37°C in a humified incubator with 5% CO2.

extract_protocol:
Nuclei were incubated for 1 hour at room temperature with rotation with rabbit anti-H3K4me3 (Millipore Sigma, Cat# 05-745R, 3697296). Control samples were treated in the same conditions without antibody. Samples were washed twice with wash buffer and incubated for 30 min at room temperature with rotation in wash buffer containing recombinant Protein A-MNase (pA-MN) (1:250). Samples were washed twice with wash buffer and equilibrated at 0°C in an ice bath. Three mM CaCl2 was added to each sample to activate MNase cleavage and digested in an ice bath for 30 min. Digestion for H3K4me3 samples was stopped after 30 min using a stop buffer (20 mM EDTA. 4 mM EGTA, 200 mM NaCl, 50 ug/mL RNase A). Samples were incubated at 37°C for 20 min to release genomic fragments and fragments were then separated through centrifugation. Samples were incubated at 4°C for 1 hr to release genomic fragments. The salt concentration was increased to 500 mM for Chd1 samples, RNase A was added, and samples were incubated at 37°C for 20 min to release genomic fragments. Fragments for all samples were isolated and extracted to be used as input for library build.
Libraries were built using NEB Next II Ultra DNA library kit (NEB E7645L) and AMPure XP beads (Beckman Coulter A63881) purifications. Fragments were PCR amplified with 15 cycles. Samples were then pooled and paired-end sequenced on an Illumina NextSeq2000 to a depth of ~10 million uniquely mapped reads per sample.

treatment_protocol:
ES cells treated with an RNAi reagent targeting control (non-targeting GFP), Chd1, or Chd2 for 48 hours prior to harvesting nuclei for CUT&RUN.
CUT&RUN was performed for aliquots of 100,00 nuclei. Three replicates for wild-type and mutant lines were assayed, except for chd1∆CHCT where two technical replicates of two cell lines were used. Nuclei were extracted using a nuclear extraction buffer (20 mM HEPES-KOH, pH 7.9, 10 mM KCl, 0.5 mM spermidine, 0.1% Triton X-100, 20% glycerol, protease inhibitors) and flash frozen.

value: embryonic stem cells

value: wild type

value: Chd2 esiRNA KD

value: IgG

tag: batch


title: 4T1-MHCII, Replicate3

value: WT


title: Chd2KD_rep2_noab

description:
Library name: Chd2KD_rep2_noab
Protein A- MNase-digested DNA


title: Chd2KD_rep1_noab

description:
Library name: Chd2KD_rep1_noab
Protein A- MNase-digested DNA


title: isw1_null_chd1_null_bio4

data_processing:
Integrity of sequencing data was verified by fastqc version 0.11.9. Fastq files were trimmed with trimmomatic version 0.38 with parameters ILLUMINACLIP:TruSeq3-PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 CROP:36 MINLEN:24. Reads were aligned to a combined genome containing S. cerevisiae and S. pombe using bowtie2 version 2.4.1 with parameters -q -N 1 -X 1000 for paired-end sequencing. S. cerevisiae and S. pombe reads were then separated into different bam files for each respective genome. Reads were counted with SAMtools version 1.12 flagstat. Although S. pombe was added to samples, spike-in normalization was not used to generate spike-in normalized bigwigs. Normalized bigwigs were generated using deepTools version 3.3.0 bamcoverage with parameters --normalizeUsing CPM --MNase --binSize 1 --smoothLength 10 --minFragmentLength 137 --maxFragmentLength 157 to examine mononucleosome-sized fragments [93]. Other MNase-protected fragments were bioinformatically size-selected using bamCoverage, including subnucleosomes (90-110bp), hexasome-nucleosomes (230-270bp), and dinucleosomes (290-350bp). Normalized bigwigs for two to four biological replicates were averaged using WiggleTools and the ‘mean’ function.
Assembly: sacCer3
Supplementary files format and content: Bigwig files contain CPM-normalized fragment sizes corresponding to mononucleosomes (137-157bp), subnucleosomes (90-110bp), hexasome-nucleosomes (230-270bp), or dinucleosomes (290-350bp)

organism: Saccharomyces cerevisiae

growth_protocol: Strains were cultured at 30°C in YPD medium supplemented with 400 µM tryptophan to log phase (OD=0.5-0.6).

extract_protocol:
Cell pellets were washed in 10 mL water, transferred to 15 mL tubes, and then re-spun for 5 min at 4000 rpm at 4°C. Liquid was removed from cell pellets and then cells were flash frozen in liquid nitrogen. Cell pellets were resuspended in sorbitol-Tris buffer (1 M sorbitol, 50 mM Tris-HCl pH 7.4, 125 mM ß-mercaptoethanol) and then spheroplasted with Zymolyase 100T (US Biological, NC0439195) for 30 min at 30°C while rotating. Spheroplasting efficiency was visually determined under the microscope after mixing 10 µL spheroplasts with 10 µL 10% SDS. Spheroplasted cells were centrifuged at 4000 rpm for 10 min at 4°C. The supernatant was removed, and the pellet was resuspended to 5 mL volume in NP buffer (1 M sorbitol, 50 mM NaCl, 10 mM Tris-HCl pH 7.4, 5 mM MgCl2, 1 mM CaCl2, 0.075% NP40, 1 mM ß-mercaptoethanol, and 500 µM spermidine). MNase (500 units; Sigma, #N5386) was resuspended from lyophilized powder in 500 µL Ex50 buffer (10 mM HEPES pH 7.5, 50 mM NaCl, 1.5 mM MgCl2, 0.5mM EGTA pH 8.0, 10% glycerol v/v, 1 mM DTT, and 0.2 mM PMSF) and stored in aliquots at -20°C. Spheroplasted cells in 600 µL aliquots were treated with MNase in a titration ranging from 2 µL to 4.5 µL MNase for 20 min at 37°C with rotation. Then, the reaction was quenched with 100 µL STOP buffer (5% SDS, 100 mM EDTA). Protein was digested and crosslinks were reversed using 30 µL Proteinase K (20 mg/mL; Meridian Bioscience, #BIO-37084) overnight at 65°C.   DNA was purified using equal volume PCI followed by vortexing and centrifugation for 10 min max speed at 4°C in a microcentrifuge. The aqueous layer was transferred to a new tube and thoroughly mixed with equal volume chloroform isoamyl alcohol (24:1 ratio). Samples were centrifuged again for 10 min at 14,000 rpm at 4°C. The aqueous layer was transferred to a new tube and treated with 2 µL glycogen (20 mg/mL), 0.2 M NaCl, and 0.7x-1x volume isopropanol. DNA was precipitated at -20°C for 1 hr, and then centrifuged in a microcentrifuge at maximum speed for 30 min at 4°C. The supernatant was removed and the DNA pellet was washed using 70% ethanol and air dried for 2 mins. The DNA pellet was resuspended in 40 µL 10 mM Tris-HCl pH 7.5. Resuspended DNA was treated with 5 µL RNase A (Thermo Fisher Scientific, EN0531) for 1 hr at 37°C.   To verify MNase digestion, a 15 µL sample of DNA was purified using the E.Z.N.A. Cycle Pure Kit (Omega Bio-Tek, D6492) and separated on a 2% TBE gel. The 3.5 µL MNase-treated condition was chosen for all samples based on the titration series and prepared without DNA size selection. S. pombe MNase-treated chromatin was separately prepared and mononucleosome-sized DNA fragments were prepared by gel isolation and spiked in to S. cerevisiae MNase-digested DNA
. Spiked-in MNase-treated DNA was purified using the E.Z.N.A. Cycle Pure kit. Sequencing libraries were prepared with the NEB Next II Ultra DNA library kit (NEB, E7645L) using 50 ng DNA input and 3 PCR cycles. Library quality was verified using fragment analysis (Fragment Analyzer, Advanced Analytical) and submitted for sequencing on an Illumina NextSeq 500 or 2000 instrument for paired-end sequencing to a depth of ~15million uniquely mapped reads per sample.

treatment_protocol: 100 mL cells were treated with 2% formaldehyde for 30 min at room temperature with constant shaking. Crosslinking was quenched with 125 mM final concentration glycine for 10 min with constant shaking. Cells were centrifuged for 10 min at 4000 rpm at 4°C. Cell pellets were washed in 10 mL water, transferred to 15 mL tubes, and then re-spun for 5 min at 4000 rpm at 4°C. Liquid was removed from cell pellets and then cells were flash frozen in liquid nitrogen.

tag: strain

tag: genetic information

value: his3∆200 lys2-128∂ leu2∆1 ura3-52 trp1∆63  chd1∆::LEU2 3xHA-RTF1 isw1∆::HIS3

tag: molecule subtype

value: MNase-digested DNA


title: isw1_null_chd1_null_bio3


title: Chd1KD_rep3_noab

description:
Library name: Chd1KD_rep3_noab
Protein A- MNase-digested DNA

value: Chd1 esiRNA KD


title: Chd1KD_rep2_noab

description:
Library name: Chd1KD_rep2_noab
Protein A- MNase-digested DNA


title: Chd1KD_rep1_noab

description:
Library name: Chd1KD_rep1_noab
Protein A- MNase-digested DNA


title: 4T1-MHCII, Replicate1


title: 4T1-Angio, Replicate4


title: control_rep2_noab

description:
Library name: control_rep2_noab
Protein A- MNase-digested DNA

value: non-targeted esiRNA KD


title: isw1_null_chd1_null_bio2


title: control_rep3_noab

description:
Library name: control_rep3_noab
Protein A- MNase-digested DNA


title: 4T1-Angio, Replicate3


title: control_rep1_noab

description:
Library name: control_rep1_noab
Protein A- MNase-digested DNA


title: Chd2KD_rep3_H3K4me3

description:
Library name: Chd2KD_rep3_H3K4me3
Protein A- MNase-digested DNA

value: H3K4me3 (Millipore Sigma, Cat# 05-745R, 3697296)


title: isw1_null_rtf1_null_bio4

value: his3∆200 lys2-128∂ leu2∆1 ura3-52 trp1∆63  3xHSV-CHD1 rtf1∆101::LEU2 isw1∆::HIS3


title: 4T1-Angio, Replicate1

value: Primary macrophages


title: 4T1-Angio, Replicate2

value: Tumor infiltrating immune cells


title: 4T1-Mono, Replicate4


title: isw1_null_rtf1_null_bio3


title: Chd1KD_rep3_H3K4me3

description:
Library name: Chd1KD_rep3_H3K4me3
Protein A- MNase-digested DNA


title: isw1_null_rtf1_null_bio2


title: Chd1KD_rep2_H3K4me3

description:
Library name: Chd1KD_rep2_H3K4me3
Protein A- MNase-digested DNA


title: Chd1KD_rep1_H3K4me3

description:
Library name: Chd1KD_rep1_H3K4me3
Protein A- MNase-digested DNA


title: 4T1-Mono, Replicate3


title: isw1_null_rtf1_null_bio1


title: 4T1-Mono, Replicate2


title: control_rep1_H3K4me3

description:
Library name: control_rep1_H3K4me3
Protein A- MNase-digested DNA


title: control_rep2_H3K4me3

description:
Library name: control_rep2_H3K4me3
Protein A- MNase-digested DNA


title: control_rep3_H3K4me3

description:
Library name: control_rep3_H3K4me3
Protein A- MNase-digested DNA


title: isw1_null_chd1_chct_bio3

value: his3∆200 lys2-128∂ leu2∆1 ura3-52 trp1∆63  3xHSV-chd1∆CHCT 3xHA-RTF1 isw1∆::HIS3


title: 4T1-Mono, Replicate1


title: isw1_null_chd1_null_bio1


title: chd1_chct_bio2b_H3K36me3_set2

description:
Library name: chd1_chct_bio2b_H3K36me3_set2
Protein A- MNase-digested DNA

