title: Rh30_PAX3-FOXO1-FKBP cells_PolIIS5_ChIP-seq_dTAG2hr_rep2


title: Chern_City_103

status: Public on Dec 14 2022

type: genomic

city: Bethesda

first: Alexander

middle: Christian

last: Harris

state: Maryland

address: 50 South Drive

department: National Human Genome Research Institute

country: USA

institute: National Institutes of Health

hyb_protocol: Resuspended DNA was loaded onto BeadChips arrays and hybridized overnight at at 48oC.  Single-base extension and allele-specific staining was performed by hand.

scan_protocol: After allele-specific staining BeadChip arrays were coated with XC4/ethanol , dried for 1 hour and scanned on a BeadArray Reader (Illumina).

data_processing: Image data was analyzed using GenomeStudio with GT module (Illumina).

label: Cy3, Cy5

molecule: genomic DNA

organism: Canis lupus familiaris

source_name: Whole Blood

label_protocol: 200ng of genomic DNA was amplified in an overnight reaction at 37oC. The amplified DNA was enzymatically fragmented, precipitated with isopropanol, and resuspended in hybridization buffer.

extract_protocol: Genomic DNA was extracted from whole blood using Proteinase K and phenol/chloroform with standard protocols.

tag: location

value: Chernobyl City

tag: tissue

value: Whole Blood

tag: breed

value: Mixed Breed


title: SupFig3C 28 Celsius WT background version1 T1 plant 05

type: SRA

city: Los Angeles

first: Zhenhui

last: Zhong

address: 610 Charles E Young Dr East

department: Department of Molecular, Cell and Developmental Biology

institute: University of California, Los Angeles

library_source: genomic

data_processing:
Amplicon sequencing:  Reads were first quality and adaptor trimmed using Trim Galore and then mapped to the target genomic region by the BWA aligner. Sorted and indexed bam files were used as input files for further analysis by the CrispRvariants R package. Each mutation pattern with corresponding read counts was exported by the CrispRvariants R package. After assessing all control samples, a criterion to classify reads as edited reads was established: only reads with a >= 3 bp deletion or insertion (indel, mainly as deletions) of the same pattern (indels of same size starting at the same location) with >= 100 read counts from a sample were counted as edited reads. This criterion is established due to the observation of 1 bp indels and occasionally 2 bp indels with read numbers >100 in control samples. Also, larger indels that occur at very low frequencies (much lower than 100 reads) were observed in control samples. These observations indicate that occasional PCR inaccuracy and low-quality sequencing in a small fraction of reads can result in the indel patterns with corresponding read number ranges as stated above in control samples with the typical sequencing depth in our experiments (1-5 million reads/sample). By employing such stringent criteria, it is believed that the editing signals counted are true signals indicating editing events. Additionally, for FWA gRNA5 and gRNA6 targeted regions, there are long stretches of adenines near these target regions. Due to the high error rate of polymerases amplifying long stretches of adenines, reads with indels only within these stretches of adenines were not counted as true deletions. For amplicon sequencing result analysis of maize protoplast, the criterion to classify reads as edited reads was established: only reads with a >= 3bp deletion or insertion (indel, mainly as deletions) of the same pattern (indels of same size starting at the same location) with >= 10 read counts from a sample were counted as edited reads. The adjustment of the criterion was based on the fact that these amplicon sequencing was of less depth (performed by the iSeq 100) compared to the amplicon libraries of Arabidopsis protoplasts.
Whole genome sequencing for off-target analysis: For variant calling, whole genome sequencing reads were aligned to the TAIR10 reference genome using BWA mem (v0.7.17)53 with default parameters. GATK (4.2.0.0)39 MarkDuplicatesSpark was used to remove PCR duplicate reads. Then GATK HaplotypeCaller was used to call raw variants. Raw SNPs were filtered with QD < 2.0, FS > 60.0, MQ < 40.0, and SOR > 4.0. Raw InDels were filtered with QD < 2.0, FS > 200.0, and SOR > 10.0 and used for base quality score recalibration. The recalibrated bam file was further applied to GATK and Strelka (v2.9.2)40 for SNPs/InDel calling. Only SNPs/InDels called by both GATK and Strelka were used for further analysis. The intersection of GATK and Strelka  SNPs/InDels were filtered by removing identical SNPs/InDels in the rdr6-15 background by BedTools (v2.26.0)54. Variants with coverage lower than 30 reads were removed. Variant loci at which the ratio of the reads with the WT allele over the reads with variant allele larger than three were removed. For heterozygous alleles, at a coverage level of 30 reads, the chance of observing WT reads /mutation allele reads >3 is 0.26% (binomial distribution, one-tailed P=0.0026).
Assembly: tair10
Supplementary files format and content: Crispvariant_result, with detected SNV and indels in amplicon sequencing  vcf, raw variants called with GATK or strelka2 comparing to tair10 reference genome sequence
Library strategy: amplicon sequencing

organism: Arabidopsis thaliana

source_name: Arabidopsis leaf tissue

growth_protocol: To grow Arabidopsis plants for protoplast preparation, Col-0 and fwa-4 epi-mutant plants were grown under a 12-hour light/12-hour dark photoperiod and with low light condition for 3-4 weeks. To grow maize plants for protoplast isolation, B73 seeds were soaked in water overnight and planted in half peat moss and half vermiculite. After three days of light incubation, emerged seedlings were transferred to dark until the 2nd leaf was 10-15 cm long.   Transgenic T1 plants were screened with half MS plates with 40 μg/ml hygromycin B. For 28 °C treatment of T1 plants, stratified seeds on half MS plates with hygromycin B were incubated at 28 °C and resistant T1 plants were transferred to soil after about a week, and put back to 28 °C for a total of two weeks incubation at 28 °C. T1 plants were then moved to a greenhouse (23 °C) for the rest of the life cycle.  To support the growth of albino seedlings in T2 generation, 3% sucrose was supplemented to half MS plates when needed.

