title: rde-1(ne219) rep2

status: Public on Jan 29 2024

city: Fort Collins

first: Taiowa

middle: A

last: Montgomery

state: CO

address: 1878 Campus Delivery

department: Department of Biology

institute: Colorado State University

description:
16-30 nt purified RNAs from cell lysate
wt_rde-1_rpm_normalized_counts.csv

library_source: other

data_processing:
Small RNA data processing was done using the default configuration in the tinyRNA pipeline (https://github.com/MontgomeryLab/tinyRNA). mRNA data prcocessing was done using a custom pipeline including fastp, RSEM, STAR, and DESeq2.
Assembly: WS279
Supplementary files format and content: wt_rde-1_rpm_normalized_counts.csv: CSV formatted file containing reads per million total mapped reads for each feature in wild type and rde-1 mutants.
Supplementary files format and content: GFP-RDE-1_co-IP_normalized_counts.csv: CSV formatted file containing reads per million total mapped reads for each feature in GFP::RDE-1 co-IPs and cell lysates.

molecule: other

organism: Caenorhabditis elegans

source_name: gravid hermaphroditic adult whole animals

growth_protocol: Worms were grown for 72-75 hours from synchronized L1 larvae at 20C on media containing E. coli (OP50 or HT115).

extract_protocol: Small RNAs (~16-30-nt) were purified from total RNA by size selection using 17% polyacrylamide gels and in some instances treated with NEB RNA 5' Pyrophosphohydrolase (RppH)to facilitate capture of 22G-RNAs. Libraries were then prepared according to the NEBNext Multiplex Small RNA kit protocol. PCR products (~134-148 bp) were size selected using 10% polyacrylamide gels. For mRNA-seq DNase-treated total RNA was depleted of rRNA using Ribo-Zero and libraries were prepared using the Illumina TruSeq Stranded Total RNA kit.

value: pyrophosphohydrolase


title: rde-1(ne219) rep1

type: SRA

country: USA

tag: tissue

value: gravid hermaphroditic adult whole animals

tag: genotype

tag: treatment


title: wild type, rep 1

value: wild type (N2)


title: GFP::RDE-1 co-IP rep2

description:
16-30 nt purified RNAs from RDE-1 co-IP
GFP-RDE-1_co-IP_normalized_counts.csv

value: USC1080[rde-1(rde-1(cmp133[(gfp + loxP + 3xFLAG)::rde-1]) V]


title: wild type, rep 3


title: H3K27Ac_ChIP_LPS2h_Rep2

status: Public on Mar 04 2024

city: La Jolla

first: Nathanael

middle: Judge

last: Spann

state: CA

address: 9500 Gilman Drive CMMW 219A

department: Cellular and Molecular Medicine

institute: UCSD

description:
formaldehyde cross-linked
processed data file:
BMDM_ChIP_H3K27Ac_TFmerge.txt, BMDM_ChIP_H3K27Ac_AllMerged.txt

library_source: genomic

data_processing:
Preprocessing: FASTQ files from sequencing experiments were mapped to the mouse mm10 genome. Bowtie2 with default parameters was used to map ChIP-seq experiments (Langmead and Salzberg, 2012). HOMER was used to convert aligned reads into “tag directories” for further analysis (Heinz et al., 2010).
For p300, SREBP and LXR ChIP-seq experiments peaks were called with HOMER for each tag directory with default peak finding parameters -style factor against the corresponding input directory. Only peaks with > 16 normalized tags (normalized to total tags of 1e7) were kept. Overlapping peak sets were determined using mergePeaks command. The pooled tag directory from two replicates was used for track visualization. To annotate p300 signal in ATAC-seq or LXR,SREBP, p65 ChIP-seq peaks the parameter -size 200 was used. Subsequently, DESeq2 (Love et al., 2014) was used to identify differential p300 signal > 2 fold-change and p-adj < 0.05, unless stated otherwise in the text.
For H3K27ac analysis: To annotate H3K27ac signal around ATAC-seq or LXR,SREBP, p65 ChIP-seq peaks the parameter -size 1000 was used. Subsequently, DESeq2 (Love et al., 2014) was used to identify differential H3K27ac signal or chromatin accessibility with > 2 fold-change and p-adj < 0.05, unless stated otherwise in the text.
For p65 and ATAC-Seq analysis of data from GSE79423 and GSE109965 respectively: Relevant raw FASTQ files were mapped to mm10 genome with Bowtie2 with default parameters (Langmead and Salzberg, 2012). HOMER was used to convert aligned reads into “tag directories” for further analysis (Heinz et al., 2010). For p65 peaks were called with HOMER findPeaks for each tag directory with default peak finding parameters -style factor against the corresponding input directory. Peak files across various timepoints for vehicle and KLA treated timepoints were merged using HOMER mergePeaks. Merged peaks were annotated for H3K27ac and p300 signal as indicated. For ATAC-Seq, mm10 mapped, IDR defined peaks from GSE109965, for both vehicle and KLA treatment conditions, were used. Peaks were merged using HOMER mergePeaks, then merged peak file was used for further analysis as indicated in text.
To identify motifs enriched in peak regions over the background, HOMER’s motif analysis (findMotifsGenome.pl) including known default motifs and de novo motifs was used. The background sequences were either from random genome sequences or from peaks from the comparing condition indicated in the main text and in the figure legends.
Genome_build: mm10
Supplementary files format and content: Processed files include peak text files (ChIP-Seq, ATAC, and H3K27Ac peak or region data, using default HOMER parameters). Peak or region files BMDM_ChIP_p300_AllTFmerged.txt and BMDM_ChIP_H3K27Ac_AllTFmerged.txt are summed transcription factor peak files annotated with normalized tag counts from either p300 or H3K27Ac ChIP-seq data as indicated. Peak files BMDM_ChIP_p300_ATACmerged.txt and BMDM_ChIP_H3K27Ac_ATACmerged.txt are summed ATAC-Seq peak files annotated with normalized tag counts from either p300 or H3K27Ac ChIP-seq data. Peak annotation, with p300 and H3K27Ac tag directories, was done using HOMER annotatePeaks command, with option -size 200 or -size 1000, respectively. All genomic coordinates are relative to mm10 mouse assembly.

molecule: genomic DNA

organism: Mus musculus

source_name: H3K27Ac ChIP-seq LPS2h

growth_protocol: Bone marrow derived macrophages (BMDMs): Mouse bone marrow was harvested and washed once with PBS, seeded/cultured in DMEM containing 20 % FCS, 30 % L-cell conditioned media (as source of macrophage colony stimulating factor, M-CSF), and 100 U/ml penicillin/streptomycin in non-tissue culture-treated petri dishes. After 6-8 days of culture, non-adherent cells were washed off with room temperature PBS and macrophages were obtained as a homogeneous population of adherent cells which were scraped and subsequently seeded onto tissue culture-treated petri dishes overnight in RPMI-1640 containing 10% FCS, 100 U/ml penicillin/streptomycin, and 10ng/ml M-CSF.

extract_protocol:
For H3K27ac ChIP-seq, culture media was removed and plates were washed once with PBS and then fixed with 1% formaldehyde (Thermo Fisher Scientific) in PBS for 10 minutes at room temperature. The reaction was quenched by adding glycine (Thermo Fisher Scientific) to 0.125M. For p300, LXR and SREBP ChIP-seq, cells were crosslinked with 3mM DSG (ProteoChem) in PBS for 30 minutes at room temperature, and then fixed with 1% formaldehyde (Thermo Fisher Scientific) in PBS for 10 minutes at room temperature. The reaction was quenched by adding glycine (Thermo Fisher Scientific) to 0.125M. After fixation, cells were washed once with cold PBS and then pelleted at 700 X G for 5 minutes at 4°C. Crosslinked cells were stored at –80°C until ready for ChIP-seq library preparation. Fixed cells were thawed on ice, resuspended in either ice-cold LB3 (10 mM Tris/HCl pH 7.5, 100 mM NaCl, 1mM EDTA, 0.5mM EGTA, 0.1% Na-deoxycholate, 0.5% N-lauroylsarcosine, 1 X protease inhibitor cocktail, 1mM Na-Butyrate, for H3K27ac ChIP) or ice-cold RIPA-NR lysis buffer (20 mM Tris-HCl, pH 7.5, 150 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.4% Na-Deoxycholate, 0.1% SDS, 1% NP-40, 1x protease inhibitors, for p300, LXR, and SREBP ChIP). Frozen crosslinked nuclei were resuspended in wash buffer (10mM HEPES/KOH pH7.9, 85mM KCl, 1mM EDTA, 0.2% IGEPAL CA-630, 1x protease inhibitor cocktail (Sigma), 1 mM PMSF) for 5minutes on ice. Cells were spun down and then resuspended in RIPA-NR lysis buffer. Chromatin was sheared by sonication. Samples were sonicated in a 96 Place microTUBE Rack (Covaris cat#500282) using a Covaris E220 for 12 cycles (samples in LB3) or 18 cycles (samples in RIPA-NR buffer) with the following setting: time, 60 seconds; duty, 5.0; PIP, 140; cycles, 200; amplitude, 0.0; velocity, 0.0; dwell, 0.0. Samples were recovered and spun down at max speed, 4°C for 10 minutes. The LB3 lysate was diluted 1.1-fold with ice-cold 10% Triton X-100 after sonication. One percent of the lysate was kept as ChIP input. For each immunoprecipitation, aliquots of diluted lysate equivalent to 500,000 cells (for H3K27ac ChIP) or 1-2 million cells  (for p300, SREBP ChIP), 20 µl of Dynabeads Protein A (for rabbit polyclonal antibodies) or Dynabeads protein A/G (for p300, LXR, and SREBP ChIP) bound to specific antibodies for H3K27ac (2 μg, Active Motif, 39133), p300 (2 μg, Millipore, cat# 05-257,Diagenode, cat# C15200211), LXR (Santa Cruz Biotechnology: sc-1000X, sc- 133221X, sc-271064X) , and SREBP (2 μg, Santa Cruz Biotechnology: sc-8984X, Thermo Fisher Scientific: PA1-337, R&D Systems: AF7119) were combined and rotated overnight at 4°C. For H3K27ac ChIP, beads were collected on a magnet and washed three times each with wash buffer I (20 mM Tris/HCl pH 7.5, 150 mM NaCl, 1% Triton X-100, 0.1% SDS, 2 mM EDTA), wash buffer III (10 mM Tris/HCl pH 7.4, 250 mM LiCl, 1% Triton X-100, 0.7% Na-Deoxycholate, 1 mM EDTA) and twice with ice-cold TET (10 mM Tris/HCl pH7.5, 1 mM EDTA, 0.2% Tween-20). For p300, LXR and SREBP ChIP, beads were washed three times with RIPA-NR buffer (20 mM Tris-HCl/pH7.5, 150 mM NaCl, 0.1% SDS, 1% NP-40, 0.4 % Na-Deoxycholate, 1 mM EDTA, 0.5mM EGTA, 0.5mM DTT), six times with RIPA-LiCl buffer (10 mM Tris-HCl/pH 7.5, 250 mM LiCl, 1% NP-40, 0.7% Na-Deoxycholate, 1 mM EDTA), three times with ice-cold TET (10 mM Tris/HCl pH7.5, 1 mM EDTA, 0.2% Tween-20), and one time with IDTE (10mM Tris-HCl pH 8.0, 0.1mM EDTA). Bead complexes were resuspended in 25 μl TT (10 mM Tris/HCl pH 8.0, 0.05% Tween-20, 1x protease inhibitor cocktail) and sequencing libraries were prepared on-bead as described below.
ChIP libraries were prepared while bound to Dynabeads using NEBNext Ultra II Library preparation kit with reaction volumes reduced by half, essentially as previously described (Heinz et al., 2018). Libraries were eluted and crosslinks reversed by adding to the 46.5 μl NEB reaction 20 μl water, 4 μl 10% SDS, 4.5 μl 5M NaCl, 3 μl 0.5 M EDTA, and 1 μl 20 mg/ml proteinase K, followed by incubation at 55C for 1 hour and 65C for 30 minutes to overnight in a thermal cycler. Dynabeads were removed from the library using a magnet and libraries cleaned by adding 2 μl SpeedBeads 3 EDAC in 61 μl 20% PEG 8000/1.5 M NaCl, mixing well, then incubating at room temperature for 10 minutes. SpeedBeads were collected on a magnet and washed two times with 150 μl 80% ethanol for 30 seconds. Beads were collected and ethanol removed following each wash. After the second ethanol wash, beads were air dried and DNA eluted in 25 μl 10 mM Tris/HCl pH 8.0 and 0.05% Tween-20. DNA was amplified by PCR for 14 cycles in a 50 μl reaction volume using NEBNext Ultra II PCR master mix and 0.5 μM each Solexa 1GA and Solexa 1GB primers. Libraries were cleaned up with SpeedBeads as above using 36.5 μl 20% PEG 8000/1.5 M NaCl and 2 μl SpeedBeads. After ethanol washing and drying, PCR amplified libraries were eluted from the SpeedBeads using 20 μl 10 mM Tris/HCl pH 8.0 and 0.05% Tween- 20. Next, libraries were size selected 250-500 bp using gel extraction using 10% TBE acrylamide gels. Libraries were single-end sequenced using either a HiSeq 4000 or a NextSeq 500 to a depth of 10-20 million reads.

treatment_protocol: The following day after replating BMDMs, fresh medium containing 0.5% fetal bovine serum was added to the cells and serum starvation was carried overnight. After serum starvation the cells were treated with or without 100 µg/ml 3'SL , with 10 ng/ml of LPS for 1 – 24 hours as indicated. For LXR and SREBP experiments cells were treated with 1uM GW3965.

tag: strain

tag: cell type

value: bone marrow derived macrophages

value: LPS for 2 hours

tag: antibody

value: H3K27Ac (Vendor:Active Motif, cat# 39133)


title: GFP::RDE-1 co-IP rep1

description:
16-30 nt purified RNAs from RDE-1 co-IP
GFP-RDE-1_co-IP_rpm_normalized_counts.csv


title: GFP::rde-1 input rep 2

description:
16-30 nt purified RNAs from cell lysate
GFP-RDE-1_co-IP_rpm_normalized_counts.csv


title: rde-1(ne219) rep3


title: wild type, rep 2


title: GFP::rde-1 input rep 1


title: Line#2, D3 HES6-KO, tam-inducible, Multiome-seq, ATAC

status: Public on Jan 10 2024

city: Brookline

first: Ramesh

last: Shivdasani

state: Massachusetts

address: SM1052, Smith10, 450 Brookline Ave

department: Medical Oncology

institute: DFCI

description:
read1 file contains cell barcode and transposase-accessible chromatin; read2 file contains transposase-accessible chromatin
PSD3HES6_barcodes.tsv.gz
PSD3HES6_features.tsv.gz
PSD3HES6_matrix.mtx.gz

data_processing:
Pre-processing of sequencing results to generate count matrices (gene expression and ATAC barcode counts) was performed using the 10x genomics Cell Ranger ARC pipeline aligning to the hg19 genome build.
Assembly: hg19
Supplementary files format and content: 10x Genomics output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz
Supplementary files format and content: atac_fragments.tsv.gz: ATAC fragments file
Supplementary files format and content: atac_fragments.tsv.gz.tbi: ATAC fragments file index
Supplementary files format and content: atac_peaks.bed: CellRanger called Peaks file

organism: Homo sapiens

source_name: Ileum

growth_protocol: DMEM, 20 % F12K, 20% FBS, 10% R-Spondin-2 conditioned medium, 10 mM nicotinamide, 100µg/ml Primocin, 1 μM A8301, 5 μg/ml  insulin, 10 μM Y-27632, 1 μM DMH1, 50 ng/ml EGF and 2 μM T3. Cells were cultured at 37oC at 7.5% CO2.

