title: TotalRNA_Tha strain ST-RIG-I cells replicate 3

city: Paris

first: Rachel

last: Legendre

address: 28, rue du docteur Roux

department: Research and Resource Center for Scientific Informatics

institute: Institut Pasteur

data_processing:
Reads were cleaned of adapter sequences and low-quality sequences using cutadapt version 2.9. Only sequences at least 25 nucleotides (nt) in length were considered for further analysis.
Bowtie version 2.1.0 (with –very-sensitive mode) was used for alignment on the reference genome
Rabies genome coverages were computed with bedtools 2.17.0 genomecov for each strand with -d parameter
Genome_build: RABV field isolate THA (ENA accession: n°GCA_927797755) and RABV vaccine strain SAD (ENA accession: n°GCA_927797725)
Supplementary_files_format_and_content: Depth at each genome position with 1-based coordinates reported by genomeCoverage (bedtools)

organism:
Homo sapiens
Lyssavirus rabies

source_name: HEK293 cells expressing  RIGI RLR cells

growth_protocol: ST-RLRs cells (15x10^6cells) were infected at MOI of 0.5 by either THA or SAD. The cells were harvested after 24h

extract_protocol:
The cell lysate was left on ice for 20 min with gentle mixing and then clarified by centrifugation at 13,000 rpm for 15 minutes at 4°C. For total RNA (input) extraction, an aliquot of 100 µl of each cell lysate was used in the presence of TRI reagent LS (#T3934, SIGMA). The remaining lysate supernatant was incubated for 2 h on a spinning wheel with 200 µl of high-Peformance strepTactin Sepharose beads (#28-9355-99, GE healthcare). The beads were collected by centrifugation at 1600 g at 4°C for 5 min, washed three times on spinning wheel for 5 min with 5 ml washing buffer (20 mM MOPS pH 7.4, 120 mM KCl, 2 mM MgCl2, 2 mM -mercaptoethanol) supplemented with protease inhibitor cocktail and 200 unit/ml RNasein. RNAs bound to RLR (output) were eluted using biotin elution buffer (IBA), extracted with TRI reagent LS and resuspended in 40 µl ultrapure RNase free water. The quality of input and output RNAs was checked by Bioanalyzer RNA pico and nano kits, respectively (Agilent, Santa Clara, California).
The libraries were prepared with the TruSeq stranded total RNA library prep kit (Illumina), according to manufacturer’s protocol. The quality of all libraries was checked with the DNA-1000 kit (Agilent) on a 2100 Bioanalyzer and quantification was performed with Quant-It assays on a Qubit 1.0 fluorometer (Invitrogen). Sequencing was performed with the Illumina NextSeq500 system. Runs were carried out over 75 cycles, including seven indexing cycles, to obtain 75-bp single-end reads. Sequencing data were processed with Illumina Pipeline software (Casava version 1.9).

treatment_protocol: The cells were lysed in 6 ml lysis buffer (20 mM MOPS pH 7.4, 120 mM KCl, 0.5% igepal, 2 mM MgCl2, 2 mM b-mercaptoethanol) supplemented with protease inhibitor cocktail (#11873580001, Roche) and 200 unit/ml RNAsin (#N2515, Promega).

tag: viral infection

value: RABV field isolate THA

value: HEK293 cells expressing  RIGI RLR

tag: molecule subtype

value: Total RNA


title: UVABCO37_3D

status: Public on Mar 22 2024

type: SRA

city: Charlottesville

first: Kevin

middle: A.

last: Janes

state: VA

address: Box 800759 Health System

department: Department of Biomedical Engineering

country: USA

institute: University of Virginia

library_source: transcriptomic

data_processing:
RNA-seq data was aligned to the human assembly GRCh38.86 and quantified using STAR v2.5 {23104886}.
Gene counts were batch corrected using ComBat_seq R package {33015620} where each patient was considered as a batch.
Assembly: GRCh38.86
Supplementary files format and content: ReadsPerGene.out.tab - STAR aligned counts in column 4 #column1: geneID #column2: countsforunstrandedRNA-seq #column3: countsforthe1streadstrandalignedwithRNA(htseq-countoption-syes) #column4: countsforthe2ndreadstrandalignedwithRNA(htseq-countoption-sreverse)
Supplementary files format and content: Aligned.out.bam - alignment
Supplementary files format and content: allcounts_batchcorr.csv - batch corrected counts

molecule: total RNA

organism: Homo sapiens

source_name: breast cancer organoids

growth_protocol: Organoid initiation. The 50-ml conical tubes containing glass slides of tumor scrapes were centrifuged at 450 rcf for 5 minutes at 8ºC to detach and pellet cells. The slides and supernatant were removed, and the pellet was washed with DMEM GlutaMAX (Gibco, #10569010) containing penicillin–streptomycin (Gibco, #15140122; final concentration = 100 U/ml) and 0.1% (wt/vol) fatty acid-free BSA (Sigma, #A6003) (D-BSA). Pellets were washed with D-BSA three times in 15 ml or 1.5 ml tubes depending on pellet size to remove dead cells, debris, and fat. Next, the pellet was digested in Type 1 medium {33692550} containing collagenase II (Fisher, #17101015; final concentration = 1 mg/ml) and ROCK inhibitor (StemCell #72304; final concentration = 10 μM) for 15 minutes at 37ºC with shaking. 15 ml conical tubes were placed at a ~20° angle in the orbital shaker at 140 rpm (New Brunswick I26 Incubator Shaker) while 1.5ml were inserted in a small benchtop shaker at 350 rpm (Eppendorf Thermomixer 5350 Mixer). The digestion was stopped by adding 1/10th volume of FBS (Gibco, #16170086) directly to the tube and pipetting vigorously with a 1-ml micropipette. If large particulates were present, the sample was passed through a pre-wet 100 μm strainer (VWR, #76327102). To remove red blood cells, the cell pellet was mixed with RBC lysis buffer (Sigma, #11814389001) and incubated at RT for 2 min. After a final wash with D-BSA, the pellet was suspended in growth factor-reduced matrigel (Corning, #354230). The volume of matrigel depended on the cellular yield, with 40 μl matrigel used to resuspend a pellet of 10 μl and scaling linearly for larger pellets. The matrigel suspension was serially dispensed a one 5 μl drop per well in a 96-well plate. The first 20 cases were initiated as 20 µl drops in a 48-well plate according to published recommendations {33692550}, and volumes of 2 µl or 7 µl were tested in Fig. 3.The drops were solidified upside down in a 37ºC incubator for 30 minutes and then100 μl pre-warmed Type 2 medium {33692550} was added to each well. Organoid maintenance. Organoids were kept in a humidified 37ºC incubator with 5% CO2 and refed every 2–4 of days by gently removing old media and adding fresh Type 2 medium, which was prepared every 7 days. For the first 20 cases when passaging was attempted,TrypLE (Gibco, #12604013) was used to dissociate the matrigel and organoids were mechanically sheared by forcefully pipetting up and down. The cells were washed with ice-cold adDMEM+, and centrifuged at 300 rcf for 5 minutes. Matrigel-free dissociated organoids were resuspended in fresh ice-cold matrigel by carefully pipetting up and down. The matrigel-suspended cells were plated in one 20 μl drop per well in a 48-well plate. The drops were solidified upside down in a 37ºC incubator for 15 minutes and then 100 μl of pre-warmed Type 2 medium was added to each well. Cell culture. MCF7 (ATCC, #HTB-22) were cultured in EMEM (ATCC, #30-2003) supplemented with 10% FBS, 1% penicillin-streptomycin, and 0.01 mg/ml insulin (Gibco, #12585014). T47D (ATCC, #HTB-133) were cultured in RPMI-1640 (ATCC, #30-2001) supplemented with 10% FBS, 1% penicillin-streptomycin, and 0.2 Units/ml insulin. CAMA1 (ATCC, #HTB-21) were cultured in EMEM (ATCC, #30-2003) supplemented with 10% FBS and 1% penicillin-streptomycin. EFM19 (DSMZ, #ACC231) were cultured in RPMI-1640 (ATCC, #30-2001) supplemented with 10% heat-inactivated FBS and 1% penicillin-streptomycin. HCC1500 (ATCC, #CRL-2329) were cultured in RPMI-1640 (ATCC, #30-2001) supplemented with 10% FBS and 1% penicillin-streptomycin. ZR-75-1 (ATCC, #CRL-1500) were cultured in RPMI-1640 (ATCC, #30-2001) supplemented with 10% heat-inactivated FBS and 1% penicillin-streptomycin. Cells were grown and passaged according to ATCC or DSMZ guidelines.

extract_protocol:
RNA from primary tumors, organoids, 2D cultures, and cell lines was isolated with TRIzol reagent (Life Technologies, #15596018) followed by purification with the Direct-zol RNA MicroPrep Plus Kit including DNase treatment (Zymo Research, #R2062).
RNA-seq was performed by Genome Sciences Laboratory at Center for Public Health Genomics on 50-550 ng total RNA (TruSeq® Stranded Total RNA Library Prep, Illumina, #20020596)

tag: tissue

value: breast cancer organoids


title: PBS treated day31 rep2

type: RNA

city: Washington

first: Lu

last: Jin

address: 3970 Reservoir Rd NW

department: Oncology

institute: Georgetown University

hyb_protocol: Hybridiztion wes performed using standard Nanostring nCounter protocol

scan_protocol: samples were scanned following standard Nanostring nCounter protocol

data_processing: ruv package (v0.9.7.1) in R (v4.1) was used to normalize the raw count and the batch effect for Nanostring data

label: Biotin

organism: Mus musculus

source_name: primary mammary tumor

label_protocol: Labeling was performed using standard Nanostring nCounter protocol

growth_protocol: All mice were palpated for mammary tumors beginning at age of 7 months.

extract_protocol: Total RNA was isolated from tissues using Qiagen kit and purity of the DNAse-treated RNA was measured by Agilent Tapestation

treatment_protocol: HuHER2 transgenic tumor bearing mice were treated with PBS or BP (5 mg Fe) on the day of tumor detection (n = 12/group). Three mice from each group were sacrificed on day 1, 3, 7, or 31 and primary tumors collected for RNA isolation

value: primary mammary tumor

tag: treatment

value: PBS

tag: time


title: TotalRNA_Tha strain ST-RIG-I cells replicate 1

country: France

source_name: HEK293 cells expressing RIGI RLR cells

tag: cell type

value: HEK293 cells expressing RIGI RLR


title: ZR-75-1

source_name: breast cancer cell line

value: breast cancer cell line

tag: cell line


title: TotalRNA_Tha strain ST-RIG-I  cells replicate 2


title: TotalRNA_SAD strain ST-RIG-I  cells replicate 2

organism:
Homo sapiens
Rabies virus SAD B19

value: RABV vaccine strain SAD


title: TotalRNA_SAD strain ST-RIG-I cells replicate 3


title: PBS treated day31 rep1


title: BP treated day7 rep3

value: BP


title: TotalRNA_Tha strain ST-MDA5cells replicate 3

source_name: HEK293 cells expressing MDA5 RLR cells

value: HEK293 cells expressing MDA5 RLR


title: BP treated day7 rep2


title: TotalRNA_Tha strain ST-MDA5 cells replicate 2


title: T47D


title: TotalRNA_SAD strain ST-MDA5cells replicate 3


title: TotalRNA_SAD strain ST-MDA5 cells replicate 2


title: TotalRNA_Tha strain ST-MDA5 cells replicate 1


title: PBS treated day31 rep3


title: BP treated day7 rep1


title: TotalRNA_SAD strain ST-MDA5 cells replicate 1


title: EFM19


title: HCC1500


title: TotalRNA_Tha strain ST-CH cells replicate 3

source_name: HEK293 cells expressing cherry RLR cells

value: HEK293 cells expressing cherry RLR


title: PBS treated day7 rep3


title: PBS treated day7 rep2


title: TotalRNA_SAD strain ST-CH cells replicate 3


title: UVABCO37_TS

source_name: breast cancer tissue

value: breast cancer tissue


title: PBS treated day7 rep1


title: TotalRNA_SAD strain ST-RIG-I cells replicate 1


title: TotalRNA_Tha strain ST-CH cells replicate 2


title: TotalRNA_Tha strain ST-CH cells replicate 1


title: TotalRNA_SAD strain ST-CH cells replicate 2


title: TotalRNA_SAD strain ST-CH cells replicate 1


title: BP treated day3 rep3


title: M0068714187 - nsCLP

city: shenyang

first: Shanshan

last: Jia

state: China

address: Shengjing Hospital, China Medical University Street #36, SanHao,  HePing Distric

country: China

institute: Shengjing Hospital

data_processing:
FASTQ files for each sample were generated using the bcl2fastq software (Illumina Inc.)
After quality control, the reads were 3’5'-adaptor trimmed and filtered 15 bp reads with cutadapt software
The trimmed reads were aligned to reference genome with bowtie software
For each sample, known miRNAs, and predicted novel miRNAs were identified and enumerated using miRDeep2 software package (Freedlander et al. Nature Biotechnology, 26, 407-415 (2008) )
Raw reads where normalized by dividing the number of reads by the total number of mapped reads in millions, i.e., RPM
Genome_build: miRBase Release 22

source_name: nsCLP group rep5

extract_protocol:
Total RNA was extracted from plasma using Qiagen miRNeasy Serum/Plasma Kit (Qiagen, Valencia, CA, USA; Cat# 217184) according to the manufacturer’s protocol. RNA concentration was quantitated using the NanoDrop ND-1000 Spectrophotometer (NanoDrop Technologies, Wilmington, DE).  Small RNA libraries were constructed using New England Biolabs (NEB) NEBNext Multiplex Small RNA Library Prep Set for Illumina sequencers and the NEB standard protocol. Individual libraries were constructed using 1µg of total RNA isolated from each sample.
1) 3’-adaptor ligation;2) 5’-adaptor ligation;3) cDNA synthesis;4) PCR amplification;5) size selection of 135   155 bp PCR amplified fragments (corresponding to 15   35 nt small RNAs).

