title: Smarcc2 knockout + addback of Smarcc2(S586E) mouse cortical neuron DIV18, 30 min depolarized, rep 2

description: Library name: BAF170_S586E_stim_2

data_processing:
ATAC-seq reads were checked for quality using fastqc (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
Reads were trimmed from adapters using trim_galore (https://github.com/FelixKrueger/TrimGalore) with parameters --paired --nextera.
Trimmed reads were aligned to the mouse mm10 genome using bowtie2 with parameters --very-sensitive -X2000.
Low quality reads, duplicated reads and reads with multiple alignments were removed using samtools and Picard (https://broadinstitute.github.io/picard/).
Positions of Tn5 inserts were determined as read start position offset by +4 bp for reads aligned to the + strand and as a read start position offset by -5 bp for reads aligned to the - strand.
macs2 callpeak was used for peak calling with Tn5 insert positions and parameters -p 0.01 --nolambda --shift -75 --extsize 150 --nomodel --call-summits --keep-dup all.
Bedtools was used to find consensus set of peaks by merging peaks across multiple conditions (bedtools merge), count number of reads in peaks (bedtools intersect -c) and generate genome coverage (bedtools genomecov -bga).
Assembly: mm10
Supplementary files format and content: Reconstructed peaks as narrowPeak files

extract_protocol:
ATAC-seq libraries were constructed from on-plate nuclear prep of neurons plated at 1M/6-well of a 6-well plate as described in PMC8496302. Briefly, DNase at a final concentration of 200 U/mL was added to wells for 30 mins at 37 ºC concurrent with indicated treatment timepoints (such as stimulation, and/or drug addition). Neuronal media was quickly dumped and neurons were washed 4X with cold PBS. 1mL of RSB-Lysis buffer/well (10mM Tris pH 7.4, 10mM NaCl, 3 mM MgCl2, 0.1% NP-40 (v/v), 0.1% Tween-20 (v/v), 0.01% Digitonin (v/v) ) was added and incubated for 10 mins on ice, then nuclei were gently lifted, counted by a hematocytometer, and spun down at 500 g for 4ºC for 10 mins in a swing-bucket centrifuge. 75,000 nuclei were taken for further processing. Lysis buffer was washed out with RSB-Wash (containing 0.1% Tween-20 but no NP-40 or Digitonin). The pellet was resuspended in transposition mixture (25 µL 2X TD Buffer (20mM Tris pH 7.6, 10mM MgCl2, 20% DMF (v/v)), 100 nM final Tn5 transposase (homemade, gift from William Greenleaf), 16.5 µL PBS, 0.5 µL 1% digitonin, 0.5 µL 10% Tween-20 (v/v), 5 µL H¬2O) and incubated for 30 mins at 37ºC with 1000 rpm shaking.
Reactions were cleaned up, amplified into libraries, indexed, and quantified using published protocol (PMC4374986). Library size distributions were confirmed using an Agilent Bioanalyzer and High Sensitivity DNA reagents (Agilent #5067) and concentrations determined by qPCR. Equimolar pooled libraries were sequenced on an Illumina NextSeq or NovaSeq.

treatment_protocol: Membrane Depolarization by KCl Stimulation in Neurons At the designated DIV, neurons were silenced overnight with 1 µM tetrodotoxin (Tocris #1069) and 100 µM D-AP5 (Tocris #79055-68-8) to reflect the resting state and then depolarized with 50 mM KCl for indicated time points as described (PMID 26139371, PMID 27830782, PMID 2498163). Briefly, to avoid excitotoxic death, depolarization proceeded as follows: 3/10th of neuronal media was reserved and charged with 170 mM KCl, 2 mM CaCl2, 1 mM MgCl2, and 10 mM HEPES pH 7.9 by adding 69.72 µL/1 mL reserved media of concentrated isotonic stimulation buffer (2.44M KCl, 28.7 mM CaCl2, 14.4 mM MgCl2, and 143.4 mM HEPES pH 7.9). At this point, the reserved media contains 3x the final concentration for the neuron. Control wells underwent media removal without addition of any components. The mix was restored to each well and gently swirled for 3 seconds, then the plate was placed back in the incubator for the appropriate incubation time. The excitotoxicity-induced gene Clca1 was verified not to be upregulated in our RNA-seq datasets, excluding toxic reaction. Neurons were then immediately moved to ice, media was then immediately exchanged to ice-cold PBS and harvested for downstream assays. Inhibition of BAF ATPase activity: FHT1015 was obtained as lyophilized powder as a kind gift from Steve Bellon, Foghorn Therapeutics. A final concentration of 100 nM FHT1015 or DMSO at final 0.1% DMSO concentration was added to reserved neuronal media during depolarization or in the resting unstimulated state and added back to wells. The concentration was chosen from the reported biochemical in vitro IC50 of inhibition of BAF ATPase activity as compared to other remodelers

value: E16.5 cortex

value: primary neuron

value: 50 mM KCl (30 min)


title: DSP-1001660021422-D-A01

status: Public on Mar 15 2025

type: SRA

city: Houston

first: Scott

middle: Andrew

last: Ochsner

state: TX

address: One Baylor Plaza

department: Molecular and Cellular Biology

country: USA

institute: Baylor College of Medicine

library_source: transcriptomic

data_processing:
Fastq files were automatically generated with the Illumina BaseSpace Sequence Hub
Assembly: n/a
Supplementary files format and content: Digital count conversion (.dcc) files produced from fastq files using the GeoMx NGS Pipeline 2.3.3.10 desktop application.
Library strategy: Nanostring GeoMx

molecule: total RNA

organism: synthetic construct

source_name: no associated tissue

extract_protocol:
Default Nanostring GeoMx extraction protocol
Default Nanostring GeoMx library consruction protocol

tag: tissue

value: no associated tissue

tag: slide name

value: No Template Control


title: Patient 23, lymph node tumor

city: Durham

first: Katherine

middle: Ismei

last: Zhou

state: NC

address: 2301 Erwin Rd

institute: Duke University

data_processing:
RNA-seq reads for clinical patient were mapped to the human genome (build hg38) using STAR (v2.7.11b)  (PMCID:PMC3530905)  to generate bam files.
Samtools (v1.9a) (PMCID: PMC2723002) were used to sort the bam files.
Assembly: build hg38 (Ensembl)
Supplementary files format and content: quant.sf (read count)

organism: Homo sapiens

source_name: lymph node

extract_protocol:
Total RNA was extracted from 10 mg of snap-frozen tissue on a KingFisher Flex instrument (Thermo Scientific, 5400610) using the MagMAX mirVana total RNA isolation kit (Applied Biosystems, A27828).
Nucleic acid quantification was performed on a Qubit Flex Fluorometer (Thermo Scientific, Q33327) using the Qubit RNA broad range assay (Invitrogen, Q10211), and RNA quality was evaluated on a TapeStation 4200 instrument (Agilent, G2991AA) by RNA ScreenTape Analysis (Agilent, 5067-5576). Libraries were prepared from 1 µg of total RNA on a Hamilton NGS STAR instrument using the TruSeq Stranded Total RNA Library Prep Gold Kit (Illumina, 20020599). Library quantification was performed on a Qubit 3.0 Fluorometer (Thermo Scientific, Q33216) using the Qubit 1X dsDNA broad range assay (Invitrogen, Q33266). Library quality was evaluated on a TapeStation 4200 instrument (Agilent, G2991AA) by DNA ScreenTape Analysis (Agilent, 5067-5582).

tag: subject

value: Patient 23

value: lymph node


title: Patient 28, breast tumor

source_name: breast tumor

value: Patient 28

value: breast tumor


title: Smarcc2 knockout + addback of Smarcc2(S586A) mouse cortical neuron DIV18, 30 min depolarized, rep 2

city: Stanford

first: Sai

last: Gourisankar

state: CA

address: 240 Pasteur Dr, Rm 4700

department: Chemical Systems Biology

institute: Stanford

description: Library name: BAF170_S586A_stim_2

library_source: genomic

molecule: genomic DNA

organism: Mus musculus

source_name: E16.5 cortex

growth_protocol: Primary Neuron Culture Coating plates: Culture plates (Corning #353003) were coated overnight at room temperature by flooding with poly-D-lysine (Sigma #P6407) at 0.1 mg/mL in borate buffer (1.55 g boric acid/2.4 g sodium tetraborate in 500 mL sterile water). Plates were washed 3x with water and 1x with PBS before plating neurons. Dissection and culture: Cortical neurons were dissected and cultured following established protocols (PMID 32312822, PMID 26139371). Brefly, embryonic cortical neurons were harvested from embryonic day 16.5 (E16.5) mice using sterile tools. Pregnant female mice were anesthetized with isoflurane and euthanized by cervical dislocation on E16.5. A 4 cm long, V-shaped incision was made through the derma and muscle layers of the lower abdomen just above the vaginal opening of the euthanized mouse. After pulling back skin and muscle, the uterus was carefully disconnected and the string of embryos gently pulled from the abdomen and placed in a dish of sterile PBS on ice. Fetuses were removed from the amniotic sac using forceps and baby scissors and placed in a second dish of fresh PBS on ice. From this point onwards, the cortex from each embryo was considered a biological replicate. Individual embryos were transferred on sterile filter paper in ice cold PBS and stabilized from behind the neck using a curved forcep. Using a sharp pair of forceps, two incisions were made: above the olfactory bulbs between the eyes and upwards between the hemispheres skimming along the underside of the skull. The flat side of a curved forcep was then used to apply gentle pressure from the brainstem to the eyes to push the brain out of the skull. The brain was scooped up and placed in a fresh dish of sterile PBS on ice. The brain was anchored vertically under a dissecting microscope by grasping near the brainstem using forceps. The meninges and remaining olfactory bulb were removed by gently tugging along the length of the tissue. Using forceps, each hemisphere was gently lifted, avoiding the hippocampus, striatum and basal ganglia, and transferred to a 15 mL sterile Falcon tube of ice-cold PBS and allowed to settle. Then, cortices were enzymatically dissociated to single neurons with Neural Tissue Dissociation Kit (P) (Miltenyi Biotech #130-092-628). Neurons were resuspended in plating media [DMEM (Life Technologies #11960-077), 10% FBS (Omega #FB-01), 1x penicillin-streptomycin (ThermoFisher #15140122)], counted, and plated at a density of 25-30M neurons per 15 cm plate, 6-10M per 10 cm plate, 1M per well of a 6-well plate, 0.5M per well of a 12-well plate, or 0.1M per well of a 24-well plate. After incubation for 1 hour at 37 ºC/5% CO2, neurons were attached to the plates and media was changed to neuron maintenance media [Neurobasal Medium (Life Technologies #21103049), 2.5% B27 (ThermoFisher #17504044), 1% penicillin-streptomycin (Life Technologies #15070-063), 0.25% GlutaMax (Life Technologies #35050061)]. On day in vitro 2 (DIV2), ara-c (Sigma #C1768) was added to a final concentration of 0.5 µM to inhibit proliferation of any contaminating glial cells. Beginning on DIV3, half the media was exchanged for fresh neuron maintenance media every three days. Cultures were kept at 37 ºC/5% CO2.

tag: cell type

tag: treatment


title: Patient 15, breast tumor

value: Patient 15


title: Patient 1, lymph node tumor

value: Patient 1


title: Smarcc2 knockout + addback of Smarcc2(S586E) mouse cortical neuron DIV18, 30 min depolarized, rep 1

description: Library name: BAF170_S586E_stim_1


title: Smarcc2 knockout + addback of Smarcc2(S586A) mouse cortical neuron DIV18, 30 min depolarized, rep 1

description: Library name: BAF170_S586A_stim_1


title: Patient 9, breast tumor

value: Patient 9


title: Patient 27, lymph node tumor

value: Patient 27


title: Patient 19, lymph node tumor

value: Patient 19


title: Patient 17, breast tumor

value: Patient 17


title: Smarcc2 knockout + addback of WT Smarcc2 mouse cortical neuron DIV18, 30 min depolarized, rep 1

description: Library name: BAF170_stim_1


title: DSP-1001660021422-D-G02

source_name: lung

value: lung

tag: panel

value: (v1.0) Human NGS Whole Transcriptome Atlas RNA

tag: patient

tag: age

tag: fvc%

tag: smoking history

value: former

tag: pack years

tag: gender

value: female

tag: roi

tag: scan name

value: paraffin


title: Non-targeting gRNA mouse cortical neuron DIV18, 30 min depolarized, rep 1

description: Library name: vector_neg_stim_1

value: E16.5 cortex

value: primary neuron

value: 50 mM KCl (30 min)


title: Non-targeting gRNA mouse cortical neuron DIV18, 30 min depolarized, rep 2

description: Library name: vector_neg_stim_2


title: Smarcc2 knockout + addback of WT Smarcc2 mouse cortical neuron DIV18, 30 min depolarized, rep 2

description: Library name: BAF170_stim_2


title: Smarcc2 knockout + vector mouse cortical neuron DIV18, 30 min depolarized, rep 2

description: Library name: BAF170KO_stim_2


title: DSP-1001660021422-D-F11


title: Smarcc2 knockout + addback of Smarcc2(S586E) mouse cortical neuron DIV18, unstimulated, rep 2

description: Library name: BAF170_S586E_unstim_2


title: Smarcc2 knockout + addback of Smarcc2(S586E) mouse cortical neuron DIV18, unstimulated, rep 1