extract_protocol:
Amplicon sequencing: DNA was extracted from protoplast samples and leaves of transgenic plants with Qiagen DNeasy plant mini kit. The amplicon was obtained using two rounds of PCR. Amplification primers for the first round of PCR were designed to have the 3’ sequence of the primers flanking a 200-300 bp fragment of the genomic area targeted by the guide RNA of interest. The 5’ part of the primer contained a sequence which will be bound by common sequencing primers. After 25 cycles of the first round of PCR amplification, the reaction was purified using 1x Ampure XP beads (Beckman Coulter A63881). The eluate was used as template for the second round of PCR using the Phusion enzyme and 12 cycles of amplification. The second round of PCR was designed so that indexes were added to each sample. The samples were then purified using 0.8x Ampure XP beads. Part of the purified libraries were run on a 2% agarose gel to check for size and absence of primer dimer (fragments below 200 bp considered as primer dimer). Then amplicons were sent for sequencing with NovaSeq 6000 or iSeq 100 platform.
Whole genome sequencing: DNA from single Arabidopsis seedlings was extracted with the Qiagen DNeasy plant mini kit and sheared to 300 bp size with a Covaris. Library preparation was performed with Tecan Ovation Ultralow V2 DNA-seq kit. The libraries were sequenced with the NovaSeq 6000 platform.

value: leaf tissue

tag: developmental stage

value: 3-4 weeks

tag: strain

tag: background genotype

value: wild type

tag: target locus


title: Rh30_PAX3-FOXO1-FKBP cells_PolIIS5_ChIP-seq_dTAG2hr_rep1

city: Boston

first: Susu

last: Zhang

state: MA

address: 360 Longwood Ave, LC6102

department: Pediatric Oncology

institute: Dana-Farber Cancer Institute

data_processing:
Raw FASTQ data were trimmed by Trimmomatic (v0.32).
Paired end reads were aligned to a concatenated human and Drosophila genome (hg19 and dm3) using Bowtie2.
Peaks were called using MACS2.
Differential analysis was performed using DiffBind and DESeq2.
BigWig files were generated and normalized using DESeq2 normalization factor
Assembly: hg19 and dm3
Supplementary files format and content: bigWig file
Supplementary files format and content: peak file

organism: Homo sapiens

source_name: Rh30 cell line

growth_protocol: Cells were cultured in RPMI-1640 containing 10% FetalPlex and supplemented with 1% L-Glutamine and 1% penicillin/streptomycin.

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody.
NEBNext Ultra II DNA Library Prep Kit

treatment_protocol: DMSO, 500 nM dTAG47

tag: cell line

value: Rh30 cell line

tag: treatment

value: 500nM dTAG47

tag: antibody

value: anti-PolII-Ser5 (Abcam, #ab5131)


title: SupFig3C 28 Celsius WT background version1 T1 plant 02


title: SupFig3B Version2 PDS3gR10 23 Celsius rep2

source_name: Arabidopsis mesophyll protoplast

value: mysophyll protoplast


title: SupFig3B Version2 PDS3gR10 28 Celsius rep2


title: SupFig3C 28 Celsius WT background version1 T1 plant 08


title: Chern_City_101


title: Rh30_PAX3-FOXO1-FKBP cells_PolIIS5_ChIP-seq_DMSO_rep2

value: DMSO


title: SupFig3B GFPcontrol PDS3gR10region 23 Celsius


title: SupFig3B Version2 PDS3gR10 23 Celsius rep1


title: SupFig6A WT protoplast vCasphi RNP PDS3gR10 rep3


title: SupFig3B Version2 PDS3gR10 28 Celsius rep1


title: SupFig3B GFPcontrol PDS3gR10region 28 Celsius


title: Rh30_PAX3-FOXO1-FKBP cells_PolIIS2_ChIP-seq_dTAG4hr_rep1

value: anti-PolII-Ser2 (Abcam, #ab5059)


title: Chern_City_100


title: Chern_City_105


title: Rh30_PAX3-FOXO1-FKBP cells_PolIIS2_ChIP-seq_dTAG2hr_rep1


title: Rh30_PAX3-FOXO1-FKBP cells_PolIIS2_ChIP-seq_dTAG4hr_rep2


title: Chern_City_99


title: Chern_City_98


title: SupFig3AandSupFig3D 23 Celsius incubated rdr6 background version1 T1 plant 42


title: SupFig3AandSupFig3D 23 Celsius incubated rdr6 background version1 T1 plant 41


title: SupFig3AandSupFig3D 23 Celsius incubated rdr6 background version1 T1 plant 40


title: SupFig3AandSupFig3D 23 Celsius incubated rdr6 background version1 T1 plant 39


title: Rh30_PAX3-FOXO1-FKBP cells_PolIIS2_ChIP-seq_DMSO_rep2


title: SupFig3AandSupFig3D 23 Celsius incubated rdr6 background version1 T1 plant 37


title: SupFig3AandSupFig3D 23 Celsius incubated rdr6 background version1 T1 plant 38


title: SupFig3AandSupFig3D 23 Celsius incubated rdr6 background version1 T1 plant 36


title: Rh30_PAX3-FOXO1-FKBP cells_PolIIS2_ChIP-seq_dTAG2hr_rep2


title: Chern_City_96


title: SupFig3AandSupFig3D 23 Celsius incubated rdr6 background version1 T1 plant 35


title: Chern_City_94


title: Chern_City_95


title: Rh30_PAX3-FOXO1-FKBP cells_PolIIS2_ChIP-seq_DMSO_rep1


title: SupFig3AandSupFig3D 23 Celsius incubated rdr6 background version1 T1 plant 34


title: SupFig3AandSupFig3D 23 Celsius incubated rdr6 background version1 T1 plant 33


title: Rh30_PAX3-FOXO1-FKBP cells_PolII_ChIP-seq_dTAG4hr_rep2

value: anti-PolII (Santa Cruz, #sc899)


title: SupFig3AandSupFig3D 23 Celsius incubated rdr6 background version1 T1 plant 32


title: SupFig3AandSupFig3D 23 Celsius incubated rdr6 background version1 T1 plant 31


title: Chern_City_93


title: Chern_City_97


title: Rh30_PAX3-FOXO1-FKBP cells_PolII_ChIP-seq_dTAG4hr_rep1


title: Rh30_PAX3-FOXO1-FKBP cells_PolII_ChIP-seq_dTAG2hr_rep1


title: Rh30_PAX3-FOXO1-FKBP cells_PolII_ChIP-seq_dTAG2hr_rep2


title: SupFig3AandSupFig3D 23 Celsius incubated rdr6 background version1 T1 plant 30


title: SupFig3AandSupFig3D 23 Celsius incubated rdr6 background version1 T1 plant 29


title: Chern_City_11


title: Chern_City_92


title: SupFig3AandSupFig3D 23 Celsius incubated rdr6 background version1 T1 plant 25


title: SupFig3AandSupFig3D 23 Celsius incubated rdr6 background version1 T1 plant 24