value: human maternal plasma

tag: bmi of pregnant women

tag: pregnancy weeks

tag: pregnancy ages


title: MCF7


title: IP_Tha strain ST-RIG-I cells replicate 3

value: immunoprecipitated RNA


title: M006456249 - nsCLP

source_name: nsCLP group rep4


title: IP_Tha strain ST-RIG-I  cells replicate 2


title: M006392349 - nsCLP

source_name: nsCLP group rep3


title: IP_SAD strain ST-RIG-I  cells replicate 2


title: IP_Tha strain ST-RIG-I cells replicate 1


title: M006201943 - nsCLP

source_name: nsCLP group rep2


title: PBS treated day3 rep3


title: BP treated day3 rep1


title: IP_Tha strain ST-MDA5cells replicate 3


title: M004612943 - nsCLP

source_name: nsCLP group rep1


title: IP_SAD strain ST-MDA5cells replicate 3


title: IP_SAD strain ST-RIG-I cells replicate 1


title: IP_Tha strain ST-MDA5 cells replicate 2


title: PBS treated day3 rep2


title: CAMA1


title: IP_SAD strain ST-MDA5 cells replicate 2


title: 1700066BSCBP11 - Control

source_name: Control group rep5


title: 1700020BSCBP16 - Control

source_name: Control group rep4


title: BP treated day1 rep3


title: IP_Tha strain ST-CH cells replicate 3


title: IP_SAD strain ST-RIG-I cells replicate 3


title: IP_SAD strain ST-MDA5 cells replicate 1


title: BP treated day3 rep2


title: IP_Tha strain ST-MDA5 cells replicate 1


title: 1700017BSCBP13 - Control

source_name: Control group rep3


title: IP_Tha strain ST-CH cells replicate 2


title: IP_SAD strain ST-CH cells replicate 3


title: 1700014BSCBP22 - Control

source_name: Control group rep2


title: BP treated day1 rep1


title: BP treated day1 rep2


title: IP_SAD strain ST-CH cells replicate 2


title: PBS treated day1 rep2


title: IP_Tha strain ST-CH cells replicate 1


title: 1700013BSCBP10 - Control

source_name: Control group rep1


title: IP_SAD strain ST-CH cells replicate 1


title: PBS treated day3 rep1


title: P2 Six2TGC; Tsc1-2

status: Public on Mar 21 2024

city: Cincinnati

first: Alison

middle: Jarmas

last: Perl

state: Ohio

address: 3333 Burnet Ave.

institute: CCHMC

library_source: genomic

data_processing:
Raw reads in fastq format were processed using Computational Suite For Bioinformaticians and Biologists (CSBB-v3.0)
Raw reads were mapped to mm10 version of Mouse genome
CSBB uses fastqc for quality check, Bowtie2 for mapping and MACS2 for peak calling
Assembly: mm10
Supplementary files format and content: .bw files were generated and peaks were called using MACS2

molecule: genomic DNA

source_name: Nephron progenitor cells

growth_protocol: Single-cell suspensions of nephron progenitor cells were isolated by FACS from the kidneys of mice of the indicated strains/timepoints using antibodies for Itga8+, Pdgfra-; and GFP+ if applicable to the sample.

extract_protocol:
Nuclei were isolated from purified nephron progenitor cells as described by Buenrostro et al (2013)
ATAC-Seq (Buenrostro et al, 2013)

value: Nephron progenitor cells

tag: strain

tag: genotype

value: Six2TGC; Tsc1

tag: age


title: P2 Six2KI-2

value: Six2 +/CE


title: P2 Six2KI-3


title: PBS treated day1 rep1

source_name: primary mammary tumor


title: P2 Six2TGC; Tsc1-1


title: P2 129-1

value: Wild type


title: P2 B6-3


title: P2 129-3


title: P2 B6-2


title: P2 Cited1-3

value: Cited1 +/GCE


title: P2 B6-1


title: E18 Cited1-3


title: E18 Cited1-2


title: P2 129-2


title: P2 Cited1-1


title: E18 Cited1-1


title: E14 Cited1-3


title: E14 Cited1-2


title: P2 Cited1-2


title: BN1417, Rep2, Dam::RPB-6, RAPID

city: Seville

first: Peter

last: Askjaer

address: UPO Carretera de Utrera km 1

country: Spain

institute: Centro Andaluz de Biología del Desarrollo

data_processing:
FASTQ files from the NextSeq500 platform were processed in R Studio using the pipeline RGeneDamIDSeq (https://github.com/damidseq/-RGeneDamIDSeq-) (Sharma et al. 2016) for mapping of reads to genes. The pipeline includes a quality check where only reads that contain the DamID adapter (“CGCGGCCGAG”) and map to GATC sites in the C. elegans genome are retained for further analysis. The number of reads fulfilling these criteria ranged from 7.2 to 27 million. The pipeline also provides mapped read numbers per individual GATC fragment. For mapping to genes, the script was modified to include 500 bp distal to transcriptional start and termination sites. UCSC genome version ce11 (BSgenome.Celegans.UCSC.ce11) was used for alignment.
Normalization of Dam::RPB-6 reads to GFP::Dam reads was performed using the damidseq_pipeline package (https://owenjm.github.io/damidseq_pipeline/) (Marshall and Brand 2015) on the bam files generated by the RDamIDSeq pipeline. Gene occupancy was computed as log2(Dam::RPB-6/GFP::Dam) with polii.gene.call  (https://github.com/owenjm/polii.gene.call) using bedgraph output files from the damidseq_pipeline and WBCel235 gene annotation. A FDR of 0.05 was used as threshold to call transcribed genes.
Assembly: ce11
Supplementary files format and content: csv file polii.gene.call from script; contains for each gene log2 score, number of GATC fragments and FDR.

organism: Caenorhabditis elegans

source_name: Intestine

growth_protocol: Worms were grown asynchronically at 20C on NGM plates seeded with E. coli GM119 for at least two generations before egg-prepping with hypochlorite. Hatched L1s were counted the day after and 1000 L1s were aliquoted onto 10 cm NGM plates seeded with E. coli GM119 as described above. Worms were grown at 20C for 48 h before collecting 4000 L4 stage nematodes per strain and washed 8 times with 15 ml of M9 with 0.01% Tween-20. Worms were transferred to 1.5 ml tubes with M9 with 0.01% Tween-20 using Pasteur pipettes followed by two additional washes. Supernatants were aspirated and aliquots of 30 µl were snap frozen in liquid nitrogen and maintained at -80C until DNA extraction.

extract_protocol:
To purify genomic DNA, samples were lysed in 5 freeze/thaw cycles (1min in liquid nitrogen; 3min in 37C shaker) and processed with DNeasy Blood and Tissue Kit (QIAGEN #69504).
DamID was performed on 200 ng genomic DNA  extracted from 4000 L4 animals cultured and collected as indicated above. Two replicates were performed as described (de la Cruz Ruiz et al. 2022). A pool of 3 AdR primers (5'-N(4-6)GTCCTCGCGGCCGAGGATC) and 14 PCR cycles were used. Successful amplification of Dam-methylated genomic DNA yielded a smear of ~400-~1500 bp fragments when analyzed on Agilent Bioanalyzer. 40 ng of PCR amplified fragments were used for library preparation as described (de la Cruz Ruiz et al. 2022), using E7370 NEBNext® Ultra™ DNA Library Prep Kit for Illumina. Library amplicons’ size distribution was checked to be maintained as for PCR fragments indicated above followed by pooling, repurification and sequencing on a Illumina NextSeq500 platform at EMBL GeneCore.

value: Intestine


title: BN1415, Rep2, Dam::RPB-6, RAPID

value: WT


title: BN1416, Rep2, Dam::RPB-6, RAPID

source_name: Hypodermis

value: Hypodermis


title: E14 Cited1-1


title: BN1414, Rep2, Dam::RPB-6, RAPID


title: P2 Six2TGC; Tsc1-3


title: BN1053, Rep2, GFP::Dam, RAPID


title: BN1048, Rep2, GFP::Dam, RAPID


title: P2 Six2KI-1


title: BN1417, Rep1, Dam::RPB-6, RAPID


title: BN1051, Rep2, GFP::Dam, RAPID


title: BN561, Rep2, GFP::Dam, RAPID


title: BN1416, Rep1, Dam::RPB-6, RAPID


title: BN1414, Rep1, Dam::RPB-6, RAPID


title: BN1415, Rep1, Dam::RPB-6, RAPID


title: BN1051, Rep1, GFP::Dam, RAPID


title: BN561, Rep1, GFP::Dam, RAPID


title: Wild-type 6h post fertilization biol rep 2

city: Bergen

first: Simon

last: Henriet

address: Thormøhlensgate 55

country: Norway

institute: University of Bergen

data_processing:
Adaptor trimming with flexbar 3.4.0
Alignment to transcript models from annotated genes with kallisto 0.46.0
Differential gene expression analysis with DESeq2
Assembly: Oikopleura dioica genome assembly version 3.0
Supplementary files format and content: tab-delimited text files includes raw read counts produced by kallisto for each library

molecule: polyA RNA

organism: Oikopleura dioica

source_name: whole animal

growth_protocol: Animals from single crosses between Pax37b+/- parents were raised until 4, 8 and 6 hours post-fertilization. Individual animals were collected and transferred in RNA extraction buffer, and 10% of the lysate was used for genotyping Pax37b.

extract_protocol:
Animals with the same genotype were pooled together, and we extracted RNA with Nucleospin RNA XS kit (Macherey-Nagel)
Libraries were prepared with the NEBNext Single-cell/Low-input RNA library prep kit for Illumina (New England Biolabs), following the manufacturer's protocol

value: whole animal


title: Pax37b mutant 6h post fertilization biol rep 1


title: Pax37b mutant 6h post fertilization biol rep 2


title: Wild-type 8h post fertilization biol rep 2


title: Pax37b mutant 8h post fertilization biol rep 1


title: Pax37b mutant 8h post fertilization biol rep 3


title: Wild-type 6h post fertilization biol rep 1


title: Wild-type 8h post fertilization biol rep 1


title: wild type live cells, no treatment, replicate 2

city: Bethesda

first: David

middle: Johannes

last: Clark

state: MD

address: 6 Center Drive Bldg 6A Rm 2A02

department: DDB

institute: NICHD, NIH

data_processing:
Basecalling with Guppy version 6.3.8 (or newer)
Indexing of basecalled reads with Nanopolish version 0.14.0
Alignment of basecalled reads to yeast genome with Minimap version 2.24 and sorting/indexing of aligned reads with samtools version 1.17
Likelihood of methylation at CpGs scored by Nanopolish v0.14.0: 'fmeth'.
The data were processed to obtain a wig file to display the fraction of C methylated at each CG in the genome (or unresolved group of CG sites), 'fmeth',  for each sample.
Assembly: sacCer3
Supplementary files format and content: wig files containing fmeth values for each CG or group of CG sites in the yeast genome for display in IGV
Library strategy: whole genome sequencing

organism: Saccharomyces cerevisiae

source_name: Not Applicable

extract_protocol:
Replicate 1 and YDC111 DNA samples were purified from yeast cells using New England Biolabs Monarch High Molecular Weight DNA kit. Replicate 2 DNA samples were purified yeast cells by extracting proteins three times with SDS, washing out the SDS, then removing the cell wall using lytic enzyme. The DNA was purified by chloroform extraction and isopropanol precipitation and a 70% ethanol wash. The DNA was further purified using Beckman-Coulter Ampure beads at a 0.4:1 volume ratio.
Libraries were prepared following Oxford Nanopore Technologies protocols.  Replicate 1 and YDC111 samples were prepared with SQK-LSK110 kit protocols, while Replicate 2 samples were prepared with SQK-LSK109 and Native Barcoding (EXP-NBD104) kit protocols.

value: Not Applicable


title: wild type live cells, no treatment, replicate 1


title: wild type live cells, 240 m SM, replicate 2

value: MATa ade2-1 can1-100 leu2-3,112 trp1-1 ura3-1 ho::TIR1-MSssI-degron-3HA-KanMX


title: Pax37b mutant 8h post fertilization biol rep 2


title: wild type live cells, 30 m SM, replicate 2


title: wild type live cells, 0 m SM, replicate 2


title: wild type live cells, 60 m SM, replicate 2


title: wild type live cells, 120 m SM, replicate 1


title: wild type live cells, 30 m SM, replicate 1


title: wild type live cells, 240 m SM, replicate 1


title: wild type live cells, 0 m SM, replicate 1


title: BN1048, Rep1, GFP::Dam, RAPID


title: wild type live cells, 60 m SM, replicate 1


title: Pax37b mutant 6h post fertilization biol rep 3


title: Arid5a, 1 µM

city: Marburg

first: Julia

middle: E.

last: Weigand

address: Marbacher Weg 6

department: Pharmacy

country: Germany

institute: University of Marburg

data_processing:
NGS data were analyzed using the to the RBNS pipeline available at https://bitbucket.org/pfreese/rbns_pipeline/overview.
Assembly: other
Supplementary files format and content: An Excel file containing the R-values and corresponding z-values generated by the RBNS analysis pipeline for the reported 4- to 8-mer sequences. R is the enrichment of a k-mer and is defined as the frequency of the k-mer in the pulldown reads divided by its frequency in the input reads.