description: Library name: BAF170_S586E_unstim_1


title: Smarcc2 knockout + vector mouse cortical neuron DIV18, 30 min depolarized, rep 1

description: Library name: BAF170KO_stim_1


title: Smarcc2 knockout + addback of Smarcc2(S586A) mouse cortical neuron DIV18, unstimulated, rep 2

description: Library name: BAF170_S586A_unstim_2


title: Smarcc2 knockout + addback of Smarcc2(S586A) mouse cortical neuron DIV18, unstimulated, rep 1

description: Library name: BAF170_S586A_unstim_1


title: DSP-1001660021422-D-F09


title: DSP-1001660021422-D-F08


title: DSP-1001660021422-D-F07


title: Smarcc2 knockout + addback of WT Smarcc2 mouse cortical neuron DIV18, unstimulated, rep 2

description: Library name: BAF170_unstim_2


title: DSP-1001660021422-D-F10


title: Smarcc2 knockout + addback of WT Smarcc2 mouse cortical neuron DIV18, unstimulated, rep 1

description: Library name: BAF170_unstim_1


title: DSP-1001660021422-D-F06


title: Non-targeting gRNA mouse cortical neuron DIV18, unstimulated, rep 2

description: Library name: vector_neg_unstim_2


title: DSP-1001660021422-D-G01


title: DSP-1001660021422-D-F02


title: Non-targeting gRNA mouse cortical neuron DIV18, unstimulated, rep 1

description: Library name: vector_neg_unstim_1


title: Smarcc2 knockout + vector mouse cortical neuron DIV18, unstimulated, rep 1

description: Library name: BAF170KO_unstim_1


title: WT mouse cortical neuron DIV7, DMSO treated and 30 min depolarized, rep 2

description: Library name: SH4

data_processing:
Raw reads were checked for quality using fastqc (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
Reads were trimmed from adapters using cutadapt using parameters cutadapt -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCA -b AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT --nextseq-trim=20 --minimum-length 1.
Transcripts were quantified using kallisto against a mouse Gencode vM24 indexed transcriptome and annotations.
Assembly: Gencode vM24
Supplementary files format and content: abundance.tsv containing transcripts counts quantified by kallisto, used for downstream differential gene analyses

molecule: polyA RNA

extract_protocol:
Cells were harvested in TRIsure (Bioline #38033). RNA was extracted using Direct-zol RNA MicroPrep columns (Zymo #R2062) treated with DNAseI.
For sequencing library preparation, rRNA was depleted (NEB #E7400) and prepared into paired-end libraries (NEB #E7760). For naïve (WT) DIV7 neuron RNA-seq, polyA-enriched mRNAs were isolated (NEB #E7490). Library size distributions were confirmed using an Agilent Bioanalyzer and High Sensitivity DNA reagents (Agilent 5067) and concentrations determined by qPCR. Equimolar pooled libraries were sequenced on an Illumina NextSeq or HiSeq.

treatment_protocol: Membrane Depolarization by KCl Stimulation in Neurons At the designated DIV, neurons were silenced overnight with 1 µM tetrodotoxin (Tocris #1069) and 100 µM D-AP5 (Tocris #79055-68-8) to reflect the resting state and then depolarized with 50 mM KCl for indicated time points as described (PMID 26139371, PMID 27830782, PMID 2498163). Briefly, to avoid excitotoxic death, depolarization proceeded as follows: 3/10th of neuronal media was reserved and charged with 170 mM KCl, 2 mM CaCl2, 1 mM MgCl2, and 10 mM HEPES pH 7.9 by adding 69.72 µL/1 mL reserved media of concentrated isotonic stimulation buffer (2.44M KCl, 28.7 mM CaCl2, 14.4 mM MgCl2, and 143.4 mM HEPES pH 7.9). At this point, the reserved media contains 3x the final concentration for the neuron. Control wells underwent media removal without addition of any components. The mix was restored to each well and gently swirled for 3 seconds, then the plate was placed back in the incubator for the appropriate incubation time. The excitotoxicity-induced gene Clca1 was verified not to be upregulated in our RNA-seq datasets, excluding toxic reaction. Neurons were then immediately moved to ice, media was then immediately exchanged to ice-cold PBS and harvested for downstream assays. Other Pharmacological Treatments in Neurons: Neurons were treated with 0.1% DMSO during depolarization or before harvesting (unstimulated) for the indicated times (30 mins or less).

value: 0.1% DMSO + 50 mM KCl (30 min)


title: DSP-1001660021422-D-F12


title: DSP-1001660021422-D-F04


title: WT mouse cortical neuron DIV7, DMSO treated and 30 min depolarized, rep 1

description: Library name: SH3


title: WT mouse cortical neuron DIV7, DMSO treated and unstimulated, rep 2

description: Library name: SH2

value: 0.1% DMSO


title: WT mouse cortical neuron DIV7, DMSO treated and unstimulated, rep 1

description: Library name: SH1


title: patient3_PA

city: Beijing

first: Song

last: Jiangping

address: 167A Beilishi Rd

department: Fuwai Hospital, National Center for Cardiovascular Diseases

country: China

institute: Chinese Academy of Medical Sciences and Peking Union Medical College

data_processing:
The Cellranger software (Version 3.0.2) provided by 10x Genomics was used to process FASTQ files. Cellular barcode de-multiplexing read alignment to the prebuilt GRCh38/hg38 reference genome and unique molecular identifier (UMI) counting were performed using cellranger count for each sample.
Outputs from samples were then aggregated using Cellranger aggr to generate a matrix of UMI counts per gene versus cells.
Assembly: hg38
Supplementary files format and content: The filtered_feature_bc_matrix from Cellranger output.

source_name: cardiac artery

extract_protocol:
Excised arteries were collected in 10 mL DMEM (Gibco, 11885084) containing 10% fetal bovine serum (Gibco, 10091148) on ice. Three CA samples of each patient were mixed to get enough cells. Samples were washed by PBS to remove the remaining blood cells and then cut into small pieces. These small pieces were washed by PBS again and digested in PBS containing 1000 U/mL Collagenase II (Worthington, 43J14367B) at 37 °C for 25 minutes, followed by gently shaking until the solution became cloudy. The single-cell suspension was filtered with a 40 μm cell strainer and collected by centrifugation at 400g, 4 °C for 5 minutes. The supernatant was discarded, and the cell pellets were resuspended in 1 mL of 2% cold fetal bovine serum/DMEM. These steps were repeated 2 to 3 times. Arterial cell suspension was subsequently filtered through a 40-μm cell strainer (Falcon, 431750) and then centrifuged at 400g, 4 °C for 5 minutes. The cell pellet was resuspended in 200 μL red blood cell lysis buffer (Beyotime, C3702) and incubated for 10 minutes on ice. The resulting suspension was further diluted to 10× the initial volume with PBS, and centrifuged at 400g, 4 °C for 5 minutes. The cell precipitate was resuspended in 1 mL cold DMEM containing 2% fetal bovine serum.
Single-cell suspensions were loaded onto a Chromium Single Cell Controller (10x Genomics) to generate Gel Bead-In-Emulsions (GEMs). cDNA libraries were prepared using the single cell 5’ solution v2 reagent kit (Chromium, 1000020) according to the protocol provided in the 10x Genomics Chromium Single Cell Immune Profiling Solution. Briefly, FACS-sorted cells (>90% viability) were encapsulated into droplets. After the reverse transcription step, droplets were disrupted and barcoded cDNAs were purified with DynaBeads, followed by 14 cycles of PCR amplification (98 °C for 45 seconds; [98 °C for 20 seconds, 67 °C for 30 seconds, and 72 °C for 1 minute]×14 cycles; 72 °C for 1 minute). The resulting amplified cDNAs were sufficient to construct 5′ gene expression libraries. The cDNAs from single-cell transcriptomes (50 ng) were fragmented, subjected to 2 rounds of size selection with SPRI beads (avg. size 450 bp), and sequenced on the Illumina NextSeq platform (High Output V2 Kit, 150 cycles). All libraries were sequenced by an Illumina HiSeq 4000 sequencer.

value: pulmonary artery

value: patient 3

tag: condition

value: Non-diseased


title: DSP-1001660021422-D-E09


title: DSP-1001660021422-D-E10


title: patient3_CA2

value: coronary arteries


title: DSP-1001660021422-D-E07


title: DSP-1001660021422-D-E08


title: patient3_AO2

value: aorta


title: patient3_CA1


title: DSP-1001660021422-D-E06


title: patient3_AO1


title: DSP-1001660021422-D-E05


title: DSP-1001660021422-D-F03


title: DSP-1001660021422-D-F05


title: Smarcc2 knockout + vector mouse cortical neuron DIV18, unstimulated, rep 2

description: Library name: BAF170KO_unstim_2


title: DSP-1001660021422-D-E04


title: patient2_PA

value: patient 2


title: DSP-1001660021422-D-F01


title: patient2_CA2


title: DSP-1001660021422-D-E02

value: male


title: DSP-1001660021422-D-E03

value: lung


title: DSP-1001660021422-D-E12

value: (v1.0) Human NGS Whole Transcriptome Atlas RNA


title: patient2_CA1


title: patient1_CA

value: patient 1


title: DSP-1001660021422-D-E01

value: former


title: patient1_AO


title: DSP-1001660021422-D-D12

value: paraffin


title: DSP-1001660021422-D-E11

value: female


title: 4T1-mCh/rLuc, Snord67KO2, replicate 2

data_processing:
D3H2LN RNA-seq reads were trimmed using fastp (PMCID:PMC6129281)
RNA-seq reads of the 4T1 (mouse) and the D3H2LN samples (human) were mapped to the mouse genome (build m38) and human genome (build hg38), respectively, using STAR (v2.7.11b)  (PMCID:PMC3530905), to generate bam files.
Samtools (v1.9a) (PMCID: PMC2723002) were used to sort the bam files.
Further analyzed by DESeq2 (v3.19) (PMCID: PMC4302049) for differential gene expression analysis. Significant genes were quantified by having a |log2foldchange| > 1 and an adjusted P value < 0.05. The mapped reads were further analyzed with RMATS (PMCID: PMC4280593) to calculate alternative splicing (AS). Significant Events were identified with a delta PSI of 10 percent or greater and an FDR < 0.05 and having either a Inclusion or Exclusion read count >= 5.
Gene Ontology (GO) analyses were preformed using the R/Bioconductor clusterProfiler (PMCID: PMC8454663) functions enrichGO. The hyper-geometric test was used to calculate the significance of overlapping datasets, where only co-detected genes or events were used. Spearman’s rank correlation was used in correlation analysis.
Assembly: For mouse build: m38. For human build: hg38 (Ensembl).
Supplementary files format and content: quant.sf (read count)
Supplementary files format and content: .bam, .bai (mapped reads)

growth_protocol: 4T1 cells transduced with lentiviral constructs expressing mCherry and Renilla luciferase (mCh/rLuc) were maintained in RPMI medium supplemented with 10% FBS, 100 U/mL penicillin/streptomycin, and 4 µg/mL puromycin. MDA-MB-231-D3H2LN-luc cells were maintained in DMEM medium with 4.5 g/L D-glucose supplemented with 10% FBS, 100 U/mL penicillin/streptomycin, and 300 µg/mL zeocin.

extract_protocol:
For 4T1 cells, total RNA was isolated using the Purelink RNA Mini Kit (Invitrogen), and mRNA was enriched using the NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB). For MDA-MB-231-D3H2LN-luc cells, total RNA was extracted using the RNeasy kit (Qiagen).
For 4T1 cells, the KAPA Stranded mRNA-seq kit (Roche) was used to prepare libraries for mRNA-seq. For MDA-MB-231-D3H2LN cells, libraries were prepared from 1 µg of total RNA for each sample using the KAPA mRNA HyperPrep Kit (Roche) and Illumina adapters (NEB).