title: SupFig3AandSupFig3D 23 Celsius incubated rdr6 background version1 T1 plant 23


title: SupFig3AandSupFig3D 23 Celsius incubated rdr6 background version1 T1 plant 26


title: SupFig3AandSupFig3D 23 Celsius incubated rdr6 background version1 T1 plant 27


title: SupFig3AandSupFig3D 23 Celsius incubated rdr6 background version1 T1 plant 28


title: Chern_City_9


title: Rh30_PAX3-FOXO1-FKBP cells_PolII_ChIP-seq_DMSO_rep2


title: Chern_City_8


title: Rh4_PAX3-FOXO1-FKBP cells CUT&RUN_CDK8_dTAG4hr_rep2

data_processing:
Raw FASTQ data were trimmed by Trimmomatic (v0.32).
Paired end reads were aligned to a concatenated human and E.coli genome (hg19 and ecK12MG1655) using Bowtie2.
Peaks were called using Genrich (v. 0.6.1).
Differential analysis was performed using DiffBind and DESeq2.
BigWig files were generated and normalized using the DESeq2 size factors using Deeptools.
Assembly: hg19 and ecK12MG1655
Supplementary files format and content: bigWig file
Supplementary files format and content: peak file
Library strategy: CUT&RUN

source_name: Rh4 cell line

extract_protocol:
Cells were collected and incubated with Concanavalin A-coated beads. Antibodies were used to bind targeted DNA-associated proteins. pAG-Mnase was used to digest targeted regions of the genome. DNA was then extracted using phenol-chloroform
NEBNext Ultra II DNA Library Prep Kit

value: Rh4 cell line

value: anti-CDK8 (Santa Cruz, sc-13155)


title: Rh30_PAX3-FOXO1-FKBP cells_PolII_ChIP-seq_DMSO_rep1


title: SupFig3AandSupFig3D 23 Celsius incubated rdr6 background version1 T1 plant 21


title: SupFig3AandSupFig3D 23 Celsius incubated rdr6 background version1 T1 plant 22


title: SupFig3AandSupFig3D 23 Celsius incubated rdr6 background version1 T1 plant 18


title: SupFig3AandSupFig3D 23 Celsius incubated rdr6 background version1 T1 plant 19


title: Rh4_PAX3-FOXO1-FKBP cells CUT&RUN_CDK8_dTAG4hr_rep1


title: Chern_City_7


title: Chern_City_6


title: Chern_City_5


title: SupFig3AandSupFig3D 23 Celsius incubated rdr6 background version1 T1 plant 17


title: Rh4_PAX3-FOXO1-FKBP cells CUT&RUN_CDK8_dTAG2hr_rep2


title: SupFig3AandSupFig3D 23 Celsius incubated rdr6 background version1 T1 plant 15


title: Chern_City_4


title: SupFig3AandSupFig3D 23 Celsius incubated rdr6 background version1 T1 plant 14


title: Rh4_PAX3-FOXO1-FKBP cells CUT&RUN_CDK8_DMSO_rep2


title: Rh4_PAX3-FOXO1-FKBP cells CUT&RUN_CDK8_dTAG2hr_rep1


title: SupFig3AandSupFig3D 23 Celsius incubated rdr6 background version1 T1 plant 16


title: SupFig3AandSupFig3D 23 Celsius incubated rdr6 background version1 T1 plant 13


title: CNPP_121

value: Chernobyl Nuclear Power Plant


title: Rh4_PAX3-FOXO1-FKBP cells CUT&RUN_CDK8_DMSO_rep1


title: CNPP_120


title: SupFig3AandSupFig3D 23 Celsius incubated rdr6 background version1 T1 plant 10


title: SupFig3AandSupFig3D 23 Celsius incubated rdr6 background version1 T1 plant 20


title: SupFig3AandSupFig3D 23 Celsius incubated rdr6 background version1 T1 plant 08


title: Rh4_PAX3-FOXO1-FKBP cells CUT&RUN_SPT16_dTAG4hr_rep2

value: anti-SPT16 (Cell Signaling, D7I2K #12191)


title: Rh4_PAX3-FOXO1-FKBP cells CUT&RUN_SPT16_dTAG4hr_rep1


title: SupFig3AandSupFig3D 23 Celsius incubated rdr6 background version1 T1 plant 07


title: SupFig3AandSupFig3D 23 Celsius incubated rdr6 background version1 T1 plant 06


title: Chern_City_2

value: Chernobyl City


title: SupFig3AandSupFig3D 23 Celsius incubated rdr6 background version1 T1 plant 05


title: Rh4_PAX3-FOXO1-FKBP cells CUT&RUN_SPT16_dTAG2hr_rep2


title: Chern_City_3

value: Whole Blood


title: Rh4_PAX3-FOXO1-FKBP cells CUT&RUN_SPT16_dTAG2hr_rep1


title: Chern_City_1

value: Mixed Breed


title: SupFig3AandSupFig3D 23 Celsius incubated rdr6 background version1 T1 plant 12

value: leaf tissue


title: SupFig3AandSupFig3D 23 Celsius incubated rdr6 background version1 T1 plant 01

value: 3-4 weeks


title: SupFig3AandSupFig3D 23 Celsius incubated rdr6 background version1 T1 plant 02


title: SupFig3AandSupFig3D 23 Celsius incubated rdr6 background version1 T1 plant 11


title: SupFig3AandSupFig3C WT control plant4

value: wild type


title: Rh4_PAX3-FOXO1-FKBP cells CUT&RUN_SPT16_DMSO_rep1


title: CNPP_119


title: CNPP_122


title: SupFig3AandSupFig3D 23 Celsius incubated rdr6 background version1 T1 plant 04


title: Rh4_PAX3-FOXO1-FKBP cells CUT&RUN_SPT16_DMSO_rep2


title: CNPP_118


title: SupFig3AandSupFig3D 23 Celsius incubated rdr6 background version1 T1 plant 09


title: SupFig3AandSupFig3D 23 Celsius incubated rdr6 background version1 T1 plant 03


title: Rh4_PAX3-FOXO1-FKBP cells CUT&RUN_HEB_dTAG4hr_rep2

value: anti-HEB (Santa Cruz, sc-357)


title: SupFig3AandSupFig3C WT control plant2


title: CNPP_117


title: SupFig3AandSupFig3C 23 Celsius incubated WT background version2 T1 plant 41