organism: synthetic construct

source_name: synthetic construct based on mouse Arid5a

extract_protocol:
For the RBNS experiment, a random 20-mer RNA input pool generated by in vitro transcription was used. For this as a template, a T7 promoter sequence and a random 20-mer containing oligonucleotide was annealed to an equimolar amount of a shorter oligonucleotide containing only the complementary T7 promoter sequence. The resulting RNA was folded by snap cooling prior to use. Adapted from https://doi.org/10.1016/bs.mie.2015.02.007, an RBNS assay was performed using the random 20-mer RNA input pool and a Twin-Strep-labelled Arid5a49-152 domain. The protein, equilibrated for 30 min at 4°C in binding buffer (25 mM Tris-HCl pH 7.5, 150 mM KCl, 3 mM MgCl2, 0.01% Tween, 500 µg/mL BSA, 1 mM DTT), was incubated with the input RNA pool (1 µM) and 40 U of ribonuclease inhibitor (moloX, Berlin). This was done for 1 h at room temperature at three different protein concentrations (0.25, 1, 5 µM). The final pull-down was performed using MagStrep "type3" XT beads (IBA Lifesciences, Göttingen) by incubating the RNA/RBP mixture for 1 h at 4 °C. After three washing steps with wash buffer (25 mM Tris-HCl pH 8.0, 150 mM KCl, 60 μg/ml BSA, 0.5 mM EDTA, 0.01% Tween), 25 µL of elution buffer (wash buffer plus 50 mM biotin) was used twice to elute the RNA/RBP complexes from the beads. RNA was then extracted using the Zymo RNA Clean & Concentrator-5 Kit (Zymo Research, Freiburg, Germany) according to the manufacturer's instructions.
The RNA extracted after pulldown was transcribed into cDNA. The cDNA was then amplified by PCR, using primers to insert an index for each concentration and Illumina adapters. Deep sequencing was then performed at GENEWIZ (Leipzig, Germany).


title: Arid5a, 5 µM

value: synthetic construct based on mouse Arid5a


title: wild type live cells, 120 m SM, replicate 2


title: BN1053, Rep1, GFP::Dam, RAPID


title: Arid5a, 0.25 µM


title: ZnF, 5 µM

data_processing:
NGS data were analyzed using the to the RBNS pipeline available at https://bitbucket.org/pfreese/rbns_pipeline/overview.
Supplementary files format and content: Excel file containing the R-values and the corresponding z-values generated by the RBNS analysis pipeline for the indicated 4-, 5-, 6- and 7-mer sequences. R represents the enrichment of a k-mer and is defined as the frequency of the k-mer in the reads of the pulldown divided by its frequency in input reads.
Library strategy: RNA Bind-n-Seq

source_name: synthetic construct based on mouse Roquin-1

extract_protocol:
The RNA input pool for the RBNS experiment was generated by in vitro transcription. Therfore, a T7 promoter-containing oligonucleotide was annealed to an equimolar quantity of a oligonucleotide posessing a T7 promotor sequence followed by a random 20-mer flanked by partial Illumina adapters. The produced RNA was always folded by snap-cooling befor usage. Based on (https://doi.org/10.1016/bs.mie.2015.02.007) an RBNS assay was performed with the random 20-mer input RNA pool and a Twin-Strep-tagged ZnF. Protein was equilibrated in binding buffer (25 mM Tris-HCl pH 7.5, 150 mM KCl, 3 mM MgCl2, 3 mM ZnCl2, 0.01% Tween, 500 µg/mL BSA, 1 mM DTT) for 30 min at 4°C at three different concentrations (1, 5, 20 µM). The RNA pool was added to a final concentration of 1 µM with 40 U Ribonuclease Inhibitor (moloX, Berlin) and incubated for 1 h at room temperature. With MagStrep ”type3” XT beads (IBA Lifesciences, Göttingen) a pulldown was performed by incubating the RNA/ZnF mixture for 1 h at 4°C. Unbound RNA was removed by washing three times with 25 mM Tris-HCl pH 8.0, 150 mM KCl, 60 μg/ml BSA, 0.5 mM EDTA, 0.01% Tween. For elution of the RNA/ZnF complexes 25 µL of Elution Buffer (wash buffer plus 50 mM biotin) was used twice. Then the RNA was extracted with the Zymo RNA Clean & Concentrator-5 kit (Zymo Research, Freiburg) according to the manufacturer’s instructions.
The extracted RNA was transcribed into cDNA and amplified by PCR, whereby an Illumina adapter and an index for each concentration were inserted through the primers. The resulting libraries were then deep sequenced (GENEWIZ, Leipzig).

tag: concentration

value: Strep-tagged ZnF domain (5 µM)


title: 20-month-old fibroblasts reprogrammed to iPSCs replicate 1

type: genomic

city: Boston

first: Wayne

last: Mitchell

state: MA

address: 77 Avenue Louis Pasteur

institute: Brigham and Women's Hospital

hyb_protocol: Standard Illumina protocol

scan_protocol: Standard Illumina protocol

data_processing:
Raw methylation array data were normalized using SeSAMe (Zhou et al., 2018 Nucleic Acids Res. 46(20))
Normalized (SeSAMe, noob background subtraction) data in RDS format.

label: Cy3 and Cy5

source_name: Dermal fibroblasts from male C57BL/6 mice

label_protocol: Standard Illumina Protocol

extract_protocol: DNA was isolated from fibroblasts using the DNeasy Blood & Tissue kit according to the manufacturer's protocol (Qiagen)

tag: Sex

value: male

value: Dermal fibroblasts

value: reprogrammed to iPSCs


title: 4-month-old fibroblasts reprogrammed to iPSCs replicate 1


title: 4-month-old fibroblasts reprogrammed to iPSCs replicate 2


title: ZnF, 1 µM

value: synthetic construct based on mouse Roquin-1

value: Strep-tagged ZnF domain (1 µM)


title: ZnF, 20 µM

value: Strep-tagged ZnF domain (20 µM)


title: 20-month-old fibroblasts reprogrammed to iPSCs replicate 2


title: 20mer Input library

source_name: synthetic sequence library

value: synthetic sequence library

value: input


title: Arid5a, 20mer Input library


title: 4-month-old fibroblasts reprogrammed to iPSCs replicate 3


title: 4-month-old fibroblasts treated with 2c replicate 5


title: 20-month-old fibroblasts reprogrammed to iPSCs replicate 3


title: 20-month-old fibroblasts treated with 2c replicate 5


title: 20-month-old fibroblasts treated with vehicle replicate 5

value: vehicle


title: 4-month-old fibroblasts treated with 7c replicate 5


title: 4-month-old fibroblasts treated with vehicle replicate 5


title: 20-month-old fibroblasts treated with 2c replicate 4


title: 4-month-old fibroblasts treated with 7c replicate 4


title: 20-month-old fibroblasts treated with 7c replicate 5


title: 4-month-old fibroblasts treated with 2c replicate 4


title: 4-month-old fibroblasts treated with vehicle replicate 4


title: 20-month-old fibroblasts treated with 2c replicate 3


title: 20-month-old fibroblasts treated with 7c replicate 3


title: 20-month-old fibroblasts treated with vehicle replicate 4


title: 20-month-old fibroblasts treated with vehicle replicate 3


title: 4-month-old fibroblasts treated with 7c replicate 3


title: 4-month-old fibroblasts treated with 7c replicate 1


title: 20-month-old fibroblasts treated with 7c replicate 4


title: 4-month-old fibroblasts treated with 2c replicate 2


title: 4-month-old fibroblasts treated with vehicle replicate 3


title: 4-month-old fibroblasts treated with 2c replicate 3


title: 4-month-old fibroblasts treated with vehicle replicate 1


title: 20-month-old fibroblasts treated with 7c replicate 2


title: 20-month-old fibroblasts treated with 2c replicate 1


title: 20-month-old fibroblasts treated with vehicle replicate 1


title: 20-month-old fibroblasts treated with 7c replicate 1


title: 4-month-old fibroblasts treated with vehicle replicate 2


title: 20-month-old fibroblasts treated with vehicle replicate 2


title: 20-month-old fibroblasts treated with 2c replicate 2


title: 4-month-old fibroblasts treated with 2c replicate 1


title: S462TY, Selumetinib&Rigosertib, 24 hr, batch 2, biol rep2

city: Minneapolis

last: Largaespada

state: MN

address: 515 Delaware St SE

department: Department of Pediatrics

institute: University of Minnesota

data_processing:
Quality and adapter trimming via Trimmomatic v0.33
Mapping via Hisat2 v2.1.0 to ensembl annotation GRCh38 v105
Gene count quantification via Stringtie v1.3.4d
Read quality analysis via fastqc v0.11.7
Assembly: Homo sapiens GRCh38
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: Malignant Peripheral Nerve Sheath Tumor

growth_protocol: Cell lines were maintained and passaged at 37°C with 5% CO2 in DMEM high glucose media supplemented with 10% FBS and penicillin/streptomycin. If antibiotic selection was needed, puromycin was used at 500 µg/ml as indicated below.

extract_protocol:
RNA was harvested from cells using Qiagen RNEasy mini purification kits and subjected to TURBO DNAse to remove any residual genomic DNA contamination.
TruSeq stranded mRNA libraries

treatment_protocol: Cells were exposed to vehicle (DMSO), digoxin, rigosertib, selumetinib, digoxin+ selumetinib, or rigosertib+ selumetinib for 2 hours or 24 hours. At the indicated time point, cells were harvested, washerswith cold PBS, pelleted via centrifugation, and the pellets flash frozen in LiN2. Cell pellets were stored at -80°C until RNA purification.

value: Malignant Peripheral Nerve Sheath Tumor

tag: vehicle

value: DMSO

tag: treatment 1

value: Selumetinib

tag: dosage 1

value: 2 microM

tag: treatment 2

value: Rigosertib

tag: dosage 2

value: 0.1 microM

value: 24 hr

tag: batch


title: S462TY, Selumetinib&Rigosertib, 24 hr, batch 2, biol rep3

tag: tissue

tag: time


title: NF14

city: Aurora

first: Vladimir

last: Amani

state: CO

address: 12800 East 19th Avenue, Building: RC-1 North; Room: P184402A

institute: University of Colorado Anschutz Medical Campus

description:
single_nuclei_features.tsv.gz
single_nuclei_barcodes.tsv.gz
single_nuclei_matrix.mtx.gz
single_nuclei_metadata.csv.gz

library_source: transcriptomic single cell

data_processing:
Raw sequencing reads were processed using CellRanger (10× Genomics) and Seurat 3.1.0.C Cells from individual subpopulations were reanalyzed separately using Harmony alignment [13]. Presto was used for determining differential expression and marker gene identification.
Assembly: GRCh38
Supplementary files format and content: UMI counts, barcodes, and genes in sparseMatrix format, and cell metadata in CSV format.

source_name: Plexiform Neurofibroma

extract_protocol:
Human NF1-associated plexiform neurofibroma samples were collected from surgeries at Children’s Hospital Colorado (COM-IRB-13-1672). Bulk frozen samples were processed using CHAPS-based buffer as previously described by Slyper et al.  that provided nuclei that were not only high in membrane integrity, but also nuclear yield [12].  An additional wash step was utilized to prevent the presence of cell-free RNA that has been shown to confound downstream snRNA-sequencing. Bright field microscopy was employed to determine yield, quality and membrane integrity of single-nuclei. Single-nuclei generated from PN were analyzed using the 10xGenomics Chromium drop-seq platform. The snRNA-seq was performed at the UC Cancer Center Microarray and Genomics Core, where 4000 nuclei per sample were captured and barcoded to generate cDNA libraries. Libraries will subsequently be sequenced using the Illumina NovaSeq6000 platform at approximately 50,000 reads per nuclei.
Chromium Single Cell V2 and V3 Chemistry Library Kits, Gel Bead & Multiplex Kit and Chip Kit (10X Genomics)

value: Plexiform Neurofibroma


title: S462TY, Selumetinib&Rigosertib, 24 hr, batch 2, biol rep1

tag: cell line


title: 4-month-old fibroblasts treated with 7c replicate 2

value: male

tag: cell type

tag: treatment


title: S462TY, Selumetinib, 24 hr, batch 2, biol rep3

value: 125 microM


title: S462TY, Selumetinib, 24 hr, batch 2, biol rep1


title: S462TY, Selumetinib&Rigosertib, 24 hr, batch 1, biol rep3


title: S462TY, Rigosertib, 24 hr, batch 2, biol rep3

value: 0.5 microM


title: S462TY, Selumetinib&Digoxin, 24 hr, batch 1, biol rep1

value: 4 microM

value: Digoxin

value: 0.0308 microM

value: 2 hr


title: S462TY, Digoxin, 24 hr, batch 1, biol rep3


title: S462TY, Selumetinib&Digoxin, 24 hr, batch 1, biol rep3


title: S462TY, Selumetinib&Rigosertib, 24 hr, batch 1, biol rep1


title: S462TY, Rigosertib, 24 hr, batch 2, biol rep1


title: S462TY, DMSO, 24 hr, batch 1, biol rep1


title: S462TY, untreated, 24 hr, batch 1, biol rep3


title: S462TY, DMSO, 24 hr, batch 1, biol rep2


title: S462TY, Digoxin, 24 hr, batch 1, biol rep2


title: S462TY, Digoxin, 24 hr, batch 1, biol rep1


title: S462TY, untreated, 24 hr, batch 1, biol rep1


title: S462TY, Selumetinib&Digoxin, 24 hr, batch 1, biol rep2


title: S462TY, Selumetinib&Rigosertib, 2 hr, batch 1, biol rep3


title: S462TY, Selumetinib&Rigosertib, 2 hr, batch 1, biol rep2


title: S462TY, DMSO, 24 hr, batch 1, biol rep3


title: mESC_9d_RNA_5

city: Xiamen

first: Xi

last: Zeng

address: No. 422, Siming South Road

institute: Xiamen University

data_processing:
The original sequencing data acquired includes 150-bp paired-end sequences. Trim Galore version 0.6.7 was used to remove the adaptor prior to alignment. With hg38/mm10, trimmed clean sequences were aligned and de-duplicated using Bismark version v0.15.0, a bisulfite alignment program that invokes bowtie2 version 2.2.9. The alignment was carried out using non-directional library options as a result of the amplification procedure, using the following settings: -fastq --non_directional -bowtie2. The duplicates in aligned BAM file were removed using the script deduplicate_bismark provided by Bismark with the command: deduplicate_bismark -p –bam Aligned_Sample.bam.
As a supplementary script of bismark, bismark_methylation_extractor was used to operate deduplicated Bismark result files and extract the coverage and methylation information of cytosine positions with command: bismark_methylation_extractor -p --ample_memory --cytosine_report –CX Path_to_genome Deduplicated_Aligned_Sample.bam. The coverage2cytosine script from Bismark was used to extract the methylation status of cytosines specifically in GpC and CpG from the generated coverage files. The GCG context contained in the coverage file represents a cytosine position both in CpG and GpC, which is ambiguous. These ambiguous positions were located using OligoMatch and removed from the coverage files.
Assembly: hg38, mm10
Supplementary files format and content: CpG.cov and GpC.cov files containing methylation information for CpG and GpC sites.
Supplementary files format and content: counts.txt file containing gene expression information.