data_processing:
Fastq files were trimmed to 25 bp using an awk command. Integrity of sequencing data was verified by fastqc version 0.11.9. Reads were aligned to the Mus musculus (mm10) and Drosophila melanogaster (dm6) genomes using bowtie2 version 2.4.5 with parameters -I 10 -X 1000 -N 1 --very-sensitive for paired end-sequencing. Low quality reads were filtered using Picard version 2.5.0 and filtered for mapping quality (MAPQ ≥ 10) using SAMtools version 1.14. Reads were counted with SAMtools version 1.14 flagstat. Datasets were computationally size selected using SAMtools, with 150-500 bp for H3K36me3 and 130-500 bp for CHD1. For H3K36me3, normalized bigwigs were generated using bamcoverage with parameters --centerReads --binSize 5 –scaleFactor x, where the scaling factor was determined for each sample using Drosophila reads. For CHD1 CUT&RUN, normalized bigwigs were generated using bamcoverage with parameters --centerReads --binSize 5 --normalizeUsing RPGC --effectiveGenomeSize 2308125349. Normalized bigwigs for three or four replicates were averaged using WiggleTools and the ‘mean’ function. Browser tracks were generated from merged bigwig files using IGV genome browser. To generate metaplots, the output of deepTools plotProfile containing binned data (10 bp) from TSS to 2 kb or -1 kb to +2 kb. Output from plotProfile was plotted in GraphPad Prism 10 to generate final metaplots. The mm10 Encode Blacklisted regions were also excluded from the normalized bigwigs.
Assembly: mm10, dm6
Supplementary files format and content: Bigwig files contain Drosophila spike in normalized fragment sizes corresponding to 150-500bp for H3K36me3 CUT&RUNs and RPGC-normalized fragment sizes corresponding to 130-500bp for CHD1 CUT&RUNs
Library strategy: CUT&Run

extract_protocol:
Nuclei were incubated for 1 hour at room temperature with rotation with rabbit anti-H3K36me3 (Invitrogen, Cat# MA5-24687, ZJ4521201). Control samples were treated in the same conditions without antibody. Samples were washed twice with wash buffer and incubated for 30 min at room temperature with rotation in wash buffer containing recombinant Protein A-MNase (pA-MN) (1:250). Samples were washed twice with wash buffer and equilibrated at 0°C in an ice bath. Three mM CaCl2 was added to each sample to activate MNase cleavage and digested in an ice bath for 30 min. Digestion for H3K36me3 samples was stopped after 30 min using a stop buffer (20 mM EDTA. 4 mM EGTA, 200 mM NaCl, 50 ug/mL RNase A). Samples were incubated at 37°C for 20 min to release genomic fragments and fragments were then separated through centrifugation. Samples were incubated at 4°C for 1 hr to release genomic fragments. The salt concentration was increased to 500 mM for Chd1 samples, RNase A was added, and samples were incubated at 37°C for 20 min to release genomic fragments. Fragments for all samples were isolated and extracted to be used as input for library build.
Libraries were built using NEB Next II Ultra DNA library kit (NEB E7645L) and AMPure XP beads (Beckman Coulter A63881) purifications. Fragments were PCR amplified with 15 cycles. Samples were then pooled and paired-end sequenced on an Illumina NextSeq2000 to a depth of ~10 million uniquely mapped reads per sample.

treatment_protocol: CUT&RUN was performed for aliquots of 100,00 nuclei. Three replicates for wild-type and mutant lines were assayed, except for chd1∆CHCT where two technical replicates of two cell lines were used. Nuclei were extracted using a nuclear extraction buffer (20 mM HEPES-KOH, pH 7.9, 10 mM KCl, 0.5 mM spermidine, 0.1% Triton X-100, 20% glycerol, protease inhibitors) and flash frozen.


title: chd1_chct_bio2a_H3K36me3_set2

description:
Library name: chd1_chct_bio2a_H3K36me3_set2
Protein A- MNase-digested DNA


title: chd1_chct_bio1b_H3K36me3_set2

description:
Library name: chd1_chct_bio1b_H3K36me3_set2
Protein A- MNase-digested DNA


title: 4T1-MHC-II, Replicate3

data_processing:
The fastq files were processed using the ENCODE ATAC-seq pipeline to generate bam files and bigwig files. Peaks were called by Genrich in ATAC-seq mode.
Deeptools was used for the heatmap plots. ATAC-seq peaks from all study samples were merged to create a union set of sites. Read densities were calculated for each peak for each sample, and differential peaks between the treatment group and the control group were identified by DiffBind.
Assembly: mm10
Supplementary files format and content: BigWig files generated by merging the replicates.

value: Primary cells

value: Tumor-infiltrating immune cells


title: Chd2KD_rep2_H3K4me3

description:
Library name: Chd2KD_rep2_H3K4me3
Protein A- MNase-digested DNA


title: isw1_null_chd1_chct_bio1


title: isw1_null_chd1_chct_bio2


title: chd1_chct_bio1a_H3K36me3_set2

description:
Library name: chd1_chct_bio1a_H3K36me3_set2
Protein A- MNase-digested DNA


title: Chd2KD_rep1_H3K4me3

description:
Library name: Chd2KD_rep1_H3K4me3
Protein A- MNase-digested DNA


title: isw1_null_rtf1_11_A_bio2

value: his3∆200 lys2-128∂ leu2∆1 ura3-52  3xHSV-CHD1 3XHA-rtf1(11A) isw1∆::HIS3


title: 4T1-MHC-II, Replicate2

value: Tumor


title: 4T1-MHC-II, Replicate1


title: chd2_chct_bio3_H3K36me3_set1

description:
Library name: chd2_chct_bio3_H3K36me3_set1
Protein A- MNase-digested DNA

value: embryonic stem cells


title: wildtype_bio2_H3K36me3_set2

description:
Library name: wildtype_bio2_H3K36me3_set2
Protein A- MNase-digested DNA

value: wild type


title: isw1_null_rtf1_11_A_bio1


title: 4T1-Angio, Replicate3


title: rtf1_AAAA_bio3_H3K36me3_set1

description:
Library name: rtf1_AAAA_bio3_H3K36me3_set1
Protein A- MNase-digested DNA


title: rtf1_AAAA_bio2_H3K36me3_set1

description:
Library name: rtf1_AAAA_bio2_H3K36me3_set1
Protein A- MNase-digested DNA


title: isw1_null_rtf1_8_9_A_bio2

value: his3∆200 lys2-128∂ leu2∆1 ura3-52 trp1∆63  3xHSV-CHD1 3XHA-rtf1(8-9A) isw1∆::HIS3


title: 4T1-Angio, Replicate2

value: WT


title: chd2_chct_bio1_H3K36me3_set1

description:
Library name: chd2_chct_bio1_H3K36me3_set1
Protein A- MNase-digested DNA


title: 4T1-Angio, Replicate1


title: rtf1_AAAA_bio1_H3K36me3_set1

description:
Library name: rtf1_AAAA_bio1_H3K36me3_set1
Protein A- MNase-digested DNA


title: wildtype_bio3_H3K36me3_set1

description:
Library name: wildtype_bio3_H3K36me3_set1
Protein A- MNase-digested DNA


title: isw1_null_bio2

value: his3∆200 lys2-128∂ leu2∆1 ura3-52 trp1∆63  3xHSV-CHD1 3xHA-RTF1 isw1∆::HIS3


title: 4T1-Mono, Replicate3


title: wildtype_bio2_H3K36me3_set1

description:
Library name: wildtype_bio2_H3K36me3_set1
Protein A- MNase-digested DNA


title: wildtype_bio1_H3K36me3_set1

description:
Library name: wildtype_bio1_H3K36me3_set1
Protein A- MNase-digested DNA


title: chd1_chct_bio2b_noab

description: Protein A- MNase-digested DNA

data_processing:
Integrity of sequencing data was verified by fastqc version 0.11.9. Reads were aligned to the Mus musculus (mm10) and Drosophila melanogaster (dm6) genomes using bowtie2 version 2.4.5 with parameters -I 10 -X 1000 -N 1 --very-sensitive for paired end-sequencing. Low quality reads were filtered using Picard version 2.5.0 and filtered for mapping quality (MAPQ ≥ 10) using SAMtools version 1.14. Reads were counted with SAMtools version 1.14 flagstat. Datasets were computationally size selected using SAMtools, with 150-500 bp for noab and 130-500 bp for CHD1. For noab, normalized bigwigs were generated using bamcoverage with parameters --centerReads --binSize 5 –scaleFactor x, where the scaling factor was determined for each sample using Drosophila reads. For CHD1 CUT&RUN, normalized bigwigs were generated using bamcoverage with parameters --centerReads --binSize 5 --normalizeUsing RPGC --effectiveGenomeSize 2308125349. Normalized bigwigs for three or four replicates were averaged using WiggleTools and the ‘mean’ function. Browser tracks were generated from merged bigwig files using IGV genome browser. To generate metaplots, the output of deepTools plotProfile containing binned data (10 bp) from TSS to 2 kb or -1 kb to +2 kb. Output from plotProfile was plotted in GraphPad Prism 10 to generate final metaplots. The mm10 Encode Blacklisted regions were also excluded from the normalized bigwigs.
Assembly: mm10, dm6
Supplementary files format and content: Bigwig files contain normalized fragment sizes corresponding to 150-500bp
Library strategy: CUT&RUN

extract_protocol:
Control samples (noab) were treated in the same conditions without antibody. Samples were washed twice with wash buffer and incubated for 30 min at room temperature with rotation in wash buffer containing recombinant Protein A-MNase (pA-MN) (1:250). Samples were washed twice with wash buffer and equilibrated at 0°C in an ice bath. Three mM CaCl2 was added to each sample to activate MNase cleavage and digested in an ice bath for 30 min. Digestion for noab samples was stopped after 30 min using a stop buffer (20 mM EDTA. 4 mM EGTA, 200 mM NaCl, 50 ug/mL RNase A). Samples were incubated at 37°C for 20 min to release genomic fragments and fragments were then separated through centrifugation. Digestion for Chd1 samples was stopped after 30 min using a low salt stop treatment (10 mM EDTA, 2 mM EGTA, 150 nM NaCl, 5 mM Triton-X). Samples were incubated at 4°C for 1 hr to release genomic fragments. The salt concentration was increased to 500 mM for Chd1 samples, RNase A was added, and samples were incubated at 37°C for 20 min to release genomic fragments. Fragments for all samples were isolated and extracted to be used as input for library build.
Libraries were built using NEB Next II Ultra DNA library kit (NEB E7645L) and AMPure XP beads (Beckman Coulter A63881) purifications. Fragments were PCR amplified with 15 cycles. Samples were then pooled and paired-end sequenced on an Illumina NextSeq2000 to a depth of ~10 million uniquely mapped reads per sample.

tag: cut&run antibody

value: no primary antibody


title: Hnf1a KO mouse islets NS 3

city: Barcelona

first: Edgar

last: Bernardo

state: Barcelona

address: C/ del Dr. Aiguader, 88,

country: Spain

institute: CRG

data_processing:
RNA-seq reads were aligned to the mouse (GRCm38.p6 v.M24) or human (GRCh38 gencode v.42) transcriptomes using STAR (v2.7.10b) and Salmon (v1.9.0)
Salmon quant files we employed for differential gene expression using DESeq2 (v1.38.0)
For RNA-seq track visualization, STAR was used to generate BAM files that were subsequently converted into bigwig files with Deeptools (v3.5.1)
BAM files were used for differential alternative splicing analysis with rMATS (turbo v4.1.2)
Assembly: mm10
Assembly: hg38
Supplementary files format and content: tab-delimited Excel files including TPM counts (mouse islets) or Log2 TPM (EndoC-BH3 cells), differential gene expression analysis (DESeq2) and differential alternative splicing analysis (rMATS)

source_name: Pancreatic islets

growth_protocol:
EndoC-βH3 cells were cultured in plates coated with extracellular matrix gel from murine sarcoma and 2μg/mL fibronectin using Advanced DMEM/F12 supplemented with 2% fatty acid-free Bovine Serum Albumin Fraction V, 6.7ng/mL sodium selenite, 50μM 2-mercaptoethanol, 5.5μg/mL human transferrin, 10mM nicotinamide, 1% GlutaMAX and 100 U/mL Penicillin-Streptomycin.
MIN6 cells were cultured in DMEM High Glucose supplemented with 15% FBS, 1% GlutaMAX, 1% Penicillin-Streptomycin and 2.5μl β-mercaptoethanol.
Mouse pancreatic Islets cultured after isolation for 1-2 days in RPMI with 10% FBS and Pen-Strep (1:100) at 37ºC and 5% CO2.