title: SupFig3AandSupFig3C WT control plant3


title: Rh4_PAX3-FOXO1-FKBP cells CUT&RUN_HEB_dTAG4hr_rep1

value: 500nM dTAG47


title: SupFig3AandSupFig3C 23 Celsius incubated WT background version2 T1 plant 39


title: SupFig3AandSupFig3C 23 Celsius incubated WT background version2 T1 plant 40


title: SupFig3AandSupFig3C WT control plant1


title: CNPP_116


title: CNPP_115


title: SupFig3AandSupFig3C 23 Celsius incubated WT background version2 T1 plant 38


title: Rh4_PAX3-FOXO1-FKBP cells CUT&RUN_HEB_dTAG2hr_rep1


title: Rh4_PAX3-FOXO1-FKBP cells CUT&RUN_HEB_dTAG2hr_rep2


title: SupFig3AandSupFig3C 23 Celsius incubated WT background version2 T1 plant 37


title: SupFig3AandSupFig3C 23 Celsius incubated WT background version2 T1 plant 36


title: Chern_City_91


title: Rh4_PAX3-FOXO1-FKBP cells CUT&RUN_HEB_DMSO_rep2


title: SupFig3AandSupFig3C 23 Celsius incubated WT background version2 T1 plant 35


title: SupFig3AandSupFig3C 23 Celsius incubated WT background version2 T1 plant 33


title: SupFig3AandSupFig3C 23 Celsius incubated WT background version2 T1 plant 34


title: CNPP_113


title: SupFig3AandSupFig3C 23 Celsius incubated WT background version2 T1 plant 31


title: Rh4_PAX3-FOXO1-FKBP cells CUT&RUN_RUNX1_dTAG4hr_rep2

value: anti-RUNX1 (Santa Cruz, sc-365644)


title: Rh4_PAX3-FOXO1-FKBP cells CUT&RUN_HEB_DMSO_rep1


title: SupFig3AandSupFig3C 23 Celsius incubated WT background version2 T1 plant 30


title: SupFig3AandSupFig3C 23 Celsius incubated WT background version2 T1 plant 29


title: CNPP_114


title: CNPP_29


title: Rh4_PAX3-FOXO1-FKBP cells CUT&RUN_RUNX1_dTAG4hr_rep1


title: SupFig3AandSupFig3C 23 Celsius incubated WT background version2 T1 plant 27


title: CNPP_28


title: SupFig3AandSupFig3C 23 Celsius incubated WT background version2 T1 plant 28


title: Rh4_PAX3-FOXO1-FKBP cells CUT&RUN_RUNX1_dTAG2hr_rep2


title: SupFig3AandSupFig3C 23 Celsius incubated WT background version2 T1 plant 25


title: SupFig3AandSupFig3C 23 Celsius incubated WT background version2 T1 plant 24


title: Rh4_PAX3-FOXO1-FKBP cells CUT&RUN_RUNX1_dTAG2hr_rep1


title: SupFig3AandSupFig3C 23 Celsius incubated WT background version2 T1 plant 23


title: CNPP_26


title: CNPP_27


title: SupFig3AandSupFig3C 23 Celsius incubated WT background version2 T1 plant 22


title: SupFig3AandSupFig3C 23 Celsius incubated WT background version2 T1 plant 32


title: SupFig3AandSupFig3C 23 Celsius incubated WT background version2 T1 plant 21


title: Rh4_PAX3-FOXO1-FKBP cells CUT&RUN_RUNX1_DMSO_rep1


title: CNPP_25


title: SupFig3AandSupFig3C 23 Celsius incubated WT background version2 T1 plant 19


title: SupFig3AandSupFig3C 23 Celsius incubated WT background version2 T1 plant 18


title: CNPP_24


title: Rh4_PAX3-FOXO1-FKBP cells CUT&RUN_MYOD_dTAG4hr_rep2

value: anti-MYOD (Santa Cruz, sc-377460)


title: SupFig3AandSupFig3C 23 Celsius incubated WT background version2 T1 plant 26


title: SupFig3AandSupFig3C 23 Celsius incubated WT background version2 T1 plant 16


title: CNPP_30


title: CNPP_23


title: SupFig3AandSupFig3C 23 Celsius incubated WT background version2 T1 plant 13


title: SupFig3AandSupFig3C 23 Celsius incubated WT background version2 T1 plant 17


title: SupFig3AandSupFig3C 23 Celsius incubated WT background version2 T1 plant 14


title: SupFig3AandSupFig3C 23 Celsius incubated WT background version2 T1 plant 15


title: Rh4_PAX3-FOXO1-FKBP cells CUT&RUN_MYOD_dTAG4hr_rep1


title: Chern_City_89


title: SupFig3AandSupFig3C 23 Celsius incubated WT background version2 T1 plant 12


title: Chern_City_90


title: SupFig3AandSupFig3C 23 Celsius incubated WT background version2 T1 plant 09


title: Rh4_PAX3-FOXO1-FKBP cells CUT&RUN_RUNX1_DMSO_rep2

value: DMSO


title: SupFig3AandSupFig3C 23 Celsius incubated WT background version2 T1 plant 20


title: CNPP_22


title: SupFig3AandSupFig3C 23 Celsius incubated WT background version2 T1 plant 10


title: SupFig3AandSupFig3C 23 Celsius incubated WT background version2 T1 plant 11


title: Rh4_PAX3-FOXO1-FKBP cells CUT&RUN_MYOD_DMSO_rep2


title: Rh4_PAX3-FOXO1-FKBP cells CUT&RUN_MYOD_dTAG2hr_rep2


title: SupFig3AandSupFig3C 23 Celsius incubated WT background version2 T1 plant 08


title: CNPP_21


title: SupFig3AandSupFig3C 23 Celsius incubated WT background version2 T1 plant 06


title: Rh4_PAX3-FOXO1-FKBP cells CUT&RUN_MYOD_DMSO_rep1


title: Rh4_PAX3-FOXO1-FKBP cells CUT&RUN_BRD4_dTAG4hr_rep2

value: anti-BRD4 (Cell Signaling, #E2A7X)


title: Rh4_PAX3-FOXO1-FKBP cells CUT&RUN_MYOD_dTAG2hr_rep1


title: SupFig3AandSupFig3C 23 Celsius incubated WT background version2 T1 plant 05


title: SupFig3AandSupFig3C 23 Celsius incubated WT background version2 T1 plant 07