growth_protocol: All cultures were maintained at 37ºC in a humidified incubator with 5% CO2. The human chronic myeloid leukemia cell line K562 were cultured in IMDM, supplemented with 10% Fetal Bovine Serum and 1% Penicillin-Streptomycin-Glutamine.

extract_protocol:
AMAR-seq employs a stepwise strategy to lyse cell and nuclear membranes. Then, the RNA fraction undergoes transcriptome library construction on the chip based on the smart-seq2 protocol. For nuclear , cytosines on the GpC sites in the open chromatin regions are methylated with GpC methylation transferase, M.CviPI, to mark the chromatin accessibility. Subsequent bisulphite conversion converts all normal cytosines to uracil, leaving endogenously methylated CpG and artificially labelled methylated GpC unchanged. Since DNA methylation information occurs predominantly at the CpG site and the endogenous GpC methylation level is less than 2%, it is reasonable to use CG methylation to indicate DNA methylation level. The treated GC methylation marks open regions to obtain bilayer molecular information on the nuclear fraction of the cell, culminating in individual cell tri-omics data.
Subsequently, AMAR-seq employs a stepwise strategy to lyse cell and nuclear membranes. Specifically, glycoproteins expressed on the surface of the cell membrane are used to encapsulate the cell in a layer of ConA beads, where the cell is lysed in a hypotonic environment, with the cytoplasm flowing out while the nucleus remains intact. Neighboring electrodes are then energized to drag away droplets of cytoplasmic RNA and leave the nucleus at the hydrophilic site. Then, the RNA fraction undergoes transcriptome library construction on the chip based on the smart-seq2 protocol, including reverse transcription, cDNA amplification, and Tn5 transposase-based library construction. After nuclear membrane lysis, cytosines on the GpC sites in the open chromatin regions are methylated with GpC methylation transferase, M.CviPI, to mark the chromatin accessibility. Subsequent bisulphite conversion converts all normal cytosines to uracil, leaving endogenously methylated CpG and artificially labelled methylated GpC unchanged. Since DNA methylation information occurs predominantly at the CpG site and the endogenous GpC methylation level is less than 2%, it is reasonable to use CG methylation to indicate DNA methylation level. The treated GC methylation marks open regions to obtain bilayer molecular information on the nuclear fraction of the cell, culminating in individual cell tri-omics data.
smart-seq2 and scNOMe-seq

treatment_protocol: Mouse embryonic stem cells (mESCs; E14, 129/Ola) were grown on 6-cm culture dishes with MEF feeder cells and cultured in a complete medium supplemented with leukemia inhibitory factor (LIF) to prevent differentiation. To induce undirectional differentiation, mESCs were dissociated and replated onto 0.1% gelatin-coated dishes, and cultured without LIF in a feeder-free manner.

value: mouse embryonic stem cell

value: withdrawal of Leukemia inhibitory factor


title: S462TY, untreated, 24 hr, batch 1, biol rep2

value: Malignant Peripheral Nerve Sheath Tumor


title: mESC_9d_RNA_4


title: S462TY, Selumetinib, 24 hr, batch 2, biol rep2

value: DMSO


title: S462TY, Selumetinib&Rigosertib, 2 hr, batch 1, biol rep1

value: Selumetinib


title: S462TY, Selumetinib&Rigosertib, 24 hr, batch 1, biol rep2

value: 2 microM


title: S462TY, Rigosertib, 24 hr, batch 2, biol rep2

value: Rigosertib


title: mESC_9d_RNA_3


title: S462TY, Selumetinib&Digoxin, 2 hr, batch 1, biol rep3


title: mESC_9d_RNA_2


title: S462TY, Selumetinib&Digoxin, 2 hr, batch 1, biol rep1


title: S462TY, Digoxin, 2 hr, batch 1, biol rep3


title: mESC_9d_RNA_1


title: mESC_6d_RNA_5


title: mESC_6d_RNA_2


title: S462TY, Digoxin, 2 hr, batch 1, biol rep2


title: mESC_6d_RNA_4


title: mESC_6d_RNA_6


title: mESC_3d_RNA_7


title: S462TY, Rigosertib, 2 hr, batch 1, biol rep1


title: S462TY, Digoxin, 2 hr, batch 1, biol rep1


title: mESC_3d_RNA_5


title: S462TY, Rigosertib, 2 hr, batch 1, biol rep3


title: mESC_6d_RNA_1


title: mESC_3d_RNA_6


title: S462TY, DMSO, 24 hr, batch 2, biol rep1


title: S462TY, Selumetinib, 2 hr, batch 1, biol rep3


title: S462TY, DMSO, 24 hr, batch 2, biol rep2


title: mESC_3d_RNA_4


title: S462TY, Selumetinib&Digoxin, 2 hr, batch 1, biol rep2


title: mESC_3d_RNA_3


title: S462TY, Rigosertib, 2 hr, batch 1, biol rep2


title: mESC_6d_RNA_3


title: S462TY, DMSO, 24 hr, batch 2, biol rep3


title: S462TY, Selumetinib, 2 hr, batch 1, biol rep2


title: mESC_3d_RNA_2


title: pTT-18_M

city: Gothenburg

first: Helena

last: Carén

address: Medicinaregatan 1F

country: Sweden

institute: University of Gothenburg

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium MethylationEPIC beadchips using standard Illumina protocols.

data_processing: Raw methylation data were processed on the Illumina methylationEPIC array and normalized with dasen using the statistical software R.

label: Cy5 and Cy3

source_name: Pediatric brain tumour_Metastatic

label_protocol: Standard Illumina protocol

extract_protocol: Genomic DNA from fresh-frozen tumours was extracted using the DNeasy®Blood&Tissue Kit (Qiagen) according to the manufacturer's intructions.

value: Brain tumour

tag: tissue type

value: Metastatic

tag: subject status

value: patient with brain tumours


title: pTT-12_R

source_name: Pediatric brain tumour_Recurrent

value: Recurrent


title: pTT-18_P

source_name: Pediatric brain tumour_Primary

value: Primary


title: pTT-12_P


title: S462TY, Selumetinib, 2 hr, batch 1, biol rep1

value: 125 microM


title: S462TY, DMSO, 2 hr, batch 1, biol rep1


title: mESC_3d_RNA_1


title: S462TY, DMSO, 2 hr, batch 1, biol rep3


title: S462TY, DMSO, 2 hr, batch 1, biol rep2


title: mESC_0d_RNA_3


title: mESC_0d_RNA_6


title: mESC_0d_RNA_5


title: S462TY, untreated, 0 hr, batch 1, biol rep2

value: 0 hr


title: mESC_0d_RNA_4


title: S462TY, untreated, 0 hr, batch 1, biol rep1


title: S462TY, untreated, 2 hr, batch 1, biol rep1


title: smart_seq2_4

value: chronic myeloid leukemia cells


title: S462TY, untreated, 0 hr, batch 1, biol rep3


title: mESC_0d_RNA_2


title: mESC_0d_RNA_1


title: mESC_9d_nucleus_1

data_processing:
*library strategy: NOMe-seq
The original sequencing data acquired includes 150-bp paired-end sequences. Trim Galore version 0.6.7 was used to remove the adaptor prior to alignment. With hg38/mm10, trimmed clean sequences were aligned and de-duplicated using Bismark version v0.15.0, a bisulfite alignment program that invokes bowtie2 version 2.2.9. The alignment was carried out using non-directional library options as a result of the amplification procedure, using the following settings: -fastq --non_directional -bowtie2. The duplicates in aligned BAM file were removed using the script deduplicate_bismark provided by Bismark with the command: deduplicate_bismark -p –bam Aligned_Sample.bam.
As a supplementary script of bismark, bismark_methylation_extractor was used to operate deduplicated Bismark result files and extract the coverage and methylation information of cytosine positions with command: bismark_methylation_extractor -p --ample_memory --cytosine_report –CX Path_to_genome Deduplicated_Aligned_Sample.bam. The coverage2cytosine script from Bismark was used to extract the methylation status of cytosines specifically in GpC and CpG from the generated coverage files. The GCG context contained in the coverage file represents a cytosine position both in CpG and GpC, which is ambiguous. These ambiguous positions were located using OligoMatch and removed from the coverage files.
Assembly: hg38, mm10
Supplementary files format and content: CpG.cov and GpC.cov files containing methylation information for CpG and GpC sites.
Supplementary files format and content: counts.txt file containing gene expression information.


title: mESC_9d_nucleus_4


title: smart_seq2_3


title: mESC_6d_nucleus_6


title: mESC_9d_nucleus_3


title: mESC_9d_nucleus_2


title: mESC_9d_nucleus_5


title: smart_seq2_2


title: mESC_6d_nucleus_5


title: mESC_6d_nucleus_4


title: smart_seq2_1


title: S462TY, untreated, 2 hr, batch 1, biol rep2


title: S462TY, untreated, 2 hr, batch 1, biol rep3


title: AMAR_RNA_12


title: mESC_6d_nucleus_2


title: mESC_3d_nucleus_7


title: mESC_6d_nucleus_3


title: AMAR_RNA_10


title: mESC_6d_nucleus_1


title: AMAR_RNA_8


title: mESC_3d_nucleus_6


title: AMAR_RNA_7


title: AMAR_RNA_9


title: AMAR_RNA_6


title: mESC_3d_nucleus_4


title: AMAR_RNA_5


title: mESC_3d_nucleus_3


title: mESC_3d_nucleus_2


title: bulk_RNA_2


title: AMAR_RNA_4


title: AMAR_RNA_3


title: mESC_0d_nucleus_5


title: mESC_3d_nucleus_1


title: bulk_RNA_1


title: mESC_0d_nucleus_6


title: AMAR_RNA_2


title: AMAR_RNA_1


title: scBS_3


title: mESC_0d_nucleus_3


title: scBS_2


title: AMAR_RNA_11


title: mESC_0d_nucleus_4


title: mESC_0d_nucleus_2


title: mESC_3d_nucleus_5


title: scBS_1


title: mESC_0d_nucleus_1


title: pgWAT TG, CNO 1h_9

first: Johan

last: Ruud

address: Medicinaregatan 11

description:
Ruud_4_S4_L001_R1_001
rawcounts_pgWAT_CNO1h.txt

data_processing:
Raw data fastq files were created using BCL to FASTQ file converter bcl2fastq v2.20.0.422 and then further processed following the recommended workflow on the Lexogen BlueBee QuantSeq platform (quadriceps clamped and pgWAT CNO 1h) or Lexogen’s in-house pipeline (pgWAT CNO 6h).
Unique Molecular Identifiers (UMIs) were identified using UMI-tools v1.1.2, sequencing adapters and low-quality bases were trimmed with BBMap/BBDuk v38.96 (quadriceps clamped and pgWAT CNO 1h). For pgWAT 6h, no UMIs were used, and trimming was performed using cutadapt v1.18.
Trimmed reads were aligned to the mouse reference genome (GRCm39 for quadriceps clamped and pgWAT CNO 1h  and mmu_GRCm38.101 for pgWAT CNO 6h) with the Star aligner v2.7.10 (quadriceps clamped and pgWAT CNO 1h) or v2.6.1a (pgWAT CNO 6h).
Assembly: GRCm39 for quadriceps and pgWAT CNO 1h; mmu_GRCm38.101 for pgWAT CNO 6h
Supplementary files format and content: Tab-delimited text files include raw counts for each sample.

source_name: pgWAT

extract_protocol:
RNA was extracted using RNeasy Lipid Tissue Mini Kit (perigonadal WAT) and RNeasy Fibrous Tissue Midi Kit with Proteinase K digestion (whole m. quadriceps from clamped mice), according to Qiagen’s instructions. On-column DNase digestion using RNAse-Free DNAse Set (Qiagen) was applied.
Libraries were generated using the QuantSeq 3' mRNA-Seq Library Prep kit from Lexogen (FWD), purified with the Purification module kit from Lexogen, indexed with the UMI Second Strand Synthesis Module for QuantSeq FWD (Illumina, Read 1), and Lexogen UDI 12 nt Unique Dual Indexing Add-on Kits: A2 (UDI 12A 0097-0192, Cat. No. 119.384, Lexogen)(quadriceps clamped and pgWAT CNO 1h), or using the QuantSeq 3' mRNA-Seq Library Prep Kit FWD for Illumina (Lexogen, 015UG009V0260) following standard procedures (as outlined in the user guide: https://www.lexogen.com/wp-content/uploads/2021/08/015UG009V0260_QuantSeq_Illumina_2021-08-16.pdf) (pgWAT CNO 6h).