tag: cell line

value: breast cancer cells

tag: genotype

value: Snord67 knockout 2


title: 4T1-mCh/rLuc, Snord67KO2, replicate 3


title: wildtype C57/BL6 distal colonic tumor from mouse 6

city: Nashville

first: guoqiang

last: Gu

state: Tennessee

address: 9415D Medical Research Building IV

department: Department of Cell and Developmental Biology

institute: Vanderbilt University Medical Center

description: Library name: WT4

library_source: transcriptomic single cell

data_processing:
PIPseeker was used to preprocess scRNAseq reads and to align reads to the reference genome mm10 to generate count matrices of each gene in each cell.
Cells with low proportion of uniquely mapping reads (unique molecular identifier [UMI]<1000), low proportion of expressed genes (<300), or high proportion of reads mapped to the mitochondrial RNA (>20%) were considered as low quality and excluded from downstream analysis.
After quality control, scRNAseq data were normalized using UMI-filtered counts. Common and rare cell populations were identified simultaneously by adaptive k-nearest neighbor graph with optimization and visualized by UMAP using Seurat based on the first 30 principal components generated from the top 2000 highly variable genes.
Cell subpopulations were automatically annotated by single cell multiresolution marker-based annotation (scMRMA), and then further manually checked by known marker genes. Cell cycle scores of cancer cells were estimated by CellCycleScoring function in Seurat.
Differentially expressed genes between DPEP1 KO and WT in cancer cells were identified by FindMarkers function in Seurat. Functional-class-scoring GSEA analysis were performed and plotted with Genekitr R package  (https://github.com/GangLiLab/genekitr).
Assembly: mm10
Supplementary files format and content: *_barcodes.tsv.gz: compressed table file with contents of cell barcode per line
Supplementary files format and content: *_features.tsv.gz: compressed table file with contents of gene ensembl id at the first column, the gene symbol at the second column
Supplementary files format and content: *_matrix.mtx.gz: compressed matrix file with sparse matrix of expression values

source_name: colon tumor

extract_protocol:
Mouse tumors were incubated rotating at 4˚ C for 1.25 h in a chelating buffer of Dulbecco’s PBS (DPBS) with 20mM HEPES, 3mM EDTA, and 0.5mM DTT, then gently washed in DPBS. Tumors were then resuspended in DPBS with 5mg/ml cold active protease and 2.5mg/ml DNase and incubated at 4˚ C for 25 minutes with rotation. Tissues were then pipetted 10-20 times with a pipette to liberate single cells, which were passed through a 70μm filter into a new tube for washes. Cells were washed in DPBS with 0.02% BSA before proceeding immediately to scRNA-seq.
scRNA sequencing was performed using Pipseq T2 V4plus kits from Fluent Biosciences. In summary, cells were co-encapsulated with capture beads through vortexing. The resulting emulsion was then incubated to allow for lysis of cells and hybridization of mRNA to barcoded oligos on the beads. Beads were released from droplets and washed, before undergoing reverse transcription and PCR reactions, resulting in amplified barcoded transcript libraries. Libraries were then fragmented, a-tailed and indexed for sequencing. Sequencing was erformed on Novaseq XP, targeting 100M reads per sample. scRNA-seq was performed on tumors isolated from two WT mice and three DPEP1 KO mice.

treatment_protocol: Mice were injected intraperitoneally (i.p.) with 10 mg/kg of AOM (Sigma-Aldrich) in PBS once a week for two weeks. A week after the second AOM injection, mice were given ad lib access via water bottle to 2% colitis-grade DSS for 5 days. After approximately 3 months of growth, tumor number was counted, and tumor volume was measured with calipers and calculated as follows: volume = (w x h x d)/2 (w, shortest diameter; h, longest diameter; d, depth).

tag: tissue

value: colon tumor

value: WT

value: AOM/DSS


title: 4T1-mCh/rLuc, Snord67KO2, replicate 1


title: DSP-1001660021422-D-D09

tag: slide name


title: 4T1-mCh/rLuc, Snord67KO1, replicate 3

value: Snord67 knockout 1


title: 4T1-mCh/rLuc, Snord67KO1, replicate 2


title: 4T1-mCh/rLuc, Snord67KO1, replicate 1


title: wildtype C57/BL6 distal colonic tumor from mouse 4

description: Library name: WT1


title: wildtype C57/BL6 distal colonic tumor from mouse 5

description: Library name: WT3


title: DSP-1001660021422-D-D07


title: 4T1-mCh/rLuc, wild-type, replicate 3


title: 4T1-mCh/rLuc, wild-type, replicate 2


title: DPEP1 KO distal colonic tumor from mouse 3

description: Library name: KR250


title: 4T1-mCh/rLuc, wild-type, replicate 1


title: patient2_AO

value: Non-diseased


title: DSP-1001660021422-D-D06


title: DSP-1001660021422-D-D11


title: 4T1-mCh/rLuc, Snord67KO-2, oxidized, replicate 2

description:
oxidized
67AC5_2_OXI

data_processing:
Data processing overall follows the published riboxi-seq workflow: https://github.com/yz201906/RibOxi-seq. Briefly, `cutadapt` was used to removed any read-through adapters due to the a significant portion of inserts being short.
UMI sequences were then moved from read 2 of the PE reads to the name of the reads, which will be used for PCR deduplication during a later step
3' adapter sequence was then removed using `cutadapt`, while any reads lacking 3' adapter were discarded
`STAR` was used to map reads against reference genome with the following parameters: `--outMultimapperOrder Random --outFilterScoreMinOverLread 0.4 --alignEndsType EndToEnd --outFilterMatchNminOverLread 0.4 --outFilterMismatchNoverLmax 0.05 --outSAMtype BAM SortedByCoordinate`
Resulting BAM files were deduplicated using `UMITools`, and the deduplicated BAM files were then converted into BED files prior to feeding to `riboxi_bed_parsing.py` script available from github riboxi repository.
Assembly: mm10
Supplementary files format and content: There are 9 data columns in the processed data file, whereas there are 18 samples listed in the metadata file, because for RibOxi-seq, each data column is derived from 2 samples (control and oxidized).

growth_protocol: 4T1 cells transduced with lentiviral constructs expressing mCherry and Renilla luciferase (mCh/rLuc) were maintained in RPMI medium supplemented with 10% FBS, 100 U/mL penicillin/streptomycin, and 4 µg/mL puromycin

extract_protocol:
Total RNA was isolated using the Purelink RNA Mini Kit (Invitrogen), and mRNA was enriched using the NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB)
Poly(A) enriched RNA was denatured for 3 min at 90°C and fragmented by Benzonase (final RNA concentration: 100 ng/µL, enzyme 0.5 units/100µL reaction) on ice for 90 minutes. Following extraction with acidic phenol-chloroform, the fragmented samples underwent 2 rounds oxidation-elimination cycles. The oxidized RNA was then ligated to the NEB Universal miRNA cloning linker using T4 RNA ligase 2, truncated KQ (NE Biolabs, M0373S) at 16°C overnight. 25 µM RibOxi RT primer was then annealed to the reaction before ligation of 5’ RNA linker using T4 RNA ligase I at room temperature for 1 hour and subsequent reverse-transcription using Protoscript II (NE Biolabs, M0368S). cDNA was then purified with Ampure XP beads with 1:1.8 ratio. 10 µM Illumina-compatible forward and reverse PCR primers were added together with Q5 master mix (NEB, M0544S) followed by Ampure XP purification with 1:1 ratio. A custom cycling program was used to amplify the final PE libraries where 5 cycles were with annealing temperature of 55°C, while the remaining 23 cycles had annealing temperature of 62°C.


title: 4T1-mCh/rLuc, Snord67KO-2, oxidized, replicate 3

description:
oxidized
67AC5_3_OXI


title: DSP-1001660021422-D-D05


title: DPEP1 KO distal colonic tumor from mouse 2

description: Library name: KR249


title: 4T1-mCh/rLuc, Snord67KO-2, oxidized, replicate 1

description:
oxidized
67AC5_1_OXI


title: DPEP1 KO distal colonic tumor from mouse 1

description: Library name: KR247


title: DSP-1001660021422-D-D10


title: 4T1-mCh/rLuc, Snord67KO-2, control, replicate 2

description: control


title: Arid2KO mouse cortical neuron DIV7, depolarized (30 min), rep 2

description: Library name: ATAC_2_4

value: E16.5 cortex

value: primary neuron

value: 50 mM KCl (30 min)


title: 4T1-mCh/rLuc, Snord67KO-2, control, replicate 1

description: control


title: DSP-1001660021422-D-D04

value: male


title: DSP-1001660021422-D-D08

value: lung


title: 4T1-mCh/rLuc, Snord67KO-1, oxidized, replicate 3

description:
oxidized
67AC4_3_OXI


title: Arid2KO mouse cortical neuron DIV7, unstimulated, rep 2

description: Library name: ATAC_2_3


title: 4T1-mCh/rLuc, Snord67KO-1, oxidized, replicate 2

description:
oxidized
67AC4_2_OXI


title: 4T1-mCh/rLuc, Snord67KO-1, oxidized, replicate 1

description:
oxidized
67AC4_1_OXI


title: Non-targeting gRNA mouse cortical neuron DIV7, depolarized (30 min), rep 2

description: Library name: ATAC_2_2


title: 4T1-mCh/rLuc, Snord67KO-1, control, replicate 3

description: control


title: DSP-1001660021422-D-D02

value: (v1.0) Human NGS Whole Transcriptome Atlas RNA


title: DSP-1001660021422-D-D01


title: 4T1-mCh/rLuc, Snord67KO-1, control, replicate 2

description: control


title: 4T1-mCh/rLuc, Snord67KO-1, control, replicate 1

description: control


title: Non-targeting gRNA mouse cortical neuron DIV7, unstimulated, rep 2

description: Library name: ATAC_2_1


title: Arid2KO mouse cortical neuron DIV7, depolarized (30 min), rep 1

description: Library name: ATAC_1_4


title: 4T1-mCh/rLuc, wild-type, oxidized, replicate 3

description:
oxidized
4T1_3_OXI


title: 4T1-mCh/rLuc, wild-type, oxidized, replicate 2

description:
oxidized
4T1_2_OXI


title: 4T1-mCh/rLuc, wild-type, oxidized, replicate 1

description:
oxidized
4T1_1_OXI


title: Arid2KO mouse cortical neuron DIV7, unstimulated, rep 1

description: Library name: ATAC_1_3


title: DSP-1001660021422-D-C12


title: DSP-1001660021422-D-C11


title: 4T1-mCh/rLuc, wild-type, control, replicate 1

description: control


title: 4T1-mCh/rLuc, wild-type, control, replicate 2

description: control


title: 4T1-mCh/rLuc, Snord67KO-2, control, replicate 3

description: control


title: DSP-1001660021422-D-D03


title: Non-targeting gRNA mouse cortical neuron DIV7, depolarized (30 min), rep 1

description: Library name: ATAC_1_2


title: F#38 IFNR 400

city: Seoul

first: Sung Noh

last: Hong

state: South Korea

address: 81 Irwon-Ro, Gangnam-gu

department: Gastroenterolgy

country: South Korea

institute: Samsung Medical Center

description:
Library name: NL6_IFN
NL6_IFN

data_processing:
Reads from FASTQ format files were mapped to the Homo sapiens reference genome (hg38) using HISAT2 version 2.2.1 with default parameters (http://daehwankimlab.github.io/hisat2/). Gene-level read counts were quantified using featureCounts (Subread version 2.0.1).
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: small intestine (ileum)

growth_protocol: Human intestinal organoids were constructed using a previously described method. In brief, we obtained small intestinal mucosa specimens using endoscopic biopsy from the non-IBD patients without any mucosal lesions in small intestine, who underwent single-balloon enteroscopy (SBE) at the Samsung Medical Center, Seoul, Korea, after receiving informed consent. The intestinal crypts were isolated from endoscopic biopsy specimens using 10 mM EDTA (Thermo Scientific, San Jose, CA, USA) and 1 mM DTT (Thermo Scientific) chelation. The isolated crypts were resuspended into Matrigel (Corning) and plated in 48-well culture plates (Corning). The 250 μl of maintenance medium (50 % Wnt3a-conditioned medium (ATCC#CRL-2647, Manassas, VA, USA) + 50 % 2× basal medium (Basal medium: advanced DMEM/F12 (Thermo Scientific) supplemented with antibiotic–antimycotic solution (Thermo Scientific), 10 mmol/L HEPES (Thermo Scientific), GlutaMAX (Thermo Scientific), 1× N2 (Thermo Scientific), 1× B27 (Thermo Scientific), and 1 mmol/L N-acetylcysteine (Sigma–Aldrich, St. Louis, MO, USA)), supplemented with 50 ng/ml recombinant human epidermal growth factor (Sigma–Aldrich), 100 ng/ml recombinant human noggin (R&D Systems, Minneapolis, MN, USA), 500 ng/ml recombinant human R-spondin 1 (PeproTech, Cranbury, NJ, USA), 10 mM nicotinamide (Sigma–Aldrich), 10 μM p160ROCK inhibitor (Y27632, Selleckchem, Houston, TX, USA), 10 μM p38 MAP kinase inhibitor (SB202190, Sigma–Aldrich), and 10 nM Prostaglandin E2 (PGE2, Cayman Chemical, Ann Arbor, MI, USA) were added. GSK3 inhibitor (CHIR99021, Stemgent, Cambridge, MA, USA) was added to the medium during the first 2 days. After culturing the organoids for 7 days, the organoids in Matrigel were mechanically disrupted by pipetting, and then enzymatically dissociated using TrypLE Express Enzyme (Thermo Scientific). The cell pellet was resuspended in Matrigel and plated in 48-well culture plates (Corning). The medium was changed every 2 days, and organoids were passaged at a ratio of 1:2 – 1:4 on 7 days after crypt plating. To recapitulate the structure and function of the intestinal epithelium, the intestinal organoids (enteroids) were cultured in a differentiation medium (maintenance medium without Wnt3A conditional medium, SB202190, nicotinamide, and PGE2). The differentiation medium was changed every 2 days.

extract_protocol:
On day 7 after embedding (day 5 of IFNγ treatment), total RNA was extracted from enteroids using the RNeasy Mini Kit (QIAGEN, Hilden, Germany).
RNA sequencing was performed using total RNA samples with >10 μg of RNA and an RNA integrity number (RIN) > 8. Reverse transcription reactions were performed with 2 μg of isolated total RNA, poly(dT) primers, and SuperScript™ II Reverse Transcriptase (Invitrogen, Carlsbad, CA, USA). cDNA libraries were prepared via complementary DNA amplification, end repair, 3'-end adenylation, adapter ligation, and amplification. The libraries were sequenced with HiSeq2500 using the 100 bp paired-end mode of the TruSeq Rapid PE Cluster Kit and the TruSeq Rapid SBS Kit (Illumina).