extract_protocol:
Total RNA isolated using NucleoSpin Plus RNA kit (Cultek). 1ug of RNA was used for library preparation
RNAseq libraries were prepared using Trueseq Stranded mRNA Sample Prep Kit (Illumina)

value: Pancreatic islets

value: Hnf1a KO


title: 4T1-Mono, Replicate2


title: chd2_chct_bio2_H3K36me3_set1

description:
Library name: chd2_chct_bio2_H3K36me3_set1
Protein A- MNase-digested DNA


title: Hnf1a KO mouse islets NS 4


title: 4T1-Mono, Replicate1


title: chd1_null_bio2

value: his3∆200 lys2-128∂ leu2∆1 ura3-52 trp1∆63 KanMx::GAL1p-FLO8-HIS3 chd1∆::LEU2 3xHA-RTF1

value: MNase-digested DNA


title: isw1_null_bio1


title: Hnf1a KO mouse islets NS 2


title: chd1_chct_bio1b_noab

description: Protein A- MNase-digested DNA


title: chd1_chct_bio2a_noab

description: Protein A- MNase-digested DNA


title: 1-sgFlcn, Replicate3

source_name: Bone marrow

extract_protocol:
RNA from 5*10^5 cells was extracted and purified with TRIzol reagent (Thermo Fisher) according to manufacturer’s instructions.
RNA-seq libraries were prepared using Illumina TruSeq Stranded mRNA kit following manufacturer’s instructions with 5 mg of input RNA.

value: Bone marrow

value: Primary macrophages

value: Bone marrow-derived macrophages

value: sgRNA targeting Flcn transduction and 4T1 tumor conditioned medium


title: Hnf1a KO mouse islets NS 1


title: chd1_null_bio1


title: rtf1_null_bio4

value: his3∆200 lys2-128∂ leu2∆1 ura3-52 trp1∆63 KanMx::GAL1p-FLO8-HIS3 3xHSV-CHD1 rtf1∆101::LEU2


title: isw1_null_rtf1_8_9_A_bio1


title: 1-sgFlcn, Replicate2


title: 1-sgFlcn, Replicate1


title: Hnf1a WT mouse islets Control 4


title: rtf1_null_bio3


title: Hnf1a WT mouse islets Control 3


title: rtf1_null_bio2


title: chd2_chct_bio2_noab

description: Protein A- MNase-digested DNA


title: 1-sgRreb1, Replicate3

value: sgRNA targeting Rreb1 transduction and 4T1 tumor conditioned medium


title: rtf1_null_bio1


title: Hnf1a WT mouse islets Control 2


title: 1-sgRreb1, Replicate2


title: Hnf1a WT mouse islets Control 1


title: rtf1_AAAA_bio3_noab

description: Protein A- MNase-digested DNA


title: chd1_chct_bio2

value: his3∆200 lys2-128∂ leu2∆1 ura3-52 trp1∆63 KanMx::GAL1p-FLO8-HIS3 3xHSV-chd1∆CHCT 3xHA-RTF1


title: 2-sgHif1a,Replicate3

value: sgRNA targeting Hif1a transduction and 4T1 tumor conditioned medium


title: 1-sgRreb1, Replicate1


title: 2-sgHif1a,Replicate2


title: input_chd1_null_input_set2

data_processing:
Integrity of sequencing data was verified by fastqc version 0.11.9. Fastq files were trimmed with trimmomatic version 0.38 with parameters ILLUMINACLIP:TruSeq3-PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 CROP:36 MINLEN:24. Reads were aligned to a combined genome containing S. cerevisiae and S. pombe using bowtie2 version 2.4.1 with parameters -q -N 1 -X 1000 for paired-end sequencing. S. cerevisiae and S. pombe reads were then separated into different bam files for each genome. Reads were counted with SAMtools version 1.12 flagstat. Normalized bigwigs were generated using deepTools version 3.3.0 bamcoverage with parameters --extendReads --binSize 10 –scaleFactor x, where the scaling factor was determined for each sample using S. pombe reads as described.[93,94] Normalized bigwigs for two to five biological replicates were averaged using WiggleTools and the ‘mean’ function.
Assembly: sacCer3, ASM294v2
Supplementary files format and content: Bigwig files contain spike-in normalized data from S. cerevisiae immunoprecipitated DNA.

growth_protocol: Yeast cultures (250 mL) were grown to log phase (OD=0.5-0.7) in YPD+Trp.

extract_protocol:
Cell pellets were resuspended in 1xFA buffer containing 0.5% SDS and 1 mM PMSF. Cells were lysed with acid-washed glass beads using 15 cycles of vortexing at maximum speed (30s on, 30s rest on ice). Lysate was separated from beads via syringe (10 mL, with P200 tip as filter), transferred to an ultracentrifuge tube (Beckman Coulter, #355603, Brea, CA), and centrifuged at 50,000 rpm for 20 min at 4°C in an ultracentrifuge (Beckman Coulter, Optima XPN-100). The supernatant was decanted, and the pellet was resuspended in 8 mL 1xFA buffer containing 0.1% SDS and 1 mM PMSF. The resuspension was spun in the ultracentrifuge as above, and the supernatant decanted. The resulting chromatin pellet was resuspended in 1.5 mL 1xFA containing 0.1% SDS and 1 mM PMSF and transferred to a 15 mL Bioruptor tube with sonication beads (Diagenode, C30010017). Chromatin  was sheared for 25 cycles (30s on and 30s off) at 4°C in a Bioruptor Pico (Diagenode, B01060010). Chromatin was transferred to an ultracentrifuge tube and 4.2 mL of 1xFA buffer containing 0.1% SDS and 1 mM PMSF was added. Chromatin was centrifuged at 50,000 rpm for 20 min at 4°C and the supernatant was retained, aliquoted, and flash frozen in liquid nitrogen. Chromatin aliquots were stored at -80°C.  S. pombe chromatin from strain KP08 was spiked-in to S. cerevisiae chromatin at a 1:9 protein ratio upon thawing of sheared chromatin. Chromatin was quantified using the Pierce BCA kit (Thermo Scientific, 23225). IPs were performed with 500 µg (for histone IPs) or 1000 µg (for all other IPs) spiked-in chromatin and samples were diluted to 700 µL or 1.4 mL in 1xFA buffer containing 0.1% SDS and 1 mM PMSF, respectively. ChIPs were performed with antibodies against the following epitopes/proteins: HSV (Sigma-Aldrich, H6030; 5 µl per 1000 µg), HA (Santa Cruz, HA-probe Antibody (F-7) AC, sc-7392; 60 µl per 1000 µg), Rpb1 (8WG16; BioLegend, 664906; 4 µL per 1000 µg), H3 (Abcam, ab1791; 1µL per 500 µg), H3K4me3 (Active Motif 39159, 39160; 2.5 µl per 500 µg), and H3K36me3 (Abcam ab9050: 6 µg per 500 µg). After overnight incubation of primary antibodies with chromatin, Protein A Sepharose beads (Cytiva, 17-5280-01) were added to HSV, 8WG16, and H3K4me3 reactions in an amount of 30 µL beads (50% slurry) per 500 µg chromatin. Protein G Sepharose beads (Cytiva, 17-0618-01) were added to H3 and H3K36me3 in an amount of 30 µL beads (50% slurry) per 500 µg chromatin. Samples with Protein A or G beads were rotated end-over-end for 2 hr at 4°C. IP reactions were performed as described above for ChIP-qPCR, with input samples performed in parallel. DNA was eluted in 100 µL 0.5X TE.
Libraries were prepared with the NEB Next II Ultra DNA library kit (NEB, E7645L) using 500 pg DNA input. Library quality was verified using fragment analysis (Fragment Analyzer, Advanced Analytical) and submitted for sequencing on an Illumina NextSeq 500 or 2000 instrument.

treatment_protocol: Cells were crosslinked with 1% formaldehyde for 20 min at room temperature with constant shaking, and quenched with a glycine-Tris solution (3 M glycine, 20 mM Tris-HCl). Cells were centrifuged at 3000 rpm for 10 min at 4°C, washed twice with 200 mL TBS (20 mM Tris-HCl pH 7.5, 150 mM NaCl), and centrifuged at 3000 rpm for 2 min at 4°C. Cells were resuspended in 1 mL 1xFA buffer containing 0.1% SDS (50 mM HEPES-KOH pH 7.5, 150 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate, 1 mM PMSF) and transferred to 15 mL tubes to spin at 3000 rpm for 5 min at 4°C. Supernatant was removed from cell pellets and cell pellets were flash frozen in liquid nitrogen.

tag: chip antibody

value: no antibody

value: input DNA from sonicated chromatin


title: chd1_chct_bio1a_noab

description: Protein A- MNase-digested DNA

value: embryonic stem cells


title: 2-sgHif1a,Replicate1


title: rtf1_11_A_bio4

value: his3∆200 lys2-128∂ leu2∆1 ura3-52 trp1∆63 KanMx::GAL1p-FLO8-HIS3 3xHSV-CHD1 3XHA-rtf1(11A)


title: wildtype_bio3_noab

description: Protein A- MNase-digested DNA

value: wild type

value: no primary antibody


title: chd2_chct_bio3_noab

description: Protein A- MNase-digested DNA


title: input_chd1_null_input_set3


title: 2-sgPtger4,Replicate3

value: sgRNA targeting Ptger4 transduction and 4T1 tumor conditioned medium


title: rtf1_11_A_bio2


title: 2-sgPtger4,Replicate2


title: input_rtf1_11_A_input_set1


title: wildtype_bio2_noab

description: Protein A- MNase-digested DNA


title: wildtype_bio1_noab

description: Protein A- MNase-digested DNA


title: input_chd1_null_input_set1


title: rtf1_11_A_bio1


title: input_rtf1_11_A_input_set2


title: chd2_chct_bio1_noab

description: Protein A- MNase-digested DNA


title: 2-sgPtger4,Replicate1


title: chd1_chct_bio2b

description: Tagmentase-digested DNA

data_processing:
ATAC-seq data quality was verified with Pepatac version 0.10.3. Pepatac parameters were: -Q paired -M 90G --aligner bowtie2 --trimmer trimmomatic --deduplicator picard --peak-caller macs2 --peak-type fixed -G mm10 -P 24 -R. De-duplicated bam files obtained from Pepatac were shifted for ATAC-seq analysis using the deepTools alignmentSieve function using alignmentSieve –ATACshift. Resulting bam files were then size-selected into accessible fragments (length 1 to 100bp) or mononucleosome-sized fragments (length 180 to 247 bp) using deepTools bamCoverage with settings --normalizeUsing RPGC --effectiveGenomeSize 2652783500 --MNase --binSize 1 –extendReads and by removing the mm10 Encode Blacklisted regions. Normalized bigwigs for three to four replicates were averaged using WiggleTools and the ‘mean’ function. Output from plotProfile was plotted in GraphPad Prism 10 to generate final metaplots. NucleoATAC was used to call nucleosomes in wild type replicates. NucleoATAC called nucleosomes from two or more wild-type replicates were then selected. Nucleosomes over all genes or CHD1 top quintile occupied genes were subset using bedtools intersect and used to assess mononucleosome ATAC-seq enrichment in wild type and mutant cell lines
Assembly: mm10
Supplementary files format and content: Bigwig files contain 1-100bp fragments for accessible or 180-247 for mononucleosome files

source_name: Cell line

extract_protocol:
Nuclei were resuspended in 50 µL Transposase mix (25 µL 2x Tagmentation Buffer, 16.5µL 1x PBS, 0.5 µL 10% Tween-20, 0.5 µL 1 % Digitonin, 2.5 µL Tagmentase, 5 µL nuclease-free water) and incubated at 37°C for 30 min in a thermomixer shaking at 1000 rpm. Immediately, DNA was purified using the Zymo DNA Clean and Concentrator Kit per manufacturer guidelines and eluted in 10 µL water.
DNA fragments were PCR amplified (2.5 µL 25µM Nextera i5 and i7 primers, 10 µL water, 25 mL NEBNEXT High-Fidelity 2x PCR Master Mix, and 10 µL DNA). Initial amplification occurred for 5 cycles with conditions: 72°C 5 min, 98°C 30 sec, and 5 cycles (98°C 10 sec and 63°C 30 sec) and 72°C 1 min elongation. Quantitative PCR was performed to determine the number of additional cycles required (1µL library DNA, 1 µL NXT PCR primers at 2 µM, 3 µL nuclease-free water, 5 µL 2x KAPA SYBR green, and 9 µL qPCR Master Mix). qPCR conditions were 98°C 30 sec followed by 20 cycles (98°C 10 sec, 63°C 30 sec, 72°C 1 min). Remaining library was PCR amplified for 4 cycles. Amplified libraries were run on a 1.5% agarose gel and fragments sized 150-700 bp were then gel-extracted. Libraries were paired-end sequenced on a Illumina NextSeq2000 to a depth of ~50 million uniquely mapped reads per sample.