value: pgWAT

tag: genotype

value: TG

value: CNO 1 mg/kg 1h


title: bulk_nuclei_2


title: PAX6-barcode phasing

city: Edinburgh

first: Grzegorz

last: Kudla

address: Crewe Road

department: MRC HGU

country: United Kingdom

institute: University of Edinburgh

description:
a region of the plasmid containing the barcodes, PAX6, and GAL4 was excised from the vector followed by BluePippin purification and sequenced using PacBio Sequel II and 20 hours of movie collection time
barcode_consensus.csv

library_source: other

data_processing:
For pax6_le9_assay, Data from the run was transferred from the NextSeq 550 instrument to a computer running Linux and a sample sheet was created to allow the generation of demultiplexed FASTQ files using Bcl2fastq2 v2.20.0.422, using adapter stringency 0.9.
For pax6_blx_assay, Basecall data was produced by the NextSeq 1000/2000 Control Software (Version 1.4.1.39716).
Following demultiplexing of the pax6_le9_assay and pax6_blx_assay, the regions flanking the 30 nt barcodes were trimmed using trimgalore then barcodes counted and variant fitness scores calculated using the Enrich2 tool (Rubin et al. 2017)
Assembly: NA
Supplementary files format and content: barcode counts calculated with the Enrich2 tool (Rubin et al. 2017)
Supplementary files format and content: Barcode:variant phasing was achieved using the alignparse Python package (Crawford et al. 2016)
Library strategy: Barcode amplicon sequencing

molecule: other

source_name: synthetic DNA

growth_protocol: Competition assays were performed using a complete supplement mixture without histidine (Formedium) and yeast nitrogen base without amino acids (Formedium) media, supplemented with 2% glucose. To begin, the barcoded PAX6 variant library was transformed into two separate strains, LE9 and BLX, in two independent assays. The transformation process followed the protocol described in the Yeastmaker™ Yeast Transformation System 2 User Manual (Takara Bio), yielding approximately 2 x 106 and 7 x 106 transformants for LE9 and BLX strains, respectively. Transformed cells were then inoculated into 500 ml of liquid media and incubated at 30°C and 230 RPM for 12-24 hours until reaching an OD600 of approximately 1.0. Subsequently, approximately 7.5 x 108 cells were transferred to fresh media and grown for an additional 12 hours (T0). The T0 cultures were then split into two parallel lineages. All cultures were then maintained between an OD600 of 0.05 and 1.0 by passaging every 12 hours for a total of 36 hours (Timepoints 1-3).

extract_protocol:
Plasmid isolation was achieved using the protocol described by Fowler et al. (2014), which in summary used a freeze-thaw cycle and zymolyase cell wall digestion steps were coupled with Qiaprep spin miniprep kit (Qiagen) column purification
Samples from each timepoint were prepared for next-generation sequencing using a single limited-cycle PCR. Barcodes were amplified using primers possessing overhangs that contained sequencing primer annealing sequences, unique dual indexes, and P5/P7 Illumina adapter sequences (Table S1). 50 µl PCR reactions were performed for each timepoint using Phusion High-Fidelity PCR Master Mix with HF Buffer (NEB) with 20 to 50ng of template isolated plasmid DNA. Each reaction was then thermocycled using the following conditions: (1) initial denaturation at 98°C for 30 seconds, (2) incubation at 98°C for 8 seconds, (3) incubation at 69°C for 20 seconds, (4) incubation at 72°C for 8 seconds, (5) incubation at 72°C for 7 minutes. Steps 2 to 4 were repeated for 12 to 19 cycles (< 20). Multiple replicate 50 µl reactions were performed for each timepoint to ensure enough PCR product was generated. 2.5ul of Exo I nuclease (NEB) was then added directly to each ‘dirty’ PCR product and incubated at 37°C for 1 hour, followed by purification using QIAquick PCR Purification Kit (Qiagen). Samples were further purified by 2% E-Gel SizeSelect agarose gel (Invitrogen). The resulting products were purified using QIAquick PCR Purification Kit (Qiagen), after which all samples were pooled at equimolar amounts (quantified by QuBit [Invitrogen]) and then quantitated by Bioanalyzer (Agilent).

treatment_protocol: Geneticin was  added to one lineage of each strain (LE9; 400 µg/ml, BLX; 500 µg/ml) starting from timepoint 0

value: synthetic DNA


title: pgWAT TG, CNO 1h_8

description:
Ruud_82_S82_L001_R1_001
rawcounts_pgWAT_CNO1h.txt


title: bulk_nuclei_1


title: AMAR_nucleus_12


title: DMS Plasmid Library, full long-read sequence

city: SAINT LOUIS

first: Barak

middle: Alon

last: Cohen

state: MO

address: 4523 CLAYTON AVE CB #8510

department: Genetics

institute: Washington University School of Medicine

description: instrument model: PacBio Revio

data_processing:
*library strategy: Barcode amplicon sequencing
Reads were cleaned with fastp (v0.23, with default parameters). Barcodes were extracted and counted using a custom script. vBCs were mapped to variants using the results of the PacBio long-read sequencing of the barcoded plasmid library. vBCs failing to match an expected barcode from the PacBio sequencing were error-corrected up to a Hamming distance of 1, if and only if they could be unambiguously mapped to an expected variant.
Assembly: Alignment not performed
Supplementary files format and content: *.extracted_barcodes.counts.parquet: table of read counts for each vBC-rBC pair, including assigned library variant
Supplementary files format and content: barcode_to_variant_map.tsv: table mapping vBC sequences to library variants, as called from long-read plasmid sequencing data

extract_protocol:
Genomic DNA was extracted from each fraction using a Monarch Genomic DNA Purification Kit (NEB #T3010) following the manufacturer's recommended protocol.
Barcode sequences were amplified from gDNA using a two-step protocol: gDNA was first amplified with primers JLSPr141–144 and JLSPr165–168+171+172 using Q5 High-Fidelity DNA Polymerase (NEB #M0491) for 20 cycles with an annealing temperature of 65°C, and then with primers IDT10_i7_NN and IDT10_i5_NN, where NN is replaced with the unique indexing barcode ID, for sample multiplexing (10 cycles, 65°C annealing temperature).


title: Replicate 4, Fraction C

source_name: LP+Reporter cells (this study)

value: LP+Reporter cells (this study)


title: pgWAT TG, CNO 1h_7

description:
Ruud_12_S12_L001_R1_001
rawcounts_pgWAT_CNO1h.txt


title: Replicate 4, Fraction B


title: Replicate 4, Fraction D


title: Replicate 4, Fraction A


title: AMAR_nucleus_11


title: pgWAT TG, CNO 1h_6

description:
Ruud_83_S83_L001_R1_001
rawcounts_pgWAT_CNO1h.txt


title: Replicate 3, Fraction D


title: Replicate 3, Fraction B


title: Replicate 3, Fraction C


title: AMAR_nucleus_10


title: AMAR_nucleus_9


title: pgWAT TG, CNO 1h_5

description:
Ruud_75_S75_L001_R1_001
rawcounts_pgWAT_CNO1h.txt


title: pgWAT TG, CNO 1h_4

description:
Ruud_27_S27_L001_R1_001
rawcounts_pgWAT_CNO1h.txt


title: Replicate 2, Fraction C


title: Replicate 3, Fraction A


title: AMAR_nucleus_8


title: Replicate 2, Fraction B


title: Replicate 2, Fraction D


title: pgWAT TG, CNO 1h_3

description:
Ruud_11_S11_L001_R1_001
rawcounts_pgWAT_CNO1h.txt


title: pgWAT TG, CNO 1h_2

description:
Ruud_3_S3_L001_R1_001
rawcounts_pgWAT_CNO1h.txt


title: Replicate 2, Fraction A


title: AMAR_nucleus_6


title: Replicate 1, Fraction B


title: pgWAT WT, CNO 1h_9

description:
Ruud_90_S90_L001_R1_001
rawcounts_pgWAT_CNO1h.txt

value: WT


title: AMAR_nucleus_5


title: Replicate 1, Fraction A


title: pgWAT WT, CNO 1h_8

description:
Ruud_74_S74_L001_R1_001
rawcounts_pgWAT_CNO1h.txt


title: AMAR_nucleus_3


title: AMAR_nucleus_4


title: pgWAT WT, CNO 1h_7

description:
Ruud_66_S66_L001_R1_001
rawcounts_pgWAT_CNO1h.txt


title: pgWAT WT, CNO 1h_6

description:
Ruud_35_S35_L001_R1_001
rawcounts_pgWAT_CNO1h.txt


title: AMAR_nucleus_2


title: Canine cutaneous histiocytoma, group 3 according to Cockerell & Slauson 1979, reanalysis, lymphocyte enriched, FFPE, 3

city: Berlin

first: Alina

middle: Katharina

last: Loriani Fard

address: Robert-von-Ostertag Straße 15

department: Department of Veterinary Medicine

institute: Freie Universität Berlin

description: re-analysis of GSM8142034

hyb_protocol: 150 to 250ng of total RNA were hybridized to the nCounter Canine IO Panel XT CodeSets (NanoString Technologies, Inc., Seattle, WA, USA). Hybridized samples were processed following the manufacturer’s protocols (protocol ID: MAN-10023-11, MAN-10056-06) and loaded onto the nCounter MAX Analysis System’s (NanoString) Prep Station for purification and immobilization on sample cartridges.

scan_protocol: These were transferred to the Digital Analyzer for data collection following the manufacturer’s user manual (protocol ID: MAN-C0035-08).

data_processing: Following the workflow described in the manufacturer’s user manuals (MAN-C0019-08, MAN-C0011-04), the reporter library files (RLF) and reporter code count (RCC) files were imported into the nSolver 4.0 Analysis Software. Quality control and normalisation followed default settings.

label: NanoString

organism: Canis lupus familiaris

source_name: FFPE tumor tissue, group 3

extract_protocol: Total RNA was extracted utilizing the PureLink FFPE Total RNA Isolation Kit (Thermo Fisher Scientific Inc.). After DNase I treatment 150 to 250ng total RNA was used for library construction.

tag: pooled sample

value: no

tag: breed

value: Pug

tag: age (years)

value: male


title: Canine cutaneous histiocytoma, group 3 according to Cockerell & Slauson 1979, reanalysis, lymphocyte enriched, FFPE, 1

description: re-analysis of GSM8142032

value: Rottweiler

tag: Sex

value: male neutered


title: Canine cutaneous histiocytoma, group 3 according to Cockerell & Slauson 1979, reanalysis, lymphocyte enriched, FFPE, 2

description: re-analysis of GSM8142033

value: Beagle

value: female


title: AMAR_nucleus_1


title: Canine cutaneous histiocytoma, group 3 according to Cockerell & Slauson 1979, reanalysis, lymphocyte enriched, FFPE, 5

description: re-analysis of GSM8142036

value: Jack Russell Terrier


title: Canine cutaneous histiocytoma group 1 according to Cockerell & Slauson 1979, reanalysis, FFPE, 5

description: re-analysis of GSM8142020

source_name: FFPE tumor tissue, group 1

value: French Bulldog


title: AMAR_nucleus_7


title: Canine cutaneous histiocytoma, group 3 according to Cockerell & Slauson 1979, reanalysis, lymphocyte enriched, FFPE, 4

description: re-analysis of GSM8142035

value: Bullterrier


title: Canine cutaneous histiocytoma, group 1 according to Cockerell & Slauson 1979, reanalysis, FFPE, 4

description: re-analysis of GSM8142019

value: Boxer


title: Canine cutaneous histiocytoma, group 1 according to Cockerell & Slauson 1979, reanalysis, FFPE, 3

description: re-analysis of GSM8142018

value: Terrier

value: n/s


title: pgWAT TG, CNO 6h_6

description:
Ruud_0082
rawcounts_pgWAT_CNO6h.txt

value: pgWAT

value: TG

value: CNO 1 mg/kg 6h


title: pgWAT TG, CNO 6h_5

description:
Ruud_0080
rawcounts_pgWAT_CNO6h.txt


title: pgWAT TG, CNO 1h_1

description:
Ruud_51_S51_L001_R1_001
rawcounts_pgWAT_CNO1h.txt

value: CNO 1 mg/kg 1h


title: pgWAT WT, CNO 1h_4

description:
Ruud_19_S19_L001_R1_001
rawcounts_pgWAT_CNO1h.txt

value: WT


title: Replicate 1, Fraction D

value: LP+Reporter cells (this study)


title: pgWAT WT, CNO 1h_3

description:
Ruud_67_S67_L001_R1_001
rawcounts_pgWAT_CNO1h.txt


title: pgWAT TG, CNO 6h_4

description:
Ruud_0079
rawcounts_pgWAT_CNO6h.txt


title: Canine cutaneous histiocytoma, group 1 according to Cockerell & Slauson 1979, reanalysis, FFPE, 2

description: re-analysis of GSM8142017

value: no

value: Goldendoodle

value: male


title: Replicate 1, Fraction C


title: pgWAT WT, CNO 1h_2

description:
Ruud_59_S59_L001_R1_001
rawcounts_pgWAT_CNO1h.txt


title: A375 Lamin A KO  Nuc rep 1 (FAM120A)

city: Tel Aviv

first: Daniel

last: Benhalevy

address: Tel Aviv University, Green Bldg. Room 205

department: Shmunis School of Biomedicine and Cancer Research

country: Israel

institute: Tel-Aviv University

data_processing:
Illumina Nova-seq 6000 platform was used for sequencing
Basecalling was done using bcl2fastq V2.17.1
The reads were aligned to the hg38 genome using PARalyzer
normalized reads and clusters were combined in a csv file
Assembly: hg38
Supplementary files format and content: PARalyzer output

molecule: nuclear RNA

growth_protocol: SHSY5Y cells were cultured in RPMI media supplemented with 10% Fetal Bovine Serum and 1% Penicillin-Streptomycin. A375 cells were cultured with DMEM supplemented with 10% Fetal Bovine Serum and 1% Penicillin-Streptomycin. Lamin A knockout cells were generated in using PITCH-CRISPR-Cas9-microhomology-mediated end-joining. Lamin A knock out cells were cultured with respective complete media complemented with 2 μg/ml puromycin and 350 μg/ml G418.