treatment_protocol: To evaluate the IFNγ-induced responses in the enteroids, the intestinal organoids were cultured in a maintenance medium for 2 days to establish a stable number of organoids, before inducing organoid differentiation and IFNγ treatment. After 2 days of organoid plating, the maintenance medium was replaced with a differentiation medium every 2 days. IFNγ (100 pg/mL) was added to the culture medium every 24 hours.

value: small intestine (ileum)

value: human non-IBD enteroid F#38

value: intestinal epithelial cells

value: 100 pg/mL IFNγ treatment, Day7

tag: batch


title: Non-targeting gRNA mouse cortical neuron DIV7, unstimulated, rep 1

description: Library name: ATAC_1_1

tag: cell type


title: 4T1-mCh/rLuc, wild-type, control, replicate 3

description: control

value: breast cancer cells


title: F#38 IFNR 0

description:
Library name: NL6
NL6

tag: treatment

value: no IFNγ treatment, Day7


title: #292 IFNR 400

description:
Library name: NL5_IFN
NL5_IFN

value: human non-IBD enteroid #292


title: DSP-1001660021422-D-C08

tag: panel

value: former

value: paraffin


title: #292 IFNR 0

description:
Library name: NL5
NL5

value: WT


title: DSP-1001660021422-D-C07

tag: patient


title: #294 IFNR 100

description:
Library name: NL4_IFN
NL4_IFN

value: human non-IBD enteroid #294


title: #294 IFNR 0

description:
Library name: NL4
NL4


title: #291 IFNR 100

description:
Library name: NL3_IFN
NL3_IFN

value: human non-IBD enteroid #291


title: #291 IFNR 0

description:
Library name: NL3
NL3


title: DSP-1001660021422-D-C06

tag: age


title: WT mouse cortical neuron DIV7, DMSO treated (30 min) and depolarized (30 min), rep 2

description: Library name: ATAC_14

value: E16.5 cortex

value: primary neuron

value: 0.1% DMSO (30 min) and 50 mM KCl (30 min)


title: N2 IFN_R 100

description:
Library name: NL2_IFN
NL2_IFN

value: human non-IBD enteroid N2


title: DSP-1001660021422-D-C10

value: lung

value: (v1.0) Human NGS Whole Transcriptome Atlas RNA

tag: fvc%

value: male


title: WT mouse cortical neuron DIV7, DMSO treated (30 min) and depolarized (30 min), rep 1

description: Library name: ATAC_13


title: DSP-1001660021422-D-C05

tag: smoking history


title: N2 IFN_R 0

description:
Library name: NL2
NL2

value: small intestine (ileum)

value: intestinal epithelial cells


title: #66 IFN_R 100

description:
Library name: NL1_IFN
NL1_IFN

source_name: small intestine (jejunum)

value: small intestine (jejunum)

value: human non-IBD enteroid #67

value: 100 pg/mL IFNγ treatment, Day7


title: DSP-1001660021422-D-C04

value: former

tag: pack years


title: WT mouse cortical neuron DIV7, 100 nM FHT1015 treated (10 min) and depolarized (10 min), rep 2

description: Library name: ATAC_12

value: 100 nM FHT1015 (10 min) and 50 mM KCl (10 min)


title: #66 IFN_R 0

description:
Library name: NL1
NL1

value: WT

value: no IFNγ treatment, Day7


title: DSP-1001660021422-D-C09

tag: gender

value: paraffin


title: 389 IFNR 400

description:
Library name: CD10_IFN
CD10_IFN

value: human CD enteroid #389


title: DSP-1001660021422-D-C03

tag: roi


title: 389 IFNR 0

description:
Library name: CD10
CD10


title: WT mouse cortical neuron DIV7, 100 nM FHT1015 treated (30 min) and depolarized (30 min), rep 2

description: Library name: ATAC_16

value: E16.5 cortex

value: primary neuron

value: 100 nM FHT1015 (30 min) and 50 mM KCl (30 min)


title: F#18 IFNR 400

description:
Library name: CD9_IFN
CD9_IFN

value: human CD enteroid F#18


title: F#35 IFNR 400

description:
Library name: CD8_IFN
CD8_IFN

value: human CD enteroid F#65


title: DSP-1001660021422-D-C02

value: lung

value: (v1.0) Human NGS Whole Transcriptome Atlas RNA

value: female

tag: scan name


title: F#18 IFNR 0

description:
Library name: CD9
CD9

value: small intestine (ileum)

value: intestinal epithelial cells


title: WT mouse cortical neuron DIV7, 100 nM FHT1015 treated (30 min) and depolarized (30 min), rep 1

description: Library name: ATAC_15


title: WT mouse cortical neuron DIV7, DMSO treated (10 min) and depolarized (10 min), rep 1

description: Library name: ATAC_9

value: 0.1% DMSO (10 min) and 50 mM KCl (10 min)


title: WT mouse cortical neuron DIV7, 100 nM FHT1015 treated (10 min) and depolarized (10 min), rep 1

description: Library name: ATAC_11


title: DSP-1001660021422-D-C01

value: former


title: F#35 IFNR 0

description:
Library name: CD8
CD8


title: WT mouse cortical neuron DIV7, DMSO treated (10 min) and depolarized (10 min), rep 2

description: Library name: ATAC_10


title: 376 IFNR 400

description:
Library name: CD7_IFN
CD7_IFN

value: human CD enteroid #376

value: 100 pg/mL IFNγ treatment, Day7


title: DSP-1001660021422-D-B12


title: WT mouse cortical neuron DIV7, 100 nM FHT1015 treated (30 min) and unstimulated, rep 2

description: Library name: ATAC_8


title: DSP-1001660021422-D-B11


title: 376 IFNR 0

description:
Library name: CD7
CD7

value: WT

value: no IFNγ treatment, Day7


title: 375 IFNR 0

description:
Library name: CD6
CD6

value: human CD enteroid #375


title: WT mouse cortical neuron DIV7, 100 nM FHT1015 treated (30 min) and unstimulated, rep 1

description: Library name: ATAC_7

value: E16.5 cortex


title: F#63 IFNR 400

description:
Library name: CD5_IFN
CD5_IFN

value: human CD enteroid F#63


title: 296 IFNR 0

description:
Library name: CD4
CD4

value: human CD enteroid #296


title: DSP-1001660021422-D-B09

value: paraffin


title: F#63 IFNR 0

description:
Library name: CD5
CD5


title: 375 IFNR 400

description:
Library name: CD6_IFN
CD6_IFN


title: 296 IFNR 100

description:
Library name: CD4_IFN
CD4_IFN


title: WT mouse cortical neuron DIV7, DMSO treated (30 min) and unstimulated, rep 1

description: Library name: ATAC_5

value: primary neuron


title: DSP-1001660021422-D-B10

value: lung


title: DSP-1001660021422-D-B08

value: (v1.0) Human NGS Whole Transcriptome Atlas RNA


title: 293 IFNR 100

description:
Library name: CD3_IFN
CD3_IFN

value: human CD enteroid #293


title: 293 IFNR 0

description:
Library name: CD3
CD3

value: small intestine (ileum)


title: WT mouse cortical neuron DIV7, DMSO treated (30 min) and unstimulated, rep 2

description: Library name: ATAC_6


title: WT mouse cortical neuron DIV7, 100 nM FHT1015 treated (10 min) and unstimulated, rep 2

description: Library name: ATAC_4


title: 123 IFNR 100

description:
Library name: CD2_IFN
CD2_IFN

value: human CD enteroid #123

value: intestinal epithelial cells


title: DSP-1001660021422-D-B07

value: former

value: female


title: 123 IFNR 0

description:
Library name: CD2
CD2


title: DSP-1001660021422-D-B06


title: WT mouse cortical neuron DIV7, 100 nM FHT1015 treated (10 min) and unstimulated, rep 1

description: Library name: ATAC_3


title: WT mouse cortical neuron DIV7, DMSO treated (10 min) and unstimulated, rep 2

description: Library name: ATAC_2


title: #96 IFN_R 0

description:
Library name: CD1
CD1

value: small intestine (jejunum)

value: human CD enteroid #96


title: pIXHALO_CabSauv-B_h

city: New York

first: Shao-shan

middle: Carol

last: Huang

state: NY

address: 12 Waverly Pl

department: Biology

institute: New York University

data_processing:
Library strategy: DAP-Seq
Base calling was done with Illumina Offline Base Caller (OLB 1.9.4).
Raw reads were trimmed using TrimGalore 0.6.6 wrapper for Cutadapt 3.1 with the following parameter: "-q 20".
Trimmed reads were aligned by bowtie2 version 2.3.2 with default parameters against the genome assembly Vitis vinifera cv. Cabernet Sauvignon Cl. 08 V1.1, either to both the primary contigs and the haplotigs or to the primary contigs alone. Aligned reads were filtered by MAPQ score of at least 30.
Peaks were called using GEM peak caller version 3.3 with the default version read distribution, Vitis vinifera cv. Cabernet Sauvignon Cl. 08 V1.1 contig sequences, with the pIXHALO samples as control, and parameters "--f SAM ---t 1 --k_min 5 --k_max 14 --k_seqs 2000 --k_neg_dinu_shuffle --outNP --outBED --outMEME --outJASPAR --outHOMER --print_bound_seqs --print_aligned_seqs".
Assembly: Vitis vinifera cv. Cabernet Sauvignon Cl. 08 V1.1
Supplementary files format and content: Peak regions in narrowPeak format were created by GEM, using reads mapped to both primary contigs and haplotigs (cs) or to the primary contigs alone (csp).

organism: Vitis vinifera

source_name: young leaf

growth_protocol: Leaf material (1-2 in) was collected from young grapevine leaves of cv. ‘Cabernet Sauvignon’ CS08 located in the Foundation Plant Services Facility-UCDavis, California.

extract_protocol:
Genomic DNA was extracted by crude nuclei isolation (with PVP40) and 20% Sarkosyl-chloroflorm extraction following procedure described in Thomas et al. 1993 (M. R. Thomas, S. Matsumoto, P. Cain, N. S. Scott, Repetitive DNA of grapevine: classes present and sequences suitable for cultivar identification. Theoretical and Applied Genetics 86, 173–180 (1993)). DAP-seq experiment was performed as described in Bartlett et al., 2017 (Bartlett, A., O'Malley, RC., Huang, SC. et al. Mapping genome-wide transcription-factor binding sites using DAP-seq. Nat Protoc 12:1659-1672 (2017). https://doi.org/10.1038/nprot.2017.055).  The DAP-Seq DNA library is prepared from fragmented naked genomic DNA ligated with a short DNA sequence (20bp) encoding a truncated Illumina TruSeq adapter.  Separately, a construct containing a HALO-tagged transcription factor is translated by in vitro (rabbit reticulocyte) expression system. The affinity-tagged protein is immobilized on the appropriate affinity resin.  The DNA affinity purification step begins by combining the DNA library with the immobilized transcription factor. After the wash steps remove the unbound DNA, the bound DNA fraction is eluted.
The eluted DNA fragments are PCR amplified with a full-length indexed TruSeq primer and directly sequenced on the Illumina NextSeq 500.

treatment_protocol: Leaf material was collected and flash frozen with liquid nitrogen prior gDNA isolation.

tag: cultivar

value: Cabernet Sauvignon (clone 08)

tag: protein

value: pIXHALO

tag: protein family

value: control

tag: protein source

value: Vitis vinifera

tag: protein affinity tag

value: HALO

tag: expression system

value: rabbit reticulocyte lysate

tag: dna source

value: CabSauv-B

tag: replicate

value: h


title: WT mouse cortical neuron DIV7, DMSO treated (10 min) and unstimulated, rep 1

description: Library name: ATAC_1

tag: tissue

value: E16.5 cortex

tag: cell type

value: primary neuron

tag: treatment


title: DSP-1001660021422-D-B05

value: lung

tag: slide name

tag: panel

value: (v1.0) Human NGS Whole Transcriptome Atlas RNA

tag: patient

tag: age

tag: fvc%

value: paraffin


title: VvMYB24-SD_CabSauv-B_h

tag: gene id vcost

tag: gene id v1

value: MYB


title: dual-AAV v3em PE3,2e12, tail-vein injection,liver,rep3,off target site 10

city: Hangzhou

first: Lijia

last: Ma

state: Zhejiang

address: Shilongshan Road No.18, Cloud Town, Xihu District

department: School of Life Sciences

institute: Westlake university

description:
Library name: SP8R3liverot10
rep3,off target site 10
sPE_sep_processed_date.xls

data_processing:
*library strategy: Amplicon Sequencing
Traget site and protential off-target sites were amplified by PCR using the primer sequences, then sequenced on an Illumina NovaSeq system. Deep sequencing data analysis was processed using CRISPResso2 and untreated cells were used as negative controls to exclude PCR amplification and sequencing errors. Reads were align to the amplicon sequence by crispresso2 using --max_paired_end_reads_overlap 140 --min_paired_end_reads_overlap     10 --exclude_bp_from_left 0 --exclude_bp_from_right 0 --plot_window_size 20 --min_frequency_alleles_around_cut_to_plot 0.2
On-target editing efficiencies, which are greater than 0.1%, were quantified as a percentage of (number of on-target reads) / (number of total reads).
Assembly: sequence.txt
Supplementary files format and content: xlsx files, percentage of total sequencing reads with on-target editing or off-target editing for all libraries, percentage of total sequencing reads with indels.