treatment_protocol: Plated cells were washed with 1x PBS, trypsinized, collected and 120,000 cells were centrifuged at 600 g for 5 min at 4°C, washed with 1x PBS, and centrifuged again. Resuspension buffer (0.01 M Tris-HCl pH 7.5, 0.01 M NaCl, and 0.03 M MgCl2) was used as a base for multiple solutions. Cells were resuspended in 50 µL Lysis buffer (48.5 µL Resuspension buffer with 0.5 µL 10% NP-40, 0.5 µL 10% Tween-20, 0.5 µL 1% Digitonin) and incubated on ice for 15 min. To lysed cells, 1 mL Wash buffer was added (990 µL resuspension buffer, 10 µL 10% Tween-20). Nuclei were centrifuged and supernatant was removed. Nuclei were flash frozen in liquid nitrogen and stored at -75°C.

value: Cell line


title: input_rtf1_11_A_input_set3


title: rtf1_AAAA_bio1_noab

description: Protein A- MNase-digested DNA


title: rtf1_8_9_A_bio4

value: his3∆200 lys2-128∂ leu2∆1 ura3-52 trp1∆63 KanMx::GAL1p-FLO8-HIS3 3xHSV-CHD1 3XHA-rtf1(8-9A)

value: MNase-digested DNA


title: 2-sgPpp2r3c, Replicate3

value: Bone marrow

value: Primary macrophages

value: sgRNA targeting Ppp2r3c transduction and 4T1 tumor conditioned medium


title: chd1_chct_bio3


title: rtf1_AAAA_bio2_noab

description: Protein A- MNase-digested DNA


title: rtf1_8_9_A_bio3


title: chd1_chct_bio2a

description: Tagmentase-digested DNA


title: input_chd1_null_input_set4

value: his3∆200 lys2-128∂ leu2∆1 ura3-52 trp1∆63 KanMx::GAL1p-FLO8-HIS3 3xHSV-CHD1 rtf1∆101::LEU2


title: 2-sgPpp2r3c, Replicate2

value: Bone marrow-derived macrophages


title: input_rtf1_8_9_A_input_set1


title: chd1_chct_bio1b

description: Tagmentase-digested DNA


title: rtf1_8_9_A_bio2


title: chd1_chct_bio1a

description: Tagmentase-digested DNA


title: 2-sgPpp2r3c, Replicate1


title: chd2_chct_bio2

description: Tagmentase-digested DNA


title: input_rtf1_8_9_A_input_set2


title: wildtype_bio3

value: his3∆200 lys2-128∂ leu2∆1 ura3-52 trp1∆63 KanMx::GAL1p-FLO8-HIS3 3xHSV-CHD1 3xHA-RTF1


title: input_rtf1_8_9_A_input_set3


title: rtf1_8_9_A_bio1


title: chd2_chct_bio3

description: Tagmentase-digested DNA


title: wildtype_bio4


title: 2-sgNC1, Replicate2

value: non-targeting control sgRNA transduction and 4T1 tumor conditioned medium induction


title: 2-sgNC1, Replicate1


title: sgLamtor1, Replicate3

value: sgRNA targeting Lamtor1 transduction and 4T1 tumor conditioned medium


title: input_rtf1_null_input_set2

value: no antibody

value: input DNA from sonicated chromatin


title: chd2_chct_bio1

description: Tagmentase-digested DNA

value: embryonic stem cells


title: wildtype_bio1


title: wildtype_bio2


title: input_rtf1_null_input_set1


title: rtf1_AAAA_bio3

description: Tagmentase-digested DNA


title: rtf1_AAAA_bio2

description: Tagmentase-digested DNA


title: input_chd1_chct_input_set5

value: his3∆200 lys2-128∂ leu2∆1 ura3-52 trp1∆63 KanMx::GAL1p-FLO8-HIS3 3xHSV-chd1∆CHCT 3xHA-RTF1


title: 2-sgNC1, Replicate3


title: input_rtf1_null_input_set3


title: sgLamtor1, Replicate2


title: chd1_chct_bio1


title: sgLamtor1, Replicate1


title: rtf1_AAAA_bio1

description: Tagmentase-digested DNA


title: 1-sgNC1, Replicate3


title: input_rtf1_null_input_set4


title: 1-sgNC1, Replicate2


title: input_rtf1_8_9_A_input_set4


title: input_chd1_null_input_set5


title: input_chd1_chct_input_set7


title: wildtype_bio3

description: Tagmentase-digested DNA

value: wild type


title: input_wildtype_input_set2


title: input_wildtype_input_set3


title: wildtype_bio2

description: Tagmentase-digested DNA


title: input_wildtype_input_set1


title: input_chd1_null_input_set6


title: 1-sgNC1, Replicate1


title: wildtype_bio1

description: Tagmentase-digested DNA


title: input_wildtype_input_set4


title: input_rtf1_11_A_input_set5

value: his3∆200 lys2-128∂ leu2∆1 ura3-52 trp1∆63 KanMx::GAL1p-FLO8-HIS3 3xHSV-CHD1 3XHA-rtf1(11A)


title: sgNC1, Replicate2


title: input_chd1_chct_input_set6


title: input_rtf1_11_A_input_set4


title: wildtype_bio4

description: Tagmentase-digested DNA

value: Cell line


title: input_rtf1_11_A_input_set6


title: chd1_chct_bio2b_CHD1

description: Protein A- MNase-digested DNA

data_processing:
Fastq files were trimmed to 25 bp using an awk command. Integrity of sequencing data was verified by fastqc version 0.11.9. Reads were aligned to the Mus musculus (mm10) and Drosophila melanogaster (dm6) genomes using bowtie2 version 2.4.5 with parameters -I 10 -X 1000 -N 1 --very-sensitive for paired end-sequencing. Low quality reads were filtered using Picard version 2.5.0 and filtered for mapping quality (MAPQ ≥ 10) using SAMtools version 1.14. Reads were counted with SAMtools version 1.14 flagstat. Datasets were computationally size selected using SAMtools, with 150-500 bp for H3K4me3 and 130-500 bp for CHD1. For H3K4me3, normalized bigwigs were generated using bamcoverage with parameters --centerReads --binSize 5 –scaleFactor x, where the scaling factor was determined for each sample using Drosophila reads. For CHD1 CUT&RUN, normalized bigwigs were generated using bamcoverage with parameters --centerReads --binSize 5 --normalizeUsing RPGC --effectiveGenomeSize 2308125349. Normalized bigwigs for three or four replicates were averaged using WiggleTools and the ‘mean’ function. Browser tracks were generated from merged bigwig files using IGV genome browser. To generate metaplots, the output of deepTools plotProfile containing binned data (10 bp) from TSS to 2 kb or -1 kb to +2 kb. Output from plotProfile was plotted in GraphPad Prism 10 to generate final metaplots. The mm10 Encode Blacklisted regions were also excluded from the normalized bigwigs.
Assembly: mm10, dm6
Supplementary files format and content: Bigwig files contain Drosophila spike in normalized fragment sizes corresponding to 150-500bp for H3K4me3 CUT&RUNs and RPGC-normalized fragment sizes corresponding to 130-500bp for CHD1 CUT&RUNs
Library strategy: CUT&RUN

extract_protocol:
Nuclei were incubated overnight at 4°C with rotation in wash buffer with rabbit anti-Chd1 (Diagenode 15410334, 1:50). Nuclei were incubated for 1 hour at room temperature with rotation with rabbit anti-H3K4me3 (Sigma-Aldrich 05-745R, 1:100). Control samples were treated in the same conditions without antibody. Samples were washed twice with wash buffer and incubated for 30 min at room temperature with rotation in wash buffer containing recombinant Protein A-MNase (pA-MN) (1:250). Samples were washed twice with wash buffer and equilibrated at 0°C in an ice bath. Three mM CaCl2 was added to each sample to activate MNase cleavage and digested in an ice bath for 30 min. Digestion for H3K4me3 samples was stopped after 30 min using a stop buffer (20 mM EDTA. 4 mM EGTA, 200 mM NaCl, 50 ug/mL RNase A). Samples were incubated at 37°C for 20 min to release genomic fragments and fragments were then separated through centrifugation. Digestion for Chd1 samples was stopped after 30 min using a low salt stop treatment (10 mM EDTA, 2 mM EGTA, 150 nM NaCl, 5 mM Triton-X). Samples were incubated at 4°C for 1 hr to release genomic fragments. The salt concentration was increased to 500 mM for Chd1 samples, RNase A was added, and samples were incubated at 37°C for 20 min to release genomic fragments. Fragments for all samples were isolated and extracted to be used as input for library build.
Libraries were built using NEB Next II Ultra DNA library kit (NEB E7645L) and AMPure XP beads (Beckman Coulter A63881) purifications. Fragments were PCR amplified with 15 cycles. Samples were then pooled and paired-end sequenced on an Illumina NextSeq2000 to a depth of ~10 million uniquely mapped reads per sample.


title: sgNC1, Replicate1


title: 8wg16_chd1_null_bio1

value: his3∆200 lys2-128∂ leu2∆1 ura3-52 trp1∆63 KanMx::GAL1p-FLO8-HIS3 chd1∆::LEU2 3xHA-RTF1

value: IP'd DNA from sonicated chromatin


title: chd1_chct_bio1b_CHD1

description: Protein A- MNase-digested DNA


title: chd1_chct_bio2a_CHD1

description: Protein A- MNase-digested DNA


title: input_rtf1_8_9_A_input_set5

value: his3∆200 lys2-128∂ leu2∆1 ura3-52 trp1∆63 KanMx::GAL1p-FLO8-HIS3 3xHSV-CHD1 3XHA-rtf1(8-9A)


title: sgNC1, Replicate3

value: Bone marrow

value: Primary macrophages


title: 8wg16_chd1_null_bio2


title: 4T1 tumor conditioned medium, Replicate2

data_processing:
The fastq files were processed using the ENCODE ATAC-seq pipeline to generate bam files, bigwig files, and peaks called by MACS2.
Deeptools is used for the heatmap plots. ATAC-seq Peaks from all study samples were merged to create a union set of sites. Read densities were calculated for each peak for each sample, differential peaks between treatment group and control group were identified by DEseq2.
Assembly: mm10
Supplementary files format and content: BigWig files generated by merging the replicates.