title: Chern_City_88


title: CNPP_19


title: CNPP_20


title: SupFig3AandSupFig3C 23 Celsius incubated WT background version2 T1 plant 04


title: SupFig3AandSupFig3C 23 Celsius incubated WT background version2 T1 plant 03


title: Rh4_PAX3-FOXO1-FKBP cells CUT&RUN_BRD4_dTAG4hr_rep1


title: SupFig3AandSupFig3C 23 Celsius incubated WT background version1 T1 plant 43


title: SupFig3AandSupFig3C 23 Celsius incubated WT background version2 T1 plant 01


title: Rh4_PAX3-FOXO1-FKBP cells CUT&RUN_BRD4_dTAG2hr_rep1


title: Rh4_PAX3-FOXO1-FKBP cells CUT&RUN_BRD4_DMSO_rep2


title: Rh4_PAX3-FOXO1-FKBP cells CUT&RUN_BRD4_dTAG2hr_rep2


title: SupFig3AandSupFig3C 23 Celsius incubated WT background version1 T1 plant 40


title: CNPP_17


title: CNPP_18


title: Rh4_PAX3-FOXO1-FKBP cells CUT&RUN_BRD4_DMSO_rep1


title: SupFig3AandSupFig3C 23 Celsius incubated WT background version1 T1 plant 39


title: Chern_City_87


title: SupFig3AandSupFig3C 23 Celsius incubated WT background version1 T1 plant 38


title: SupFig3AandSupFig3C 23 Celsius incubated WT background version1 T1 plant 37


title: CNPP_16


title: SupFig3AandSupFig3C 23 Celsius incubated WT background version1 T1 plant 36


title: Chern_City_86


title: Tucidinostate -SK-UT-1 RNA rep4

city: Chicago

first: Qiwei

last: Yang

address: 5841 S. Maryland Avenue

department: Obstetrics and Gynecology

institute: University of Chicago

library_source: transcriptomic

data_processing:
Quasi-mapping and quantification: salmon 1.4.0
Assembly: GRCh38
Supplementary files format and content: gene level raw abdunance in TSV format

molecule: total RNA

source_name: uterine leiomyosarcoma cell line

growth_protocol: The uterine leiomyosarcoma cell line (SK-UT-1) was cultured and maintained in ATCC-formulated Eagle’s Minimum Essential Medium with 10% of fetal bovine serum

extract_protocol:
Cell pellets were  flash-frozen, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The SK-UT-1 cell line was treated with  Tucidinostat (5 uM) or DL-sulforaphane (5 uM) or vehicle control for 48 hours.

value: HDAC inhibitor


title: SupFig3AandSupFig3C 23 Celsius incubated WT background version2 T1 plant 02


title: SupFig3AandSupFig3C 23 Celsius incubated WT background version1 T1 plant 35


title: SupFig3AandSupFig3C 23 Celsius incubated WT background version1 T1 plant 41


title: SupFig3AandSupFig3C 23 Celsius incubated WT background version1 T1 plant 42


title: CNPP_15


title: Chern_City_85


title: SupFig3AandSupFig3C 23 Celsius incubated WT background version1 T1 plant 32


title: SupFig3AandSupFig3C 23 Celsius incubated WT background version1 T1 plant 30


title: SupFig3AandSupFig3C 23 Celsius incubated WT background version1 T1 plant 33


title: Tucidinostate -SK-UT-1 RNA rep2


title: CNPP_14


title: Tucidinostate -SK-UT-1 RNA rep1


title: SupFig3AandSupFig3C 23 Celsius incubated WT background version1 T1 plant 31


title: DL-sulforaphane -SK-UT-1 RNA rep4


title: SupFig3AandSupFig3C 23 Celsius incubated WT background version1 T1 plant 28


title: SupFig3AandSupFig3C 23 Celsius incubated WT background version1 T1 plant 29


title: CNPP_13


title: SupFig3AandSupFig3C 23 Celsius incubated WT background version1 T1 plant 25


title: SupFig3AandSupFig3C 23 Celsius incubated WT background version1 T1 plant 27


title: DL-sulforaphane -SK-UT-1 RNA rep3


title: Tucidinostate -SK-UT-1 RNA rep3


title: SupFig3AandSupFig3C 23 Celsius incubated WT background version1 T1 plant 26


title: SupFig3AandSupFig3C 23 Celsius incubated WT background version1 T1 plant 34


title: CNPP_12


title: DL-sulforaphane -SK-UT-1 RNA rep1


title: VEH SK-UT-1 RNA rep4

value: DMSO (VEH)


title: SupFig3AandSupFig3C 23 Celsius incubated WT background version1 T1 plant 22


title: CNPP_11


title: SupFig3AandSupFig3C 23 Celsius incubated WT background version1 T1 plant 24


title: SupFig3AandSupFig3C 23 Celsius incubated WT background version1 T1 plant 21


title: CNPP_112


title: VEH SK-UT-1 RNA rep3


title: SupFig3AandSupFig3C 23 Celsius incubated WT background version1 T1 plant 20


title: CNPP_111


title: SupFig3AandSupFig3C 23 Celsius incubated WT background version1 T1 plant 16


title: DL-sulforaphane -SK-UT-1 RNA rep2


title: VEH SK-UT-1 RNA rep1


title: VEH SK-UT-1 RNA rep2


title: SupFig3AandSupFig3C 23 Celsius incubated WT background version1 T1 plant 18


title: Chern_City_84


title: CNPP_131


title: SupFig3AandSupFig3C 23 Celsius incubated WT background version1 T1 plant 23


title: SupFig3AandSupFig3C 23 Celsius incubated WT background version1 T1 plant 13


title: whole blood, not ntm disease, CFB2171

city: Vancouver

first: Bradley

last: Quon

state: BC

address: 1081 Burrard Street

department: Department of Medicine

country: Canada

institute: Centre for Heart and Lung Innovation

data_processing:
Untrimmed reads were aligned to the primary human assembly GRCh38.p13 v38 (May 21, 2021) from GENCODE using STAR v 2.7
RSEM v1.3.3 with default parameters was used to produce bam formatted files with gene level quantification
Raw count data was imported to R version 4.1.1 using tximport, and annotated with the Ensembl database version 104 of Bioconductor.
Combat-seq was used to adjust counts according to extraction batch
Assembly: GENCODE GRCh38.p13 v38 (May 21, 2021)
Supplementary files format and content: comma delimited files (.csv) with DESeq raw counts
Supplementary files format and content: comma delimited files (.csv) with DESeq normalized and batch corrected counts

source_name: whole blood

growth_protocol: Whole blood extracted from patients and stored at -70° C in PAXblood gene tubes

extract_protocol:
The PAXgene Blood micro-RNA Kit was used for RNA extraction (in five batches) following the manufacturer’s (QIAGEN) instructions, but omitting the DNA depletion steps
The library preparation was performed using the strand-specific Nextera NEB mRNA kit with adapters AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC and AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT.