source_name: liver

growth_protocol: HEK293T cell and Hepa1-6 cell were grown in high-glucose Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% fetal bovine serum (FBS) (Gemini #900-108) and 1% GlutaMAX (Thermo #35050061). Cells were passaged every 2-3 days. After one day post-transduction, the medium was changed. Cells were harvested at 72 hours post-transduction.

extract_protocol:
Genomic DNA (gDNA) was isolated using TIANamp Genomic DNA Kit (TIANGEN #DP304) according to the manufacturer’s protocol.
The region that integrated with genomic DNA including RT template was PCR amplified from genomic DNA for HTS. For the first round of PCR, genomic sites of interest were amplified from 150 ng of genomic DNA using Q5 PCR Master Mix (New England Biolabs #M0544S) with the primers containing Illumina forward and reverse adapters. 50 uL of PCR 1 reaction was performed with forward and reverse primers each at 0.25 uM, ~1 uL of genomic DNA extract, and 25 uL of Q5 PCR Master Mix. To add a unique sequencing index, 50 uL of a given PCR 2 contained 2.5 uL of previous step unpurified PCR product; a unique forward or reverse primer pair, each at 0.25 uM; and 25 uL of Q5 PCR Master Mix. Primers are listed in Table S1. PCR 2 products were purified by DNA AMPure XP beads (Beckman Coulter #A63882) and eluted with 25 uL of water. DNA concentration was quantified by Nanodrop One (Thermo Fisher Scientific).

treatment_protocol: Cells were transfected at 60%-70% confluency using 3 uL of Lipofectamine 3000 (Thermo Fisher) with 1500 ng each half of the Split-PE. Three days post transfection, cells were collected. All animal experiments were conducted under the protocol approved by Institutional Animal Care and Use Committee (IACUC) of the Westlake University. C57BL/6 male mice were purchased and housed in the Laboratory Animal Resource Center (LARC) at the Westlake University. The LARC is a certified pathogen-free and environmental-control facility (21 ± 2°C, 55 ± 15% humidity and 12:12-h light: dark cycle). AAV were injected into the tail vein of six-week-old male C57BL/6 mice.

value: liver

tag: genotype

value: WT


title: DSP-1001660021422-D-B04

tag: smoking history

value: former

tag: pack years

tag: gender

value: female

tag: roi

tag: scan name


title: split ePE3 at mPcsk9 in hepa1-6 cells_Rep3- I6

description:
Library name: ePE3-hepa.R3.I6
Rep3- I6
vitro_processed_ePE3.xlsx

source_name: Hepa1-6 cell

tag: cell line

value: Hepa1-6 cell

value: mouse hepatocellular carcinoma cells

value: split ePE3 at mPcsk9


title: dual-AAV v3em PE3,2e12, tail-vein injection,liver,rep2,off target site 10

description:
Library name: SP8R2liverot10
rep2,off target site 10
sPE_sep_processed_date.xls

tag: tissue


title: dual-AAV v3em PE3,2e12, tail-vein injection,liver,rep1,off target site 10

description:
Library name: SP8R1liverot10
rep1,off target site 10
sPE_sep_processed_date.xls


title: DSP-1001660021422-D-B02


title: split ePE3 at mPcsk9 in hepa1-6 cells_Rep2- I5

description:
Library name: ePE3-hepa.R2.I5
Rep2- I5
vitro_processed_ePE3.xlsx

tag: cell type


title: dual-AAV v3em PE3,1e12, tail-vein injection,liver,rep3,off target site 10

description:
Library name: SP7R3liverot10
rep3,off target site 10
sPE_sep_processed_date.xls

tag: treatment


title: DSP-1001660021422-D-B01

tag: slide name


title: dual-AAV v3em PE3,1e12, tail-vein injection,liver,rep2,off target site 10

description:
Library name: SP7R2liverot10
rep2,off target site 10
sPE_sep_processed_date.xls


title: split ePE3 at mPcsk9 in hepa1-6 cells_Rep1- I4

description:
Library name: ePE3-hepa.R1.I4
Rep1- I4
vitro_processed_ePE3.xlsx


title: dual-AAV v3em PE3,2e12, tail-vein injection,liver,rep3,off target site 9

description:
Library name: SP8R3liverot9
rep3,off target site 9
sPE_sep_processed_date.xls


title: dual-AAV v3em PE3,1e12, tail-vein injection,liver,rep1,off target site 10

description:
Library name: SP7R1liverot10
rep1,off target site 10
sPE_sep_processed_date.xls


title: DSP-1001660021422-D-A12

tag: panel

value: male


title: split ePE3 at mPcsk9 in hepa1-6 cells_Rep3- I3

description:
Library name: ePE3-hepa.R3.I3
Rep3- I3
vitro_processed_ePE3.xlsx


title: #96 IFN_R 100

description:
Library name: CD1_IFN
CD1_IFN

value: small intestine (jejunum)

value: human CD enteroid #96

value: intestinal epithelial cells

value: 100 pg/mL IFNγ treatment, Day7

tag: batch


title: DSP-1001660021422-D-A11

tag: patient

tag: age


title: dual-AAV v3em PE3,2e12, tail-vein injection,liver,rep2,off target site 9

description:
Library name: SP8R2liverot9
rep2,off target site 9
sPE_sep_processed_date.xls


title: dual-AAV v3em PE3,2e12, tail-vein injection,liver,rep1,off target site 9

description:
Library name: SP8R1liverot9
rep1,off target site 9
sPE_sep_processed_date.xls


title: dual-AAV v3em PE3,1e12, tail-vein injection,liver,rep3,off target site 9

description:
Library name: SP7R3liverot9
rep3,off target site 9
sPE_sep_processed_date.xls


title: split ePE3 at mPcsk9 in hepa1-6 cells_Rep2- I2

description:
Library name: ePE3-hepa.R2.I2
Rep2- I2
vitro_processed_ePE3.xlsx


title: dual-AAV v3em PE3,1e12, tail-vein injection,liver,rep1,off target site 9

description:
Library name: SP7R1liverot9
rep1,off target site 9
sPE_sep_processed_date.xls


title: split ePE3 at mPcsk9 in hepa1-6 cells_Rep1- I1

description:
Library name: ePE3-hepa.R1.I1
Rep1- I1
vitro_processed_ePE3.xlsx


title: dual-AAV v3em PE3,1e12, tail-vein injection,liver,rep2,off target site 9

description:
Library name: SP7R2liverot9
rep2,off target site 9
sPE_sep_processed_date.xls


title: dual-AAV v3em PE3,2e12, tail-vein injection,liver,rep3,off target site 8

description:
Library name: SP8R3liverot8
rep3,off target site 8
sPE_sep_processed_date.xls


title: DSP-1001660021422-D-A09

tag: fvc%


title: DSP-1001660021422-D-A08


title: dual-AAV v3em PE3,1e12, tail-vein injection,liver,rep3,off target site 8

description:
Library name: SP7R3liverot8
rep3,off target site 8
sPE_sep_processed_date.xls


title: R4

city: bengbu

first: sun

middle: qi

last: ketizu

address: donghai street 2600

institute: Bengbu Medical University

description: Library name: SAMPLE6

data_processing:
Total RNA was extracted from gastric samples, purified, and used for RNA sequencing library preparation.
Shanghai OE Biotech conducted complementary DNA library construction and sequencing on an Illumina HiSeq X Ten system.
High-quality reads were aligned to the mouse reference genome using Bowtie2
Expression levels for individual genes were calculated and normalized to fragments per kilobase of exon model per million mapped reads.
For RNA-seq, we performed sequencing on samples from 3 randomly selected animals per group.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: stomach

extract_protocol:
Total RNA was extracted using the TRIzol reagent (Invitrogen, CA, USA)according to the manufacturer’s protocol. RNA purity and quantification were evaluated using the NanoDrop 2000 spectrophotometer (Thermo Scientific, USA). RNA integrity was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).
Then the libraries were constructed using VAHTS Universal V6 RNA-seq Library Prep Kit according to the manufacturer’s instructions. The transcriptome sequencing and analysis were conducted by OE Biotech Co., Ltd. (Shanghai, China)

value: stomach

value: Riclin gavage(20mg/kg)


title: R3

description: Library name: SAMPLE5


title: R2

description: Library name: SAMPLE4


title: dual-AAV v3em PE3,1e12, tail-vein injection,liver,rep2,off target site 8

description:
Library name: SP7R2liverot8
rep2,off target site 8
sPE_sep_processed_date.xls


title: dual-AAV v3em PE3,1e12, tail-vein injection,liver,rep1,off target site 8

description:
Library name: SP7R1liverot8
rep1,off target site 8
sPE_sep_processed_date.xls


title: dual-AAV v3em PE3,2e12, tail-vein injection,liver,rep3,off target site 7

description:
Library name: SP8R3liverot7
rep3,off target site 7
sPE_sep_processed_date.xls


title: DSP-1001660021422-D-A06

value: lung

value: (v1.0) Human NGS Whole Transcriptome Atlas RNA


title: DSP-1001660021422-D-A07

value: paraffin


title: CK4

description: Library name: SAMPLE3

value: Normal saline gavage(20mg/kg)


title: DSP-1001660021422-D-A05


title: dual-AAV v3em PE3,2e12, tail-vein injection,liver,rep1,off target site 7

description:
Library name: SP8R1liverot7
rep1,off target site 7
sPE_sep_processed_date.xls

value: liver

value: WT


title: DSP-1001660021422-D-A10

value: former


title: CK2

description: Library name: SAMPLE2


title: dual-AAV v3em PE3,1e12, tail-vein injection,liver,rep2,off target site 7

description:
Library name: SP7R2liverot7
rep2,off target site 7
sPE_sep_processed_date.xls


title: DSP-1001660021422-D-A04


title: dual-AAV v3em PE3,1e12, tail-vein injection,liver,rep1,off target site 7

description:
Library name: SP7R1liverot7
rep1,off target site 7
sPE_sep_processed_date.xls


title: CK1

description: Library name: SAMPLE1


title: dual-AAV v3em PE3,2e12, tail-vein injection,liver,rep2,off target site 7

description:
Library name: SP8R2liverot7
rep2,off target site 7
sPE_sep_processed_date.xls


title: dual-AAV v3em PE3,2e12, tail-vein injection,liver,rep3,off target site 6

description:
Library name: SP8R3liverot6
rep3,off target site 6
sPE_sep_processed_date.xls


title: dual-AAV v3em PE3,2e12, tail-vein injection,liver,rep2,off target site 8

description:
Library name: SP8R2liverot8
rep2,off target site 8
sPE_sep_processed_date.xls


title: D3H2LN-luc, Snord67KO, replicate 3

value: breast cancer cells

value: Snord67 knockout


title: Early_Life_RLT_Spleen

city: San Francisco

first: James

last: Gardner

address: 513 Parnassus Ave

institute: University of California, San Francisco

description: Library name: Sample 3

data_processing:
Demultiplexing, barcode processing, gene aggregation were performed using the Cell Ranger Software (v8.0.1) Downsteam analysis was performed in Python (v3.10.12) using scanpy(v1.10.2) and scVI-tools (v1.1.5).
Assembly: mm10
Supplementary files format and content: h5 file containing raw feature matrix output from Cell Ranger
Supplementary files format and content: h5ad file containing an AnnData object with processed count data. Raw and scVI normalized counts are stored as layers. Cell and gene metadata are stored in the '.obs' and '.var' attribute. UMAP coordinated are stored in the '.obsm' attribute.

source_name: spleen

extract_protocol:
Mouse spleen, mesenteric, and other lymph nodes (cervical, brachial, axillary, inguinal, and para-aortic) were procured and pooled in digestion medium consisting of RPMI 1640 with 2% foetal bovine serum (FBS) (Sigma-Aldrich), with deoxyribonuclease (DNase) (100 µg/mL; Roche) and LiberaseTM (96 µg/mL; Roche), minced and agitated at 37°C with gentle agitation for 30 min, and passed through a 70-micron filter. Cells were then sorted for live, tdTmt+ MHCII+ cells and processed for single-cell analysis.
10x Chromium V3 3' Protocol

value: spleen

value: lymphocytes


title: DSP-1001660021422-D-A03

value: male


title: DSP-1001660021422-D-A02


title: dual-AAV v3em PE3,2e12, tail-vein injection,liver,rep2,off target site 6

description:
Library name: SP8R2liverot6
rep2,off target site 6
sPE_sep_processed_date.xls


title: dual-AAV v3em PE3,2e12, tail-vein injection,liver,rep1,off target site 8

description:
Library name: SP8R1liverot8
rep1,off target site 8
sPE_sep_processed_date.xls


title: V0278R_Veh

city: Charlottesville

first: Matthew

last: Devall

state: Virginia

address: 1335 Lee Street

institute: University of Virginia

data_processing:
Resulting FASTQ files were aligned to GENCODE v45 using a STAR two-pass alignment and RSEM
Principal component analysis was used to determine the presence of any outlier pairs and differentially expressed genes (DEGs) were identified through a repeated-measures tests in DESeq2. Sample pairing was used as a blocking factor, which allowed for the comparison of gene expression differences across treatment conditions while accounting for differences observed within sample pairs (n=5 pairs).
Assembly: GrCH38: GENCODE v45
Supplementary files format and content: comma delimited file containing raw counts for each sample.