extract_protocol:
Cells were lysed in 50 μL lysis buffer(10 mM Tris-HCl (pH 7.4), 10 mM NaCl, 3 mM MgCl2，0.5% NP-40) on ice for 10min. Nuclei were isolated by centrifugation at 500 g for 10 min then resuspended in 50 μL of transposition mix (10 μL 5×TTBL, 5 μL TTE Mix V50 and 35 μL ddH2O) at 55 degrees for 10min.
Libraries were constructed by TruePrep DNA Library Prep Kit V2 for Illumina (Vazyme#TD501) as manufacturer’s instructions.

value: WT

value: 4T1-tumor conditioned medium for 4 days


title: 4T1 tumor conditioned medium, Replicate3

value: Bone marrow-derived macrophages


title: input_rtf1_null_input_set6

value: his3∆200 lys2-128∂ leu2∆1 ura3-52 trp1∆63 KanMx::GAL1p-FLO8-HIS3 3xHSV-CHD1 rtf1∆101::LEU2


title: chd1_chct_bio1a_CHD1

description: Protein A- MNase-digested DNA


title: wildtype_bio3_CHD1

description: Protein A- MNase-digested DNA


title: 8wg16_rtf1_11_A_bio1


title: wildtype_bio1_H3K36me3_set2

description:
Library name: wildtype_bio1_H3K36me3_set2
Protein A- MNase-digested DNA


title: wildtype_bio2_CHD1

description: Protein A- MNase-digested DNA


title: LGP, Replicate3

value: 25mM lactic acid,100nM PGE2 and 2ng/mL GM-CSF for 4 days


title: 8wg16_rtf1_8_9A_bio1


title: 8wg16_rtf1_11_A_bio2


title: input_wildtype_input_set5

value: no antibody

value: his3∆200 lys2-128∂ leu2∆1 ura3-52 trp1∆63 KanMx::GAL1p-FLO8-HIS3 3xHSV-CHD1 3xHA-RTF1


title: LGP, Replicate2


title: wildtype_bio1_CHD1

description: Protein A- MNase-digested DNA

value: embryonic stem cells


title: input_wildtype_input_set6

value: input DNA from sonicated chromatin


title: LGP, Replicate1


title: input_rtf1_8_9_A_input_set6


title: 8wg16_rtf1_null_bio2


title: 8wg16_rtf1_null_bio1


title: 4T1 tumor conditioned medium, Replicate1


title: chd1_chct_bio2b_H3K4me3_set2

description: Protein A- MNase-digested DNA

value: H3K4me3 (Millipore Sigma, Cat# 05-745R, 4070079)


title: 8wg16_chd1_chct_bio1

value: his3∆200 lys2-128∂ leu2∆1 ura3-52 trp1∆63 KanMx::GAL1p-FLO8-HIS3 3xHSV-chd1∆CHCT 3xHA-RTF1


title: input_rtf1_null_input_set5


title: chd1_chct_bio2a_H3K4me3_set2

description: Protein A- MNase-digested DNA

value: Cell line


title: 8wg16_wildtype_bio1


title: chd1_chct_bio1b_H3K4me3_set2

description: Protein A- MNase-digested DNA


title: GP, Replicate1

value: 100nM PGE2 and 2ng/mL GM-CSF for 4 days


title: 8wg16_wildtype_bio2

value: IP'd DNA from sonicated chromatin


title: H3K4me3_chd1_null_bio1

value: his3∆200 lys2-128∂ leu2∆1 ura3-52 trp1∆63 KanMx::GAL1p-FLO8-HIS3 chd1∆::LEU2 3xHA-RTF1


title: GP, Replicate2

value: Bone marrow


title: chd1_chct_bio1a_H3K4me3_set2

description: Protein A- MNase-digested DNA


title: LG, Replicate3

value: Primary macrophages

value: 25mM lactic acid and 2ng/mL GM-CSF for 4 days


title: 8wg16_chd1_chct_bio3


title: 8wg16_rtf1_8_9A_bio2

value: his3∆200 lys2-128∂ leu2∆1 ura3-52 trp1∆63 KanMx::GAL1p-FLO8-HIS3 3xHSV-CHD1 3XHA-rtf1(8-9A)


title: 8wg16_wildtype_bio3


title: input_wildtype_input_set7


title: H3K4me3_rtf1_11_A_bio1

value: his3∆200 lys2-128∂ leu2∆1 ura3-52 trp1∆63 KanMx::GAL1p-FLO8-HIS3 3xHSV-CHD1 3XHA-rtf1(11A)


title: wildtype_bio2_H3K4me3_set2

description: Protein A- MNase-digested DNA

value: wild type


title: LG, Replicate1

value: Bone marrow-derived macrophages

value: WT


title: wildtype_bio1_H3K4me3_set2

description: Protein A- MNase-digested DNA


title: 8wg16_wildtype_bio4

value: his3∆200 lys2-128∂ leu2∆1 ura3-52 trp1∆63 KanMx::GAL1p-FLO8-HIS3 3xHSV-CHD1 3xHA-RTF1


title: 8wg16_wildtype_bio5


title: H3K4me3_rtf1_11_A_bio2


title: LP, Replicate3

value: 25mM lactic acid and 100nM PGE2 for 4 days


title: 8wg16_chd1_chct_bio2


title: chd2_chct_bio3_H3K4me3_set1

description: Protein A- MNase-digested DNA

value: embryonic stem cells

value: H3K4me3 (Millipore Sigma, Cat# 05-745R, 3697296)


title: H3K4me3_rtf1_8_9A_bio1


title: LP, Replicate1


title: H3_chd1_chct_bio3

value: his3∆200 lys2-128∂ leu2∆1 ura3-52 trp1∆63 KanMx::GAL1p-FLO8-HIS3 3xHSV-chd1∆CHCT 3xHA-RTF1


title: LG, Replicate2


title: LP, Replicate2


title: wildtype_bio3_H3K4me3_set2

description: Protein A- MNase-digested DNA

value: Cell line

value: H3K4me3 (Millipore Sigma, Cat# 05-745R, 4070079)


title: H3_chd1_chct_bio1

value: IP'd DNA from sonicated chromatin


title: H3_chd1_chct_bio2


title: chd2_chct_bio2_H3K4me3_set1

description: Protein A- MNase-digested DNA


title: G, Replicate3

value: 2ng/mL GM-CSF for 4 days


title: H3K4me3_rtf1_null_bio1

value: his3∆200 lys2-128∂ leu2∆1 ura3-52 trp1∆63 KanMx::GAL1p-FLO8-HIS3 3xHSV-CHD1 rtf1∆101::LEU2


title: rtf1_AAAA_bio3_H3K4me3_set1

description: Protein A- MNase-digested DNA


title: H3K4me3_rtf1_8_9A_bio2


title: H3K4me3_rtf1_null_bio2


title: H3_chd1_null_bio1

value: his3∆200 lys2-128∂ leu2∆1 ura3-52 trp1∆63 KanMx::GAL1p-FLO8-HIS3 chd1∆::LEU2 3xHA-RTF1


title: G, Replicate2

value: Bone marrow

value: Primary macrophages


title: G, Replicate1


title: rtf1_AAAA_bio2_H3K4me3_set1

description: Protein A- MNase-digested DNA


title: H3_chd1_null_bio2


title: H3_rtf1_11_A_bio1

value: his3∆200 lys2-128∂ leu2∆1 ura3-52 trp1∆63 KanMx::GAL1p-FLO8-HIS3 3xHSV-CHD1 3XHA-rtf1(11A)


title: H3K4me3_wildtype_bio1


title: P, Replicate3

value: 100nM PGE2 for 4 days


title: rtf1_AAAA_bio1_H3K4me3_set1

description: Protein A- MNase-digested DNA


title: H3K4me3_wildtype_bio2


title: wildtype_bio3_H3K4me3_set1

description: Protein A- MNase-digested DNA

value: wild type


title: H3_rtf1_11_A_bio2


title: chd2_chct_bio1_H3K4me3_set1

description: Protein A- MNase-digested DNA


title: HA_chd1_null_bio1

value: HA (Santa Cruz, #sc-7392, lot #D0121)


title: P, Replicate2

value: Bone marrow-derived macrophages

value: WT


title: P, Replicate1


title: H3_rtf1_8_9A_bio2

value: his3∆200 lys2-128∂ leu2∆1 ura3-52 trp1∆63 KanMx::GAL1p-FLO8-HIS3 3xHSV-CHD1 3XHA-rtf1(8-9A)


title: wildtype_bio1_H3K4me3_set1

description: Protein A- MNase-digested DNA

value: embryonic stem cells

value: H3K4me3 (Millipore Sigma, Cat# 05-745R, 3697296)


title: L, Replicate3

value: 25mM lactic acid for 4 days


title: H3_rtf1_8_9A_bio1


title: HA_rtf1_11_A_bio1


title: L, Replicate2


title: P8_A

city: Baltimore

first: Pin

last: Lyu

address: 400 N Broadway

institute: JHU

description: Library name: P8_A

library_source: genomic single cell

data_processing:
Sequencing results for 13LGS and mouse scRNA-Seq were processed through the 10x CellRanger pipeline (version 3.1.0), using the 13LGS genome GCF_016881025.1_HiC_Itri_2 78, and the output loaded into Seurat (version 4.0.4). Cells from Cellplex-labeled libraries were deconvoluted using the cellranger multi pipeline (version 6.0). ScRNA-Seq Seurat objects were analyzed following the Seurat SCT workflow 67,68. Cell type was determined cluster by cluster based on marker gene expression derived from the Seurat function ‘FindAllMarkers’ using default parameters. Differential gene expression between Cone-like Precursors and Rods was identified using the Seurat function “FindMarkers”. ScRNA-Seq samples were aggregated using the CellRanger aggr pipeline (version 3.1.0).
Assembly: GRCm38
Supplementary files format and content: fragments for scATAC-seq

organism: Ictidomys tridecemlineatus

source_name: retina

extract_protocol:
The use of animals for these studies was conducted using protocols approved by the Johns Hopkins Animal Care and Use Committee, the UW Oshkosh Animal Care and Use Committee, and the Northwestern University Animal Care and Use Committee, in compliance with ARRIVE guidelines and the ARVO Statement for the Use of Animals in Ophthalmic and Vision Research, and were performed in accordance with relevant guidelines and regulations.Embryonic 13-lined ground squirrel (13LGS) retinal samples were collected from timed-pregnant captive dams and embryonic day was confirmed by comparison with mouse Theiler stages. Postnatal 13LGS retinal samples were collected from captive-bred litters with day of birth set as Postnatal Day 0. 13LGS were euthanized by decapitation.
Retina and explants were dissociated, methanol-fixed cells rehydrated, and nuclei isolated from flash-frozen samples as previously described 71. GEM generation and library preparation for scRNA-Seq were completed according to the 10x 3’ v3.1 user guide (Rev D) using the Chromium Next GEM Single Cell 3ʹ Kit v3.1 and Dual Index Kit TT Set A and for Cellplex samples according to the 10x Next GEM Single Cell 3’ Reagent Kits v3.1 (Dual Index) with Feature Barcode technology for Cell Multiplexing (Rev A) using the 3ʹ CellPlex Kit Set A and Dual Index Kit NN Set A. Transposition, GEM generation, and library preparation for scATAC-Seq were completed according to the 10x ATAC v1.1 user guide (Rev D) using the Chromium Next GEM Single Cell ATAC Reagent Kits v1.1 and Single Index Kit N, Set A. Quality control and sequencing were performed by the Johns Hopkins Transcriptomics and Deep Sequencing Core.