extract_protocol:
Stem cells / Differentiated EECs were dissociated using 1x TrypLE Exprress at 37 °C for 10 min. Cells were washed and re-suspended in PBS and stained with a Viability Dye, washed and resuspended in FACS buffer (HBSS without Ca+2, Mg+2 and phenol red, 0.9% Glucose, 10 mM HEPES, 500 ppm N-acetyl L-cystein, 10µM Y27632,  2% FBS). Alive cells were sorted using a FACS (BD Aria) according to the presence or absence of mCherry signal. Cells were washed and resuspended in PBS. Nuclei were extracted and resuspended in PBS supplemented with 0.04% w/v BSA.
Library was prepared using Chromium Next GEM Single Cell Multiome ATAC + Gene Expression protocol (10x Genomics). Cellular mRNA and ATAC sites were reverse-transcribed and indexed with a shared cellular barcode. Indexed cDNAs were then pooled and amplified by PCR according to the Chromium Next GEM Single Cell Multiome ATAC + Gene Expression protocol (10x Genomics) and with specific primers amplifying the ATAC sites. SPRI bead size selection was performed in order to separate both the mRNA-derived cDNA (>300bp) and the ATAC sites (>180bp). For the mRNA derived cDNA and ATAC library preparation, we further proceeded according to the manufacturer’s instructions for Next GEM Single Cell Multiome ATAC + Gene Expression protocol (10x Genomics).

value: Ileum

tag: cell line

value: D3 HES6-KO, tam-inducible

tag: library type

value: ATAC


title: Line#2, D6 NEUROD1-DBD-KO, tam-inducible, Multiome-seq, ATAC

description:
read1 file contains cell barcode and transposase-accessible chromatin; read2 file contains transposase-accessible chromatin
PSD6ND123_barcodes.tsv.gz
PSD6ND123_features.tsv.gz
PSD6ND123_matrix.mtx.gz

value: D6 NEUROD1-DBD-KO, tam-inducible


title: Line#2, D6 scrambled, tam-inducible, Multiome-seq, ATAC, rep1

description:
read1 file contains cell barcode and transposase-accessible chromatin; read2 file contains transposase-accessible chromatin
PSD6Ne_barcodes.tsv.gz
PSD6Ne_features.tsv.gz
PSD6Ne_matrix.mtx.gz

value: D6 scrambled, tam-inducible


title: Line#2, D3 scrambled, tam-inducible, Multiome-seq, ATAC, rep2

description:
read1 file contains cell barcode and transposase-accessible chromatin; read2 file contains transposase-accessible chromatin
PSD3scram_barcodes.tsv.gz
PSD3scram_features.tsv.gz
PSD3scram_matrix.mtx.gz

value: D3 scrambled, tam-inducible


title: Line#2, D6 ASCL1-KO, tam-inducible, Multiome-seq, ATAC

description:
read1 file contains cell barcode and transposase-accessible chromatin; read2 file contains transposase-accessible chromatin
PSD6AS_barcodes.tsv.gz
PSD6AS_features.tsv.gz
PSD6AS_matrix.mtx.gz

value: D6 ASCL1-KO, tam-inducible


title: Line#2, D3 scrambled, tam-inducible, Multiome-seq, ATAC, rep1

description:
read1 file contains cell barcode and transposase-accessible chromatin; read2 file contains transposase-accessible chromatin
D3Ne_barcodes.tsv.gz
D3Ne_features.tsv.gz
D3Ne_matrix.mtx.gz


title: Line#2, D6 NEUROD1-TAD-KO, tam-inducible, Multiome-seq, ATAC

description:
read1 file contains cell barcode and transposase-accessible chromatin; read2 file contains transposase-accessible chromatin
PSD3ND_barcodes.tsv.gz
PSD3ND_features.tsv.gz
PSD3ND_matrix.mtx.gz

value: D6 NEUROD1-TAD-KO, tam-inducible


title: Line#2, D3 ASCL1-KO, tam-inducible, Multiome-seq, ATAC

description:
read1 file contains cell barcode and transposase-accessible chromatin; read2 file contains transposase-accessible chromatin
PSD3AS_barcodes.tsv.gz
PSD3AS_features.tsv.gz
PSD3AS_matrix.mtx.gz

value: D3 ASCL1-KO, tam-inducible


title: Line#2, D6 HES6-KO, tam-inducible, Multiome-seq, ATAC

description:
read1 file contains cell barcode and transposase-accessible chromatin; read2 file contains transposase-accessible chromatin
PSD6HES6_barcodes.tsv.gz
PSD6HES6_features.tsv.gz
PSD6HES6_matrix.mtx.gz

value: D6 HES6-KO, tam-inducible


title: Line#2, D6, tam-inducible, Multiome-seq, ATAC

description:
read1 file contains cell barcode and transposase-accessible chromatin; read2 file contains transposase-accessible chromatin
PS6_barcodes.tsv.gz
PS6_features.tsv.gz
PS6_matrix.mtx.gz

value: D6, tam-inducible


title: Line#2, D5, tam-inducible, Multiome-seq, ATAC

description:
read1 file contains cell barcode and transposase-accessible chromatin; read2 file contains transposase-accessible chromatin
PS5_barcodes.tsv.gz
PS5_features.tsv.gz
PS5_matrix.mtx.gz

value: D5, tam-inducible


title: Line#2, D3, tam-inducible, Multiome-seq, ATAC

description:
read1 file contains cell barcode and transposase-accessible chromatin; read2 file contains transposase-accessible chromatin
PS3_barcodes.tsv.gz
PS3_features.tsv.gz
PS3_matrix.mtx.gz

value: D3, tam-inducible


title: blood from kidney stone patients, disease9

status: Public on Jan 01 2024

city: Shenzhen

first: Yuhao

last: An

state: Guangdong Province

address: 16 Lanjing Road, Kengzi Street, Pingshan District

country: China

institute: Shenzhen Bay Lab

data_processing:
Base calling using CASAVA for sequenced reads conversion.
Raw reads quality check using FastQC.
Sequence reads were trimmed for adaptor sequence / low-quality sequence using Trimmomatic.
Trimmed sequence reads were mapped to hg19 using Bowtie2.
Methylated gene sites were detected using Bismark.
Assembly: hg19
Supplementary files format and content: DNA methylation percentage in each sample. gene_regions_level.txt: Methylation patterns in the promoter, exon, intron, 5'UTR, 3'UTR, etc; gene_updown_level.txt: Methylation patterns in the area before the promoter and behind the coding gene.

source_name: blood

extract_protocol:
Genomic DNA was harvested and digested by MspI
DNA libraries for Reduced representation bisulfite sequencing (RRBS) were prepared using EZ DNA Methylation Gold Kit following manufacturer's protocols.

value: blood

value: human blood

value: disease blood


title: blood from kidney stone patients, disease8


title: Line#2, D1, tam-inducible, Multiome-seq, ATAC

description:
read1 file contains cell barcode and transposase-accessible chromatin; read2 file contains transposase-accessible chromatin
PS1_barcodes.tsv.gz
PS1_features.tsv.gz
PS1_matrix.mtx.gz

value: D1, tam-inducible


title: blood from kidney stone patients, disease7


title: blood from kidney stone patients, disease5


title: blood from kidney stone patients, disease6


title: blood from kidney stone patients, disease4


title: blood from kidney stone patients, disease2


title: blood from kidney stone patients, disease1


title: blood from normal individuals, control2

value: normal blood


title: blood from kidney stone patients, disease3


title: blood from normal individuals, control1


title: blood from normal individuals, control3


title: blood from normal individuals, control5


title: Line#2, D6 scrambled, tam-inducible, Multiome-seq, ATAC, rep2

description:
read1 file contains cell barcode and transposase-accessible chromatin; read2 file contains transposase-accessible chromatin
PSD6scram_barcodes.tsv.gz
PSD6scram_features.tsv.gz
PSD6scram_matrix.mtx.gz

value: Ileum


title: K562, H3K4me3, rep3

status: Public on Dec 24 2023

city: Moscow

first: Arkadiy

last: Golov

address: Vavilova, 34/5

country: Russia

institute: Institute of Gene Biology, RAS

data_processing:
Raw MChIP-C reads were mapped to the hg19 genome build with BWA-MEM (with -SP5M flags).
Mapped reads were parsed, uniquely mapped distal read pairs (>5,000 bp apart; cis) were selected and deduplicated with the pairtools package (v.0.3.0).
Binary BAM files were produced from pairtools output and reads mapping to the H3K4me3 ChIP-seq peaks were selected with the samtools (v.1.15.1).
BigWig proximity ligation profiles (merged or separated by individual viewpoints) were generated with the deeptools (v.3.5.1).
Assembly: hg19
Supplementary files format and content: bigWig: viewpoint specific and merged MChIP-C proximity ligation coverage in 100bp and 250bp genomic bins, ChIP-seq occupancy coverage in 50bp genomic bins
Supplementary files format and content: bed: genomic intervals corresponding to the positions of MChIP-C viewpoints
Supplementary files format and content: bedpe: pairs of genomic interval representing MChIP-C identified physical genomic interactions

growth_protocol: K562 cells were cultivated in DMEM medium supplemented with 10% fetal bovine serum and 1× penicillin/streptomycin in a humidified 37 °C incubator with 5% CO2

extract_protocol:
MChIP-C: Cells were crosslinked for 10 min at room temperature in fresh full growth medium supplemented with 2% formaldehyde. Crosslinked cells were permeabilized in PBS supplemented with 0.01% digitonin on ice, chromatin was subjected to 1h digestion with 35-40 U of micrococcal nuclease (Thermo Scientific, EN0181). Next, DNA ends were repaired with 100 U of T4 Polynucleotide Kinase (NEB, M0201L) and 50U of Klenow fragment (NEB, M0210L). Blunted DNA ends were proximity ligated with 75U of T4 DNA ligase (ThermoScientific, EL0012). Chromatin was sheared on ice with a VirSonic 100 cell disrupter with 3 15-sec pulses on “15” power setting, separated with 3 min periods of recovery, transferred to RIPA buffer and immunoprecipitated with anti-H3K4me3 antibodies (Active motif, 39016) and protein A/G magnetic beads (Thermo Scientific, 26162). DNA was reverse-crosslinked and isolated with phenol-chloroform extraction and ethanol precipitation. ChIP-seq:  Cells were crosslinked for 10 min at room temperature in fresh full growth medium supplemented with 2% formaldehyde. Crosslinked cells were permeabilized in PBS supplemented with 0.01% digitonin on ice. Permeabilized cells were resuspended in ice cold ChIP lysis buffer (50 mM Tris-HCl pH 8.0, 1% SDS, 10 mM EDTA), chromatin was sheared with 4 30-sec ultrasound pulses on “15” power setting of VirSonic 100 sonicator. Incubation with antibodies, immunoprecipitation, DNA isolation were performed as described in MChIP-C protocol.
MChIP-C and ChIP-seq NGS libraries were prepared from immunoprecipitated DNA with the NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB, E7645) according to the manufacturer’s recommendations, with the following modifications: 1) we decreased the reaction volumes two-fold; 2) instead of the adaptor included in the kit, we used 1 μL of barcoded Y-shaped Illumina TruSeq adapters (Illumina, 20015960 and 20015961) per reaction and extended ligation time to 1h.  We used either 17 μL (~0.37×) (for MChIP-C) or 35 μL (0.76×) (for ChIP-seq) of AMPure XP beads (Beckman Coulter, A63881) in the pre-PCR clean-up. Adapter-ligated material was amplified with 12-14 cycles of PCR using KAPA HiFi HotStart PCR Kit (Roche, 07958897001) and universal P5/P7 Illumina primers.
OTHER:MChIP-C, ChIP-seq

value: Human erythroleukemia


title: K562, H3K4me3, rep4


title: SUIT2 shEn1_1.2

status: Public on Dec 19 2023

city: Davis

first: Chang-il

last: Hwang

address: One Shields Ave

department: Microbiology and Molecular Genetics

institute: University of California Davis

library_source: transcriptomic

data_processing:
Paired-end sequencing reads were aligned to mm9 reference genome using HISAT2.
Aligned reads were counted by featureCounts.
Assembly: mm9
Supplementary files format and content: Tab-delimited text files include countd reads, per gene, per row.

molecule: total RNA

source_name: Pancreas

extract_protocol:
RNA was harvested using PureLink RNA mini kit (Thermo Fisher).
Library preparation and sequencing were performed by Novogene Co., LTD (Beijing, China).

value: Pancreas

value: epithelial cells

value: En1 shRNA


title: SUIT2 shEn1_2.2


title: SUIT2 shScr_4

value: Scramble shRNA


title: SUIT2 shScr_3


title: K562, H3K4me3, rep2


title: K562, H3K4me3, rep1 (NovaSeq)


title: SUIT2 shEn1_1.1


title: SUIT2 shScr_2


title: SUIT2 shScr_1


title: mM15 shEn1#2

value: Kras +/LSL-G12D; Trp53+/LSL-R172H; Pdx1-Cre


title: mM15 shEn1#1


title: mM15 shScr


title: mM3P shEn1#2


title: blood from normal individuals, control4


title: mM3P shScr


title: mT8-2D En1 Input

data_processing:
Paired-end sequencing reads were aligned to mm9 reference genome using Bowtie2.
Aligned reads were filtered using SAMtools tollkit to filter the BAM file on the mapping quality (Minimum MAPQ quality score 20).
Bigwig file of fragment or read coverages were generated using bamCoverage (Bin size in bases 50).
Assembly: mm9
Supplementary files format and content: Bigwig
Library strategy: CUT&RUN-seq

extract_protocol:
Enriched chromatin were extracted using CUT&RUN assay kit (Cell Signaling Technology).
Library preparation and sequencing were performed by Novogene Co., LTD (Beijing, China) on a NovaSeq 6000 PE150 sequencing system.