value: whole blood

tag: outcome

tag: Sex

value: male

tag: sample date_yyyymmdd

tag: baseline fevpp

tag: baseline fvcpp

tag: ethnicity

value: caucasian

tag: age years


title: SupFig3AandSupFig3C 23 Celsius incubated WT background version1 T1 plant 11


title: SupFig3AandSupFig3C 23 Celsius incubated WT background version1 T1 plant 14


title: CNPP_129

tag: location

value: Chernobyl Nuclear Power Plant


title: CNPP_130

tag: tissue

value: Whole Blood


title: SupFig3AandSupFig3C 23 Celsius incubated WT background version1 T1 plant 12


title: SupFig3AandSupFig3C 23 Celsius incubated WT background version1 T1 plant 09


title: whole blood, not ntm disease, CFB2186


title: whole blood, not ntm disease, CFB2166

value: female


title: SupFig3AandSupFig3C 23 Celsius incubated WT background version1 T1 plant 17

value: leaf tissue


title: SupFig3AandSupFig3C 23 Celsius incubated WT background version1 T1 plant 19

value: 3-4 weeks


title: SupFig3AandSupFig3C 23 Celsius incubated WT background version1 T1 plant 08

value: wild type


title: SupFig3AandSupFig3C 23 Celsius incubated WT background version1 T1 plant 07


title: SupFig3AandSupFig3C 23 Celsius incubated WT background version1 T1 plant 15


title: CNPP_128

tag: breed

value: Mixed Breed


title: whole blood, ntm disease, CFB2163


title: SupFig3AandSupFig3C 23 Celsius incubated WT background version1 T1 plant 05

tag: developmental stage


title: SupFig3AandSupFig3C 23 Celsius incubated WT background version1 T1 plant 06

tag: strain


title: SupFig3AandSupFig3C 23 Celsius incubated WT background version1 T1 plant 04

tag: background genotype


title: CNPP_127


title: Chern_City_82

value: Chernobyl City


title: Chern_City_83


title: whole blood, not ntm disease, CFB2169


title: whole blood, not ntm disease, CFB2160


title: SupFig3AandSupFig3C 23 Celsius incubated WT background version1 T1 plant 01

tag: target locus


title: whole blood, not ntm disease, CFB2152


title: SupFig3AandSupFig3C 23 Celsius incubated WT background version1 T1 plant 10


title: whole blood, ntm disease, CFB2159


title: whole blood, not ntm disease, CFB2149


title: SupFig1B Version2 PDS3gR10 T1 plant 5


title: SupFig1B Version2 PDS3gR10 T1 plant 4


title: SupFig1B Version2 PDS3gR10 T1 plant 6


title: CNPP_132


title: CNPP_126


title: SupFig1B Version2 PDS3gR10 T1 plant 3


title: SupFig1B Version2 PDS3gR10 T1 plant 2


title: SupFig1B Version2 PDS3gR10 T1 plant 1


title: whole blood, not ntm disease, CFB2146


title: CNPP_125


title: SupFig3AandSupFig3C 23 Celsius incubated WT background version1 T1 plant 02


title: whole blood, not ntm disease, CFB2142


title: CNPP_124


title: Fig5C rdr6 background vCasphi pUB10 ribozyme gR10 T1 plant 33


title: Fig5C rdr6 background vCasphi pUB10 ribozyme gR10 T1 plant 35


title: Fig5C rdr6 background vCasphi pUB10 ribozyme gR10 T1 plant 36


title: whole blood, not ntm disease, CFB2140


title: CNPP_110


title: SupFig3AandSupFig3C 23 Celsius incubated WT background version1 T1 plant 03