source_name: colon

growth_protocol: Biopsies were washed 3x with DPBS (Gibco #14190-136) at room temperature. Following this, the supernatant was aspirated, and biopsies were incubated in 10mL of DPBS containing 9mM Ultra-Pure EDTA (Invitrogen #155750-038) for 20 minutes at room temperature. Manual inversions of the samples were carried out every 2-3 minutes. During incubation, all tubes, tips and pipets were conditioned with wash media (DMEM/F-12 (Gibco #12634-010), 10% FBS (Gibco #16000-044), 10 mM HEPES (Gibco #15630-080), 2mM L-glutamine (Cellgro #25-005-CI), 1X Pen-Strep, 1X Glutamax (Gibco # 35050-061)) to avoid crypt adhesion. DPBS/EDTA was subsequently removed following incubation. 10mL of DPBS without EDTA was added. This solution was then manually pipetted up and down performed 8-10x to agitate colon crypts from colon biopsies. Tissue was allowed to settle and supernatant was collected in a 15mL tube. This process was repeated two more times. Collected supernatant was spun at 1200rpm at 4ºC for 5 minutes and all but 2mL of supernatants from each 15mL tube was then removed and combined in a clean 50mL tube, without disturbing the pellet. Using a conditioned 5mL pipet, the remaining 2mLs from each tube was then combined into one 15mL tube and spun at 1200rpm at 4ºC for 5 minutes. The resulting supernatant was carefully removed. Pellets containing intact colon crypts were then added to 10μL of complex media (45% Wash Media, 50% L-WRN conditioned media, 10nM Gastrin (Sigma #G9020), 10μM Y27632 Dihydrochloride (R&D #1254), 1X B27 Supplement (Gibco #17504-44), 1X N2 Supplement (Gibco #17502-048), 1mM n-Acetylcysteine (Sigma #A9165), 50ng/μL EGF (Life Technologies  #PHG0311L), 10mM Nicotinamide (Sigma  #N6636), 500nM A83 (R&D #2939), 10μM SB202190 (R&D  #1264)) was added. To reduce the clumping of the colon crypts, this mixture was then manually pipetted several times. 200μL of Matrigel (Corning #356237) was then added and mixed. 35-50μL of each sample was then plated at the center of wells of a 48-well plate and incubated at 37ºC for 15 minutes. 300-500μL of complex media was then added and samples were returned to the incubator. Organoids were checked and fed after 24hrs. Following this, they were passaged as needed (every 3-5 days) then frozen.

extract_protocol:
Following a 72-hour fructose exposure, Matrigel was scratched off each well using a pipette tip and placed into sterile Eppendorf tubes. A total of 1mL of complex media was added to each well and then transferred to tubes containing Matrigel, which were then centrifuged at 1200rpm at 4ºC for 5 minutes. The resulting supernatant was carefully removed and 500μL of TrypLE (Gibco #12604039) was added to each pellet, which were placed in the incubator at 37ºC for 10 minutes. Following incubation, TrypLE was neutralized using an equal volume of complex media. Matrigel containing organoids were further disrupted 8-10x using a fine needle before being centrifuged at 1200rpm at 4ºC for 5 minutes. Finally, supernatant was removed and 300µL of RNA Lysis Solution RA1 (with 6µl TCEP) (Clontech/Machery-Nagel RNA XS Kit) was added to each pellet. The contents were then vortexed and stored in a -80oC freezer prior to RNA extraction.
Illumina Tru-Stranded, with rRNA depletion

treatment_protocol: Five AA right side colon organoid lines were grown on the same 46 well plate in complex media for a period of five days. AA colon organoids were derived from a separate cohort than the original Cleveland biopsies. On day five, normal colon organoid lines were either treated with complex media containing 4.4mM of fructose or an equal volume of water (vehicle control). Fresh media containing fructose or water was replaced every 24 hours for a total exposure time of 72 hours.

value: colon

value: organoid

value: healthy epithelial

value: Water


title: dual-AAV v3em PE3,1e12, tail-vein injection,liver,rep3,off target site 6

description:
Library name: SP7R3liverot6
rep3,off target site 6
sPE_sep_processed_date.xls


title: Early_Life_RLT_other_LNs

description: Library name: Sample 1

source_name: mesenteric lymph nodes

value: mesenteric lymph nodes


title: V0278R_HFCS

value: 4.4mM Fructose


title: dual-AAV v3em PE3,1e12, tail-vein injection,liver,rep3,off target site 7

description:
Library name: SP7R3liverot7
rep3,off target site 7
sPE_sep_processed_date.xls


title: dual-AAV v3em PE3,1e12, tail-vein injection,liver,rep2,off target site 6

description:
Library name: SP7R2liverot6
rep2,off target site 6
sPE_sep_processed_date.xls


title: D3H2LN-luc, wild-type, replicate 3


title: V0166R_Veh


title: ChIPseq_CTCF_5LTR-LacZ_E11.5_FLHL_Rep2

city: Berlin

first: Juliane

last: Glaser

address: Ihnestrasse 63-73

department: Development and Disease

country: Germany

institute: Max Planck Institute for Molecular Genetics

description:
L44
ChIpseq_CTCF_5LTR-LacZ_E11.5_FLHL_merged.bw

data_processing:
Single-end and paired-end ChIP-seq reads were mapped with bowtie (v2.2.6).
Filtered for mapping quality MAPQ ≥ 10.
Duplicates were removed using samtools rmdup (v1.8).
For generating coverage tracks, reads were extended to 300 bp (H3K27ac, H3K4me1, and H3K4me3) or 200 bp (CTCF and Rad21) and scaled to r.p.m. (106 per number of unique reads) using bedtools genomecov v2.27.1
Assembly: mm10
Supplementary files format and content: bigwig

source_name: limbs

extract_protocol:
ChIP experiments were performed following the protocol described in (Distinct global shifts in genomic binding profiles of limb malformation-associated HOXD13 mutations. Ibrahim et al.,Genome Research 2013).
Snap frozen samples were first digested and chromatin was sonicated with a Diagenode Bioruptor (45 cycles- 30 sec pulse, 30 sec pause, HI power). 25-35 ug of chromatin was used in each immunoprecipitation with 1ug of the following specific antibodies: anti-H3K4me3, Millipore, cat. No. 07-473; anti-H3K4me1, Diagenode, cat. No. C15410037; anti-H3K27ac, Diagenode, cat. No. C15410174; anti-CTCF, Active Motif, cat. No. 61311; anti-Rad21, abcam, cat.No. ab992. Libraries were prepared using the Nextera adaptors and sequenced.

treatment_protocol: Limbs from  E11.5 mouse embryos were dissected in PBS, a single cell suspension was made using Trypsin, samples were fixed in 1% PFA, snap frozen, and stored at -80 °C.

value: limbs

tag: developmental stage

tag: strain

value: 5LTR-LacZ KI/WT


title: D3H2LN-luc, wild-type, replicate 2

tag: genotype


title: ChIPseq_CTCF_5LTR-LacZ_E11.5_FLHL_Rep1

description:
L43
ChIpseq_CTCF_5LTR-LacZ_E11.5_FLHL_merged.bw


title: P1239R_Veh


title: ChIPseq_CTCF_Dac1JBl6_E11.5_FLHL_Rep2

description:
L42
ChIpseq_CTCF_Dac1JBl6_E11.5_FLHL_merged.bw


title: V0166R_HFCS


title: D3H2LN-luc, wild-type, replicate 1


title: dual-AAV v3em PE3,1e12, tail-vein injection,liver,rep1,off target site 6

description:
Library name: SP7R1liverot6
rep1,off target site 6
sPE_sep_processed_date.xls


title: Early_Life_RLT_mLN

description: Library name: Sample 2

source_name: pooled cervical, axillary, inguinal and para-aortic lymph nodes


title: dual-AAV v3em PE3,2e12, tail-vein injection,liver,rep3,off target site 5

description:
Library name: SP8R3liverot5
rep3,off target site 5
sPE_sep_processed_date.xls


title: P1239R_HFCS


title: ChIPseq_CTCF_Dac1JBl6_E11.5_FLHL_Rep1

description:
L41
ChIpseq_CTCF_Dac1JBl6_E11.5_FLHL_merged.bw


title: dual-AAV v3em PE3,2e12, tail-vein injection,liver,rep2,off target site 5

description:
Library name: SP8R2liverot5
rep2,off target site 5
sPE_sep_processed_date.xls


title: ChIPseq_CTCF_Dac1J129sv_E11.5_FLHL_Rep2

description:
L40
ChIpseq_CTCF_Dac1J129sv_E11.5_FLHL_merged.bw


title: SUDHL4-TAZ-CART19-REP3

city: Philadelphia

first: Patrizia

last: Porazzi

state: PA

address: 3400 Civic Center Blvd

department: Center for Cellular Immunotherapies

institute: University of Pennsylvania

description: Library name: ATAC-12

data_processing:
Trimming was performed using Trimmomatic-0.32 with parameter -phred33 LEADING:3 TRAILING:3 SLIDINGWINDOW:3:3 MINLEN:30 in paired-end mode.
Alignment was performed using bowtie2-2.3.4.3. The output sam files were converted into bam files, and sorted and indexed using samtools-0.1.19.
Duplicates and mitochondrial reads were removed from the .bam files, and they were converted to .bed files
Peaks were called using MACS2 v2.2.9.1 with significance q-value cutoff <=0.05
Read counts for each peak were determined by the dba.count function from the R package Diffbind.
Assembly: hg38

growth_protocol: Germinal Center Diffuse Large B-cell Lymphoma (GBC-DLBCL) SU-DHL-4 [mut EZH2; Y641F] were cultured in R10 media (Roswell Park Memorial Institute medium 1640 (RPMI; Gibco; Cat#11875-085) supplemented with 10% fetal bovine serum (FBS, Gibco; Cat# 16140-071), 1% penicillin and 1% streptomycin (Gibco; Cat# 15140-163), 1% GlutaMAX supplement (Gibco; Cat# 35050-079, and 1% HEPES (Gibco; Cat# 15630-130) in a 37°C incubator with 5% CO2.

extract_protocol:
Nuclei from 80,000 sorted SU-DHL-4 cells from all the experimental conditions were isolated and were subjected to the transposition reaction using Tn5 transposase for 30 minutes at 37°C with 1000rp mixing.
ATAC-seq libraries were prepared using the Active Motif ATAC-Seq kit following the manufacturer’s protocol. The transposed DNA was purified using DNA Clean and Concentrator (Zymo) and fragments were barcoded with unique i5 and/or i7 indexed primers. Final libraries were double size selected using AMPure beads prior to sequencing. Sequencing was performed on an Illumina NextSeq 2000 instrument to produce 75-bp paired-end reads.

treatment_protocol: 3 days pre-treatment of SU-DHL-4 with tazemetostat (250 nM) or vehicle (DMSO), then add CART-19 (E:T ratio 0.25) in the presence of tazemetostat or vehicle and sorted after 48 hs.


title: ChIPseq_CTCF_Dac1J129sv_E11.5_FLHL_Rep1

description:
L39
ChIpseq_CTCF_Dac1J129sv_E11.5_FLHL_merged.bw


title: P1176R_Veh


title: D3H2LN-luc, Snord67KO, replicate 2


title: dual-AAV v3em PE3,2e12, tail-vein injection,liver,rep1,off target site 6

description:
Library name: SP8R1liverot6
rep1,off target site 6
sPE_sep_processed_date.xls


title: dual-AAV v3em PE3,2e12, tail-vein injection,liver,rep1,off target site 5

description:
Library name: SP8R1liverot5
rep1,off target site 5
sPE_sep_processed_date.xls


title: SUDHL4-TAZ-CART19-REP2

description: Library name: ATAC-11


title: D3H2LN-luc, Snord67KO, replicate 1


title: dual-AAV v3em PE3,1e12, tail-vein injection,liver,rep3,off target site 5

description:
Library name: SP7R3liverot5
rep3,off target site 5
sPE_sep_processed_date.xls


title: SUDHL4-TAZ-CART19-REP1

description: Library name: ATAC-10


title: ChIPseq_CTCF_WT_E11.5_FLHL_Rep2

description:
L38
ChIpseq_CTCF_WTBl6_E11.5_FLHL_merged.bw

value: Wild-type


title: P1114R_Veh


title: ChIPseq_CTCF_WT_E11.5_FLHL_Rep1

description:
L37
ChIpseq_CTCF_WTBl6_E11.5_FLHL_merged.bw


title: SUDHL4-DMSO-CART19-REP2

description: Library name: ATAC-8


title: P1176R_HFCS


title: SUDHL4-DMSO-CART19-REP3

description: Library name: ATAC-9


title: dual-AAV v3em PE3,1e12, tail-vein injection,liver,rep1,off target site 5

description:
Library name: SP7R1liverot5
rep1,off target site 5
sPE_sep_processed_date.xls

value: liver


title: P1114R_HFCS


title: SUDHL4-DMSO-CART19-REP1

description: Library name: ATAC-7


title: dual-AAV v3em PE3,2e12, tail-vein injection,liver,rep3,off target site 4

description:
Library name: SP8R3liverot4
rep3,off target site 4
sPE_sep_processed_date.xls

value: WT


title: 3_LPS_high

city: Epalinges

first: Julia

last: Esser-von Bieren

state: non

address: Chemin des Boveresses 155

country: Switzerland

institute: UNIL

description: GDHvsLPS.tabular

data_processing:
RNA-seq reads were demultiplexed using Galaxy
RNA-seq reads were aligned to the NCBI GRCh38 reference genome by GSNAP
FeatureCounts was used to assign the reads to genes
Analysis on the RNA-seq count-matrix was carried out using R
The DESeq2 package was used to calculate the fold change, base mean and adjusted p-values
Assembly: GRCh38
Supplementary files format and content: tab-delimited .txt files contain raw counts for all samples; GDHvsLPS.tabular.txt : 1st "LPS" column: 0.5 ng/ml; 2nd "LPS" column: 1.0 ng/ml

source_name: blood

growth_protocol: Human monocyte derived macrophages (MDM) grown in RPMI + cytokines (7 days)

extract_protocol:
RNA was extracted using a spin-column kit (Zymo Research)
TruSeq Stranded mRNA Library Prep Kit (Illumina)

treatment_protocol: Stimulated or not with heGDH (5µg/ml)

value: blood

value: monocyte derived macrophages

value: LPS (1.0 ng/ml)


title: 3_GDH

description: GDHvsctr.tabular

value: heGDH


title: anti-PD-1, asGM1+, rep3

city: Daejeon

first: Dongmin

last: Chun

address: 291, Daehak-ro, Yuseong-gu

department: Biological sciences

institute: Korea Advanced Institute of Science & Technology (KAIST)

data_processing:
HISAT2 aligned the trimmed reads to reference mouse genome
StringTie measured the gene expression in FPKM and TPM
Assembly: mm39
Supplementary files format and content: txt file_gene counts

source_name: CD8+ T cell

extract_protocol:
RNA extraction were dealt with TRIZol and TruSeq mRNA kit from illumina.
RNA libraries for RNA-seq were prepared using SMARTer Ultra low input RNA Library Prep Kit following manufacturer's protocols.