value: Epithelial cells

value: Kras +/LSL-G12D; Trp53 +/LSL-R172H; Pdx1-Cre

value: En1 cDNA


title: mM3P shEn1#1


title: mT8-2D En1 H3K27me3


title: mT8-2D En1 H3K27ac


title: mT8-2D En1 FLAG


title: mT8-2D empty H3K27me3

value: Empty Vector


title: mT5-2D En1 Input


title: mT8-2D empty H3K27ac


title: mT8-2D En1 H3K4me3


title: SUIT2 shEn1_2.1


title: mT8-2D empty H3K4me3


title: mT5-2D En1 H3K27me3


title: mT5-2D En1 H3K27ac


title: mT5-2D En1 FLAG


title: mT5-2D empty H3K27me3


title: mT5-2D empty Input


title: mT5-2D empty H3K27ac


title: mT5-2D En1 H3K4me3


title: mT4-2D En1 H3K27me3


title: mT4-2D En1 H3K27ac


title: mT4-2D En1 Input


title: mT4-2D En1 H3K4me3


title: mT4-2D En1 FLAG


title: mT4-2D empty Input


title: mT4-2D empty H3K27me3


title: mT4-2D empty H3K27ac


title: mT3-2D En1 Input


title: mT4-2D empty H3K4me3


title: mT8-2D empty Input


title: mT3-2D En1 H3K27ac


title: mT3-2D En1 H3K4me3


title: mT3-2D En1 FLAG


title: mT3-2D empty H3K27ac


title: mT5-2D empty H3K4me3


title: mT3-2D empty H3K4me3


title: 3-trimester_Brain_Saline-F_10

status: Public on Dec 15 2023

city: New York

first: Molly

middle: S

last: Estill

state: NY

address: 1 Gustave L. Levy Place

department: Neuroscience

institute: Mount Sinai School of Medicine

description:
3tri_deseq2_F_vs_M.Sal.txt
3tri_deseq2_Mor_vs_Sal.F.txt
counts_matrix.txt
4429 - 3

data_processing:
Adaptor removal was performed with trim-galore (version 0.6.6), with parameters "--paired --trim-n". Alignment of trimmed reads to murine genome (mm10) was performed using HISAT2 (version 2.2.1). Duplicate removal was performed with samtools rmdup (version 1.11). Gene expression matrices were obtained using featureCounts (version 2.0.1), with parameters "-p -O --fraction -t gene" to generate the samples' read counts in the GENCODE M25 annotation.
For each model, genes were filtered to remove those genes with fewer than 2 reads in at least 6 samples. Using R (version 4.2.1), DEseq2 (version 1.36.0) was used to determine the differential expression within each model, accounting for both drug treatment and sample gender ("~ treatment + gender + treatment:gender" or "~ gender + treatment + gender:treatment").
Assembly: mm10
Supplementary files format and content: Data files are formatted as tab-delimited text files. The files containing differential expression information provide the statistics relevant to differential expression, as well as the feature id and associated gene symbol of each feature.

source_name: brain

extract_protocol: RNA integrity was assessed with an Agilent Tapestation 4200 using the RNA ScreenTape (Agilent, Wilmington, DE). All samples had RIN values > 8. mRNA libraries were generated using the NEBNext Ultra™ II RNA Library Prep Kit for Illumina (New England BioLabs, Ipswitch, MA).

treatment_protocol: Osmotic minipump filled with morphine (10mg/kg/day) or saline was used to expose pups in utero ( PND1 sample and 3-trimseter sample) . For PND1-14 and last trimester of 3-trimester expousre, pups were injected twice a day with morphine 10mg/kg). All groups were killed 6 hours after the last morphine injection, brains were removed and flash frozen in liquid nitrogen.

value: brain

tag: gender

value: female

tag: drug

value: saline


title: 3-trimester_Brain_Saline-F_11

description:
3tri_deseq2_F_vs_M.Sal.txt
3tri_deseq2_Mor_vs_Sal.F.txt
counts_matrix.txt
4429 - 4


title: 3-trimester_Brain_Saline-M_9

description:
3tri_deseq2_F_vs_M.Sal.txt
3tri_deseq2_Mor_vs_Sal.M.txt
counts_matrix.txt
4429 - 2

value: male


title: 3-trimester_Brain_Saline-F_12

description:
3tri_deseq2_F_vs_M.Sal.txt
3tri_deseq2_Mor_vs_Sal.F.txt
counts_matrix.txt
4429 - 5


title: 3-trimester_Brain_Saline-F_5

description:
3tri_deseq2_F_vs_M.Sal.txt
3tri_deseq2_Mor_vs_Sal.F.txt
counts_matrix.txt
4431 - 5


title: 3-trimester_Brain_Saline-F_6

description:
3tri_deseq2_F_vs_M.Sal.txt
3tri_deseq2_Mor_vs_Sal.F.txt
counts_matrix.txt
4431 - 6


title: 3-trimester_Brain_Saline-M_4

description:
3tri_deseq2_F_vs_M.Sal.txt
3tri_deseq2_Mor_vs_Sal.M.txt
counts_matrix.txt
4431 - 4


title: 3-trimester_Brain_Saline-M_3

description:
3tri_deseq2_F_vs_M.Sal.txt
3tri_deseq2_Mor_vs_Sal.M.txt
counts_matrix.txt
4431 - 3


title: 3-trimester_Brain_Saline-F_7

description:
3tri_deseq2_F_vs_M.Sal.txt
3tri_deseq2_Mor_vs_Sal.F.txt
counts_matrix.txt
4431 - 7


title: 3-trimester_Brain_Saline-M_2

description:
3tri_deseq2_F_vs_M.Sal.txt
3tri_deseq2_Mor_vs_Sal.M.txt
counts_matrix.txt
4431 - 2


title: 3-trimester_Brain_Saline-M_1

description:
3tri_deseq2_F_vs_M.Sal.txt
3tri_deseq2_Mor_vs_Sal.M.txt
counts_matrix.txt
4431 - 1


title: 3-trimester_Brain_Morphine-F_12

description:
3tri_deseq2_F_vs_M.Mor.txt
3tri_deseq2_Mor_vs_Sal.F.txt
counts_matrix.txt
4436 - 5

value: morphine


title: 3-trimester_Brain_Morphine-M_8

description:
3tri_deseq2_F_vs_M.Mor.txt
3tri_deseq2_Mor_vs_Sal.M.txt
counts_matrix.txt
4436 - 1


title: 3-trimester_Brain_Morphine-M_9

description:
3tri_deseq2_F_vs_M.Mor.txt
3tri_deseq2_Mor_vs_Sal.M.txt
counts_matrix.txt
4436 - 2


title: 3-trimester_Brain_Morphine-F_10

description:
3tri_deseq2_F_vs_M.Mor.txt
3tri_deseq2_Mor_vs_Sal.F.txt
counts_matrix.txt
4436 - 3


title: mT3-2D empty Input


title: 3-trimester_Brain_Morphine-M_4

description:
3tri_deseq2_F_vs_M.Mor.txt
3tri_deseq2_Mor_vs_Sal.M.txt
counts_matrix.txt
4433 - 4


title: 3-trimester_Brain_Morphine-M_2

description:
3tri_deseq2_F_vs_M.Mor.txt
3tri_deseq2_Mor_vs_Sal.M.txt
counts_matrix.txt
4433 - 2


title: 3-trimester_Brain_Morphine-F_7

description:
3tri_deseq2_F_vs_M.Mor.txt
3tri_deseq2_Mor_vs_Sal.F.txt
counts_matrix.txt
4433 - 7


title: 3-trimester_Brain_Morphine-M_1

description:
3tri_deseq2_F_vs_M.Mor.txt
3tri_deseq2_Mor_vs_Sal.M.txt
counts_matrix.txt
4433 - 1


title: 3-trimester_Brain_Morphine-M_3

description:
3tri_deseq2_F_vs_M.Mor.txt
3tri_deseq2_Mor_vs_Sal.M.txt
counts_matrix.txt
4433 - 3


title: 3-trimester_Brain_Saline-M_8

description:
3tri_deseq2_F_vs_M.Sal.txt
3tri_deseq2_Mor_vs_Sal.M.txt
counts_matrix.txt
4429 - 1


title: 3-trimester_Brain_Morphine-F_6

description:
3tri_deseq2_F_vs_M.Mor.txt
3tri_deseq2_Mor_vs_Sal.F.txt
counts_matrix.txt
4433 - 6


title: PND14_Brain_Saline-M_8

description:
PND14_deseq2_F_vs_M.Sal.txt
PND14_deseq2_Mor_vs_Sal.M.txt
counts_matrix.txt
4425 - 2


title: PND14_Brain_Saline-F_10

description:
PND14_deseq2_F_vs_M.Sal.txt
PND14_deseq2_Mor_vs_Sal.F.txt
counts_matrix.txt
4425 - 4


title: PND14_Brain_Saline-F_6

description:
PND14_deseq2_F_vs_M.Sal.txt
PND14_deseq2_Mor_vs_Sal.F.txt
counts_matrix.txt
4424 - 6


title: PND14_Brain_Saline-M_9

description:
PND14_deseq2_F_vs_M.Sal.txt
PND14_deseq2_Mor_vs_Sal.M.txt
counts_matrix.txt
4425 - 3


title: 3-trimester_Brain_Morphine-F_5

description:
3tri_deseq2_F_vs_M.Mor.txt
3tri_deseq2_Mor_vs_Sal.F.txt
counts_matrix.txt
4433 - 5


title: PND14_Brain_Saline-M_7

description:
PND14_deseq2_F_vs_M.Sal.txt
PND14_deseq2_Mor_vs_Sal.M.txt
counts_matrix.txt
4425 - 1


title: PND14_Brain_Saline-F_5

description:
PND14_deseq2_F_vs_M.Sal.txt
PND14_deseq2_Mor_vs_Sal.F.txt
counts_matrix.txt
4424 - 5


title: PND14_Brain_Saline-M_3

description:
PND14_deseq2_F_vs_M.Sal.txt
PND14_deseq2_Mor_vs_Sal.M.txt
counts_matrix.txt
4424 - 3


title: PND14_Brain_Saline-F_4

description:
PND14_deseq2_F_vs_M.Sal.txt
PND14_deseq2_Mor_vs_Sal.F.txt
counts_matrix.txt
4424 - 4


title: 3-trimester_Brain_Morphine-F_11

description:
3tri_deseq2_F_vs_M.Mor.txt
3tri_deseq2_Mor_vs_Sal.F.txt
counts_matrix.txt
4436 - 4


title: RNAseq_8C_MC_Male_rep13

status: Public on Mar 15 2024

city: Boston

first: Chunyao

last: Wei

state: MA

address: 185 Cambridge St.

department: Molecular Biology

institute: Massachusetts General Hospital

data_processing:
On the HiSeq 2500, HiSeq 4000 and NovaSeq platform, intensity extraction from images, base calling and quality score assignment during the sequencing was performed by software RTA and RTA2, respectively.
Raw data was first examined using Trim Galore (The Babraham Bioinformatics Group) to remove adapters from reads using the following parameters: (--stringency 8 --phred33 -e 0.2 --paired --length 43 --r1 44 --r2 44), followed by the PCR duplication removal and subsequent base trimming from the 5’end of reads (22nt from read1 and 5nt from read2). Pre-processed reads were aligned to two parental mouse genomes separately using STAR (v2.7.10a) in the 2-pass mode, with the allowance of 1 mismatch in every 20 bases and a maximum of 6 mismatches per read pair. Non-canonical introns were not considered. Reads with overlapping mates were only considered with at least 5 nucleotide overlap. All discordant read pairs where two mates were aligned to different chromosomes were discarded. The coordinates of rRNA genes in mm10 mouse genome were downloaded from RepeatMasker track (v4.0.7) in UCSC genome browser and all the reads mapping to these regions were masked and ignored in the final output files (including bam, bed and bw files).
To quantify overall expression of each given gene, all unique aligned read pairs overlapping with gene exons were counted using featureCounts (v1.5.0-p1).
For allelic gene analysis, each unique aligned read that covered strain specific SNPs or indels was analyzed and the alignment quality between two alleles was compared to determine its allelic origin. Each experiment yielded three tracks: cas, mus, and composite (neutral, cas and mus combined). For better visualization of gene expression between alleles, read mapping coordinates in different parental genomes were also converted to matched coordinates in mm10 mouse genome.  Similar to overall expression quantification, only the allelic read overlapping with gene exons were considered for allelic read counts of this gene. Allelic expression level of a given gene was thus calculated by splitting its overall expression in accordance with the allelic expression ratio, which was defined by the ratio of total allelic read count from one allele relative to that of the other allele.
assembly: mm10
processed data files format and content: alignment .bw files showing RNA coverage on + and - strand from M. castaneus (cas) reads, M. musculus (mus) reads and compsoite (comp) reads.
processed data files format and content: .txt files showing gene read counts from M. castaneus (cas) reads, M. musculus (mus) reads and compsoite (comp) reads.

organism:
Mus musculus
Mus musculus castaneus

source_name: Single preimplantation embryo

extract_protocol:
Single embryo was flushed out from the mouse oviduct, and immediately lysed in 1ul lysis solution containing 1% NP-40 and 4U RNase inhibitor
A combination of 1ul of 5x 1st strand buffer and 0.1 ul of RNA spike-in or water was added into the single embryo lysis, followed by the incubation at 82C for 12 minutes. After quick chill on ice, the RNAs were next end repaired by adding 1ul PNK solution (70mM tris-HCl pH7.6, 10mM MgCl2, 15mM DTT, 4 units/ul RNase Inhibitor) containing 2 units of T4 PNK and by incubating at 37C for 10 minutes. The RNA samples were further incubated at 37C for 5 minutes after the addition of 0.5ul mix containing 1 unit of PolyA polymerase and 3 picomole ATP. Before reverse transcription, 1ul of pre-RT mix (5uM R-dT Primer (TTTCCCTACACGACGCTCTTCCGATCTNNNNNNTTTTTTTTTTTTTTTVVN), 6.25mM dNTPs, 15mM EDTA) was added to samples, followed by the heat up at 72C for 2 minutes. After RNA denaturation, samples were immediately chilled on ice, followed by the addition of 5.5ul freshly made RT mix containing 1X 1st strand Buffer, 10mM DTT, 2U/ul RNase inhibitor, 2M Betaine, 1uM GGrG oligo (iCiGiCGGAGTTCAGACGTGTGCTCTTCCGATCTrGrG+G) and 20U/ul Superscript II reverse transcriptase II. Samples were then incubated with the following temperature setting: 40C for 5 mins, 42C for 30 mins, Two cycles of 50C for 2 mins followed by 42C for 2mins, and 15 mins at 70C. First strand cDNA libraries were next amplified by 15 cycles of first round PCR (F: GTGACTGGAGTTCAGACGTGTGCTCTTC; R: ACACTCTTTCCCTACACGACGCTCTTC) in a total volume of 30ul PCR reactions and purified with Ampure XP beads at 1:1 ratio. Purified cDNAs from the PCR (13.5ul) were mixed with 130ng of RNA probes in total 30ul of hybridization buffer (10mM Tris-HCl, pH8.0, 0.5M NaCl, 5mM EDTA and 0.2% SDS), and incubated at the following temperatures: 94C for 2 mins, followed by ramp down to 50C with 1C down per 50 seconds, and finally at 50C for 5 mins. Meanwhile, 100ul of streptavidin C1 beads were washed, pre-blocked and warmed to 50C. To delete ribosomal cDNAs, samples and beads were mixed at 50 C and incubated for another 5 mins at 50 C, and immediately put on a magnetic rack. Supernatant was collected and purified with Ampure XP beads. The purified cDNAs were further amplified by 9 cycles of PCR with Multiplex oligos (NEB). The final PCR product was purified and subject to sequencing.