extract_protocol:
Cells were fractinated into cytoplasmic and nuclear lysates and clarified by centrifugation. First AGO / FAM120A proteins were enriched by immunoprecipitation with T6B peptide or anti-FAM120A antibody. After washing the beads, RNase T1 digestion was performed, 3´ends of the RNA fragments were dephosphorylated using CIP, and RNA was fluorescently 3´end-labeled using T4 Rnl2(1–249)K227Q, followed by dephosporylation with T4 PNK. RNA-protein complexes were separated by SDS-PAGE and excised. After proteinase K treatment, RNA was extracted and 5' end labelled with T4 RNA ligase. Following small RNA cDNA library preparation was performed.
Ligation products were reverse transcribed and amplified by PCR.

treatment_protocol: 16 h before cell harvesting cells were treated with  4-thiouridine (4SU)  at a final concentration of 100 μM. Just before harvesting cells were crosslinked with 312 nm UV-light for 5 min.

tag: ip molecule

value: FAM120A antibody

value: Lamin A KO

value: 4SU and 312 UV light


title: pgWAT TG, CNO 6h_2

description:
Ruud_0076
rawcounts_pgWAT_CNO6h.txt


title: pgWAT WT, CNO 1h_5

description:
Ruud_91_S91_L001_R1_001
rawcounts_pgWAT_CNO1h.txt


title: Canine cutaneous histiocytoma, group 1 according to Cockerell & Slauson 1979, reanalysis, FFPE, 1

description: re-analysis of GSM8142016

value: French Bulldog

value: male neutered


title: pgWAT WT, CNO 6h_6

description:
Ruud_0084
rawcounts_pgWAT_CNO6h.txt


title: pgWAT TG, CNO 6h_1

description:
Ruud_0073
rawcounts_pgWAT_CNO6h.txt


title: A375 Lamin A KO Cyto rep 1 (FAM120A)

molecule: cytoplasmic RNA


title: A375 Lamin A KO Nuc rep 2 (FAM120A)


title: pgWAT WT, CNO 6h_2

description:
Ruud_0075
rawcounts_pgWAT_CNO6h.txt


title: pgWAT WT, CNO 6h_1

description:
Ruud_0074
rawcounts_pgWAT_CNO6h.txt


title: pgWAT WT, CNO 1h_1

description:
Ruud_43_S43_L001_R1_001
rawcounts_pgWAT_CNO1h.txt


title: SHSY5Y Lamin A KO  Nuc rep 1 (FAM120A)


title: quadriceps TG, CNO, clamped_10

description:
Ruud_53_S53_L001_R1_001
rawcounts_quadriceps_clamped.txt

source_name: quadriceps

value: quadriceps


title: SHSY5Y Lamin A KO  Cyto rep 2 (FAM120A)


title: A375 Lamin A KO  Cyto rep 2 (FAM120A)


title: quadriceps TG, CNO, clamped_9

description:
Ruud_54_S54_L001_R1_001
rawcounts_quadriceps_clamped.txt

value: CNO 1 mg/kg clamp


title: SHSY5Y Lamin A KO Cyto rep 1 (FAM120A)


title: quadriceps TG, CNO, clamped_8

description:
Ruud_62_S62_L001_R1_001
rawcounts_quadriceps_clamped.txt


title: pgWAT WT, CNO 6h_4

description:
Ruud_0081
rawcounts_pgWAT_CNO6h.txt


title: pgWAT WT, CNO 6h_3

description:
Ruud_0077
rawcounts_pgWAT_CNO6h.txt


title: SHSY5Y Lamin A KO Nuc rep 2 (FAM120A)


title: pgWAT WT, CNO 6h_5

description:
Ruud_0083
rawcounts_pgWAT_CNO6h.txt


title: MLVQ93

city: ILLKIRCH

first: Delphine

last: Duteil

address: 1 rue Laurent Fries

institute: IGBMC

data_processing:
Image analysis and base calling were performed using RTA 2.7.7 and bclconvert 3.8.4.
Assembly: mm10

source_name: skeletal muscle

extract_protocol: P3048 : ChIP samples were purified using SPRIselect beads (Beckman-Coulter, Villepinte, France) and quantified using the Qubit 4 fluorimeter (Thermo Fischer Scientific, Illkirch, France). ChIP-seq libraries were prepared from 1.8 to 10 ng of double-stranded purified DNA using the MicroPlex Library Preparation kit v3 (C05010001, Diagenode, Seraing, Belgium), according to manufacturer's instructions. In the first step, the DNA was repaired and yielded molecules with blunt ends. In the next step, stem-loop adaptors with blocked 5 prime ends were ligated to the 5 prime end of the genomic DNA, leaving a nick at the 3 prime end. The adaptors cannot ligate to each other and do not have single-strand tails, avoiding non-specific background. In the final step, the 3 prime ends of the genomic DNA were extended to complete library synthesis and Illumina compatible indexes were added through a PCR amplification (7 + 5 cycles). Amplified libraries were purified and size-selected using SPRIselect beads (Beckman Coulter) to remove unincorporated primers and other reagents.

value: skeletal muscle

tag: antibody

value: wild-type


title: MLVQ91


title: pgWAT TG, CNO 6h_3

description:
Ruud_0078
rawcounts_pgWAT_CNO6h.txt

value: pgWAT

value: TG


title: neonatal, EC, rep2, H3K27ac

city: Chapel Hill

first: Li

last: Qian

state: North Carolina

address: 111 Mason Farm Road, MBRB

department: Department of Pathology

institute: UNC

data_processing:
bcl2convert v3.8.2-12 for demultiplexing
Standard CUT&Tag Analysis protocol used to align (bowtie2) and filter (samtools) reads
Peaks were identified using SEACR top 0.01
Differential peaks were identfied by comparing identified peaks to control samples using DESeq2
Assembly: mm10
Supplementary files format and content: bigWig
Library strategy: CUT&Tag

source_name: heart

growth_protocol: Lonza EGM2 media

extract_protocol:
Bench top CUT&Tag V.3
Bench top CUT&Tag V.3

treatment_protocol: retroviral infection of select samples

value: heart

value: endothelial


title: neonatal, EC, rep1, H3K27ac


title: quadriceps TG, CNO, clamped_7

description:
Ruud_85_S85_L001_R1_001
rawcounts_quadriceps_clamped.txt


title: A375 Lamin A KO  Nuc rep 1 (AGO)

value: T6B peptide


title: quadriceps TG, CNO, clamped_5

description:
Ruud_21_S21_L001_R1_001
rawcounts_quadriceps_clamped.txt


title: quadriceps TG, CNO, clamped_4

description:
Ruud_5_S5_L001_R1_001
rawcounts_quadriceps_clamped.txt


title: A375 Lamin A KO  Cyto rep 2 (AGO)


title: DMS Plasmid Library, barcode amplicon

data_processing:
Reads were cleaned with fastp (v0.23, with default parameters). Barcodes were extracted and counted using a custom script. vBCs were mapped to variants using the results of the PacBio long-read sequencing of the barcoded plasmid library. vBCs failing to match an expected barcode from the PacBio sequencing were error-corrected up to a Hamming distance of 1, if and only if they could be unambiguously mapped to an expected variant.
Assembly: Alignment not performed
Supplementary files format and content: *.extracted_barcodes.counts.parquet: table of read counts for each vBC-rBC pair, including assigned library variant
Supplementary files format and content: barcode_to_variant_map.tsv: table mapping vBC sequences to library variants, as called from long-read plasmid sequencing data


title: A375 Lamin A KO Cyto rep 1 (AGO)


title: quadriceps TG, CNO, clamped_3

description:
Ruud_69_S69_L001_R1_001
rawcounts_quadriceps_clamped.txt


title: quadriceps TG, CNO, clamped_2

description:
Ruud_22_S22_L001_R1_001
rawcounts_quadriceps_clamped.txt


title: Etv2, rep2, H3K27ac

value: Etv2 iEC


title: wild type nuclei, 1.25 nM Dam, rep 2

data_processing:
Paired-end data were aligned to yeast genome using Bowtie 2
bam files were analysed to obtain DNA fragment ends and coverage: "Cuts" and "Occupancy" files.
The 'fcut' ratio for each nucleotide in each chromosome was calculated as the fraction: no. of ends/coverage.
fcut data are provided here as .wig files
Assembly: SacCer3
Library strategy: qDA-seq (Chereji et al. (2019) Genome Research 29, 1985-1995)

extract_protocol:
Genomic DNA was purified from yeast cells by extracting proteins three times with SDS, washing out the SDS, then removing the cell wall using lytic enzyme. The DNA was purified by chloroform extraction and isopropanol precipitation and a 70% ethanol wash. The DNA was further purified using Beckman-Coulter Ampure beads at a 0.4:1 volume ratio.
Genomic DNA was digested with excess DpnI and sonicated to ~300 bp fragments. Paired-end libraries were prepared using the New England Biolabs kits and protocols.

value: strain


title: SEG, rep2, H3K27ac

value: SEG iEC


title: quadriceps TG, CNO, clamped_1

description:
Ruud_14_S14_L001_R1_001
rawcounts_quadriceps_clamped.txt


title: A375 WT Cyto rep 2 (AGO)

value: WT


title: A375 WT Nuc rep 1 (AGO)


title: SEG, rep1, H3K27ac


title: Etv2, rep1, H3K27ac


title: control, rep2, H3K27ac

value: fibroblast


title: A375 WT Cyto rep 1 (AGO)

value: 4SU and 312 UV light


title: quadriceps TG, CNO, clamped_6

description:
Ruud_37_S37_L001_R1_001
rawcounts_quadriceps_clamped.txt


title: wild type nuclei, 0.31 nM Dam, rep 2


title: control, rep1, H3K27ac


title: quadriceps WT, CNO, clamped_9

description:
Ruud_45_S45_L001_R1_001
rawcounts_quadriceps_clamped.txt


title: A375 Lamin A KO Nuc rep 2 (AGO)

value: Lamin A KO


title: quadriceps WT, CNO, clamped_10

description:
Ruud_61_S61_L001_R1_001
rawcounts_quadriceps_clamped.txt


title: wild type nuclei, 0.16 nM Dam, rep 2


title: DR-C-24h

city: Charlottesville

first: Ana Karina

last: de Olliiveirra

address: 1340 Jefferson Park Avenue

institute: UVA

hyb_protocol: The RNA samples (100 ng) were incubated for 16 h at 65 °C in a hybridization buffer containing the CodeSet (reporter and capture probes). Hybridized samples were processed using the Prep Station using high sensitivity protocol, 3 h per 12-sample cartridge.

scan_protocol: The Prep Station purifies the RNA/probe complexes and places them in a cartridge where they are immobilized and aligned for data collection. Data acquisition was carried out in the NanoString nCounter Digital Analyzer with the ‘Max’ Field of View (FOV) setting to 555 images per sample in a 6 h scan per cartridge.

data_processing:
NanoString gene expression profiling was conducted using the mouse nCounter Fibrosis V2 Panel (NanoString Technologies, Seattle, WA, USA), which contains probes specific to 760 endogenous genes and 10 housekeeping genes (ACAD9, ARMH3, CNOT10, GUSB, MTMR14, NOL7, NUBBP1, PGK1, PPIA, RPLP0).   Data were analyzed using ROSALIND (https://rosalind.bio/), with a hyper-scale cloud developed by ROSALIND, Inc. (San Diego, CA), accessed on March 05, 2023. The quality control of samples was verified using spike-ins of positive and negative probes, and housekeeping expression levels.
Normalization, fold changes, and p-values were calculated using criteria provided by NanoString. ROSALIND follows the nCounter Advanced Analysis protocol of dividing counts within a lane by the geometric mean of the normalizer probes from the same lane. The geNorm algorithm was used to select normalizer probes in the Bioconductor package NormqPCR, removing candidate housekeepers with the least stable expression relative to other candidates.

label: Barcode probe

source_name: gastrocnemius muscle

label_protocol: A total of 21 blocks of FFPE muscle mouse tissue (Control, B. asper (BA) BA-1h, BA-6h, BA-24h, D. russelii (DR) DR-1h, DR-6h, DR-24h) were used for RNA extraction.

extract_protocol: Four slices of 10 µm thickness from each selected block were deparaffinized using D-Limonene (Sigma), digested with proteinase K, and isolated using RNeasy® Plus Mini Kit QIAGEN, according to the manufacturer's protocol. The final volume of extracted RNA was 14 µL. RNA concentration and purity were assessed using a NanoDrop instrument. Sample concentration was measured at 260 nm and 280 nm, and the ratio of optical density 260/280 and 260/230 were used to test for protein and phenol contamination respectively.

treatment_protocol: Groups of mice (CD-1 strain, 18-20 grams) received an intramuscular injection, in the right gastrocnemius, of 30 µg venom. Control mice were injected with 50 µL PBS only. At the time intervals of 1 h, 6 h, 24 h following injection, groups of three mice were sacrificed by CO2 inhalation, and the tissue was excised and added to 10% formalin solution in water.