title: Chern_City_81


title: whole blood, not ntm disease, CFB2138


title: CNPP_109


title: CNPP_108


title: Fig5C rdr6 background vCasphi pUB10 ribozyme gR10 T1 plant 30


title: Fig5C rdr6 background vCasphi pUB10 ribozyme gR10 T1 plant 28


title: Fig5C rdr6 background vCasphi pUB10 ribozyme gR10 T1 plant 29


title: Fig5C rdr6 background vCasphi pUB10 ribozyme gR10 T1 plant 27


title: CNPP_107


title: whole blood, ntm disease, CFB2128


title: Fig5C rdr6 background vCasphi pUB10 ribozyme gR10 T1 plant 31


title: whole blood, not ntm disease, CFB2127


title: Fig5C rdr6 background vCasphi pUB10 ribozyme gR10 T1 plant 25


title: Fig5C rdr6 background vCasphi pUB10 ribozyme gR10 T1 plant 34


title: Fig5C rdr6 background vCasphi pUB10 ribozyme gR10 T1 plant 32


title: whole blood, not ntm disease, CFB2112


title: CNPP_106


title: Fig5C rdr6 background vCasphi pUB10 ribozyme gR10 T1 plant 23


title: Fig5C rdr6 background vCasphi pUB10 ribozyme gR10 T1 plant 22


title: Fig5C rdr6 background vCasphi pUB10 ribozyme gR10 T1 plant 24


title: CNPP_104


title: CNPP_105


title: Fig5C rdr6 background vCasphi pUB10 ribozyme gR10 T1 plant 19


title: whole blood, not ntm disease, CFB2134


title: Fig5C rdr6 background vCasphi pUB10 ribozyme gR10 T1 plant 21


title: Fig5C rdr6 background vCasphi pUB10 ribozyme gR10 T1 plant 20


title: CNPP_103


title: CNPP_102


title: Fig5C rdr6 background vCasphi pUB10 ribozyme gR10 T1 plant 18


title: CNPP_101


title: whole blood, not ntm disease, CFB2108


title: whole blood, not ntm disease, CFB2102


title: whole blood, ntm disease, CFB2098


title: Fig5C rdr6 background vCasphi pUB10 ribozyme gR10 T1 plant 13


title: Fig5C rdr6 background vCasphi pUB10 ribozyme gR10 T1 plant 26


title: CNPP_100


title: Fig5C rdr6 background vCasphi pUB10 ribozyme gR10 T1 plant 17


title: Fig5C rdr6 background vCasphi pUB10 ribozyme gR10 T1 plant 15


title: Fig5C rdr6 background vCasphi pUB10 ribozyme gR10 T1 plant 16


title: whole blood, not ntm disease, CFB2088


title: CNPP_99


title: whole blood, not ntm disease, CFB2087


title: Fig5C rdr6 background vCasphi pUB10 ribozyme gR10 T1 plant 14


title: Fig5C rdr6 background vCasphi pUB10 ribozyme gR10 T1 plant 10


title: Fig5C rdr6 background vCasphi pUB10 ribozyme gR10 T1 plant 12


title: whole blood, ntm disease, CFB2084


title: Fig5C rdr6 background vCasphi pUB10 ribozyme gR10 T1 plant 11


title: CNPP_98


title: Fig5C rdr6 background vCasphi pUB10 ribozyme gR10 T1 plant 09


title: whole blood, ntm disease, CFB2105


title: Fig5C rdr6 background vCasphi pUB10 ribozyme gR10 T1 plant 08


title: CNPP_97


title: whole blood, not ntm disease, CFB2082


title: Fig5C rdr6 background vCasphi pUB10 ribozyme gR10 T1 plant 07


title: whole blood, not ntm disease, CFB2075


title: SLAV_2

value: Slavutych


title: Fig5C rdr6 background vCasphi pUB10 ribozyme gR10 T1 plant 05


title: Fig5C rdr6 background vCasphi pUB10 ribozyme gR10 T1 plant 06


title: whole blood, ntm disease, CFB2071

value: asian


title: Fig5C rdr6 background vCasphi pUB10 ribozyme gR10 T1 plant 02


title: Fig5C rdr6 background vCasphi pUB10 ribozyme gR10 T1 plant 01


title: whole blood, not ntm disease, CFB2074


title: Fig5C rdr6 background vCasphi pUB10 ribozyme gR10 T1 plant 03


title: SLAV_6


title: Fig5C rdr6 background vCasphi pUB10 ribozyme gR10 T1 plant 04


title: Fig5C rdr6 background vCasphi CmYLCVp ribozyme gR10 T1 plant 43


title: SLAV_1


title: SLAV_5


title: Fig5C rdr6 background vCasphi CmYLCVp ribozyme gR10 T1 plant 42


title: Fig5C rdr6 background vCasphi CmYLCVp ribozyme gR10 T1 plant 45


title: whole blood, not ntm disease, CFB2059

value: unknown


title: whole blood, ntm disease, CFB2060


title: SLAV_4


title: whole blood, ntm disease, CFB2061


title: Fig5C rdr6 background vCasphi CmYLCVp ribozyme gR10 T1 plant 46


title: SLAV_3


title: Fig5C rdr6 background vCasphi CmYLCVp ribozyme gR10 T1 plant 44


title: Fig5C rdr6 background vCasphi CmYLCVp ribozyme gR10 T1 plant 41


title: Fig5C rdr6 background vCasphi CmYLCVp ribozyme gR10 T1 plant 40


title: Fig5C rdr6 background vCasphi CmYLCVp ribozyme gR10 T1 plant 39


title: whole blood, not ntm disease, CFB2058


title: SLAV_7


title: Fig5C rdr6 background vCasphi CmYLCVp ribozyme gR10 T1 plant 37


title: Fig5C rdr6 background vCasphi CmYLCVp ribozyme gR10 T1 plant 38


title: whole blood, ntm disease, CFB2049

value: mixed


title: Fig5C rdr6 background vCasphi CmYLCVp ribozyme gR10 T1 plant 36


title: Fig5C rdr6 background vCasphi CmYLCVp ribozyme gR10 T1 plant 35


title: Fig5C rdr6 background vCasphi CmYLCVp ribozyme gR10 T1 plant 34


title: whole blood, ntm disease, CFB2045


title: SLAV_15


title: Fig5C rdr6 background vCasphi CmYLCVp ribozyme gR10 T1 plant 32


title: Fig5C rdr6 background vCasphi CmYLCVp ribozyme gR10 T1 plant 33


title: whole blood, not ntm disease, CFB2044


title: SLAV_16


title: SLAV_13


title: SLAV_12


title: whole blood, not ntm disease, CFB2039


title: whole blood, not ntm disease, CFB2022


title: Fig5C rdr6 background vCasphi CmYLCVp ribozyme gR10 T1 plant 28


title: Fig5C rdr6 background vCasphi CmYLCVp ribozyme gR10 T1 plant 31


title: Fig5C rdr6 background vCasphi CmYLCVp ribozyme gR10 T1 plant 29


title: SLAV_14


title: SLAV_11


title: whole blood, not ntm disease, CFB2013


title: Fig5C rdr6 background vCasphi CmYLCVp ribozyme gR10 T1 plant 25


title: Fig5C rdr6 background vCasphi CmYLCVp ribozyme gR10 T1 plant 30


title: SLAV_8


title: Fig5C rdr6 background vCasphi CmYLCVp ribozyme gR10 T1 plant 27


title: Fig5C rdr6 background vCasphi CmYLCVp ribozyme gR10 T1 plant 26


title: whole blood, not ntm disease, CFB2009


title: Fig5C rdr6 background vCasphi CmYLCVp ribozyme gR10 T1 plant 24


title: whole blood, not ntm disease, CFB2007


title: SLAV_10


title: whole blood, not ntm disease, CFB2006


title: Fig5C rdr6 background vCasphi CmYLCVp ribozyme gR10 T1 plant 22


title: Chern_City_80


title: Fig5C rdr6 background vCasphi CmYLCVp ribozyme gR10 T1 plant 21


title: Fig5C rdr6 background vCasphi CmYLCVp ribozyme gR10 T1 plant 20


title: whole blood, ntm disease, CFB2001


title: Fig5C rdr6 background vCasphi CmYLCVp ribozyme gR10 T1 plant 19


title: Chern_City_79


title: Fig5C rdr6 background vCasphi CmYLCVp ribozyme gR10 T1 plant 18


title: Fig5C rdr6 background vCasphi CmYLCVp ribozyme gR10 T1 plant 23


title: CAG-WT

city: Nanjing

first: Zigen

last: Lin

address: No.138 Xianlin Avenue, Qixia District, Nanjing city, Jiangsu Province, China

country: China

institute: Nanjing University of Chinese Medicine

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Data filtering steps.Prior to assembly, the low quality reads(1,reads containing sequencing adaptors; 2,reads containing sequencing primer;3, nucleotide with q quality score lower than 20 )were removed .software CutAdapter,parameters -o 5 -p 100
Read alignment software,software HISAT ,version 2.0 ,parameters -l fr-firststrand -mi 20 -mx 500000 -p 2 -b dta -q phred33-quals -x 9
perform expression level for mRNAs by calculating FPKM.stimate the expression levels of all transcripts.software StringTie ,version 1.3.0,parameters -b dta -q phred33-quals.
Assembly: Beta_vulgaris.GCF_000511025.2_RefBeet-1.2.2
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample
Supplementary files format and content: "S gene number" refers to the number of genes with significant differences between CAG_OE vs CAG_WT in a given KEGG pathway.  "TS gene number" is the number of genes that are significantly different in CAG_OE vs CAG_WT.  "B gene number" refers to the number of genes in a specific KEGG pathway.  "TB gene number" is the total number of genes.