value: retina


title: P8_B

description: Library name: P8_B


title: rtf1_11_A_bio3

value: MNase-digested DNA


title: HA_rtf1_11_A_bio2

value: IP'd DNA from sonicated chromatin


title: H3_rtf1_null_bio1

value: his3∆200 lys2-128∂ leu2∆1 ura3-52 trp1∆63 KanMx::GAL1p-FLO8-HIS3 3xHSV-CHD1 rtf1∆101::LEU2


title: H3_rtf1_null_bio2


title: P4_B

description: Library name: P4_B


title: H3_wildtype_bio1

value: his3∆200 lys2-128∂ leu2∆1 ura3-52 trp1∆63 KanMx::GAL1p-FLO8-HIS3 3xHSV-CHD1 3xHA-RTF1


title: L, Replicate1

value: Bone marrow


title: HA_rtf1_8_9A_bio1


title: ctrl, Replicate3

value: Primary macrophages

value: PBS and DMSO for 4 days


title: H3K4me3_chd1_null_bio2

value: his3∆200 lys2-128∂ leu2∆1 ura3-52 trp1∆63 KanMx::GAL1p-FLO8-HIS3 chd1∆::LEU2 3xHA-RTF1


title: P4_A

description: Library name: P4_A


title: HA_rtf1_8_9A_bio2


title: HA_rtf1_null_bio1


title: ctrl, Replicate2


title: H3_wildtype_bio2


title: P21_B

description: Library name: P21_B


title: HA_chd1_null_bio2


title: wildtype_bio2_H3K4me3_set1

description: Protein A- MNase-digested DNA

value: Cell line

value: wild type


title: H3_wildtype_bio3


title: ctrl, Replicate1

value: Bone marrow-derived macrophages


title: P21_A

description: Library name: P21_A


title: HA_wildtype_bio1

value: HA (Santa Cruz, #sc-7392, lot #D0121)


title: HA_rtf1_null_bio2


title: LGP-sgRNA,CROP-seq

data_processing:
Raw reads from scRNA-seq were processed to generate gene expression matrixes using CeleScope (https://github.com/singleron-RD/CeleScope) (version 1.11.1) pipeline. Briefly, raw reads were first processed with CeleScope to remove low quality reads with Cutadapt v3.7 to trim poly-A tail and adapter sequences. Cell barcode and UMI were extracted. After that, we used STAR v2.6.1b to map reads to the reference genome GRCm39. UMI counts and gene counts of each cell were acquired with featureCounts v2.0.1 , and used to generate expression matrix files for subsequent analysis.
To assign sgRNAs to corresponding cell barcodes, we used the multi_tag module of CeleScope. This module enabled us to demultiplex and quantify sgRNA sequences in each cell. In brief, it first check the mismatches between linker sequence (we set it as the constant 26 nt sequence before sgRNA sequence). If no mismatch < len(linker) / 10 + 1, the read is classified as “invalid”. Next, we determine the minimum Unique Molecular Identifier (UMI) threshold, denoted as UMI_min. UMI_min is calculated as the lesser of the 5th percentile and one-tenth of the median of the total UMI counts across all cells. If the calculated value is less than 1, UMI_min is set to 1.  Cells with valid UMIs below this threshold are classified as "undetermined". Simultaneously, the method calculates the minimum signal-to-noise ratio (SNR_min) for each cell barcode. SNR is computed as the ratio of the signal (the second highest UMI count) to the noise (the highest UMI count). If the signal is zero, the SNR is defined as zero; if the noise is zero, the SNR is defined as infinity. Cell barcodes with UMIs at least equal to UMI_min but with an SNR less than SNR_min are classified as "multiplets". Cell barcodes passed above thresholds were assigned a guide based on the highest guide counts. To ensure the accuracy of sgRNA sequences, we modified the source code in multi_tag module of CeleScope and set the n_mismatch parameter to 0. This alteration ensures that no mismatches are allowed between sgRNA sequences, thereby eliminating potential errors that could arise from allowing mismatches. The guide assignments were added to the Scanpy annotation of observations for downstream processing.
Scanpy (version 1.9.3) was used for quality control, dimensionality reduction and clustering. All data were processed using the Scanpy standard analysis workflow (https://www.sc-best-practices.org/preamble.html), and clusters of each dataset were annotated according to the marker genes. In vivo CROP-seq and LGP CROP-seq data were integrated using Harmony. Initial clusters with fewer than 100 cells were eliminated, reclustering was performed to refine the cell groupings. The cluster-specific or gene-knockout-specific marker genes were identified by using the scanpy.tl.rank_genes_groups function with default parameters.
Assembly: GRCm39
Supplementary files format and content: csv files include raw counts for each cell
Supplementary files format and content: csv files include normalized counts for each cell
Supplementary files format and content: csv files include tag (sgRNA) counts for each cell

extract_protocol:
Single-cell suspensions with PBS were loaded onto microwell chip using the Singleron Matrix® Single Cell Processing System. Barcoding Beads are subsequently collected from the microwell chip, followed by reverse transcription of the mRNA captured by the Barcoding Beads and to obtain cDNA, and PCR amplification.
The amplified cDNA is then fragmented and ligated with sequencing adapters. The scRNA-seq libraries were constructed according to the protocol of the GEXSCOPE® Single Cell RNA Library Kits (Singleron). The  sgRNA information was enriched by three rounds of amplification in cDNA library.  Individual libraries were diluted to 4 nM, pooled, and sequenced on Illumina novaseq 6000 with 150 bp paired end reads.

value: Tumor

value: Lewis lung cancer

value: tumor infiltrating immune cells

value: Loxp-Stop-Loxp-Cas9, Lyz2-Cre


title: H3K36me3_chd1_chct_bio2

value: his3∆200 lys2-128∂ leu2∆1 ura3-52 trp1∆63 KanMx::GAL1p-FLO8-HIS3 3xHSV-chd1∆CHCT 3xHA-RTF1


title: P17_B

description: Library name: P17_B

value: retina


title: HA_wildtype_bio2

value: IP'd DNA from sonicated chromatin


title: Adar,scRNA-seq

data_processing:
Raw reads from scRNA-seq were processed to generate gene expression matrixes using CeleScope (https://github.com/singleron-RD/CeleScope) (version 1.11.1) pipeline. Briefly, raw reads were first processed with CeleScope to remove low quality reads with Cutadapt v3.7 to trim poly-A tail and adapter sequences. Cell barcode and UMI were extracted. After that, we used STAR v2.6.1b to map reads to the reference genome GRCm39. UMI counts and gene counts of each cell were acquired with featureCounts v2.0.1 , and used to generate expression matrix files for subsequent analysis.
Scanpy (version 1.9.3) was used for quality control, dimensionality reduction and clustering. All data were processed using the Scanpy standard analysis workflow (https://www.sc-best-practices.org/preamble.html), and clusters of each dataset were annotated according to the marker genes. The cluster-specific marker genes were identified by using the scanpy.tl.rank_genes_groups function with default parameters.
Assembly: GRCm39
Supplementary files format and content: csv file includes cell meta-infomation in Scanpy annotation of observations
Supplementary files format and content: csv file includes gene meta-infomation in Scanpy annotation of variables/features
Supplementary files format and content: csv file includes normalized counts for each cell
Supplementary files format and content: csv file includes raw counts for each cell

extract_protocol:
Single-cell suspensions with PBS were loaded onto microwell chip using the Singleron Matrix® Single Cell Processing System. Barcoding Beads are subsequently collected from the microwell chip, followed by reverse transcription of the mRNA captured by the Barcoding Beads and to obtain cDNA, and PCR amplification.
The amplified cDNA is then fragmented and ligated with sequencing adapters. The scRNA-seq libraries were constructed according to the protocol of the GEXSCOPE® Single Cell RNA Library Kits (Singleron). Individual libraries were diluted to 4 nM, pooled, and sequenced on Illumina novaseq 6000 with 150 bp paired end reads.

value: sgRNA targeting Adar transduction


title: P17_A

description: Library name: P17_A


title: HSV_chd1_null_bio1

value: HSV (Sigma-Aldrich, #H6030, lot 086M4845V)


title: LGP,CROP-seq


title: H3K36me3_chd1_chct_bio3


title: HSV_chd1_null_bio2


title: NC,scRNA-seq

value: Non-targeting control sgRNA transdcution


title: H3K36me3_chd1_null_bio1


title: P12_B

description: Library name: P12_B


title: P12_A

description: Library name: P12_A


title: H3K36me3_chd1_null_bio2


title: HSV_rtf1_11_A_bio1

value: his3∆200 lys2-128∂ leu2∆1 ura3-52 trp1∆63 KanMx::GAL1p-FLO8-HIS3 3xHSV-CHD1 3XHA-rtf1(11A)


title: sgAdar, Replicate2

description:
sgAdar-2-4T1
Adar_ko_and_ctrl_ko_counts.txt

data_processing:
Sequencing reads were aligned to the mouse reference genome (GRCm38/mm10) using Hisat2 (version 2.2.1), subsequent to trimming with Trim Galore (version 0.6.7).
Gene counts were obtained using featureCounts (version 2.0.1).
Assembly: mm10
Supplementary files format and content: tab-delimited text files include raw counts for each Sample
Supplementary files format and content: csv file includes TPM values for each Sample

source_name: Primary macrophages

extract_protocol:
RNA from 5´ 105 cells was extracted and purified with TRIzol reagent (Thermo Fisher) according to manufacturer’s instructions.
RNA-seq libraries were prepared using Illumina TruSeq Stranded mRNA kit following manufacturer’s instructions with 5 mgof input RNA.

value: Bone marrow

value: Bone-marrow derived macrophages

value: sgRNA targeting Adar transduction and 4T1 tumor conditoned medium transdcution


title: sgAdar, Replicate1

description:
sgAdar-1-4T1
Adar_ko_and_ctrl_ko_counts.txt


title: H3K36me3_rtf1_11_A_bio1


title: P1_A

description: Library name: P1_A


title: H3K36me3_rtf1_11_A_bio2


title: P1_B

description: Library name: P1_B


title: HSV_rtf1_8_9A_bio1

value: his3∆200 lys2-128∂ leu2∆1 ura3-52 trp1∆63 KanMx::GAL1p-FLO8-HIS3 3xHSV-CHD1 3XHA-rtf1(8-9A)


title: HSV_rtf1_11_A_bio2


title: sgNC, Replicate2

description:
sgNC1-2-4T1
Adar_ko_and_ctrl_ko_counts.txt

value: non-targeting control sgRNA transduction and 4T1 tumor conditioned medium induction


title: H3K36me3_chd1_chct_bio1


title: H3K36me3_rtf1_8_9A_bio1


title: HSV_rtf1_8_9A_bio2


title: sgNC, Replicate1

description:
sgNC1-1-4T1
Adar_ko_and_ctrl_ko_counts.txt


title: HSV_rtf1_null_bio1

value: his3∆200 lys2-128∂ leu2∆1 ura3-52 trp1∆63 KanMx::GAL1p-FLO8-HIS3 3xHSV-CHD1 rtf1∆101::LEU2


title: H3K36me3_rtf1_8_9A_bio2


title: 4T1-tumor conditioned medium, Replicate2

description:
4T1-2
TPM_TEM_complete.csv

value: WT

value: 4T1-tumor conditioned medium for 5 days


title: H3K36me3_rtf1_null_bio1


title: HSV_rtf1_null_bio2


title: 4T1-tumor conditioned medium, Replicate1

description:
4T1-1
TPM_TEM_complete.csv

value: 4T1-tumor conditioned medium for 4 days


title: H3K36me3_rtf1_null_bio2


title: E24_A

description: Library name: E24_A


title: rluB_TOB_replicate3

city: paris

first: Zeynep

last: Baharoglu

address: 25 rue du dr roux

institute: Institut Pasteur

description: Vibrio cholerae N16961 hapR+

data_processing:
Count data were analyzed using R version 3.2.0 and the Bioconductor package DESeq2 version 1.8.1
Data were normalized with DESeq2 and the “shorth” parameter
The dispersion estimation and statistical test for differential expression were performed with default parameters
The generalized linear model was set with a single covariate corresponding to the biological condition, biological replicates being included into each condition
Raw p-values were adjusted for multiple testing according to the Benjamini and Hochberg procedure and genes with an adjusted p-value lower than 0.001 were considered differentially expressed.
Assembly: V. cholerae N16961 accession numbers AE003852 and AE003853
Supplementary files format and content: excel files containing number of reads and differencial expression values