tag: strain

value: CD-1 strain

value: 30 ug D. russelli venom

tag: group


title: DR-B-24h

description: NanoString gene expression profiling was conducted using the mouse nCounter Fibrosis V2 Panel (NanoString Technologies, Seattle, WA, USA), which contains probes specific to 760 endogenous genes and 10 housekeeping genes

growth_protocol: Groups of mice (CD-1 strain, 18-20 grams)


title: SHSY5Y Lamin A KO Nuc rep 2 (AGO)


title: A375 WT Nuc rep 2 (AGO)


title: wild type nuclei, No Dam, rep 2


title: wild type nuclei, 1.25 nM Dam, rep 1


title: wild type nuclei, 0.63 nM Dam, rep 2


title: DR-A-24h


title: quadriceps WT, CNO, clamped_6

description:
Ruud_93_S93_L001_R1_001
rawcounts_quadriceps_clamped.txt

value: quadriceps

value: CNO 1 mg/kg clamp


title: wild type nuclei, 0.63 nM Dam, rep 1


title: DR-C-6h


title: SHSY5Y Lamin A KO Cyto rep 1 (AGO)


title: wild type nuclei, 0.31 nM Dam, rep 1


title: SHSY5Y Lamin A KO  Cyto rep 2 (AGO)


title: DR-B-6h


title: SHSY5Y WT Nuc rep 2 (AGO)


title: DR-A-6h


title: wild type nuclei, No Dam, rep 1


title: quadriceps WT, CNO, clamped_8

description:
Ruud_29_S29_L001_R1_001
rawcounts_quadriceps_clamped.txt


title: SHSY5Y WT Nuc rep 1 (AGO)


title: wild type nuclei, 0.16 nM Dam, rep 1


title: SHSY5Y WT Cyto rep 2 (AGO)


title: DR-C-1h


title: quadriceps WT, CNO, clamped_3

description:
Ruud_30_S30_L001_R1_001
rawcounts_quadriceps_clamped.txt


title: Isw1/Chd1-degron live cells, 480 min auxin, 240 min SM, rep 2

value: MATa ade2-1 can1-100 leu2-3,112 trp1-1 ura3-1 isw1-degron-3HA::URA3 chd1-degron-3HA::LEU2 ho::TIR1-Dam-degron-3HA-KanMX


title: quadriceps WT, CNO, clamped_5

description:
Ruud_77_S77_L001_R1_001
rawcounts_quadriceps_clamped.txt


title: quadriceps WT, CNO, clamped_7

description:
Ruud_13_S13_L001_R1_001
rawcounts_quadriceps_clamped.txt


title: quadriceps WT, CNO, clamped_2

description:
Ruud_38_S38_L001_R1_001
rawcounts_quadriceps_clamped.txt


title: quadriceps WT, CNO, clamped_1

description:
Ruud_6_S6_L001_R1_001
rawcounts_quadriceps_clamped.txt


title: SHSY5Y WT Cyto rep 1  (AGO)


title: Isw1/Chd1-degron live cells, 360 min auxin, 120 min SM, rep 2


title: DR-A-1h


title: KO naïve CD4+ T cells biol rep 3

city: Frederick

first: Thiruvaimozhi

last: Abimannan

address: Building 560, Room 22-6

department: CDBL

institute: National Cancer Institute

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene
Assembly: Mus Musculus(GRCm38/mm10)
Supplementary files format and content: gene_count.xls
Supplementary files format and content: gene_fpkm.xls

source_name: CD4+T cells

growth_protocol: Cells were cultured in RPMI 1640 supplemented with 10% fetal bovine serum, 100 U/ml penicillin, 100 mg/ml streptomycin and 50 mM 2-mercaptoethanol referred as complete medium (CM)

extract_protocol:
Total RNA was extracted for each of the 3 bioological replicates from WT Th17, KO Th17, WT Th17 with NAC, KO Th17 with NAC, WT Th17 with 3-KDS, KO Th17 with 3-KDS, WT naive and KO naive CD4+ T cells using Trizol and RNA-Clean and concentrater column. About 1.3 ug of RNA in 25ul was submitted for bulk RNAseq using Illumina machine (HWI-ST1276). Total RNA sample quality was measured using Nanodrop (OD260/280), gel electrophoresis and Agilent 2100 to measure RNA integrity.
Susequently, mRNA was enriched using oligo(dT) beads, fragmented, cDNA was synthesized using random hexamers, followed by the second strand cDNA synthesis using dTTP. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries was pooled and sequenced on Illumina platforms, according to effective library concentration and data amount.

treatment_protocol: For Th17 differentiation, naïve CD4+ T cells at 1 million cells/ml concentration were activated by plate bound anti-CD3 (5 mg/ml) and soluble anti-CD28 (2 mg/ml) for 4 days along with hTGF-β1 (5 ng/ml), IL-6 (40 ng/ml), anti-IL-4 (10 mg/ml) and anti-IFN-γ (10 mg/ml).

value: CD4+T cells

value: SPTLC1 defecient (KO)

value: KO naive CD4+ T cells


title: BA-C-24h

value: 30 ug B. asper venom


title: A375 Lamin A KO AGO1-4 IP rep 3

first: Aishe

last: Sarshad

address: Medicinaregatan 9C

department: Dept.of Biochemistry & Cell Biology

data_processing:
Illumina Nova-seq 6000 platform was used for sequencing
sequences were aligned to human miRNAs using bowtie2 and quantified using bedtools coverage
normalized counts in excel file
Assembly: hg38
Supplementary files format and content: raw counts file

extract_protocol:
Cells were fractinated into cytoplasmic and nuclear lysates and clarified by centrifugation. First AGO proteins were enriched by immunoprecipitation with T6B peptide. After washing the beads they were treated with Trizol and the RNA extracted. 3'adapter and 5'adapter were added generating small RNA cDNA library preparation
Ligation products were reverse transcribed and amplified by PCR.

treatment_protocol: no treatment

value: T6B peptide


title: A375 Lamin A KO AGO1-4 IP rep 2


title: quadriceps WT, CNO, clamped_4

description:
Ruud_46_S46_L001_R1_001
rawcounts_quadriceps_clamped.txt


title: Isw1/Chd1-degron live cells, 300 min auxin, 60 min SM, rep 2

last: Clark

address: 6 Center Drive Bldg 6A Rm 2A02


title: SHSY5Y Lamin A KO  Nuc rep 1 (AGO)


title: A375 Lamin A KO AGO1-4 IP rep 1


title: DR-B-1h


title: Isw1/Chd1-degron live cells, 270 min auxin, 30 min SM, rep 2


title: BA-B-24h


title: Isw1/Chd1-degron live cells, 420 min auxin, 180 min SM, rep 2


title: BA-A-24h


title: KO naïve CD4+ T cells biol rep 2


title: KO naïve CD4+ T cells biol rep 1


title: Isw1/Chd1-degron live cells, 240 min auxin, 0 min SM, rep 2


title: BA-B-6h


title: Isw1/Chd1-degron live cells, 180 min auxin, rep 2


title: A375 WT AGO1-4 IP rep 2


title: BA-C-6h


title: Isw1/Chd1-degron live cells, 0 min auxin, rep 2


title: WT naïve CD4+ T cells biol rep 2

value: WT naive CD4+ T cells


title: A375 WT AGO1-4 IP rep 1


title: WT naïve CD4+ T cells biol rep 1


title: BA-A-6h


title: Isw1/Chd1-degron live cells, 480 min auxin, 240 min SM, rep 1

value: strain


title: BA-C-1h


title: SHSY5Y Lamin A KO AGO1-4 IP rep 3


title: Isw1/Chd1-degron live cells, 420 min auxin, 180 min SM, rep 1


title: SHSY5Y Lamin A KO AGO1-4 IP rep 2


title: Isw1/Chd1-degron live cells, 360 min auxin, 120 min SM, rep 1


title: BA-B-1h


title: KO Th17 with NAC biol rep 3

value: KO Th17 with NAC


title: KO Th17 with NAC biol rep 2


title: SHSY5Y Lamin A KO AGO1-4 IP rep 1


title: KO Th17 with NAC biol rep 1


title: SHSY5Y WT AGO1-4 IP rep 2

value: WT


title: BA-A-1h


title: A375 WT AGO1-4 IP rep 3


title: SHSY5Y WT AGO1-4 IP rep 3


title: Control-2

value: 50 ul PBS

value: Control


title: Isw1/Chd1-degron live cells, 300 min auxin, 60 min SM, rep 1


title: Isw1/Chd1-degron live cells, 270 min auxin, 30 min SM, rep 1


title: WT Th17 with NAC biol rep 3

value: WT Th17 with NAC


title: WT Th17 with NAC biol rep 2


title: WT Th17 with NAC biol rep 1


title: Isw1/Chd1-degron live cells, 240 min auxin, 0 min SM, rep 1


title: Control-1

value: CD-1 strain


title: SHSY5Y WT AGO1-4 IP rep 1


title: Isw1/Chd1-degron live cells, 180 min auxin, rep 1


title: D7 Postpartum

city: Ann Arbor

first: Alexander

last: Vargo

state: United States

address: 4909 Buhl Building, 1241 E. Catherine St.

department: Human Genetics

institute: University of Michigan

description: 10x Genomics

data_processing:
Raw paired-end sequence data were processed and aligned using CellRanger v4+ (version noted in each matrix.mtx file)
The filtered gene expression matrix is uploaded, containing only cell-associated reads
Assembly: GRCh38
Supplementary files format and content: matrix.mtx.gz: sparse matrix (MEX format) listing nonzero entries in the cell-by-gene matrix (rows correspond to genes, columns correspond to cells)
Supplementary files format and content: features.tsv.gz: tab-separated array providing the correspondence between the rows of the cell-by-gene matrix and genes (Ensembl IDs and gene names)
Supplementary files format and content: barcodes.tsv.gz: list of barcodes used as unique cell identifiers (column names for cell-by-gene matrix)

source_name: Uterus

extract_protocol:
Fresh full thickness human uterus samples obtained both during surgery for benign indications and from organ donors were used as tissue sources.  When possible, the whole tissue sample was dissected into two anatomic segments (endometrium, myometrium).  These segments separately were used to create a single cell suspensions by mechanical dissociation and digestion with collagenase at 37C. Live cells were collected by flow cytometry.
10x Chromium scRNA-seq; Single-cell suspensions were processed and single cell RNA-seq data were generated using the 10X Genomics Chromium Controller by the University of Michigan Advanced Genomics Core.

value: Uterus


title: KO Th17 with 3-KDS biol rep 3

value: KO Th17 with 3-KDS


title: D6 Postmenopausal

description: 10x Genomics


title: KO Th17 with 3-KDS biol rep 2


title: Myo5

description: 10x Genomics


title: Isw1/Chd1-degron live cells, 0 min auxin, rep 1

first: David


title: RH4_neopetrotaurine_B_2uM_6h

first: Javed

last: Khan

address: 37 Convent Dr.

department: Genetics Branch

institute: NCI, NIH

data_processing:
RNA-seq was mapped using STAR with hg19 as reference.
RNA-seq read abundance for each gene counted (TPM) using RSEM
RNA-seq raw reads normalized using DESeq2
Assembly: hg19/GRCh37
Supplementary files format and content: RNA-seq processed files are quantification matrices of TPM (transcripts per million) at the gene level.

source_name: muscle

growth_protocol: Cells were maintained in DMEM with 10% FBS and Penn/Strep at 37 °C incubation.

extract_protocol:
Bulk RNA is extracted using QIAGEN Rneasy Plus Mini Kit.
Illumina TruSeq Stranded mRNA and Total RNA library prep

treatment_protocol: Cells were treated with either DMSO or compound of interest for 6 hours.

value: muscle

value: Rhabdomyosarcoma

value: wt

value: 6 hr

value: Neopetrotaurine B


title: KO Th17 with 3-KDS biol rep 1

value: CD4+T cells

value: SPTLC1 defecient (KO)


title: RH4_neopetrotaurine_A_2uM_6h

value: Neopetrotaurine A


title: WT Th17 with 3-KDS biol rep 3

value: WT Th17 with 3-KDS


title: RH4_DMSO_6h_220228

value: DMSO


title: Chd1-degron live cells, 420 min auxin, 180 min SM, rep 2

institute: NICHD, NIH

value: strain

value: MATa ade2-1 can1-100 leu2-3,112 trp1-1 ura3-1 chd1-degron-3HA::LEU2 ho::TIR1-Dam-degron-3HA-KanMX


title: SCMC_neopetrotaurine_C_11uM_6h

value: SCMC

value: Neopetrotaurine C


title: WT Th17 with 3-KDS biol rep 2

value: WT


title: Endo4

description: 10x Genomics

source_name: Uterus (Endometrium)

value: Uterus (Endometrium)


title: Myo4

description: 10x Genomics

source_name: Uterus (Myometrium)

value: Uterus (Myometrium)


title: Chd1-degron live cells, 270 min auxin, 30 min SM, rep 2


title: Myo3

description: 10x Genomics


title: RH4_neopetrotaurine_C_3uM_6h

value: muscle


title: KO Th17 biol rep 3

value: KO Th17


title: SCMC_neopetrotaurine_A_7uM_6h

value: Rhabdomyosarcoma

value: wt


title: SCMC_neopetrotaurine_B_7uM_6h

value: 6 hr

value: Neopetrotaurine B


title: Chd1-degron live cells, 240 min auxin, 0 min SM, rep 2


title: Chd1-degron live cells, 300 min auxin, 60 min SM, rep 2


title: KO Th17 biol rep 2

value: CD4+T cells

value: SPTLC1 defecient (KO)