value: Single preimplantation embryo

value: wild type (MC)

tag: Sex

value: Male

value: C57BL/6J x CAST/EiJ

tag: developmental stage


title: PND14_Brain_Morphine-F_12

description:
PND14_deseq2_F_vs_M.Mor.txt
PND14_deseq2_Mor_vs_Sal.F.txt
counts_matrix.txt
4423 - 6


title: PND14_Brain_Morphine-F_10

description:
PND14_deseq2_F_vs_M.Mor.txt
PND14_deseq2_Mor_vs_Sal.F.txt
counts_matrix.txt
4423 - 4


title: PND14_Brain_Morphine-F_11

description:
PND14_deseq2_F_vs_M.Mor.txt
PND14_deseq2_Mor_vs_Sal.F.txt
counts_matrix.txt
4423 - 5


title: PND14_Brain_Morphine-M_9

description:
PND14_deseq2_F_vs_M.Mor.txt
PND14_deseq2_Mor_vs_Sal.M.txt
counts_matrix.txt
4423 - 3


title: PND14_Brain_Saline-M_2

description:
PND14_deseq2_F_vs_M.Sal.txt
PND14_deseq2_Mor_vs_Sal.M.txt
counts_matrix.txt
4424 - 2


title: PND14_Brain_Morphine-M_8

description:
PND14_deseq2_F_vs_M.Mor.txt
PND14_deseq2_Mor_vs_Sal.M.txt
counts_matrix.txt
4423 - 2


title: PND14_Brain_Morphine-M_7

description:
PND14_deseq2_F_vs_M.Mor.txt
PND14_deseq2_Mor_vs_Sal.M.txt
counts_matrix.txt
4423 - 1


title: PND14_Brain_Morphine-F_6

description:
PND14_deseq2_F_vs_M.Mor.txt
PND14_deseq2_Mor_vs_Sal.F.txt
counts_matrix.txt
4422 - 6


title: PND14_Brain_Saline-F_12

description:
PND14_deseq2_F_vs_M.Sal.txt
PND14_deseq2_Mor_vs_Sal.F.txt
counts_matrix.txt
4425 - 6


title: PND14_Brain_Morphine-M_3

description:
PND14_deseq2_F_vs_M.Mor.txt
PND14_deseq2_Mor_vs_Sal.M.txt
counts_matrix.txt
4422 - 3


title: PND14_Brain_Morphine-F_4

description:
PND14_deseq2_F_vs_M.Mor.txt
PND14_deseq2_Mor_vs_Sal.F.txt
counts_matrix.txt
4422 - 4


title: PND14_Brain_Saline-F_11

description:
PND14_deseq2_F_vs_M.Sal.txt
PND14_deseq2_Mor_vs_Sal.F.txt
counts_matrix.txt
4425 - 5


title: PND14_Brain_Morphine-M_2

description:
PND14_deseq2_F_vs_M.Mor.txt
PND14_deseq2_Mor_vs_Sal.M.txt
counts_matrix.txt
4422- 2


title: PND14_Brain_Morphine-F_5

description:
PND14_deseq2_F_vs_M.Mor.txt
PND14_deseq2_Mor_vs_Sal.F.txt
counts_matrix.txt
4422 - 5


title: PND14_Brain_Morphine-M_1

description:
PND14_deseq2_F_vs_M.Mor.txt
PND14_deseq2_Mor_vs_Sal.M.txt
counts_matrix.txt
4422- 1


title: PND1_Brain_Saline-M_14

description:
PND1_deseq2_F_vs_M.Sal.txt
PND1_deseq2_Mor_vs_Sal.M.txt
counts_matrix.txt
M_Sal_7


title: PND1_Brain_Saline-M_13

description:
PND1_deseq2_F_vs_M.Sal.txt
PND1_deseq2_Mor_vs_Sal.M.txt
counts_matrix.txt
M_Sal_6


title: PND1_Brain_Saline-M_12

description:
PND1_deseq2_F_vs_M.Sal.txt
PND1_deseq2_Mor_vs_Sal.M.txt
counts_matrix.txt
M_Sal_5


title: PND1_Brain_Saline-M_10

description:
PND1_deseq2_F_vs_M.Sal.txt
PND1_deseq2_Mor_vs_Sal.M.txt
counts_matrix.txt
M_Sal_3


title: PND14_Brain_Saline-M_1

description:
PND14_deseq2_F_vs_M.Sal.txt
PND14_deseq2_Mor_vs_Sal.M.txt
counts_matrix.txt
4424 - 1


title: PND1_Brain_Saline-M_11

description:
PND1_deseq2_F_vs_M.Sal.txt
PND1_deseq2_Mor_vs_Sal.M.txt
counts_matrix.txt
M_Sal_4


title: PND1_Brain_Saline-M_9

description:
PND1_deseq2_F_vs_M.Sal.txt
PND1_deseq2_Mor_vs_Sal.M.txt
counts_matrix.txt
M_Sal_2


title: PND1_Brain_Saline-M_8

description:
PND1_deseq2_F_vs_M.Sal.txt
PND1_deseq2_Mor_vs_Sal.M.txt
counts_matrix.txt
M_Sal_1


title: PND1_Brain_Saline-F_7

description:
PND1_deseq2_F_vs_M.Sal.txt
PND1_deseq2_Mor_vs_Sal.F.txt
counts_matrix.txt
F_Sal_7


title: PND1_Brain_Saline-F_4

description:
PND1_deseq2_F_vs_M.Sal.txt
PND1_deseq2_Mor_vs_Sal.F.txt
counts_matrix.txt
F_Sal_4


title: PND1_Brain_Saline-F_5

description:
PND1_deseq2_F_vs_M.Sal.txt
PND1_deseq2_Mor_vs_Sal.F.txt
counts_matrix.txt
F_Sal_5


title: PND1_Brain_Saline-F_1

description:
PND1_deseq2_F_vs_M.Sal.txt
PND1_deseq2_Mor_vs_Sal.F.txt
counts_matrix.txt
F_Sal_1


title: PND1_Brain_Saline-F_2

description:
PND1_deseq2_F_vs_M.Sal.txt
PND1_deseq2_Mor_vs_Sal.F.txt
counts_matrix.txt
F_Sal_2


title: PND1_Brain_Morphine-M_10

description:
PND1_deseq2_F_vs_M.Mor.txt
PND1_deseq2_Mor_vs_Sal.M.txt
counts_matrix.txt
M_Mor_6


title: PND1_Brain_Saline-F_3

description:
PND1_deseq2_F_vs_M.Sal.txt
PND1_deseq2_Mor_vs_Sal.F.txt
counts_matrix.txt
F_Sal_3


title: PND1_Brain_Morphine-M_8

description:
PND1_deseq2_F_vs_M.Mor.txt
PND1_deseq2_Mor_vs_Sal.M.txt
counts_matrix.txt
M_Mor_4


title: PND1_Brain_Morphine-M_9

description:
PND1_deseq2_F_vs_M.Mor.txt
PND1_deseq2_Mor_vs_Sal.M.txt
counts_matrix.txt
M_Mor_5


title: PND1_Brain_Morphine-F_4

description:
PND1_deseq2_F_vs_M.Mor.txt
PND1_deseq2_Mor_vs_Sal.F.txt
counts_matrix.txt
F_mor_4


title: PND1_Brain_Morphine-M_5

description:
PND1_deseq2_F_vs_M.Mor.txt
PND1_deseq2_Mor_vs_Sal.M.txt
counts_matrix.txt
M_Mor_1


title: PND1_Brain_Morphine-F_3

description:
PND1_deseq2_F_vs_M.Mor.txt
PND1_deseq2_Mor_vs_Sal.F.txt
counts_matrix.txt
F_Mor_3


title: PND1_Brain_Morphine-F_2

description:
PND1_deseq2_F_vs_M.Mor.txt
PND1_deseq2_Mor_vs_Sal.F.txt
counts_matrix.txt
F_Mor_2


title: PND1_Brain_Morphine-F_1

description:
PND1_deseq2_F_vs_M.Mor.txt
PND1_deseq2_Mor_vs_Sal.F.txt
counts_matrix.txt
F_Mor_1


title: Illumina_M1+gR1+Booster_biol, rep_3

status: Public on Oct 30 2023

city: Zurich

first: Richard

last: Chahwan

address: Winterthurerstrasse 190

department: Institute of Experimental Immunology

country: Switzerland

institute: University of Zurich

data_processing:
To analyse base editing outcome the webtool CRISPResso2 (https://crispresso.pinellolab.partners.org) was used. Fastq.gz files were uploaded together with the reference sequenc and the gRNA sequences. Option Base Editing was choosen and minimum alignment homology were set to 80 %. Adapters were trimmed by choosingNEXTERA PE.
Supplementary files format and content: Selected_nucleotide_percentage_table_around_sgRNA_XYZ.txt (Txt file given by CRISPResso2; shows all possible nucleotide changes in percentage within the protospacer sequence as well as 10 nts +/- of protospacer.)
Supplementary files format and content: Modification_count_vectors.txt (Txt file given by CRISPResso2; shows percentage of deletions, insertions and substitions for each  position of the analyzed sequenced)
Supplementary files format and content: CRISPResso_quantification_of_editing_frequency.txt (Txt file given by CRISPResso2; overall read number per position and the overall substitution and deletion frequency )
Supplementary files format and content: Nucleotide_percentage_table.txt (Txt file given by CRISPResso2; shows all possible nucleotide changes in percentage of the whole input sequence)

extract_protocol:
Cells were harvested and genomic DNA was extracted using GeneJet Genomic DNA Purification Kit (Thermo Fisher) following manufacturers protocol. Concentration of isolated gDNA was measured with Nanodrop2000 and stored until further use at -80 °C
Targeted amplicon deep sequencing was performed. Locus of interest was amplified through PCR with barcoded Primers for multiplexing. In total 100 ng gDNA were used together with 0.5 µM each forward and reverse primer and 0.2 µM dNTPs and 0.2 µl phusion polymerase (Thermo Fisher). In total three independent PCR reactions were merged. All barcoded amplicons were pooled in an equal molar ratio.

value: Human Embyonic Kidney Cells with GFP

value: Lipid-based transfection of plasmids encoditing base editor M1, GFP-spcific gRNA R1 and UGI, respectively. For Illumina Sequencing

tag: time

value: Cells harvest 72 h post transfection


title: Illumina_M1+gR1_biol, rep_3

value: Lipid-based transfection of plasmids encoditing base editor M1 and GFP-spcific gRNA R1, respectively. For Illumina Sequencing


title: Illumina_M1+gR1+Booster_biol, rep_1


title: Brainstem at 10 weeks of gestation

status: Public on Oct 31 2023

city: XiaMen

first: chao

last: tu

state: FuJian

address: JiMei street,668

department: Center for precision medicine

institute: HuaQiao university

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
Aligned and quantified using the Cell Ranger Single-Cell Software Suite (v.3.0.1, 10x Genomics).
Assembly: GRCh38
Supplementary files format and content: gzip files and raw count matrix files

molecule: polyA RNA

source_name: brainstem

extract_protocol:
Human fetal brainstem tissue was dissected and digested to prepare single cell suspensions.
Using chromium next GEM single cell 3’ GEM protocol (Library &Gel Bead Kit v3.1, 16 rxns PN-1000121)

value: brainstem

tag: gestational age

value: 10 weeks


title: PND1_Brain_Saline-F_6

description:
PND1_deseq2_F_vs_M.Sal.txt
PND1_deseq2_Mor_vs_Sal.F.txt
counts_matrix.txt
F_Sal_6


title: Illumina_M1+gR1+Booster_biol, rep_2


title: Illumina_M1+gR1_biol, rep_1


title: M1 + gB + Booster_biol, rep3

value: Lipid-based transfection of plasmids encoditing base editor M1, 53BP1-specific gRNA B and mutation booster UGI, respectively.


title: M1 + gB_biol, rep2

value: Lipid-based transfection of plasmids encoditing base editor M1 and 53BP1-specific gRNA B , respectively.


title: M1 + gB_biol, rep1


title: M1 + gB + Booster_biol, rep2


title: M1 + gB_biol, rep3


title: M1 + gB + Booster_biol, rep1


title: Exp_53BP1_Untreated_biol, rep2

value: Untreated cells that were cultured under same conditions but did not get transfected as control for 53BP1 samples


title: Exp_53BP1_Untreated_biol, rep1


title: PND1_Brain_Morphine-M_7

description:
PND1_deseq2_F_vs_M.Mor.txt
PND1_deseq2_Mor_vs_Sal.M.txt
counts_matrix.txt
M_Mor_3

value: brain


title: Exp_53BP1_Untreated_biol, rep3


title: M1 + g1/A_biol, rep3

value: Lipid-based transfection of plasmids encoditing base editor M1, GFP-spcific gRNA R1 and ATP1A1-specific gRNA A , respectively.


title: M1 + g1/A + Booster_biol, rep3

value: Lipid-based transfection of plasmids encoditing base editor M1, GFP-spcific gRNA R1, ATP1A1-specific gRNA A and mutation booster UGI, respectively.