organism: Vibrio cholerae

source_name: bacterial culture

growth_protocol: growth in liquid MH up to OD 0,25

extract_protocol:
Cultures were centrifuged, and RNA was harvested using Trizol reagent. Illumina TruSeq mRNA Sample Prep Kit (20020595) was used with 7 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols (Krin et al., 2018, PMID: 29783948)

treatment_protocol: tobramycin 0,4 µg/ml

value: bacterial culture

tag: growth phase

value: exponential phase OD 0.25

value: delta-rluB

value: TOB 0,4 ug/ml


title: E21_CB

description: Library name: E21_CB

value: retina


title: rluB_TOB_replicate2

description: Vibrio cholerae N16961 hapR+


title: LA_PGE2_GM-CSF, Replicate1

description:
LA_PGE2_GM-CSF-1
TPM_TEM_complete.csv

value: 25mM lactate, 100nM PGE2 and 2ng/mL GM-CSF for 4 days


title: LA_PGE2_GM-CSF, Replicate2

description:
LA_PGE2_GM-CSF-2
TPM_TEM_complete.csv


title: E21_CA

description: Library name: E21_CA


title: rluB_TOB_replicate1

description: Vibrio cholerae N16961 hapR+


title: PGE2_GM-CSF, Replicate1

description:
PGE2_GMCSF-1
TPM_TEM_complete.csv

value: 100nM PGE2 and 2ng/mL GM-CSF for 4 days


title: E21_A

description: Library name: E21_A


title: E21_B

description: Library name: E21_B


title: E26_B

description: Library name: E26_B


title: WT_TOB_replicate3

description: Vibrio cholerae N16961 hapR+


title: PGE2_GM-CSF, Replicate2

description:
PGE2_GMCSF-2
TPM_TEM_complete.csv


title: H3K36me3_wildtype_bio3

value: his3∆200 lys2-128∂ leu2∆1 ura3-52 trp1∆63 KanMx::GAL1p-FLO8-HIS3 3xHSV-CHD1 3xHA-RTF1

value: IP'd DNA from sonicated chromatin


title: WT_TOB_replicate2

description: Vibrio cholerae N16961 hapR+


title: H3K4me3_chd1_chct_bio1

value: his3∆200 lys2-128∂ leu2∆1 ura3-52 trp1∆63 KanMx::GAL1p-FLO8-HIS3 3xHSV-chd1∆CHCT 3xHA-RTF1


title: E26_A

description: Library name: E26_A


title: E24_B

description: Library name: E24_B


title: H3K4me3_chd1_chct_bio2


title: E18_CB

description: Library name: E18_CB


title: LA_GM-CSF, Replicate2

description:
LA_GM-CSF-2
TPM_TEM_complete.csv

value: Bone marrow

value: Bone-marrow derived macrophages

value: 25mM lactate and 2ng/mL GM-CSF for 4 days


title: LA_GM-CSF, Replicate1

description:
LA_GM-CSF-1
TPM_TEM_complete.csv


title: H3K36me3_wildtype_bio2


title: WT_TOB_replicate1

description: Vibrio cholerae N16961 hapR+


title: H3K36me3_wildtype_bio1


title: E18_A

description: Library name: E18_A


title: LA_PGE2, Replicate1

description:
LA_PGE2_-1
TPM_TEM_complete.csv

value: 25mM lactate and 100nM PGE2 for 4 days


title: LA_PGE2, Replicate2

description:
LA_PGE2_-2
TPM_TEM_complete.csv

value: WT


title: H3K4me3_chd1_null_bio3

value: his3∆200 lys2-128∂ leu2∆1 ura3-52 trp1∆63 KanMx::GAL1p-FLO8-HIS3 chd1∆::LEU2 3xHA-RTF1


title: N-_14D_3

city: Bangkok

first: Apidet

last: Rakpenthai

state: Chatuchak

address: 50 Ngamwongwan Rd

country: Thailand

institute: Kasetsart University

description: Library name: Sample 9

data_processing:
Sequence read were trimmed by Trimmomatic
Trimmed read were mapped to mm10 by using HISAT2
Gene Expression Quantification and Profile were preform using StringTie
DEG analysis  were preform using DESeq2
Assembly: ASM41409v2 was used as a reference genome
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

organism: Morus notabilis

source_name: Roots

extract_protocol:
Total RNA was extracted from cells using TRIzol Reagent (Invitrogen) following the manufacturer's instructions.
TruSeq Stranded mRNA Library Prep Kit and TruSeq Stranded mRNA Reference

value: Roots


title: T cells expressing AM tag (ChIP)

city: Sapporo

first: Kensuke

last: Takada

address: N21W11 Kita-ku

country: Japan

institute: Hokkaido University

description: Library name: Sample 1

data_processing:
Mapping and peak calls were conducted using the ENCODE ChIP-seq pipeline (https://github.com/ENCODE-DCC/chip-seq-pipeline).
Reads were mapped to the mm10 reference sequence using Bowtie2 (ver. 2.3.4.3).
The duplicate reads were removed with Picard (2.20.7) and samtools (1.9).
Peak calling was performed using SPP (1.15.5) with default parameters.
After removing the blacklisted regions, the consistency of the peaks was tested at the irreproducible discovery rate (IDR) using IDR (2.0.4.2).
Assembly: mm10
Supplementary files format and content: bigWig

source_name: Spleen

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 min at room temperature. Then, 1.5 M glycine was added to the cells, followed by a 5-min incubation to stop the reaction. Chromatin digestion and immunoprecipitation were performed using the SimpleChIP Plus Enzymatic Chromatin IP Kit (Cell Signaling) with anti-AM-tag antibody (Active Motif) according to manufacturers' instructions.
Sequencing libraries were prepared from the ChIP DNAs using the SMARTer ThruPLEX Tag-seq Kit (Clontech) according to the manufacturer’s protocol. Single-read sequencing (150 bp) was performed on the DNBSEQ-G400RS sequencer (MGI Tech).

value: Spleen

value: T cells

value: OT-I-TCR tg

value: Infected with AM-expressing vector


title: T cells expressing Rora-fused AM tag (ChIP)

description: Library name: Sample 2

value: Infected with Rora-AM-expressing vector


title: PGE2, Replicate2

description:
PGE2-2
TPM_TEM_complete.csv

value: 100nM PGE2 for 4 days


title: H3K4me3_rtf1_8_9A_bio3

value: his3∆200 lys2-128∂ leu2∆1 ura3-52 trp1∆63 KanMx::GAL1p-FLO8-HIS3 3xHSV-CHD1 3XHA-rtf1(8-9A)


title: H3K4me3_rtf1_8_9A_bio4


title: H3K4me3_chd1_null_bio4


title: N-_14D_2

description: Library name: Sample 8


title: PGE2, Replicate1

description:
PGE2-1
TPM_TEM_complete.csv


title: N-_14D_1

description: Library name: Sample 7


title: O3- IAA26 Knockout line

city: College Park

first: Madhu

last: Kappagantu

state: MD

address: 4291 Fieldhouse drive

institute: University of Maryland

description: Biological replicate 3

data_processing:
CLC Genomics Workbench v 10.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05, ambiguous trim = yes)
Trimmed reads were used to perform RNA-seq analysis with Arabiospsis thaliana (TAIR10) as reference ( mismatch cost =2, insertion cost =3, deletion cost =3, length fraction =0.8, similarity fraction =0.8, global alignment =No)
Total read count and RPKM values of each gene was  calculated with default parameters  CLC genomics workbench v 10.0.1
Assembly: TAIR10
Supplementary files format and content: Excel file include RPKM values for all 9 samples

organism: Arabidopsis thaliana

source_name: Leaf

growth_protocol: Leaves from 9 week old Wild type Shahdara and IAA26 mutants of shahdara were collected

extract_protocol:
RNA was isolated leaves using Rneasy plant mini kit (Qiagen)
RNA libraries for RNA-seq were prepared using NEB NEXT ultra Prep Kit following manufacturer's protocols.

treatment_protocol: Differential expression analysis of IAA26 knockout and stable lines was performed with wild type Shahdara as control group

value: Leaf

value: Shahdara- IAA26 knockout

value: IAA26 Knockout mutant

value: 9 week old plants


title: O1- IAA26 Knockout line

description: Biological replicate 1


title: O2- IAA26 Knockout line

description: Biological replicate 2


title: FN_14D_3

description: Library name: Sample 6


title: GM-CSF, Replicate2

description:
GM-CSF-2
TPM_TEM_complete.csv

value: Bone marrow

value: Bone-marrow derived macrophages

value: 2ng/mL GM-CSF for 4 days


title: H3K4me3_wildtype_bio4

value: his3∆200 lys2-128∂ leu2∆1 ura3-52 trp1∆63 KanMx::GAL1p-FLO8-HIS3 3xHSV-CHD1 3xHA-RTF1

value: IP'd DNA from sonicated chromatin


title: FN_14D_2

description: Library name: Sample 5

value: Roots


title: E18_CA

description: Library name: E18_CA

value: retina


title: P3- IAA26 stable line

description: Biological replicate 3

value: Shahdara- IAA26 stable

value: IAA26 Stable mutant


title: H3K4me3_wildtype_bio3


title: H3K4me3_chd1_chct_bio3

value: his3∆200 lys2-128∂ leu2∆1 ura3-52 trp1∆63 KanMx::GAL1p-FLO8-HIS3 3xHSV-chd1∆CHCT 3xHA-RTF1


title: LA, Replicate2

description:
LA-2
TPM_TEM_complete.csv

value: WT

value: 25mM lactate for 4 days


title: GM-CSF, Replicate1

description:
GM-CSF-1
TPM_TEM_complete.csv


title: FN_14D_1

description: Library name: Sample 4


title: P1- IAA26 stable line

description: Biological replicate 1


title: CHI_14D_3

description: Library name: Sample 3


title: LA, Replicate1

description:
LA-1
TPM_TEM_complete.csv


title: HA_chd1_chct_bio1

value: HA (Santa Cruz, #sc-7392, lot #D0121)


title: Wt3- Wildtype Shahdara

description: Biological replicate 3

value: Leaf

value: Shahdara

value: Control


title: Control,Replicate2

description:
PBS_DMSO-2
TPM_TEM_complete.csv

value: PBS and DMSO for 4 days


title: HA_chd1_chct_bio2


title: CHI_14D_2

description: Library name: Sample 2


title: Control,Replicate1

description:
PBS_DMSO-1
TPM_TEM_complete.csv

value: Bone marrow


title: CHI_14D_1

description: Library name: Sample 1


title: Wt2- Wildtype Shahdara

description: Biological replicate 2

value: 9 week old plants


title: HA_chd1_chct_bio3


title: Panc02, Replicate2

description:
Panc02-day6-2
Panc02_counts.txt

value: Bone-marrow derived macrophages

value: M-CSF differentiation and Panc02 tumor-conditioned medium induction


title: HA_wildtype_bio3

value: his3∆200 lys2-128∂ leu2∆1 ura3-52 trp1∆63 KanMx::GAL1p-FLO8-HIS3 3xHSV-CHD1 3xHA-RTF1

value: IP'd DNA from sonicated chromatin


title: Wt1- Wildtype Shahdara

description: Biological replicate 1


title: P2- IAA26 stable line

description: Biological replicate 2


title: 2396G Mock

city: Minneapolis

first: Craig

middle: John

last: Bierle

state: Minnesota

address: 2001 6th Street SE

department: Pediatrics

institute: University of Minnesota

description:
Library name: 2396G
Dam infected at 35 days gestation and euthanized at 56 days gestation

data_processing:
Space Ranger (10x Genomics, version 1.3.0) was used to process the raw Illumina sequencing data.
Space Ranger outputs were uploaded to Partek® Flow® software (v10.0)
Reads that aligned to the GPCMV genome from each sample of infected placenta were visualized with Geneious (v11.1.5)
Assembly: Cavpor3.0 (GCF_000151735.1, Annotation Release 103) amended with the GPCMV genome (strain 22122, NC_020231), and a list of Guinea pig Y chromosome transcripts
Supplementary files format and content: filtered_feature_bc_matrix.h5: Filtered feature-barcode matrices
Supplementary files format and content: spatial.tar: Compressed spatial output files generated by Space Ranger.
Supplementary files format and content: .tif: High resolution slide scan images of capture areas
Library strategy: Spatial Transcriptomics

molecule: polyA RNA

organism: Cavia porcellus

source_name: Maternal-fetal interface

growth_protocol: Guinea pigs were time mated during postpartum estrus and euthanized at 56 days gestation.