title: Chd1-degron live cells, 480 min auxin, 240 min SM, rep 2


title: Endo2

description: 10x Genomics


title: SCMC_DMSO_6h_220228


title: Chd1-degron live cells, 180 min auxin, rep 2


title: Myo2

description: 10x Genomics


title: Chd1-degron live cells, 360 min auxin, 120 min SM, rep 2


title: KO Th17 biol rep 1


title: MOLM13 CUT&RUN IgG 24h GSK2879552

city: Portland

first: William

middle: Montgomery

last: Yashar

state: OR

address: 3181 SW Sam Jackson Park Rd

department: Knight Cancer Institute

institute: OHSU

description: CUT&RUN

data_processing:
Library strategy: CUT&RUN
Libraries were aligned to the human genome (hg38) using Bowtie2 and the following options --local --very-sensitive-local --no-unal --no-mixed --no-discordant --phred33 -I 10 -X 700
Peaks were called using GoPeaks and the following option -mdist 1000
CPM normalized tracks were generated with DeepTools
CPM normalized bigwigs merged with UCSC bigWigMerge
Bedgraphs coverted to bigwigs with UCSC bedGraphToBigWig
Differential peaks were identified using DESeq2 with default parameters
Genome_build: hg38

source_name: MOLM13 cell line

extract_protocol:
Libraries were prepared using NEBNext Ultra II DNA Library Prep Kit (NEB)
The OHSU Massively Parallel Sequencing Shared Resource (MPSSR) performed the sequencing at 37 BP PE

tag: time point

value: 24 hours

value: Normal Rabbit IgG (#2729, Cell Signaling Technologies)


title: Chd1-degron live cells, 480 min auxin, 240 min SM, rep 1

city: Bethesda

value: strain


title: WT Th17 with 3-KDS biol rep 1

value: WT Th17 with 3-KDS


title: Endo3

description: 10x Genomics

tag: tissue


title: Myo1

description: 10x Genomics


title: Endo1

description: 10x Genomics


title: WT Th17 biol rep 2

value: WT Th17


title: MOLM13 CUT&RUN IgG 24h Combination

description: CUT&RUN

value: 1 nM quizartinib + 100 nM GSK2879552


title: WT Th17 biol rep 1

value: WT


title: Chd1-degron live cells, 300 min auxin, 60 min SM, rep 1

value: MATa ade2-1 can1-100 leu2-3,112 trp1-1 ura3-1 chd1-degron-3HA::LEU2 ho::TIR1-Dam-degron-3HA-KanMX


title: rNAPC2 replicate 5

city: Mainz

first: Wolfram

last: Ruf

address: Langenbeckstrasse 1

institute: CTH Mainz

data_processing:
Reads were mapped to GRCm39 build 39 genome with Star on the fly
Assembly: MM GRCm39 build 39
Supplementary files format and content: Tab delimited text file

source_name: Spleen

growth_protocol: mice were bred under identical housing conditions  in the central animal facility of the University Medical Center Mainz

extract_protocol:
CD11c+cells were isolated by MACS and trizol treated
Libraries were constructed at Novogene

treatment_protocol: MRL-lpr mice receiving 0.5 mg/kg rNAPc2 or saline control every other day for 3 weeks starting at an age of 11 weeks

value: Spleen

value: Dendritic Cell

value: MRL/MpJ-Faslpr/J


title: rNAPC2 replicate 4


title: MOLM13 CUT&RUN PU.1 24h Combination replicate 3

description: CUT&RUN

value: PU.1 (MA5-15064, Invitrogen)


title: MOLM13 CUT&RUN PU.1 24h Combination replicate 2

description: CUT&RUN


title: MOLM13 CUT&RUN PU.1 24h Combination replicate 1

description: CUT&RUN


title: rNAPC2 replicate 3


title: Chd1-degron live cells, 0 min auxin, rep 2


title: Chd1-degron live cells, 240 min auxin, 0 min SM, rep 1


title: WT Th17 biol rep 3


title: MOLM13 CUT&RUN PU.1 24h GSK2879552 replicate 3

description: CUT&RUN


title: rNAPC2 replicate 2


title: Chd1-degron live cells, 180 min auxin, rep 1


title: MOLM13 CUT&RUN PU.1 24h GSK2879552 replicate 1

description: CUT&RUN


title: Chd1-degron live cells, 0 min auxin, rep 1


title: MOLM13 CUT&RUN PU.1 24h Quizartinib replicate 3

description: CUT&RUN

value: 1 nM quizartinib


title: rNAPC2 replicate 1


title: Saline replicate 5

value: Saline


title: Chd1-degron live cells, 360 min auxin, 120 min SM, rep 1


title: MOLM13 CUT&RUN PU.1 24h Quizartinib replicate 2

description: CUT&RUN


title: Isw1-degron live cells, 480 min auxin, 240 min SM, rep 2

value: MATa ade2-1 can1-100 leu2-3,112 trp1-1 ura3-1 isw1-degron-3HA::URA3 ho::TIR1-Dam-degron-3HA-KanMX


title: MOLM13 CUT&RUN IgG 24h DMSO

description: CUT&RUN

value: DMSO


title: Chd1-degron live cells, 420 min auxin, 180 min SM, rep 1


title: Saline replicate 4


title: Saline replicate 3


title: MOLM13 CUT&RUN PU.1 24h Quizartinib replicate 1

description: CUT&RUN


title: Isw1-degron live cells, 300 min auxin, 60 min SM, rep 2


title: Isw1-degron live cells, 360 min auxin, 120 min SM, rep 2


title: Saline replicate 2


title: MOLM13 CUT&RUN PU.1 24h DMSO replicate 2

description: CUT&RUN


title: MOLM13 CUT&RUN IgG 24h Quizartinib

description: CUT&RUN


title: MOLM13 CUT&RUN PU.1 24h DMSO replicate 3

description: CUT&RUN


title: 4mo, 2c treated, replicate 4

city: Boston

first: Wayne

last: Mitchell

address: 77 Avenue Louis Pasteur

institute: Brigham and Women's Hospital

data_processing:
Fastq files were mapped to the genome using STAR v.2.7.2b
Assembly: mm10 (GRCm38.p6)
Supplementary files format and content: excel file containing raw counts for each sample

source_name: ear

growth_protocol: Fibroblasts were cultured in DMEM/F12 media supplemented with 1X anti-anti, 10% FBS, 1X beta-mercaptoethanol, and 1X non-essential amino acids (Gibco). Cells were grown at 37°C with 5% CO2 and 3% O2.

extract_protocol:
Cells were washed 3x with PBS, and lysed in the dish with Trizol. Isolation of total RNA was performed according to manufacturer's protocol (direct-zol, Zymo Research)
Libraries were prepared with TruSeq Stranded mRNA LT Sample Prep Kit according to TruSeq Stranded mRNA Sample Preparation Guide, Part # 15031047 Rev. E
mRNA-seq (polyA-enrichment)

treatment_protocol: Cells were cultured in 6-well plates with 3 ml media in each well. Chemical cocktails were added to the media such that final DMSO and PBS concentration was each 0.5%. Media and treatments were replaced every 3 days.

value: ear

tag: age

value: fibroblast

value: 2c treated


title: MOLM13 CUT&RUN GFI1 24h Combination replicate 3

description: CUT&RUN

value: 24 hours

value: GFI1 (ab21061, Abcam)


title: Saline replicate 1


title: Isw1-degron live cells, 270 min auxin, 30 min SM, rep 2

tag: cell line

value: strain


title: MOLM13 CUT&RUN PU.1 24h DMSO replicate 1

description: CUT&RUN

tag: cell type


title: Isw1-degron live cells, 180 min auxin, rep 2


title: 4mo, 7c treated, replicate 4

tag: treatment

value: 7c treated


title: Isw1-degron live cells, 240 min auxin, 0 min SM, rep 2


title: Chd1-degron live cells, 270 min auxin, 30 min SM, rep 1


title: 4mo, untreated, replicate 4

value: untreated


title: Isw1-degron live cells, 420 min auxin, 180 min SM, rep 2


title: MOLM13 CUT&RUN GFI1 24h Combination replicate 2

description: CUT&RUN

value: 1 nM quizartinib + 100 nM GSK2879552


title: 4mo, 2c treated, replicate 3


title: MOLM13 CUT&RUN GFI1 24h Combination replicate 1

description: CUT&RUN


title: MOLM13 CUT&RUN GFI1 24h GSK2879552 replicate 3

description: CUT&RUN


title: Isw1-degron live cells, 480 min auxin, 240 min SM, rep 1


title: 4mo, 7c treated, replicate 3


title: Isw1-degron live cells, 420 min auxin, 180 min SM, rep 1


title: Isw1-degron live cells, 360 min auxin, 120 min SM, rep 1


title: Isw1-degron live cells, 0 min auxin, rep 2


title: 4mo, 2c treated, replicate 2


title: Isw1-degron live cells, 300 min auxin, 60 min SM, rep 1


title: Isw1-degron live cells, 270 min auxin, 30 min SM, rep 1


title: 4mo, 7c treated, replicate 2


title: 4mo, untreated, replicate 3


title: 4mo, untreated, replicate 2


title: Isw1-degron live cells, 240 min auxin, 0 min SM, rep 1


title: 4mo, 2c treated, replicate 1


title: Isw1-degron live cells, 0 min auxin, rep 1


title: MOLM13 CUT&RUN GFI1 24h DMSO replicate 2

description: CUT&RUN


title: MOLM13 CUT&RUN GFI1 24h Quizartinib replicate 2

description: CUT&RUN


title: MOLM13 CUT&RUN GFI1 24h DMSO replicate 1

description: CUT&RUN


title: 4mo, 7c treated, replicate 1


title: Isw1-degron live cells, 180 min auxin, rep 1


title: MOLM13 CUT&RUN GFI1 24h DMSO replicate 3

description: CUT&RUN


title: Rsc8-degron live cells, 480 min auxin, 240 min SM, rep 2

value: MATa ade2-1 can1-100 leu2-3,112 trp1-1 ura3-1 rsc8-degron-3HA::LEU2 ho::TIR1-Dam-degron-3HA-KanMX


title: 4mo, untreated, replicate 1


title: MOLM13 CUT&RUN GFI1 24h GSK2879552 replicate 1

description: CUT&RUN


title: 20mo, 7c treated, replicate 4


title: 20mo, 2c treated, replicate 4


title: WT naïve CD4+ T cells biol rep 3

value: CD4+T cells

value: WT

value: WT naive CD4+ T cells


title: MOLM13 CUT&RUN GFI1 24h GSK2879552 replicate 2

description: CUT&RUN


title: MOLM13 CUT&Tag IgG with CEBPA 24h Combination replicate 3

description: CUT&Tag

data_processing:
Library strategy: CUT&Tag
Libraries were aligned to the human genome (hg38) using Bowtie2 and the following options --local --very-sensitive-local --no-unal --no-mixed --no-discordant --phred33 -I 10 -X 700
Peaks were called using GoPeaks and the following option -mdist 1000
CPM normalized tracks were generated with DeepTools
CPM normalized bigwigs merged with UCSC bigWigMerge
Bedgraphs coverted to bigwigs with UCSC bedGraphToBigWig
Differential peaks were identified using DESeq2 with default parameters
Genome_build: hg38

extract_protocol:
Libraries were prepared according to published protocol Kaya-Okur et al 2019
The OHSU Massively Parallel Sequencing Shared Resource (MPSSR) performed the sequencing at 37 BP PE

value: Normal Rabbit IgG (#2729, Cell Signaling Technologies)


title: MOLM13 CUT&Tag IgG with CEBPA 24h Combination replicate 2

description: CUT&Tag


title: 20mo, 2c treated, replicate 3


title: Rsc8-degron live cells, 360 min auxin, 120 min SM, rep 2


title: MOLM13 CUT&Tag IgG with CEBPA 24h GSK2879552 replicate 3

description: CUT&Tag


title: 20mo, untreated, replicate 4


title: Rsc8-degron live cells, 270 min auxin, 30 min SM, rep 2


title: Rsc8-degron live cells, 300 min auxin, 60 min SM, rep 2


title: MOLM13 CUT&RUN GFI1 24h Quizartinib replicate 3

description: CUT&RUN

value: 1 nM quizartinib


title: MOLM13 CUT&RUN GFI1 24h Quizartinib replicate 1

description: CUT&RUN


title: 20mo, 7c treated, replicate 3


title: MOLM13 CUT&Tag IgG with CEBPA 24h GSK2879552 replicate 2

description: CUT&Tag


title: 20mo, untreated, replicate 3


title: Rsc8-degron live cells, 240 min auxin, 0 min SM, rep 2


title: Rsc8-degron live cells, 420 min auxin, 180 min SM, rep 2


title: 20mo, 7c treated, replicate 2


title: MOLM13 CUT&Tag IgG with CEBPA 24h Combination replicate 1

description: CUT&Tag


title: Rsc8-degron live cells, 0 min auxin, rep 2


title: MOLM13 CUT&Tag IgG with CEBPA 24h GSK2879552 replicate 1

description: CUT&Tag


title: Rsc8-degron live cells, 480 min auxin, 240 min SM, rep 1


title: 20mo, 2c treated, replicate 2


title: Rsc8-degron live cells, 180 min auxin, rep 2


title: MOLM13 CUT&Tag IgG with CEBPA 24h Quizartinib replicate 2

description: CUT&Tag


title: MOLM13 CUT&Tag IgG with CEBPA 24h Quizartinib replicate 3

description: CUT&Tag


title: 20mo, 7c treated, replicate 1


title: MOLM13 CUT&Tag IgG with CEBPA 24h DMSO replicate 3

description: CUT&Tag


title: Rsc8-degron live cells, 270 min auxin, 30 min SM, rep 1


title: 20mo, untreated, replicate 1


title: MOLM13 CUT&Tag IgG with CEBPA 24h Quizartinib replicate 1

description: CUT&Tag


title: 20mo, 2c treated, replicate 1


title: Rsc8-degron live cells, 360 min auxin, 120 min SM, rep 1


title: Rsc8-degron live cells, 300 min auxin, 60 min SM, rep 1


title: Rsc8-degron live cells, 420 min auxin, 180 min SM, rep 1


title: 20mo, untreated, replicate 2


title: MOLM13 CUT&Tag IgG with CEBPA 24h DMSO replicate 2

description: CUT&Tag