title: PND1_Brain_Morphine-M_6

description:
PND1_deseq2_F_vs_M.Mor.txt
PND1_deseq2_Mor_vs_Sal.M.txt
counts_matrix.txt
M_Mor_2

value: male

value: morphine


title: Illumina_M1+gR1_biol, rep_2


title: M1 + g1/A_biol, rep2


title: Exp_A_Untreated_biol, rep2

value: Untreated cells that were cultured under same conditions but did not get transfected as control for ATP1A1 samples


title: M1 + g1/A + Booster_biol, rep2


title: M2 + L1/2 + Booster_biol, rep3

data_processing:
To analyse base editing outcome the webtool CRISPResso2 (https://crispresso.pinellolab.partners.org) was used. Fastq.gz files were uploaded together with the reference sequenc and the gRNA sequences. Option Base Editing was choosen and  default settings were used.
Supplementary files format and content: Selected_nucleotide_percentage_table_around_sgRNA_XYZ.txt (Txt file given by CRISPResso2; shows all possible nucleotide changes in percentage within the protospacer sequence as well as 10 nts +/- of protospacer.)
Supplementary files format and content: Modification_count_vectors.txt (Txt file given by CRISPResso2; shows percentage of deletions, insertions and substitions for each  position of the analyzed sequenced)
Supplementary files format and content: CRISPResso_quantification_of_editing_frequency.txt (Txt file given by CRISPResso2; overall read number per position and the overall substitution and deletion frequency )
Supplementary files format and content: Nucleotide_percentage_table.txt (Txt file given by CRISPResso2; shows all possible nucleotide changes in percentage of the whole input sequence)

value: Lipid-based transfection of plasmids encoditing base editor M2, GFP-spcific gRNA L1,GFP-specific gRNA L2 and mutation booster UGI , respectively.


title: M3 + L1/2 + Booster_biol, rep3

value: Lipid-based transfection of plasmids encoditing base editor M3, GFP-spcific gRNA L1, GFP-specific gRNA L2 and mutation booster UGI, respectively.


title: M1 + g1/A_biol, rep1

value: Human Embyonic Kidney Cells with GFP


title: M1 + g1/A + Booster_biol, rep1


title: Exp_ATP1A1_Untreated_biol, rep1


title: M3 + L1/2 + Booster_biol, rep2


title: M1 + L1/2 + Booster_biol, rep2

value: Lipid-based transfection of plasmids encoditing base editor M1, GFP-spcific gRNA L1, GFP-specific gRNA L2 and mutation booster UGI, respectively.


title: M3 + L1/2 + Booster_biol, rep1

value: Cells harvest 72 h post transfection


title: M4 + L1/2 + Booster_biol, rep3

value: Lipid-based transfection of plasmids encoditing base editor M4, GFP-spcific gRNA L1, GFP-specific gRNA L2 and mutation booster UGI, respectively.


title: M2 + L1/2 + Booster_biol, rep1


title: C + L1/2+ Booster_biol, rep3

value: Lipid-based transfection of plasmids encoditing wild type S. pyogenes Cas9, GFP-specific gRNA L1 and GFP-spcific gRNA L1 and mutation booster UGI, respectively.


title: M1 + L1/2 + Booster_biol, rep3


title: M4 + L1/2 + Booster_biol, rep2


title: C + L1/2+ Booster_biol, rep2


title: M2 + L1/2 + Booster_biol, rep2


title: C + L1/2_biol, rep1

value: Lipid-based transfection of plasmids encoditing wild type S. pyogenes Cas9, GFP-specific gRNA L1 and GFP-spcific gRNA L2, respectively.


title: M4 + L1/2 + Booster_biol, rep1


title: M3 + L1/2_biol, rep3

value: Lipid-based transfection of plasmids encoditing base editor M3, GFP-spcific gRNA L1 and GFP-specific gRNA L2 , respectively.


title: C + L1/2_biol, rep3


title: M1 + L1/2 + Booster_biol, rep1


title: C + L1/2+ Booster_biol, rep1


title: Exp_ATP1A1_Untreated_biol, rep3


title: M4 + L1/2_biol, rep3

value: Lipid-based transfection of plasmids encoditing base editor M4, GFP-spcific gRNA L1 and GFP-specific gRNA L2 , respectively.


title: M2 + L1/2_biol, rep3

value: Lipid-based transfection of plasmids encoditing base editor M2, GFP-spcific gRNA L1 and GFP-specific gRNA L2 , respectively.


title: M1 + L1/2_biol, rep3

value: Lipid-based transfection of plasmids encoditing base editor M1, GFP-spcific gRNA L1 and GFP-specific gRNA L2 , respectively.


title: M4 + L1/2_biol, rep2


title: C + L1/2_biol, rep2


title: M2 + L1/2_biol, rep2


title: M3 + L1/2_biol, rep1


title: M2 + L1/2_biol, rep1


title: C + L2 + Booster_biol, rep3

value: Lipid-based transfection of plasmids encoditing wild type S. pyogenes Cas9, GFP-spcific gRNA L2 and mutation booster UGI, respectively.


title: C + L2 + Booster_biol, rep2


title: C + L1 + Booster_biol, rep3

value: Lipid-based transfection of plasmids encoditing wild type S. pyogenes Cas9, GFP-spcific gRNA L1 and mutation booster UGI, respectively.


title: M1 + L1/2_biol, rep2


title: C + L1 + Booster_biol, rep2


title: C + L2_biol, rep2

value: Lipid-based transfection of plasmids encoditing wild type S. pyogenes Cas9 and GFP-spcific gRNA L2, respectively.


title: C + L1_biol, rep3

value: Lipid-based transfection of plasmids encoditing wild type S. pyogenes Cas9 and GFP-spcific gRNA L1, respectively.


title: C + L1 + Booster_biol, rep1


title: C + L2 + Booster_biol, rep1


title: C + L1_biol, rep2


title: C + L2_biol, rep1


title: M3 + L1/2_biol, rep2


title: C + L1_biol, rep1


title: M1 + L2 + Booster_biol, rep3

value: Lipid-based transfection of plasmids encoditing base editor M1, GFP-spcific gRNA L2 and mutation booster UGI, respectively.


title: M1 + L1 + Booster_biol, rep3

value: Lipid-based transfection of plasmids encoditing base editor M1, GFP-spcific gRNA L1 and mutation booster UGI, respectively.


title: M1 + L1 + Booster_biol, rep2


title: M1 + L2_biol, rep3

value: Lipid-based transfection of plasmids encoditing base editor M1 and GFP-spcific gRNA L2, respectively.


title: M1 + L2_biol, rep2

value: Human Embyonic Kidney Cells with GFP


title: M1 + L1/2_biol, rep1


title: M1 + L1_biol, rep3

value: Lipid-based transfection of plasmids encoditing base editor M1 and GFP-spcific gRNA L1, respectively.


title: M1 + L2 + Booster_biol, rep2

value: Cells harvest 72 h post transfection


title: M1 + L1_biol, rep2


title: M1 + L2 + Booster_biol, rep1


title: M1 + L1 + Booster_biol, rep1


title: M1 + L2_biol, rep1


title: M1 + L1_biol, rep1


title: C + gV3_biol, rep3

value: Lipid-based transfection of plasmids encoditing wild type S. pyogenes Cas9 and mouse_specific gRNA V3 as control, respectively.


title: M4 + L1/2_biol, rep1


title: M3 + gV3_biol, rep3

value: Lipid-based transfection of plasmids encoditing base editor M3 and mouse_specific gRNA V3 as control, respectively.


title: M2 + gV3_biol, rep3

value: Lipid-based transfection of plasmids encoditing base editor M2 and mouse_specific gRNA V3 as control, respectively.


title: C + gV3_biol, rep2


title: M1 + gV3_biol, rep3

value: Lipid-based transfection of plasmids encoditing base editor M1 and mouse_specific gRNA V3 as control, respectively.


title: M4 + gV3_biol, rep2

value: Lipid-based transfection of plasmids encoditing base editor M4 and mouse_specific gRNA V3 as control, respectively.


title: M3 + gV3_biol, rep2


title: C + L2_biol, rep3


title: M2 + gV3_biol, rep2


title: M1 + gV3_biol, rep2


title: C + gV3_biol, rep1


title: M2 + gV3_biol, rep1


title: M3 + gV3_biol, rep1


title: M4 + gV3_biol, rep1


title: C + R1_biol, rep3

value: Lipid-based transfection of plasmids encoditing wild type S. pyogenes Cas9 and GFP-spcific gRNA R1, respectively.


title: M1 + gV3_biol, rep1


title: M1 + R2 + Booster_biol, rep3

value: Lipid-based transfection of plasmids encoditing base editor M1, GFP-spcific gRNA R2 and mutation booster UGI, respectively.


title: C + R1 + Booster_biol, rep3

value: Lipid-based transfection of plasmids encoditing wild type S. pyogenes Cas9, GFP-spcific gRNA R1 and mutation booster UGI, respectively.


title: Exp_PBS_GFP_Untreated_biol, rep3

value: Untreated cells that were cultured under same conditions but did not get transfected


title: M1 + R1 + Booster_biol, rep3

value: Lipid-based transfection of plasmids encoditing base editor M1, GFP-spcific gRNA R1 and mutation booster UGI, respectively.


title: M1 + R2_biol, rep3

value: Lipid-based transfection of plasmids encoditing base editor M1 and GFP-spcific gRNA R2, respectively.


title: C + R2 + Booster_biol, rep3

value: Lipid-based transfection of plasmids encoditing wild type S. pyogenes Cas9, GFP-spcific gRNA R2 and mutation booster UGI, respectively.


title: C + R2_biol, rep3

value: Lipid-based transfection of plasmids encoditing wild type S. pyogenes Cas9 and GFP-spcific gRNA R2, respectively.


title: M4 + gV3_biol, rep3


title: C + R1_biol, rep2


title: C + R2_biol, rep2


title: C + R2 + Booster_biol, rep2


title: Exp_PBS_GFP_Untreated_biol, rep2


title: C + R1 + Booster_biol, rep2


title: M1 + R1_biol, rep3

value: Lipid-based transfection of plasmids encoditing base editor M1 and GFP-spcific gRNA R1, respectively.


title: M1 + R2 + Booster_biol, rep2

value: Human Embyonic Kidney Cells with GFP


title: M1 + R1 + Booster_biol, rep2


title: M1 + R2_biol, rep2


title: C + R1 + Booster_biol, rep1


title: C + R2 + Booster_biol, rep1


title: C + R2_biol, rep1


title: M1 + R2_biol, rep1


title: M1 + R1_biolp, p1


title: M1 + gV2/gV3/gV6/gV7_biol, rep3

value: Mouse Lymphoma B Cell

value: Nucleofection of plasmids encoding base editor M1, VH-specific gRNA V2, VH-specific gRNA V3, VH-specific gRNA V6 and VH-specific gRNA V7, respectively.


title: C + R1_biol, rep1

value: Cells harvest 72 h post transfection


title: Exp_MyoD_Untreated

data_processing:
To analyse base editing outcome the webtool CRISPResso2 (https://crispresso.pinellolab.partners.org) was used. Fastq.gz files were uploaded together with the reference sequenc and the gRNA sequences. Option Base Editing was choosen and default settings were used. Adapters were trimmed with NEXTERA PE option.
Supplementary files format and content: Selected_nucleotide_percentage_table_around_sgRNA_XYZ.txt (Txt file given by CRISPResso2; shows all possible nucleotide changes in percentage within the protospacer sequence as well as 10 nts +/- of protospacer.)
Supplementary files format and content: Modification_count_vectors.txt (Txt file given by CRISPResso2; shows percentage of deletions, insertions and substitions for each  position of the analyzed sequenced)
Supplementary files format and content: CRISPResso_quantification_of_editing_frequency.txt (Txt file given by CRISPResso2; overall read number per position and the overall substitution and deletion frequency )
Supplementary files format and content: Nucleotide_percentage_table.txt (Txt file given by CRISPResso2; shows all possible nucleotide changes in percentage of the whole input sequence)

value: Mouse Embyronic Fibroblast Cells

value: Untreated cells that were cultured under same conditions but did not get transfected as control for MyoD samples


title: Exp_MyoD_M4 + gM

value: Lipid-based transfection of plasmids encoditing base editor M4 and MyoD-spcific gRNA M, respectively.


title: Exp_MyoD_M1 + gM

value: Lipid-based transfection of plasmids encoditing base editor M1 and MyoD-spcific gRNA M, respectively.


title: C + gV2/gV3/gV6/gV7_biol, rep1

value: Nucleofection of plasmids encoding wild type S. pyogenes Cas9, VH-specific gRNA V2, VH-specific gRNA V3, VH-specific gRNA V6 and VH-specific gRNA V7, respectively.


title: Exp_CH12_Untreated_biol, rep3

value: Untreated cells that were cultured under same conditions but did not get transfected as control for VH samples


title: M1 + gV2/gV3/gV6/gV7_biol, rep2


title: Exp_CH12_Untreated_biol, rep2


title: C + gV2/gV3/gV6/gV7_biol, rep3


title: Exp_CH12_Untreated_biol, rep1


title: HeLa cells, DMS CR4/5 amplicon, rep 2

status: Public on Oct 20 2023

city: Santa Cruz

first: Michael

last: Stone

address: 1156 High Street

institute: University of California Santa Cruz

data_processing:
Reads were quality filtered and size selected with TrimGalore. Command: --paired --nextera R1.fastq.gz R2.fastq.gz --length 120
Reads were mapped to the hTR sequence (451 nt) with bowtie2. Command: bowtie2 --local --no-unal --no-discordant --no-mixed --phred33
The Devonvolution of RNA Ensembles with Expectation Maximization (DREEM) program was run on BAM files of Pseudoknot and CR4/5 ampliconsusing start and end nucleotides 22-204 and 213-368, respectively.
Assembly: Human Telomerase RNA (hTR)
Supplementary files format and content: Tab delimited text file containing normalized DMS reactivities for each nucleotide of hTR from the corresponding DREEM cluster. -999 corresponds to NaN.
Supplementary files format and content: Text file containing dot bracket secondary structures for the top predictions of DMS guided structure prediction from the corresponding DREEM cluster.

source_name: HeLa cell culture

growth_protocol: HeLa and HEK293T/17 cells (ATCC CRL-11268, lot:70040949) were cultured in DMEM containing 10% fetal bovine serum, 100 units/mL of penicillin, 100 mg/m of streptomycin, and 1X Gibco GlutaMAX at 37°C, 5% CO2. Cells were seeded into 6-well plates at 0.3 x 106 cells per well and allowed to grow to 90% confluency prior to use.