extract_protocol:
Placentas were disected, halved, and flash-frozen in OCT. Frozen placentas were trimmed to ~7X7 mm squares representing similar regions of interest and 10 μm tissue sections were prepared using a cryostat and placed onto Visium capture areas.
Sequencing libraries were prepared using Visium Spatial Gene Expression Slides (10x Genomics) and an 18 minute tissue permeabilization time according to the manufacturer's recommended protocol for fresh frozen tissue (CG000239 Rev C).

treatment_protocol: At 35 days gestation, guinea pigs were either infected with guinea pig cytomegalovirus or injected with saline.

value: Maternal-fetal interface

value: Mock-infected


title: JSA06

description: Parse Biosciences SPLiT-seq

data_processing:
fastq files were demultiplexed and aligned to the genome using splitpipe from Parse Biosciences
Cell-gene count matricies were processed using Seurat v4 as described in the text
Assembly: Homo sapiens, hg38, Ensembl 105 annotation
Supplementary files format and content: .rds file of processed single-cells from kidney organoids from differentiation days 10 (untreated), 12, 14, and 18. Days 12, 14, and 18 include both control and proximal-biased (treated with 10 uM LY294002 from days 10-12) cells.

extract_protocol:
6 individual organoids per timepoint were collected for FACS sorting for DRAQ5+, DAPI- single cells, and then fixed using the Parse Biosciences fixation protocol (Evercode Cell Fixation)
Parse Biosciences Evercode WT v2

treatment_protocol: Ly29-treated samples were treated with 10 uM LY294002 between days 10 and 12 of kidney organoid differentiation

value: Kidney organoid

value: Untreated, control, and Ly29-treated (10 uM between days 10-12)


title: 735B  Mock

description:
Library name: 735B
Dam infected at 35 days gestation and euthanized at 56 days gestation


title: GP, Replicate3

value: Primary macrophages

value: Bone marrow-derived macrophages

value: WT

value: 100nM PGE2 and 2ng/mL GM-CSF for 4 days


title: HA_wildtype_bio4

value: HA (Santa Cruz, #sc-7392, lot #D0121)


title: HA_wildtype_bio5


title: 4T1, Replicate2

description:
4T1_Day6_2
4T1_edu_counts.txt

value: M-CSF differentiation and 4T1 tumor-conditioned medium induction


title: JSA07

description: Parse Biosciences SPLiT-seq


title: JSA05

description: Parse Biosciences SPLiT-seq


title: 2395C GPCMV

description:
Library name: 2395C
Dam infected at 35 days gestation and euthanized at 56 days gestation

value: GPCMV-infected


title: 4T1, Replicate1

description:
4T1_Day6_1
4T1_edu_counts.txt

value: Bone marrow


title: HSV_chd1_chct_bio1

value: HSV (Sigma-Aldrich, #H6030, lot 086M4845V)

value: his3∆200 lys2-128∂ leu2∆1 ura3-52 trp1∆63 KanMx::GAL1p-FLO8-HIS3 3xHSV-chd1∆CHCT 3xHA-RTF1


title: H3K4me3_wildtype_bio5


title: M0, Replicate2

description:
BMDM-2
M0_counts.txt

value: Bone-marrow derived macrophages

value: M-CSF differentiation for 10 days


title: 731A GPCMV

description:
Library name: 731A
Dam infected at 35 days gestation and euthanized at 56 days gestation


title: HSV_chd1_chct_bio2

value: IP'd DNA from sonicated chromatin


title: JSA08

description: Parse Biosciences SPLiT-seq


title: Panc02, Replicate1

description:
Panc02-day6-1
Panc02_counts.txt

value: M-CSF differentiation and Panc02 tumor-conditioned medium induction


title: M0, Replicate1

description:
BMDM-1
M0_counts.txt


title: 2396E Mock

description:
Library name: 2396E
Dam infected at 35 days gestation and euthanized at 56 days gestation

value: Maternal-fetal interface

value: Mock-infected


title: JSA03

description: Parse Biosciences SPLiT-seq

value: Kidney organoid

value: Untreated, control, and Ly29-treated (10 uM between days 10-12)


title: HSV_chd1_chct_bio3


title: 2396A Mock

description:
Library name: 2396A
Dam infected at 35 days gestation and euthanized at 56 days gestation


title: TAMs-sgRNA,CROP-seq

data_processing:
Raw reads from scRNA-seq were processed to generate gene expression matrixes using CeleScope (https://github.com/singleron-RD/CeleScope) (version 1.11.1) pipeline. Briefly, raw reads were first processed with CeleScope to remove low quality reads with Cutadapt v3.7 to trim poly-A tail and adapter sequences. Cell barcode and UMI were extracted. After that, we used STAR v2.6.1b to map reads to the reference genome GRCm39. UMI counts and gene counts of each cell were acquired with featureCounts v2.0.1 , and used to generate expression matrix files for subsequent analysis.
To assign sgRNAs to corresponding cell barcodes, we used the multi_tag module of CeleScope. This module enabled us to demultiplex and quantify sgRNA sequences in each cell. In brief, it first check the mismatches between linker sequence (we set it as the constant 26 nt sequence before sgRNA sequence). If no mismatch < len(linker) / 10 + 1, the read is classified as “invalid”. Next, we determine the minimum Unique Molecular Identifier (UMI) threshold, denoted as UMI_min. UMI_min is calculated as the lesser of the 5th percentile and one-tenth of the median of the total UMI counts across all cells. If the calculated value is less than 1, UMI_min is set to 1.  Cells with valid UMIs below this threshold are classified as "undetermined". Simultaneously, the method calculates the minimum signal-to-noise ratio (SNR_min) for each cell barcode. SNR is computed as the ratio of the signal (the second highest UMI count) to the noise (the highest UMI count). If the signal is zero, the SNR is defined as zero; if the noise is zero, the SNR is defined as infinity. Cell barcodes with UMIs at least equal to UMI_min but with an SNR less than SNR_min are classified as "multiplets". Cell barcodes passed above thresholds were assigned a guide based on the highest guide counts. To ensure the accuracy of sgRNA sequences, we modified the source code in multi_tag module of CeleScope and set the n_mismatch parameter to 0. This alteration ensures that no mismatches are allowed between sgRNA sequences, thereby eliminating potential errors that could arise from allowing mismatches. The guide assignments were added to the Scanpy annotation of observations for downstream processing.
Scanpy (version 1.9.3) was used for quality control, dimensionality reduction and clustering. All data were processed using the Scanpy standard analysis workflow (https://www.sc-best-practices.org/preamble.html), and clusters of each dataset were annotated according to the marker genes.In the in vivo CROP-seq data, initial clusters with fewer than 100 cells were eliminated, reclustering was performed to refine the cell groupings. The cluster-specific or gene-knockout-specific marker genes were identified by using the scanpy.tl.rank_genes_groups function with default parameters.
Assembly: GRCm39
Supplementary files format and content: csv files include cell meta-infomation in Scanpy annotation of observations
Supplementary files format and content: csv files include gene meta-infomation in Scanpy annotation of variables/features
Supplementary files format and content: csv files include normalized counts for each cell
Supplementary files format and content: csv files include raw counts for each cell
Library strategy: CROP-seq

extract_protocol:
Single-cell suspensions with PBS were loaded onto microwell chip using the Singleron Matrix® Single Cell Processing System. Barcoding Beads are subsequently collected from the microwell chip, followed by reverse transcription of the mRNA captured by the Barcoding Beads and to obtain cDNA, and PCR amplification.
The amplified cDNA is then fragmented and ligated with sequencing adapters. The scRNA-seq libraries were constructed according to the protocol of the GEXSCOPE® Single Cell RNA Library Kits (Singleron). The sgRNA information was enriched by three rounds of amplification in cDNA library.  Individual libraries were diluted to 4 nM, pooled, and sequenced on Illumina novaseq 6000 with 150 bp paired end reads.

value: Tumor

value: Lewis lung cancer

value: tumor infiltrating immune cells

value: Loxp-Stop-Loxp-Cas9, Lyz2-Cre


title: HSV_rtf1_11_A_bio3

value: his3∆200 lys2-128∂ leu2∆1 ura3-52 trp1∆63 KanMx::GAL1p-FLO8-HIS3 3xHSV-CHD1 3XHA-rtf1(11A)


title: HSV_rtf1_8_9A_bio3

value: his3∆200 lys2-128∂ leu2∆1 ura3-52 trp1∆63 KanMx::GAL1p-FLO8-HIS3 3xHSV-CHD1 3XHA-rtf1(8-9A)


title: ChIP-seq EndoC-BH3 H3K27ac

data_processing:
Adapters were removed from ChIP-seq reads using cutadapt (v1.9.1)
Reads were aligned to the mouse (mm10) or human (hg19) genomes using Bowtie2 (v2.1.0)
bam files were created by filtering for multi-mapping (min MAPQ = 30) using Samtools (v1.2)
Duplicate reads and blacklisted regions were removed using Picard (v2.6.0) and Bedtools (v2.13.3)
bam files were converted into bigWig files for data visualization using Deeptools
Peaks were called using MACS2 (v.2.1.0) with the following settings: --bw=300 --keep-dup all --qvalue 0.01
Assembly: mm10
Assembly: hg19
Supplementary files format and content: bigWig files for each sample
Supplementary files format and content: bed files showing peaks for each sample

source_name: Murine β-cell line

extract_protocol:
~5 million cells were crosslinked in 1% formaldehyde for 10 min at RT in rotation. After quenching in 0.125 M glycine for 5 min, cells were washed in PBS and lysed in ChIP lysis buffer (2% Triton X-100, 1% SDS, 100 mM NaCl, 10 mM Tris-HCl pH 8.0, 1 mM EDTA and protease inhibitors) on ice for 30 min. Chromatin lysate was sonicated for 8 min (aiming for fragments between 150-400 bp) using a S220 Focused Ultrasonicator (Covaris)
Libraries were amplified by PCR (number of cycles were determined by qPCR using the Ct + 1 value) with KAPA HiFi Hotstart Ready mix (Kapa Biosystems) and size-selected (250–350 bp) employing Agencourt AMPure XP beads (Beckman Coulter). Bioanalyzer was used for sample QC and library pooling for multiplexing.

value: EndoC-BH3 cell line

value: Human beta-cell line

value: WT


title: ChIP-seq EndoC-BH3 H3K4me3


title: TEMs-sgRNA,CROP-seq

value: Bone marrow

value: tumor educated bone marrow-derived macrophages

value: sgRNA transduction and 4T1-tumor conditioned medium


title: JSA02

description: Parse Biosciences SPLiT-seq


title: TEMs,CROP-seq


title: 2395B1 GPCMV

description:
Library name: 2395B1
Dam infected at 35 days gestation and euthanized at 56 days gestation

value: GPCMV-infected


title: TAMs,CROP-seq