value: CD8+ T cell

tag: cell population

value: DAPI- CD45.2+ CD8+ asGM+

value: wild type


title: anti-PD-1, asGM1+, rep1


title: dual-AAV v3em PE3,2e12, tail-vein injection,liver,rep2,off target site 4

description:
Library name: SP8R2liverot4
rep2,off target site 4
sPE_sep_processed_date.xls


title: anti-PD-1, asGM1+, rep2


title: SUDHL4-TAZ-UTD-REP2

description: Library name: ATAC-5


title: 3_ctr

description: GDHvsctr.tabular

value: control


title: dual-AAV v3em PE3,2e12, tail-vein injection,liver,rep1,off target site 4

description:
Library name: SP8R1liverot4
rep1,off target site 4
sPE_sep_processed_date.xls


title: 2_LPS_high

description: GDHvsLPS.tabular


title: anti-PD-1, asGM1-, rep3

value: DAPI- CD45.2+ CD8+ asGM-


title: SUDHL4-TAZ-UTD-REP1

description: Library name: ATAC-4


title: anti-PD-1, asGM1-, rep2


title: dual-AAV v3em PE3,1e12, tail-vein injection,liver,rep3,off target site 4

description:
Library name: SP7R3liverot4
rep3,off target site 4
sPE_sep_processed_date.xls


title: 2_GDH

description: GDHvsctr.tabular


title: SUDHL4-TAZ-UTD-REP3

description: Library name: ATAC-6


title: dual-AAV v3em PE3,1e12, tail-vein injection,liver,rep2,off target site 4

description:
Library name: SP7R2liverot4
rep2,off target site 4
sPE_sep_processed_date.xls


title: dual-AAV v3em PE3,1e12, tail-vein injection,liver,rep2,off target site 5

description:
Library name: SP7R2liverot5
rep2,off target site 5
sPE_sep_processed_date.xls


title: anti-PD-1, asGM1-, rep1


title: SUDHL4-DMSO-UTD-REP2

description: Library name: ATAC-2


title: dual-AAV v3em PE3,1e12, tail-vein injection,liver,rep1,off target site 4

description:
Library name: SP7R1liverot4
rep1,off target site 4
sPE_sep_processed_date.xls


title: SUDHL4-DMSO-UTD-REP1

description: Library name: ATAC-1


title: 2_ctr

description: GDHvsctr.tabular


title: 1_LPS_high

description: GDHvsLPS.tabular


title: dual-AAV v3em PE3,2e12, tail-vein injection,liver,rep3,off target site 3

description:
Library name: SP8R3liverot3
rep3,off target site 3
sPE_sep_processed_date.xls


title: isotype ctrl, asGM1+, rep2

value: isotype ctrl


title: 1_GDH

description: GDHvsctr.tabular


title: isotype ctrl, asGM1+, rep1


title: dual-AAV v3em PE3,2e12, tail-vein injection,liver,rep2,off target site 3

description:
Library name: SP8R2liverot3
rep2,off target site 3
sPE_sep_processed_date.xls


title: 1_ctr

description: GDHvsctr.tabular


title: Homo CDAHFD

city: shanghai

first: shi-qing

last: cai

address: number 320 yueyang road

institute: CAS Center for Excellence in Brain Science and Intelligence Technology

description: Library name: Homo CDAHFD

data_processing:
The HISAT aligner with –rna-strandness F 43 was used to map sequencing reads to the mouse reference genome GRCm38 (mm10) and mapped reads were counted using HTSeq to obtain raw read counts for each gene 44. The R package DESeq2 45 was used to identify the differentially expressed genes (DEGs) between groups. Genes with a P < 0.05 were designated as DEGs between groups.
Assembly: mm10
Supplementary files format and content: raw reads and counts for each group.

extract_protocol:
Total RNAs of livers were isolated and purified by using TRIzol (Invitrogen) and the RNeasy Mini kit (Qiagen), respectively.
The RNA-seq library was prepared by TruSeq Stranded Total RNA Sample Preparation kit (Illumina) for 150-bp paired-end sequencing.

value: Baz2b Homo


title: SUDHL4-DMSO-UTD-REP3

description: Library name: ATAC-3


title: WT CDAHFD

description: Library name: WT CDAHFD


title: dual-AAV v3em PE3,2e12, tail-vein injection,liver,rep1,off target site 3

description:
Library name: SP8R1liverot3
rep1,off target site 3
sPE_sep_processed_date.xls


title: isotype ctrl, asGM1-, rep3


title: Sample E4

city: Copenhagen N

first: Bjarne

middle: Winther

last: Kristensen

state: Denmark

address: Ole Maaløes Vej 5, building 2, 3 floor

department: Bartholin Institute

country: Denmark

institute: Rigshospitalet, University of Copenhagen

description: Hypermetabolic tumor (Zesto)

data_processing:
SamTools
Rsubread
edgeR
Assembly: GRCh37
Supplementary files format and content: normalised_filtered_cpm_log_data

source_name: Hypermetabolic tumor (Zesto)

growth_protocol: not applicable

extract_protocol:
We used the AllPrep DNA/RNA Mini Kit from Qiagen (#80284) to extract DNA and RNA from each sample. DNA was measured using Qubit fluorometer. RNA quality and quantity were measured using an Agilent 2100 Bioanalyzer.
mRNA libraries were generated from 10 ng of RNA from each sample using the TruSeq® RNA Library Prep for Enrichment (20020189) and TruSeq® RNA Enrichment (20020490) library prep kits, following the manufacturer's protocol. The libraries were sequenced on an Illumina NovaSeq 6000 System high-output flow cell (2 × 150bp), with one lane of an S4 flow cell used for the transcriptome sequencing of all 23 biopsies. In total 2,568,575,326 reads were obtained and aligned to the human reference genome (GRCh38) using STAR. Duplicate reads were removed and the remaining reads were sorted using SamTools. Gene expression counts were generated for each sample using featureCounts in the Rsubread package. The resulting counts were normalized to counts per million (CPM) and subjected to trimmed mean of M (TMM) normalization using edgeR. During the TMM normalization step, genes with counts below a certain CPM cutoff were filtered out to reduce noise. On an average, approximately 75% of the reads were uniquely mapped.

treatment_protocol: not applicable

value: Hypermetabolic tumor (Zesto)

value: Glioblastoma tumor

value: naive patient


title: isotype ctrl, asGM1-, rep2


title: Heter CDAHFD

description: Library name: Heter CDAHFD

value: Baz2b Heter


title: dual-AAV v3em PE3,1e12, tail-vein injection,liver,rep3,off target site 3

description:
Library name: SP7R3liverot3
rep3,off target site 3
sPE_sep_processed_date.xls

value: liver


title: isotype ctrl, asGM1-, rep1


title: Sample D9

description: Periphery (Akri)

source_name: Periphery (Akri)

value: Periphery (Akri)


title: dual-AAV v3em PE3,1e12, tail-vein injection,liver,rep2,off target site 3

description:
Library name: SP7R2liverot3
rep2,off target site 3
sPE_sep_processed_date.xls

value: WT


title: Flt3L Panc02, asGM1+, rep3


title: isotype ctrl, asGM1+, rep3


title: Sample D8

description: Periphery (Akri)


title: Sample D4

description: Periphery (Akri)


title: dual-AAV v3em PE3,1e12, tail-vein injection,liver,rep1,off target site 3

description:
Library name: SP7R1liverot3
rep1,off target site 3
sPE_sep_processed_date.xls


title: dual-AAV v3em PE3,2e12, tail-vein injection,liver,rep3,off target site 2

description:
Library name: SP8R3liverot2
rep3,off target site 2
sPE_sep_processed_date.xls


title: Homo elder rep2

description: Library name: Homo elder rep2


title: Heter control

description: Library name: Heter control


title: Homo control

description: Library name: Homo control


title: WT control

description: Library name: WT control


title: Flt3L Panc02, asGM1+, rep2


title: Sample D3

description: Periphery (Akri)


title: Flt3L Panc02, asGM1+, rep1


title: dual-AAV v3em PE3,2e12, tail-vein injection,liver,rep2,off target site 2

description:
Library name: SP8R2liverot2
rep2,off target site 2
sPE_sep_processed_date.xls


title: Homo elder rep1

description: Library name: Homo elder rep1


title: Flt3L Panc02, asGM1-, rep3


title: Sample D1

description: Periphery (Akri)


title: dual-AAV v3em PE3,2e12, tail-vein injection,liver,rep1,off target site 2

description:
Library name: SP8R1liverot2
rep1,off target site 2
sPE_sep_processed_date.xls


title: dual-AAV v3em PE3,1e12, tail-vein injection,liver,rep3,off target site 2

description:
Library name: SP7R3liverot2
rep3,off target site 2
sPE_sep_processed_date.xls


title: Sample C9

description: Hypometabolic tumor (Kryo)

source_name: Hypometabolic tumor (Kryo)

value: Hypometabolic tumor (Kryo)


title: Flt3L Panc02, asGM1-, rep2


title: Heter elder rep1

description: Library name: Heter elder rep1


title: Sample C8

description: Hypometabolic tumor (Kryo)


title: dual-AAV v3em PE3,1e12, tail-vein injection,liver,rep2,off target site 2

description:
Library name: SP7R2liverot2
rep2,off target site 2
sPE_sep_processed_date.xls


title: WT elder rep2

description: Library name: WT elder rep2


title: Sample C3

description: Hypermetabolic tumor (Zesto)


title: dual-AAV v3em PE3,1e12, tail-vein injection,liver,rep1,off target site 2

description:
Library name: SP7R1liverot2
rep1,off target site 2
sPE_sep_processed_date.xls


title: Panc02, asGM1+, rep3


title: WT elder rep1

description: Library name: WT elder rep1


title: dual-AAV v3em PE3,2e12, tail-vein injection,liver,rep3,off target site 1

description:
Library name: SP8R3liverot1
rep3,off target site 1
sPE_sep_processed_date.xls


title: Sample C2

description: Periphery (Akri)


title: Panc02, asGM1+, rep2


title: Sample C1

description: Tumor satellite

source_name: Tumor satellite

value: Tumor satellite


title: Panc02, asGM1+, rep1


title: Homo young rep1

description: Library name: Homo young rep1


title: dual-AAV v3em PE3,2e12, tail-vein injection,liver,rep1,off target site 1

description:
Library name: SP8R1liverot1
rep1,off target site 1
sPE_sep_processed_date.xls


title: Heter young rep2

description: Library name: Heter young rep2


title: Heter young rep1

description: Library name: Heter young rep1


title: Heter elder rep2

description: Library name: Heter elder rep2


title: Sample B4

description: Hypometabolic tumor (Kryo)


title: dual-AAV v3em PE3,1e12, tail-vein injection,liver,rep3,off target site 1

description:
Library name: SP7R3liverot1
rep3,off target site 1
sPE_sep_processed_date.xls


title: Panc02, asGM1-, rep2


title: Panc02, asGM1-, rep1


title: Flt3L Panc02, asGM1-, rep1


title: WT young rep2

description: Library name: WT young rep2


title: Panc02, asGM1-, rep3


title: Sample B2

description: Hypometabolic tumor (Kryo)


title: dual-AAV v3em PE3,1e12, tail-vein injection,liver,rep1,off target site 1

description:
Library name: SP7R1liverot1
rep1,off target site 1
sPE_sep_processed_date.xls


title: dual-AAV split-ePE3-367,2e12, tail-vein injection,liver,rep3,off target site 10

description:
Library name: SP4R3liverot10
rep3,off target site 10
sPE_sep_processed_date.xls


title: scRNA_129sv_Dac_E115_FL

data_processing:
The Cell Ranger pipeline version 3 (10x Genomics lnc.) was used for each scRNA-seq sample to de-multiplex the raw base call files, generate the fastq files, and perform the alignment against a custom mouse reference genome mm10, including Maenli coordinates (ENSMUSG00000099336.2), to create the UMI count matrix.
Only cells with a detected number of UMI counts among 500 and 40,000, a detected number of genes among 200 and 5,000, and less than 10% of mitochondrial UMI counts were considered for further analysis.
We used scrublet (https://doi.org/10.1016/j.cels.2018.11.005) to identify potential duplets in our dataset. We filtered out cells with a scrublet score higher than 0.2.
Each sample dataset was normalized independently using the SCT method (10.1186/s13059-019-1874-1) implemented in Seurat3 (10.1038/nbt.4096) R package and then integrated the datasets using the Seurat3 IntegrateData function and considering the top 6000 most variable genes.
The first 20 Principal Components of this joint dataset were calculated and used for UMAP projection and cell clustering. To delimitate the major forelimb bud cell types, we used the Louvain algorithm implemented in the Seurat3 function FindClusters with resolution equal 0.02. We identified marker genes for each of the main cell types using the ROC method of the Seurat3 FindAllMarkers function. We only considered genes expressed in at least 10% of each cell-cluster and a log2 fold-change average higher than 0.25.
Assembly: mm10

source_name: Forelimb

extract_protocol:
scRNA-seq 10X Genomics:
The cell concentration was determined using an automated cell counter (Bio-Rad) and cells were subjected to single-cell RNA-sequencing (10x Genomic, ChromiumTM Single Cell 3’ v2; one reaction per time point and per strain has been used) aiming for a target cell recovery of up to 10,000 sequenced cells per sequencing library (time point and strain). Single-cell libraries were generated according to the manufacturer’s instructions with the following conditions: 8 PCR cycles were ran during cDNA amplification and 12 PCR cycles were ran during library generation/sample indexing to increase library complexity. Libraries were sequenced with a minimum of 230 million paired end reads.