extract_protocol:
Total RNA was extracted using Trizol following the manufacturer's protocol.
10 μg of HeLa cell derived total RNA was DNAse treated in 1X TURBO DNAse buffer with 1 μL TURBO DNAse enzyme (Thermo Fisher Scientific), followed by column-purification with DNA Clean and Concentrator-5 columns (Zymo Research) following the manufacturer protocol. 5 μg of DNAse-treated RNA was mixed with 5 pmol hTR targeting primer containing a 4-nucleotide unique molecular identifier (UMI) in a volume of 11 μL, heated to 75°C for 3 min and annealed at 35°C for 15 min. Next, 4 μL of 5X M-MLV buffer (Promega), 1 μL 0.1M DTT, 1 μL RNAsin Plus (Promega), and 1 μL TGIRT III (Ingex) were added and the mixture was incubated at room temperature for 30 min. Then, 2 μL of 10mM dNTPs were added, and the reaction was mixed and incubated at 60 °C for 2.5 h. After RT, 1 μL of 5M NaOH was added directly to the cDNA and incubated at 95°C, followed by 2.5 μL of 2M HCl and purification by DNA Clean and Concentrator-5 columns (Zymo Research) using an 8:1 ratio of DNA Binding Buffer to cDNA volume. The cDNA was mixed into a 50 μL second strand synthesis reaction containing 10 μL 5X GC Phusion Buffer (Thermo Fisher Scientific), 1 μL 10 mM dNTP, 25 pmol of a second hTR targeting primer containing a 4 nucleotide UMI, and 1 μL Phusion polymerase. The second strand synthesis reaction was incubated in a thermocycler with the following program: 98°C 2 min, 60°C 2 min, 72°C 10 min. Second strand product was cleaned up with Ampure XP beads (Beckman Coulter) at a 0.8:1 bead to sample volume ratio and eluted in 20 μL nuclease-free H2O. Illumina sequencing libraries of two partially overlapping hTR regions (Pseudoknot: nucleotides 1-286 and CR4/5: nucleotides 193-451) were generated by two successive 50 μL PCR reactions. For the first PCR, 4 μL second strand product was added to a 50 μL PCR reaction containing primers for either the pseudoknot or CR4/5 amplicon and run with the following program: 10 cycles at 66°C annealing temperature, followed by 10 cycles at a 60°C annealing temperature. Amplicons were bead cleaned with a 0.8:1 ratio and went into a second PCR of 10 cycles at an annealing temperature of 65°C to complete the sequencing adapters and multiplexing barcodes. Libraries were bead cleaned with a 0.8:1 ratio and quantified by Qubit (Thermo Fisher Scientific) and Tapestation (Agilent) for quality metrics before sequencing by 150 bp paired end reads on the iSeq100 (Illumina).

treatment_protocol: For DMS modification, plates of HeLa cells were divided into DMS and control groups (3 wells each). Media from the DMS group was aspirated and replaced with 2 mL of a 2% DMS (Sigma) solution in cell media (prepared by brief vortexing to incorporate DMS). Cells were incubated at 37°C for 4 min, media was aspirated from each well and replaced with 10 mL of ice cold DMS quench solution (30% beta-mercaptoethanol in phosphate-buffered saline). Plates were placed on ice and the cells were collected by scraping and brief trituration, then pelleted by centrifugation at 200 x g for 5 min. Cells were washed once with cold PBS.

value: HeLa cell culture

value: HeLa

value: Cervical cancer

value: WT

value: DMS


title: Exp_PBS_GFP_Untreated_biol, rep1

value: Untreated cells that were cultured under same conditions but did not get transfected


title: HeLa cells, DMS PK amplicon, rep 1


title: HeLa cells, Untreated CR4/5 amplicon


title: M1 + R1_biol, rep2

value: Lipid-based transfection of plasmids encoditing base editor M1 and GFP-spcific gRNA R1, respectively.


title: EV, scRNA-seq

status: Public on Sep 11 2023

city: Baltimore

first: Kellie

middle: N

last: Smith

state: MD

address: 1650 Orleans Street

institute: Johns Hopkins University

description: 10X Genomics

data_processing:
Cell Ranger v3.1.0 was used to demultiplex the FASTQ reads, align them to the GRCh38 human transcriptome, and extract their cell and unique molecular identifier (UMI) barcodes. The output of this pipeline is a digital gene expression (DGE) matrix for each sample, which records the number of UMIs for each gene that are associated with each cell barcode.
To generate the single-cell V(D)J sequences and annotate each library, we aligned TCR FASTQ reads to human GRCh38 V(D)J reference (v3.1.0 from 10X Genomics) using “cellranger vdj” function from Cell Ranger (v3.1.0). The filtered contig annotations, which contained high-level annotations of each high-confident cellular contig,
Assembly: GRCh38
Supplementary files format and content: Tab separated files and matrix files

source_name: Lung

extract_protocol:
DNA was extracted from each CD8-enriched culture condition using the Qiamp micro-DNA kit according to the manufacturer’s instructions
Libraries were prepared accordingn to 10X Genomics protocols for 5' barcoded GEX, feature barcode, and V(D)J TCR (Version 1)

value: Lung

value: T cell


title: HeLa cells, DMS CR4/5 amplicon, rep 1


title: 41BBL, scRNA-seq

description: 10X Genomics


title: M1 + R2 + Booster_biol, rep1

value: Human Embyonic Kidney Cells with GFP

value: Lipid-based transfection of plasmids encoditing base editor M1, GFP-spcific gRNA R2 and mutation booster UGI, respectively.


title: M1 + gV2/gV3/gV6/gV7 + Booster_biol, rep2

value: Mouse Lymphoma B Cell

value: Nucleofection of plasmids encoding base editor M1, VH-specific gRNA V2, VH-specific gRNA V3, VH-specific gRNA V6,VH-specific gRNA V7 and UGI, respectively.

value: Cells harvest 72 h post transfection


title: C + gV2/gV3/gV6/gV7_biol, rep2


title: OX40L, scRNA-seq

description: 10X Genomics


title: ci1447_tumor-1, scRNA-seq

description: 10X Genomics


title: ci1447_normal-2, scRNA-seq

description: 10X Genomics


title: M1 + gV2/gV3/gV6/gV7 + Booster_biol, rep1


title: M1 + gV2/gV3/gV6/gV7_biol, rep1

value: Nucleofection of plasmids encoding base editor M1, VH-specific gRNA V2, VH-specific gRNA V3, VH-specific gRNA V6 and VH-specific gRNA V7, respectively.


title: ci1447_tumor-2, scRNA-seq

description: 10X Genomics


title: ci1447_normal-1, scRNA-seq

description: 10X Genomics


title: ci1453_tumor-2, scRNA-seq

description: 10X Genomics


title: ci1453_normal-2, scRNA-seq

description: 10X Genomics


title: ci1448_tumor-2, scRNA-seq

description: 10X Genomics


title: ci1453_normal-1, scRNA-seq

description: 10X Genomics


title: HeLa cells, Untreated PK amplicon


title: ci1448_normal-2, scRNA-seq

description: 10X Genomics


title: GITRL, scRNA-seq

description: 10X Genomics


title: ci1445_tumor-1, scRNA-seq

description: 10X Genomics


title: ci1448_tumor-1, scRNA-seq

description: 10X Genomics


title: ci1450_tumor-1, scRNA-seq

description: 10X Genomics


title: ci1448_normal-1, scRNA-seq

description: 10X Genomics


title: ci1450_normal-1, scRNA-seq

description: 10X Genomics


title: ci1168_tumor-3, scRNA-seq

description: 10X Genomics


title: ci1445_normal-1, scRNA-seq

description: 10X Genomics


title: ci1168_normal-1, scRNA-seq

description: 10X Genomics


title: ci1168_tumor-4, scRNA-seq

description: 10X Genomics


title: ci1168_tumor-1, scRNA-seq

description: 10X Genomics


title: ci1168_tumor-5, scRNA-seq

description: 10X Genomics


title: ci1456_tumor-1, scRNA-seq

description: 10X Genomics


title: ci1451_tumor-1, scRNA-seq

description: 10X Genomics


title: ci1168_tumor-2, scRNA-seq

description: 10X Genomics


title: ci1415_tumor-1, scRNA-seq

description: 10X Genomics


title: ci1453_tumor-1, scRNA-seq

description: 10X Genomics


title: ci1452_tumor-2, scRNA-seq

description: 10X Genomics


title: ci1452_tumor-1, scRNA-seq

description: 10X Genomics


title: ci1452_normal-2, scRNA-seq

description: 10X Genomics


title: ci1452_normal-1, scRNA-seq

description: 10X Genomics


title: ci1451_normal-1, scRNA-seq

description: 10X Genomics


title: Memo1-mutant

status: Public on Aug 03 2023

city: Iowa City

first: Eric

last: Van Otterloo

state: Iowa

address: 801 Newton Rd

institute: University of Iowa

data_processing:
Sequencing reads were processed with Cellranger (10X Genomics, v. 3.0.2) and analyzed using the Seurat R package (v. 3). The single cell libraries were filtered to exclude genes detected in fewer than 3 cells. Cells were filtered to require greater than 500 and less than 50,000 UMIs, and less than 30% of UMIs derived from mitochondrial RNAs. PCA was applied to scaled log-normalized UMI counts from the top 3,000 most variable genes. Graph-based clustering and projection into two dimensions with UMAP was performed using 40 principal components.
Assembly: mm10
Supplementary files format and content: cell_metadata.tsv.gz: TSV file with cluster annotations and additional metadata per cell
Supplementary files format and content: matrix.mtx.gz: matrixMarket sparseMatrix of UMI counts
Supplementary files format and content: barcodes.tsv.gz: cell barcodes matching columns of matrix.mtx.gz
Supplementary files format and content: features.tsv.gz: gene names matching columns of matrix.mtx.gz

source_name: Incisor tissue

extract_protocol:
Briefly, following euthanasia, the lower-jaw was removed from a P20 control and Memo1;K14CRE mouse (N = 1) and each hemimandible cleaned of soft tissue in ice-cold DEPC-PBS. The cervical loop was exposed by gently shaving away the bone with a fresh scalpel and collecting the tissue (including some enamel), using the second molar as a distal delimiter. The region harvested included both epithelial and mesenchymal components of the cervical loop. Following tissue harvest, samples were incubated in a trypsin/dispase ‘cocktail’ for ~35 minutes at 37°C and dissociated into a suspension of single cells. Any hard, non-dissociated tissue (i.e., mineralized enamel) was allowed to settle briefly, and the supernatant transferred. Cells were washed 2x with PBS+BSA, resuspended in PBS+BSA, and subsequently passed through a Scienceware Flowmi cell strainer (40 µM). After cell density quantification, ~10,000 cells from each suspension were used to generate scRNAseq libraries, using the standard 10x genomics platform.
Libraries were prepared using the 10x Genomics 3' end single cell RNA-seq platform.

value: Incisor tissue


title: BcatMyc Day60 Lesion Slide2 Rep27

status: Public on Apr 28 2023

city: Glasgow

first: Kathryn

last: Gilroy

address: Garscube

country: United Kingdom

institute: CRUK Scotland Institute

data_processing:
Fastq files were converted to Digital Count Conversion (DCC) files using the GeoMx NGS pipeline of the Illumina BaseSpace platform.
DCC files underwent quality control, filtering, Q3 normalisation and background correction using the GeoMx DSP analysis suite (Nanostring).
Assembly: mm10
Supplementary files format and content: Unnormalized counts matrix, Normalised counts matrix

source_name: Liver

extract_protocol:
Slide preparation and probe hybridisation was performed as per Nanostrong GeoMx protocols. Areas of interest were defined by imaging slides with GeoMx DSP and then exposed to UV light to release probes. Oligonucleotides were then collected with a microcapillary and deposited into 96 well plates for sequencing.
Sequencing libraries were generated by PCR from the photo-released indexing oligos and AOI-specific Illumina adapter sequences, and unique i5 and i7 sample indices were added. Each PCR used corresponding GeoMx seq code primers (Nanostring) and was performed as per manufacturer's instructions. No template controls included all kit components but no RNA.

treatment_protocol: Induction of genetic recombination was performed with AAV8.TBG.Cre, administered via intravenous tail vein injections at either 6.4X10e8 GC/ml (low dose) or 2X10e11 GC/ml (high dose) to target mutant alleles in the liver. Tissues were harvested at the timepoints specified.

tag: segment id

value: RZAJ 20.1B/20.2E | leison_RZAJ_027 | Segment 1

value: Male

value: Liver

value: AAV8Cre (low dose) Bcatenin Ex3/+ DM-Myc/DM-Myc

tag: location

value: Lesion

tag: time point

value: Day 60


title: Control

tag: tissue

value: Control


title: BcatMyc Day60 Lesion Slide2 Rep28

value: RZAJ 20.1B/20.2E | leison_RZAJ_028 | Segment 1

tag: genotype


title: BcatMyc Day60 Lesion Slide2 Rep24

value: RZAJ 20.1B/20.2E | leison_RZAJ_024 | Segment 1


title: BcatMyc Day60 Lesion Slide2 Rep26

value: RZAJ 20.1B/20.2E | leison_RZAJ_026 | Segment 1


title: BcatMyc Day60 Lesion Slide2 Rep25

value: RZAJ 20.1B/20.2E | leison_RZAJ_025 | Segment 1


title: BcatMyc Day60 Lesion Slide2 Rep22

value: RZAJ 20.1B/20.2E | leison_RZAJ_022 | Segment 1


title: BcatMyc Day60 Lesion Slide2 Rep21

value: RZAJ 20.1B/20.2E | leison_RZAJ_021 | Segment 1


title: BcatMyc Day60 Lesion Slide2 Rep19

value: RZAJ 20.1B/20.2E | leison_RZAJ_019 | Segment 1


title: BcatMyc Day60 Lesion Slide2 Rep20

value: RZAJ 20.1B/20.2E | leison_RZAJ_020 | Segment 1


title: BcatMyc Day60 Lesion Slide2 Rep23

value: RZAJ 20.1B/20.2E | leison_RZAJ_023 | Segment 1


title: BcatMyc Day60 Lesion Slide2 Rep17

value: RZAJ 20.1B/20.2E | leison_RZAJ_017 | Segment 1


title: BcatMyc Day60 Lesion Slide2 Rep15

value: RZAJ 20.1B/20.2E | leison_RZAJ_015 | Segment 1


title: BcatMyc Day60 Lesion Slide2 Rep14

value: RZAJ 20.1B/20.2E | leison_RZAJ_014 | Segment 1

value: Male


title: BcatMyc Day60 Lesion Slide2 Rep13

value: RZAJ 20.1B/20.2E | leison_RZAJ_013 | Segment 1

value: Liver

value: AAV8Cre (low dose) Bcatenin Ex3/+ DM-Myc/DM-Myc


title: BcatMyc Day60 Lesion Slide2 Rep29

value: RZAJ 20.1B/20.2E | leison_RZAJ_029 | Segment 1

value: Lesion

value: Day 60


title: BcatMyc Day60 Lesion Slide2 Rep11

value: RZAJ 20.1B/20.2E | leison_RZAJ_011 | Segment 1


title: BcatMyc Day60 Lesion Slide2 Rep8

value: RZAJ 20.1B/20.2E | leison_RZAJ_008 | Segment 1


title: BcatMyc Day60 Lesion Slide2 Rep10

value: RZAJ 20.1B/20.2E | leison_RZAJ_010 | Segment 1


title: BcatMyc Day60 Lesion Slide2 Rep12

value: RZAJ 20.1B/20.2E | leison_RZAJ_012 | Segment 1


title: BcatMyc Day60 Lesion Slide2 Rep7

value: RZAJ 20.1B/20.2E | leison_RZAJ_007 | Segment 1


title: BcatMyc Day60 Lesion Slide2 Rep5

value: RZAJ 20.1B/20.2E | leison_RZAJ_005 | Segment 1


title: No Template Control 2

organism: synthetic construct

source_name: control

value: control


title: BcatMyc Day60 Lesion Slide2 Rep4

value: RZAJ 20.1B/20.2E | leison_RZAJ_004 | Segment 1


title: BcatMyc Day60 Lesion Slide2 Rep3

value: RZAJ 20.1B/20.2E | leison_RZAJ_003 | Segment 1


title: BcatMyc Day60 Lesion Slide2 Rep6

value: RZAJ 20.1B/20.2E | leison_RZAJ_006 | Segment 1


title: BcatMyc Day60 Lesion Slide2 Rep2

value: RZAJ 20.1B/20.2E | leison_RZAJ_002 | Segment 1

value: Male


title: BcatMyc Day60 Lesion Slide2 Rep1

value: RZAJ 20.1B/20.2E | leison_RZAJ_001 | Segment 1

value: Liver


title: BcatMyc Day60 Clonal Slide2 Rep15

value: RZAJ 20.1B/20.2E | clonal_015 | Segment 1

value: AAV8Cre (low dose) Bcatenin Ex3/+ DM-Myc/DM-Myc

value: Clonal


title: BcatMyc Day60 Lesion Slide2 Rep18

value: RZAJ 20.1B/20.2E | leison_RZAJ_018 | Segment 1

value: Lesion

value: Day 60


title: BcatMyc Day60 Clonal Slide2 Rep12

value: RZAJ 20.1B/20.2E | clonal_012 | Segment 1


title: BcatMyc Day60 Clonal Slide2 Rep17

value: RZAJ 20.1B/20.2E | clonal_017 | Segment 1


title: BcatMyc Day60 Clonal Slide2 Rep16

value: RZAJ 20.1B/20.2E | clonal_016 | Segment 1


title: BcatMyc Day60 Clonal Slide2 Rep13

value: RZAJ 20.1B/20.2E | clonal_013 | Segment 1


title: BcatMyc Day60 Clonal Slide2 Rep10

value: RZAJ 20.1B/20.2E | clonal_010 | Segment 1


title: BcatMyc Day60 Lesion Slide2 Rep9

value: RZAJ 20.1B/20.2E | leison_RZAJ_009 | Segment 1


title: BcatMyc Day60 Clonal Slide2 Rep5

value: RZAJ 20.1B/20.2E | clonal_005 | Segment 1


title: BcatMyc Day60 Clonal Slide2 Rep8

value: RZAJ 20.1B/20.2E | clonal_008 | Segment 1


title: BcatMyc Day60 Clonal Slide2 Rep4

value: RZAJ 20.1B/20.2E | clonal_004 | Segment 1

value: Male


title: BcatMyc Day60 Clonal Slide2 Rep14

value: RZAJ 20.1B/20.2E | clonal_014 | Segment 1

value: Liver


title: BcatMyc Day60 Clonal Slide2 Rep6

value: RZAJ 20.1B/20.2E | clonal_006 | Segment 1

value: AAV8Cre (low dose) Bcatenin Ex3/+ DM-Myc/DM-Myc


title: BcatMyc Day60 Clonal Slide2 Rep7

value: RZAJ 20.1B/20.2E | clonal_007 | Segment 1

value: Clonal


title: BcatMyc Day60 Clonal Slide2 Rep11

value: RZAJ 20.1B/20.2E | clonal_011 | Segment 1

value: Day 60


title: BcatMyc Day60 Clonal Slide2 Rep3

value: RZAJ 20.1B/20.2E | clonal_003 | Segment 1


title: BcatMyc Day60 Clonal Slide2 Rep9

value: RZAJ 20.1B/20.2E | clonal_009 | Segment 1


title: BcatMyc Day60 Clonal Slide2 Rep2

value: RZAJ 20.1B/20.2E | clonal_002 | Segment 1


title: BcatMyc Day60 Normal Slide2 Rep10

value: Normal


title: BcatMyc Day60 Clonal Slide2 Rep1

value: RZAJ 20.1B/20.2E | clonal_001 | Segment 1


title: No Template Control 1

value: control


title: BcatMyc Day60 Normal Slide2 Rep6


title: BcatMyc Day60 Normal Slide2 Rep9


title: BcatMyc Day60 Normal Slide2 Rep8


title: BcatMyc Day60 Normal Slide2 Rep7


title: BcatMyc Day60 Normal Slide2 Rep4


title: BcatMyc Day60 Normal Slide2 Rep5


title: BcatMyc Day60 Normal Slide2 Rep3


title: BcatMyc Day60 Lesion Slide1 Rep20

value: RMAA 16.2F/16.2G | Leison_020 | Segment 1

value: Lesion


title: BcatMyc Day60 Normal Slide2 Rep1

value: Male


title: BcatMyc Day60 Lesion Slide1 Rep17

value: RMAA 16.2F/16.2G | Leison_017 | Segment 1


title: BcatMyc Day60 Lesion Slide1 Rep18

value: RMAA 16.2F/16.2G | Leison_018 | Segment 1

value: Liver


title: BcatMyc Day60 Lesion Slide1 Rep19

value: RMAA 16.2F/16.2G | Leison_019 | Segment 1

value: AAV8Cre (low dose) Bcatenin Ex3/+ DM-Myc/DM-Myc


title: BcatMyc Day60 Lesion Slide1 Rep15

value: RMAA 16.2F/16.2G | Leison_015 | Segment 1


title: BcatMyc Day60 Lesion Slide1 Rep16

value: RMAA 16.2F/16.2G | Leison_016 | Segment 1


title: BcatMyc Day60 Lesion Slide1 Rep12

value: RMAA 16.2F/16.2G | Leison_012 | Segment 1

value: Day 60


title: BcatMyc Day60 Lesion Slide1 Rep13

value: RMAA 16.2F/16.2G | Leison_013 | Segment 1


title: BcatMyc Day60 Lesion Slide1 Rep8

value: RMAA 16.2F/16.2G | Leison_008 | Segment 1


title: BcatMyc Day60 Lesion Slide1 Rep11

value: RMAA 16.2F/16.2G | Leison_011 | Segment 1


title: BcatMyc Day60 Normal Slide2 Rep2

value: Normal


title: BcatMyc Day60 Lesion Slide1 Rep7

value: RMAA 16.2F/16.2G | Leison_007 | Segment 1


title: BcatMyc Day60 Lesion Slide1 Rep14

value: RMAA 16.2F/16.2G | Leison_014 | Segment 1


title: BcatMyc Day60 Lesion Slide1 Rep4

value: RMAA 16.2F/16.2G | Leison_004 | Segment 1

value: Lesion


title: BcatMyc Day60 Lesion Slide1 Rep6

value: RMAA 16.2F/16.2G | Leison_006 | Segment 1

value: Male


title: BcatMyc Day60 Lesion Slide1 Rep3

value: RMAA 16.2F/16.2G | Leison_003 | Segment 1

value: Liver


title: BcatMyc Day60 Lesion Slide1 Rep2

value: RMAA 16.2F/16.2G | Leison_002 | Segment 1

value: AAV8Cre (low dose) Bcatenin Ex3/+ DM-Myc/DM-Myc


title: BcatMyc Day60 Clonal Slide1 Rep15

value: RMAA 16.2F/16.2G | 015clone | Segment 1

value: Clonal


title: BcatMyc Day60 Lesion Slide1 Rep5

value: RMAA 16.2F/16.2G | Leison_005 | Segment 1

value: Day 60


title: BcatMyc Day60 Lesion Slide1 Rep9

value: RMAA 16.2F/16.2G | Leison_009 | Segment 1


title: BcatMyc Day60 Clonal Slide1 Rep16

value: RMAA 16.2F/16.2G | 016clone | Segment 1


title: BcatMyc Day60 Clonal Slide1 Rep17

value: RMAA 16.2F/16.2G | 021clone | Segment 1


title: BcatMyc Day60 Clonal Slide1 Rep11

value: RMAA 16.2F/16.2G | 011clone | Segment 1


title: BcatMyc Day60 Lesion Slide1 Rep1

value: RMAA 16.2F/16.2G | Leison_001 | Segment 1


title: BcatMyc Day60 Clonal Slide1 Rep13

value: RMAA 16.2F/16.2G | 013clone | Segment 1


title: BcatMyc Day60 Clonal Slide1 Rep14

value: RMAA 16.2F/16.2G | 014clone | Segment 1


title: BcatMyc Day60 Clonal Slide1 Rep10

value: RMAA 16.2F/16.2G | 010clone | Segment 1


title: BcatMyc Day60 Clonal Slide1 Rep12

value: RMAA 16.2F/16.2G | 012clone | Segment 1

value: Male


title: BcatMyc Day60 Clonal Slide1 Rep3

value: RMAA 16.2F/16.2G | 003clone | Segment 1

value: Liver


title: BcatMyc Day60 Clonal Slide1 Rep8

value: RMAA 16.2F/16.2G | 008clone | Segment 1

value: AAV8Cre (low dose) Bcatenin Ex3/+ DM-Myc/DM-Myc


title: BcatMyc Day60 Lesion Slide1 Rep10

value: RMAA 16.2F/16.2G | Leison_010 | Segment 1

value: Lesion


title: BcatMyc Day60 Clonal Slide1 Rep1

value: RMAA 16.2F/16.2G | 001clone | Segment 1

value: Clonal

value: Day 60


title: BcatMyc Day60 Clonal Slide1 Rep9

value: RMAA 16.2F/16.2G | 009clone | Segment 1


title: Bcat Day4 PN Slide2 Rep6

value: RMV 12.1A/12.1B | PN_15 | Full ROI

value: AAV8Cre (high dose) Bcatenin Ex3/+

value: Portal Node

value: Day 4


title: Bcat Day4 PN Slide2 Rep7

value: RMV 12.1A/12.1B | PN_16 | Full ROI


title: BcatMyc Day60 Normal Slide1 Rep2

value: Normal


title: BcatMyc Day60 Normal Slide1 Rep1

value: Male


title: BcatMyc Day60 Clonal Slide1 Rep6

value: RMAA 16.2F/16.2G | 006clone | Segment 1


title: BcatMyc Day60 Clonal Slide1 Rep4

value: RMAA 16.2F/16.2G | 004clone | Segment 1

value: Liver


title: Bcat Day4 PN Slide2 Rep2

value: RMV 12.1A/12.1B | PN_11 | Full ROI


title: BcatMyc Day60 Normal Slide1 Rep4

value: AAV8Cre (low dose) Bcatenin Ex3/+ DM-Myc/DM-Myc


title: Bcat Day4 GS-low Slide2 Rep6

value: RMV 12.1A/12.1B | GS-low_15 | Full ROI

value: GS-low


title: Bcat Day4 GS-low Slide2 Rep5

value: RMV 12.1A/12.1B | GS-low_14 | Full ROI


title: BcatMyc Day60 Normal Slide1 Rep5

value: Day 60


title: BcatMyc Day60 Normal Slide1 Rep3


title: Bcat Day4 PN Slide2 Rep8

value: RMV 12.1A/12.1B | PN_9 | Full ROI


title: M1 + R1 + Booster_biol, rep1

value: Human Embyonic Kidney Cells with GFP

tag: treatment

value: Lipid-based transfection of plasmids encoditing base editor M1, GFP-spcific gRNA R1 and mutation booster UGI, respectively.