treatment_protocol: Limbs from E9.5, E10.5 and E11.5 mouse embryos were dissected in PBS. A single-cell suspension was obtained by incubating the tissue for 10 min at 37 °C in 200 µL Gibco trypsin-EDTA 0.05% (Thermo Fisher Scientific) and 20 µL 5% BSA (Sigma-Aldrich). Digestion was then blocked by adding 400 µL of BSA 5%. Cells were then resuspended by pipetting and filtered using a 0.40 µm cell strainer (Falcon). Cells were washed once with 0.04% BSA with a centrifugation step performed for 5 min at 1200 r.p.m then resuspended in 0.04% BSA.

value: Forelimb


title: WT young rep1

description: Library name: WT young rep1


title: dual-AAV v3em PE3,2e12, tail-vein injection,liver,rep2,off target site 1

description:
Library name: SP8R2liverot1
rep2,off target site 1
sPE_sep_processed_date.xls


title: Homo young rep2

description: Library name: Homo young rep2


title: dual-AAV split-ePE3-367,2e12, tail-vein injection,liver,rep2,off target site 10

description:
Library name: SP4R2liverot10
rep2,off target site 10
sPE_sep_processed_date.xls


title: Sample B1

description: Hypometabolic tumor (Kryo)


title: 1_isotype control, control

data_processing:
Sequences were base called and reads were demultiplexed using bcl2fastq with standard settings.
ChIP-seq reads were pre-processed using the nf-core/chipseq pipeline version 2.0.0 with the --read-length 75 parameter.
ChIP-seq reads were aligned to the NCBI GRCh38 reference genome (iGenomes).
Assembly: GRCh38
Supplementary files format and content: bed, differential peaks

source_name: unstimulated MDM

growth_protocol: CD14+ monocytes + TGFb1, GM-CSF

extract_protocol:
MinElute PCR Purification Kit; ChIP antibody: H3K27ac: abcam, Cat#ab4729; isotype ctr: Cat#ab171870
DNA Ultra II kit

treatment_protocol: untreated or heGDH (5 µg/ml)

value: blood

value: monocyte derived macrophages


title: Sample B9

description: Hypermetabolic tumor (Zesto)


title: 1_H3K27ac, heGDH

source_name: MDM stimulated with heGDH

value: heGDH


title: dual-AAV split-ePE3-367,2e12, tail-vein injection,liver,rep1,off target site 10

description:
Library name: SP4R1liverot10
rep1,off target site 10
sPE_sep_processed_date.xls

source_name: liver


title: Sample A9

description: Hypermetabolic tumor (Zesto)


title: scRNA_B6_WT_E105_FL

value: Wild-type


title: dual-AAV v3em PE3,1e12, tail-vein injection,liver,rep2,off target site 1

description:
Library name: SP7R2liverot1
rep2,off target site 1
sPE_sep_processed_date.xls


title: 3_input, heGDH


title: scRNA_129sv_Dac_E95_FL


title: dual-AAV split-ePE3-367,1e12, tail-vein injection,liver,rep3,off target site 10

description:
Library name: SP3R3liverot10
rep3,off target site 10
sPE_sep_processed_date.xls


title: Sample A8

description: Hypermetabolic tumor (Zesto)


title: dual-AAV split-ePE3-367,1e12, tail-vein injection,liver,rep2,off target site 10

description:
Library name: SP3R2liverot10
rep2,off target site 10
sPE_sep_processed_date.xls


title: Sample B3

description: Hypermetabolic tumor (Zesto)


title: scRNA_B6_WT_E95_FL


title: Sample A3

description: Hypometabolic tumor (Kryo)


title: 3_input, control

value: control


title: scRNA_B6_WT_E115_FL


title: dual-AAV split-ePE3-367,1e12, tail-vein injection,liver,rep1,off target site 10

description:
Library name: SP3R1liverot10
rep1,off target site 10
sPE_sep_processed_date.xls


title: 2_input, heGDH


title: RNAseq_Dac1J129sv_E11.0_FL_Rep3

data_processing:
Paired-end RNA-seq reads were mapped using the STAR mapper (splice junctions based on RefSeq; options: --alignIntronMin 20 –alignIntronMax 500000 – outFilterMismatchNmax 10).
Uniquely mapped paired-end reads were subsequently used for expression analysis using the Cufflinks package (version 2.2.1; default settings)
In a first step, transcripts of each sample were assembled using Cufflinks provided with reference gene annotations from ensembl. The resulting assemblies were then merged using Cuffmerge.
Assembly: mm10
Supplementary files format and content: bigwig

extract_protocol:
Total RNAs were extracted using the Rneasy Mini Kit (QIAGEN) according to the manufacturer's instructions.
Samples were poly-A enriched and sequenced using Illumina technology following standard protocols.

treatment_protocol: Limbs from E11.0 mouse embryos were dissected in PBS, snap frozen and stored at -80° C.

value: Dac1J +/+


title: Sample A2

description: Hypermetabolic tumor (Zesto)


title: 2_input, control


title: scRNA_129sv_Dac_E105_FL


title: Sample A1

description: Hypermetabolic tumor (Zesto)


title: 1_input, heGDH


title: RNAseq_Dac1J129sv_E11.0_FL_Rep2


title: dual-AAV split-ePE3-367,2e12, tail-vein injection,liver,rep1,off target site 9

description:
Library name: SP4R1liverot9
rep1,off target site 9
sPE_sep_processed_date.xls


title: 1_H3K27ac, control


title: dual-AAV split-ePE3-367,2e12, tail-vein injection,liver,rep2,off target site 9

description:
Library name: SP4R2liverot9
rep2,off target site 9
sPE_sep_processed_date.xls


title: 1_input, control


title: RNAseq_Dac1J129sv_E11.0_FL_Rep1


title: RNAseq_WT129sv_E11.0_FL_Rep3


title: Sample A4

description: Hypermetabolic tumor (Zesto)


title: Genomic DNA of ADARcd flies

first: Daniel

last: Guzman Gundermann

address: 100 Washington Square E

institute: NYU

description:
merged_datasets_TRIBE-seq_FigS1.csv
gDNA_ADARcd

data_processing:
For RNA-seq: Trimmed with trimmomatic 0.39 with the following parameters: -phred33 HEADCROP:6 LEADING:25 TRAILING:25 AVGQUAL:25 MINLEN:19
For RNA-seq: sequences were aligned to the Drosophila genome version dm6 with STAR 2.7.6a with the following parameters: --outFilterMismatchNoverLmax 0.07 --outFilterMatchNmin 16 --outFilterMultimapNmax 1. For DNA-seq: Samples were aligned to dm6 using BWA-MEM with the parameters -Y and -K 100000000
For RNA-seq: Alignments were cleaned up by using Samtools 1.14 with samtools view with the -q 10 parameter
For RNA-seq: Duplicates removed with Picard 2.23.8 with VALIDATION_STRINGENCY=LENIENT. For DNA-seq: Duplicates were removed with GATK4 MarkDuplicatesSpark
For RNA-seq: HyperTRIBE pipeline performed using ADARcd as the control RNA sample. For DNA-seq: Variants were called with the GATK HaplotypeCaller followed by VariantFiltration with the following parameters: -filter-name "QD_filter" -filter "QD < 2.0" -filter-name "FS_filter" -filter "FS > 60.0" -filter-name "MQ_filter" -filter "MQ < 40.0" -filter-name "SOR_filter" -filter "SOR > 4.0"  -filter-name "MQRankSum_filter" -filter "MQRankSum < -12.5" -filter-name "ReadPosRankSum_filter" -filter  ReadPosRankSum < -8.0". Then all of the A to G or reverse complement T to C SNPs were filtered out from the vcf file and transformed into a bed file using the awk command. Finally these selected SNPs were subtracted from the bedgraph files from the HyperTRIBE pipeline
Assembly: dm6
Supplementary files format and content: merged_datasets_TRIBE-seq_Fig3.csv is a csv file containing the number of edits obtained by the HyperTRIBE pipeline per experiment as well as the number of edits weighted by the average editing percentage for each gene
Supplementary files format and content: merged_datasets_TRIBE-seq_FigS1.csv is a csv file containing the number of edits obtained by the HyperTRIBE pipeline per experiment as well as the number of edits weighted by the average editing percentage for each gene after removing the possible SNPs equivalent for an A to G edit found by sequencing the genomic DNA of one of the parental strains

organism: Drosophila melanogaster

source_name: adult fly

extract_protocol:
RNA was extracted with the "Dynabeads™ mRNA Purification Kit" and DNA was extracted with the "Quick Preparation of Genomic DNA from Drosophila" from Cold Spring Harbor protocols
Libraries for RNA-seq were prepared by using bulk SMART-seq3 followed by Illumina XT DNA from 1 ng of the amplified cDNA and did 6 cycles of amplification when adding the indices. Libraries for genomic DNA were prepared with the ‘NEBNext® Ultra™ II FS DNA Library Prep Kit for Illumina’ using 30 minutes of fragmentation in the first step

value: adult fly

value: UAS-ADARcd ; Sp/TM6B


title: 3_H3K27ac, heGDH


title: RNAseq_WT129sv_E11.0_FL_Rep2


title: Genomic DNA of Fmr1-ADARcd flies

description:
merged_datasets_TRIBE-seq_FigS1.csv
gDNA_Fmr1-ADARcd

value: UAS-Fmr1-ADARcd ; +/+


title: RNAseq_WT129sv_E11.0_FL_Rep1


title: dual-AAV split-ePE3-367,2e12, tail-vein injection,liver,rep3,off target site 9

description:
Library name: SP4R3liverot9
rep3,off target site 9
sPE_sep_processed_date.xls


title: dual-AAV split-ePE3-367,1e12, tail-vein injection,liver,rep3,off target site 9

description:
Library name: SP3R3liverot9
rep3,off target site 9
sPE_sep_processed_date.xls


title: 3_H3K27ac, control


title: dual-AAV split-ePE3-367,1e12, tail-vein injection,liver,rep1,off target site 9

description:
Library name: SP3R1liverot9
rep1,off target site 9
sPE_sep_processed_date.xls


title: Sample B8

description: Hypermetabolic tumor (Zesto)

value: Hypermetabolic tumor (Zesto)

value: Glioblastoma tumor

value: naive patient


title: ChIPseq_CTCF_Dac1JBl6_E10.5_FLHL

treatment_protocol: Limbs from E10.5 mouse embryos were dissected in PBS, a single cell suspension was made using Trypsin, samples were fixed in 1% PFA, snap frozen, and stored at -80 °C.

value: limbs


title: dual-AAV split-ePE3-367,1e12, tail-vein injection,liver,rep2,off target site 9

description:
Library name: SP3R2liverot9
rep2,off target site 9
sPE_sep_processed_date.xls

value: liver

value: WT


title: 2_isotype control, heGDH


title: 2_H3K27ac, heGDH


title: ChIPseq_CTCF_Dac1J129sv_E10.5_FLHL


title: 2_isotype control, control


title: dual-AAV split-ePE3-367,2e12, tail-vein injection,liver,rep2,off target site 8

description:
Library name: SP4R2liverot8
rep2,off target site 8
sPE_sep_processed_date.xls


title: ChIPseq_CTCF_WT_E10.5_FLHL_Rep2


title: dual-AAV split-ePE3-367,2e12, tail-vein injection,liver,rep1,off target site 8

description:
Library name: SP4R1liverot8
rep1,off target site 8
sPE_sep_processed_date.xls


title: ChIPseq_CTCF_WT_E10.5_FLHL_Rep1