value: Cells harvest 72 h post transfection


title: Bcat Day4 PN Slide2 Rep1

value: RMV 12.1A/12.1B | PN_10 | Full ROI

value: AAV8Cre (high dose) Bcatenin Ex3/+

value: Portal Node

value: Day 4


title: Bcat Day4 PN Slide2 Rep5

value: RMV 12.1A/12.1B | PN_14 | Full ROI

value: Male


title: Bcat Day4 GS-high Slide2 Rep7

value: RMV 12.1A/12.1B | GS-high_16 | Full ROI

value: Liver

value: GS-high


title: Bcat Day4 GS-high Slide2 Rep8

value: RMV 12.1A/12.1B | GS-high_9 | Full ROI


title: Bcat Day4 GS-high Slide2 Rep5

value: RMV 12.1A/12.1B | GS-high_14 | Full ROI


title: BcatMyc Day60 Clonal Slide1 Rep7

value: RMAA 16.2F/16.2G | 007clone | Segment 1

value: AAV8Cre (low dose) Bcatenin Ex3/+ DM-Myc/DM-Myc

value: Clonal


title: Bcat Day4 GS-low Slide2 Rep4

value: RMV 12.1A/12.1B | GS-low_13 | Full ROI

value: GS-low


title: Bcat Day4 GS-low Slide2 Rep8

value: RMV 12.1A/12.1B | GS-low_9 | Full ROI


title: Bcat Day4 GS-low Slide2 Rep7

value: RMV 12.1A/12.1B | GS-low_16 | Full ROI


title: Bcat Day4 GS-low Slide2 Rep2

value: RMV 12.1A/12.1B | GS-low_11 | Full ROI

value: AAV8Cre (high dose) Bcatenin Ex3/+


title: Bcat Day4 GS-high Slide2 Rep6

value: RMV 12.1A/12.1B | GS-high_15 | Full ROI

value: Day 4


title: Bcat Day4 GS-adj Slide2 Rep7

value: RMV 12.1A/12.1B | GS-adj_16 | Full ROI

value: Male

value: GS-adjacent


title: Bcat Day4 GS-low Slide2 Rep1

value: RMV 12.1A/12.1B | GS-low_10 | Full ROI

value: Liver


title: Bcat Day4 GS-high Slide2 Rep3

value: RMV 12.1A/12.1B | GS-high_12 | Full ROI

value: GS-high


title: Bcat Day4 PN Slide2 Rep3

value: RMV 12.1A/12.1B | PN_12 | Full ROI

value: Portal Node


title: Bcat Day4 GS-adj Slide2 Rep4

value: RMV 12.1A/12.1B | GS-adj_13 | Full ROI


title: BcatMyc Day60 Clonal Slide1 Rep5

value: RMAA 16.2F/16.2G | 005clone | Segment 1

value: AAV8Cre (low dose) Bcatenin Ex3/+ DM-Myc/DM-Myc

value: Clonal

value: Day 60


title: Bcat Day4 GS-high Slide2 Rep4

value: RMV 12.1A/12.1B | GS-high_13 | Full ROI

value: AAV8Cre (high dose) Bcatenin Ex3/+


title: Bcat Day4 GS-high Slide2 Rep1

value: RMV 12.1A/12.1B | GS-high_10 | Full ROI

value: Day 4


title: Bcat Day4 GS-adj Slide2 Rep1

value: RMV 12.1A/12.1B | GS-adj_10 | Full ROI

value: Male


title: Bcat Day4 GS-adj Slide2 Rep3

value: RMV 12.1A/12.1B | GS-adj_12 | Full ROI

value: GS-adjacent


title: Bcat Day4 GS-adj Slide2 Rep5

value: RMV 12.1A/12.1B | GS-adj_14 | Full ROI

value: Liver


title: Bcat Day4 PN Slide2 Rep4

value: RMV 12.1A/12.1B | PN_13 | Full ROI


title: Bcat Day4 GS-low Slide2 Rep3

value: RMV 12.1A/12.1B | GS-low_12 | Full ROI

value: GS-low


title: Bcat Day4 GS-adj Slide2 Rep6

value: RMV 12.1A/12.1B | GS-adj_15 | Full ROI


title: Bcat Day4 Proliferative Slide2 Rep6

value: Proliferative


title: Bcat Day4 Proliferative Slide2 Rep8


title: Bcat Day4 Proliferative Slide2 Rep7


title: Bcat Day4 GS-high Slide2 Rep2

value: RMV 12.1A/12.1B | GS-high_11 | Full ROI

value: GS-high


title: Bcat Day4 Proliferative Slide2 Rep5


title: Bcat Day4 GS-adj Slide2 Rep8

value: RMV 12.1A/12.1B | GS-adj_9 | Full ROI


title: Bcat Day4 Proliferative Slide2 Rep3

value: AAV8Cre (high dose) Bcatenin Ex3/+


title: Bcat Day4 Proliferative Slide2 Rep4


title: Bcat Day4 Proliferative Slide2 Rep2


title: Bcat Day4 PN Slide1 Rep8

value: RMV 11.1D/12.1F | PN_8 | Full ROI

value: Female

value: Portal Node


title: Bcat Day4 Proliferative Slide2 Rep1

value: Male

value: Day 4


title: Bcat Day4 PN Slide1 Rep7

value: RMV 11.1D/12.1F | PN_7 | Full ROI


title: Bcat Day4 PN Slide1 Rep6

value: RMV 11.1D/12.1F | PN_6 | Full ROI


title: Bcat Day4 PN Slide1 Rep5

value: RMV 11.1D/12.1F | PN_5 | Full ROI

value: Liver


title: Bcat Day4 PN Slide1 Rep2

value: RMV 11.1D/12.1F | PN_2 | Full ROI


title: Bcat Day4 PN Slide1 Rep1

value: RMV 11.1D/12.1F | PN_1 | Full ROI


title: Bcat Day4 GS-low Slide1 Rep8

value: RMV 11.1D/12.1F | GS-low_8 | Full ROI

value: GS-low


title: Bcat Day4 GS-adj Slide2 Rep2

value: RMV 12.1A/12.1B | GS-adj_11 | Full ROI

value: GS-adjacent


title: Bcat Day4 PN Slide1 Rep3

value: RMV 11.1D/12.1F | PN_3 | Full ROI


title: Bcat Day4 GS-low Slide1 Rep7

value: RMV 11.1D/12.1F | GS-low_7 | Full ROI

value: AAV8Cre (high dose) Bcatenin Ex3/+


title: Bcat Day4 GS-low Slide1 Rep3

value: RMV 11.1D/12.1F | GS-low_3 | Full ROI

value: Female


title: Bcat Day4 GS-low Slide1 Rep1

value: RMV 11.1D/12.1F | GS-low_1 | Full ROI


title: Bcat Day4 GS-low Slide1 Rep6

value: RMV 11.1D/12.1F | GS-low_6 | Full ROI

value: Day 4


title: BcatMyc Day60 Clonal Slide1 Rep2

value: RMAA 16.2F/16.2G | 002clone | Segment 1

value: Male

value: AAV8Cre (low dose) Bcatenin Ex3/+ DM-Myc/DM-Myc

value: Clonal

value: Day 60


title: Bcat Day4 GS-high Slide1 Rep7

value: RMV 11.1D/12.1F | GS-high_7 | Full ROI

value: Liver

value: GS-high


title: Bcat Day4 GS-high Slide1 Rep8

value: RMV 11.1D/12.1F | GS-high_8 | Full ROI


title: Bcat Day4 GS-high Slide1 Rep6

value: RMV 11.1D/12.1F | GS-high_6 | Full ROI


title: Bcat Day4 GS-high Slide1 Rep4

value: RMV 11.1D/12.1F | GS-high_4 | Full ROI


title: Bcat Day4 GS-high Slide1 Rep5

value: RMV 11.1D/12.1F | GS-high_5 | Full ROI

value: AAV8Cre (high dose) Bcatenin Ex3/+


title: Bcat Day4 GS-high Slide1 Rep2

value: RMV 11.1D/12.1F | GS-high_2 | Full ROI

value: Female


title: Bcat Day4 GS-high Slide1 Rep3

value: RMV 11.1D/12.1F | GS-high_3 | Full ROI


title: Bcat Day4 GS-high Slide1 Rep1

value: RMV 11.1D/12.1F | GS-high_1 | Full ROI

value: Day 4


title: Bcat Day4 GS-adj Slide1 Rep8

value: RMV 11.1D/12.1F | GS-adj_8 | Full ROI

value: GS-adjacent


title: Bcat Day4 GS-adj Slide1 Rep7

value: RMV 11.1D/12.1F | GS-adj_7 | Full ROI


title: Bcat Day4 GS-adj Slide1 Rep6

value: RMV 11.1D/12.1F | GS-adj_6 | Full ROI


title: Bcat Day4 GS-adj Slide1 Rep5

value: RMV 11.1D/12.1F | GS-adj_5 | Full ROI


title: Bcat Day4 GS-adj Slide1 Rep4

value: RMV 11.1D/12.1F | GS-adj_4 | Full ROI

value: Liver


title: Bcat Day4 GS-adj Slide1 Rep3

value: RMV 11.1D/12.1F | GS-adj_3 | Full ROI


title: Bcat Day4 GS-adj Slide1 Rep1

value: RMV 11.1D/12.1F | GS-adj_1 | Full ROI


title: Bcat Day4 GS-adj Slide1 Rep2

value: RMV 11.1D/12.1F | GS-adj_2 | Full ROI


title: Bcat Day4 GS-low Slide1 Rep4

value: RMV 11.1D/12.1F | GS-low_4 | Full ROI

value: GS-low


title: Bcat Day4 GS-low Slide1 Rep5

value: RMV 11.1D/12.1F | GS-low_5 | Full ROI

value: AAV8Cre (high dose) Bcatenin Ex3/+


title: Bcat Day4 GS-low Slide1 Rep2

value: RMV 11.1D/12.1F | GS-low_2 | Full ROI

value: Female


title: Bcat Day4 Proliferative Slide1 Rep7

value: Proliferative

value: Day 4


title: Bcat Day4 Proliferative Slide1 Rep8


title: Bcat Day4 Proliferative Slide1 Rep3


title: Bcat Day4 Proliferative Slide1 Rep5


title: Bcat Day4 Proliferative Slide1 Rep4


title: Bcat Day4 Proliferative Slide1 Rep2


title: Primary muscle satellite cells (MuSC) treated with LPS

status: Public on Apr 19 2023

city: Tempe

first: Christopher

middle: L

last: Plaisier

state: Arizona

department: SBHSE

institute: Arizona State University

data_processing:
The 10X Genomics CellRanger v6.0.1 was used to align to the Mus musculus reference genome mm10-2020-A (GRCm39), quantify, and provide basic quality control metrics.
Assembly: mm10
Supplementary files format and content: Gzip compressed file containing the cellranger filtered_features_bc_matrix directory, which holds the barcodes.tsv.gz, features.tsv.gz, and matrix.mtx.gz files.

growth_protocol: Primary muscle satellite cell cultures (MuSCs) were generated from cells isolated from 12 week old B6129SF1/J as previously described (Palade et al., 2019). Briefly, hind limb quadriceps femoris muscles were excised, trimmed of fat, and connective tissue, and finely minced. The muscle tissue was digested with 1.25 mg of protease XIV (Sigma-Aldrich, St. Louis, MO) for 1 h at 37 °C. The cell suspension was filtered, differentially centrifuged and pre-plated in DMEM (Corning, Corning NY), containing 2% donor horse serum (HS) (Atlanta Biologicals, Flowery Branch, GA), and 100 μg/mL Primocin (Invivogen, San Diego, CA). Fibroblasts were removed by three pre-plating rounds of three hours. Satellite cells were grown in a humidified chamber at 37 °C with 5% CO2, on Matrigel Matrix Basement Membrane (BD Biosciences, Bedford, MA) coated plates, in growth medium, Hams F-10 (Corning), containing 20% FBS (Atlanta Biologicals), 10 ng/mL bFGF (BD Biosciences) and 100 μg/mL Primocin (Invivogen).

extract_protocol:
MuSCs were then trypsinized (0.05% trypsin 0.53M EDTA, Mediatech, Manassas VA) to create a single cell suspension.
Cells were then counted on an automated cell counter and RNA library prep was done by the ASU Genomics Core facility. Samples were processed using a 10X Chromium single cell 3’ GEM, Library and Gel Bead kit V3 with a Chromium single cell B chip. The quality of each library was determined using Agilent TapeStation automated electrophoresis.

treatment_protocol: MuSCs were seeded onto Matrigel (BD Biosciences) coated 6 well plates at a density of 1 × 10^5 cells/well in growth medium. Cells were then treated with LPS (1 mg/ml; Sigma-Aldrich,) or phosphate buffered saline (PBS) for 2 hours.

tag: age

value: 12 week old

tag: strain

value: LPS


title: Primary muscle satellite cells (MuSC) treated with PBS

source_name: Primary muscle satellite cell cultures (MuSCs)

tag: cell type

value: PBS


title: Bcat Day4 Proliferative Slide1 Rep1


title: WBC_110036138

status: Public on Dec 15 2022

city: Jerusalem

first: Tommy

last: Kaplan

address: Givat Ram Campus

department: School of Computer Science and Engineering

country: Israel

institute: Hebrew University

data_processing:
Paired-end FASTQ files were mapped to the human (hg19), lambda, pUC19 and viral genomes using bwa-meth (V 0.2.0), with default parameters (Pedersen et al., 2014), then converted to BAM files using SAMtools (V 1.9) (Li et al., 2009).
Duplicated reads were marked by Sambamba (V 0.6.5), with parameters “-l 1 -t 16 --sort-buffer-size 16000 --overflow-list-size 10000000” (Tarasov et al., 2015).
Reads with low mapping quality, duplicated, or not mapped in a proper pair were excluded using SAMtools view with parameters -F 1796 -q 10.
Reads were stripped from non-CpG nucleotides and converted to BETA files using wgbstools (V 0.1.0) (Loyfer and Kaplan).
Assembly: hg19
Supplementary files format and content: pat files were generated using wgbstools (https://github.com/nloyfer/wgbs_tools) with default parameteres
Supplementary files format and content: csi files were generated using wgbstools (https://github.com/nloyfer/wgbs_tools) with default parameteres
Supplementary files format and content: beta files were generated using wgbstools (https://github.com/nloyfer/wgbs_tools) with default parameteres
Supplementary files format and content: bigwig files were generated from beta files using wgbstools beta2bw with default parameteres

source_name: White blood cells

extract_protocol:
Up to 75 ng of sheared genomic DNA was subjected to bisulfite conversion  using the EZ-96 DNA Methylation Kit (Zymo Research), with  liquid handling on a MicroLab STAR (Hamilton).
Dual-indexed sequencing  libraries were prepared using Accel-NGS Methyl-Seq DNA library  preparation kits (Swift BioSciences) and custom liquid handling scripts  executed on the Hamilton MicroLab STAR. Libraries were quantified  using KAPA Library Quantification Kits for Illumina Platforms (Kapa  Biosystems). Four uniquely dual-indexed libraries, along with the 10%  PhiX v.3 library (Illumina), were pooled and clustered on an Illumina  NovaSeq 6000 S2 flow cell followed by 150 bp, paired-end sequencing.

value: White blood cells

tag: patient id

value: female

tag: height

tag: weight

tag: race

value: black


title: WBC_110036152

tag: gender

value: white


title: WBC_110033933


title: WBC_110036059

value: male


title: WBC_110033907


title: WBC_110036107


title: WBC_110033727


title: WBC_110033912


title: WBC_110033746


title: WBC_110033633


title: Bcat Day4 PN Slide1 Rep4

value: RMV 11.1D/12.1F | PN_4 | Full ROI

tag: Sex

value: Liver

value: Portal Node


title: WBC_110033750


title: WBC_110033745


title: WBC_110033577


title: WBC_110032789


title: WBC_110032739


title: WBC_110029639


title: WBC_110027054


title: WBC_110000264


title: WBC_110000263


title: WBC_110033397


title: cfDNA_110036152

source_name: cell-free DNA

value: cell-free DNA


title: WBC_110033253


title: Bcat Day4 Proliferative Slide1 Rep6

value: AAV8Cre (high dose) Bcatenin Ex3/+


title: WBC_110027051


title: WBC_110029979


title: cfDNA_110036138


title: cfDNA_110033912


title: cfDNA_110033746


title: cfDNA_110033907


title: cfDNA_110033727


title: cfDNA_110036107


title: cfDNA_110032739


title: cfDNA_110029639


title: cfDNA_110027054


title: cfDNA_110029979


title: cfDNA_110033745


title: cfDNA_110027051


title: cfDNA_110033933


title: cfDNA_110033397


title: cfDNA_110033577


title: cfDNA_110032789


title: cfDNA_110033633


title: cfDNA_110000264


title: RCC-PR1-Normal

status: Public on Aug 18 2022

first: Shenglin

last: Mei

address: 10 Shattuck Street

institute: Harvard medical school (DMBI)

data_processing:
FASTQ files were processed with the CellRanger software (10x Genomics, Inc., version 2.2.0). Human genome hg19 was used as the reference genome (10x Genomics, Inc.) to generate the matrix files containing cell barcodes and transcript counts. Quality control metrics were used to select cells with total UMI more than 700.
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: count matrix in csv

source_name: kidney

extract_protocol:
10X Genomics Single cell 3' gene expression V2
Single cells from the tumor and the normal adjacent kidney samples subjected to RBC lysis were surface stained with anti-CD235-PE (Biolegend) for 30 min at 4°C. Cells were washed once with 2% FBS-PBS (v/v) followed by DAPI staining (1 ug/ml). Flow sorting for live and non-erythroid cells (DAPI-neg/CD235-neg) was performed on a BD FACS Aria III equipped with a 100um nozzle (BD Biosciences, San Jose, CA) instrument. All flow cytometry data were analyzed using FlowJo software (Treestar, San Carlos, CA).

tag: condition

value: Normal

tag: Stage

value: pRCC

value: No

tag: metastasic sites


title: cfDNA_110000263


title: cfDNA_110033253


title: cfDNA_110036059


title: RCC-PR2-Normal

value: ccRCC


title: cfDNA_110033750