source_name: Multiple Myeloma cells

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0. Approximately 10 ug of total RNA representing a specific adipose type was subjected to isolate Poly (A) mRNA with poly-T oligoattached magnetic beads (Invitrogen). Following purification, the poly(A)- or poly(A)+ RNA fractions is fragmented into small pieces using divalent cations under elevated temperature. Then the cleaved RNA fragments were reverse-transcribed to create the final cDNA library in accordance with the protocol for the mRNA-Seq sample preparation kit (Illumina, San Diego, USA), the average insert size for the paired-end libraries was 300 bp (±50 bp). And then we performed the paired-end sequencing on an Illumina Novaseq™ 6000 at the (lc-bio, China) following the vendor's recommended protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell type

value: CAG

tag: genotype

value: WT


title: CAG-OE

value: CD229 OE


title: Fig5C rdr6 background vCasphi CmYLCVp ribozyme gR10 T1 plant 16


title: Chern_City_76


title: Fig5C rdr6 background vCasphi CmYLCVp ribozyme gR10 T1 plant 15


title: Fig5C rdr6 background vCasphi CmYLCVp ribozyme gR10 T1 plant 14


title: Chern_City_77


title: Rh4_PAX3-FOXO1-FKBP cells CUT&RUN_P3F-HA_Xlink_dTAG4hr_rep2

data_processing:
Raw FASTQ data were trimmed by Trimmomatic (v0.32).
Paired end reads were aligned to a concatenated human and E.coli genome (hg19 and ecK12MG1655) using Bowtie2.
Peaks were called using Genrich (v. 0.6.1).
Differential analysis was performed using DiffBind and DESeq2.
BigWig files were generated and normalized using the Ecoli reads normalization factors using Deeptools.
Genome_build: hg19 and ecK12MG1655
Supplementary_files_format_and_content: bigWig file
Supplementary_files_format_and_content: peak file

growth_protocol: Cells were cultured in DMEM containing 10% FBS and supplemented with 1% L-Glutamine and 1% penicillin/streptomycin.

extract_protocol:
Cells were collected and incubated with Concanavalin A-coated beads. Antibodies were used to bind targeted DNA-associated proteins. pAG-Mnase was used to digest targeted regions of the genome. DNA was then extracted using phenol-chloroform
NEBNext Ultra II DNA Library Prep Kit
CUT&RUN

tag: treatment

value: 500nM dTAG47

tag: antibody

value: Anti-HA (Cell Signaling, (C29F4) #3724)


title: Fig5C rdr6 background vCasphi CmYLCVp ribozyme gR10 T1 plant 12


title: Fig5C rdr6 background vCasphi CmYLCVp ribozyme gR10 T1 plant 11


title: Fig5C rdr6 background vCasphi CmYLCVp ribozyme gR10 T1 plant 13


title: Fig5C rdr6 background vCasphi CmYLCVp ribozyme gR10 T1 plant 10


title: Rh4_PAX3-FOXO1-FKBP cells CUT&RUN_P3F-HA_Xlink_dTAG4hr_rep1


title: Chern_City_75


title: Chern_City_74


title: Rh4_PAX3-FOXO1-FKBP cells CUT&RUN_P3F-HA_Xlink_dTAG2hr_rep1


title: Fig5C rdr6 background vCasphi CmYLCVp ribozyme gR10 T1 plant 09


title: Rh4_PAX3-FOXO1-FKBP cells CUT&RUN_P3F-HA_Xlink_dTAG2hr_rep2


title: Fig5C rdr6 background vCasphi CmYLCVp ribozyme gR10 T1 plant 08


title: Chern_City_73


title: Fig5C rdr6 background vCasphi CmYLCVp ribozyme gR10 T1 plant 06


title: Fig5C rdr6 background vCasphi CmYLCVp ribozyme gR10 T1 plant 07


title: Rh4_PAX3-FOXO1-FKBP cells CUT&RUN_P3F-HA_Xlink_DMSO_rep2

value: DMSO


title: Chern_City_78

value: Whole Blood


title: Fig5C rdr6 background vCasphi CmYLCVp ribozyme gR10 T1 plant 05


title: Fig5C rdr6 background vCasphi CmYLCVp ribozyme gR10 T1 plant 17


title: Chern_City_72


title: Fig5C rdr6 background vCasphi CmYLCVp ribozyme gR10 T1 plant 04


title: Rh4_PAX3-FOXO1-FKBP cells CUT&RUN_P3F-HA_Xlink_DMSO_rep1


title: Fig5C rdr6 background vCasphi CmYLCVp ribozyme gR10 T1 plant 03


title: Chern_City_71


title: Fig5C rdr6 background vCasphi CmYLCVp ribozyme gR10 T1 plant 02


title: Rh4_PAX3-FOXO1-FKBP cells CUT&RUN_P3F-HA_nonXlink_DMSO


title: Fig5C rdr6 background vCasphi CmYLCVp ribozyme gR10 T1 plant 01


title: Rh4_PAX3-FOXO1-FKBP cells ATAC-seq_dTAG2hr_rep2

data_processing:
Raw FASTQ data were trimmed by Trimmomatic (v0.32).
Paired end reads were aligned to a concatenated human and Drosophila genome (hg19 and dm3) using Bowtie2.
Peaks were called using Genrich (v. 0.6.1).
Differential analysis was performed using DiffBind and DESeq2.
BigWig files were generated and normalized using the DESeq2 size factors using Deeptools.
Genome_build: hg19 and dm3
Supplementary_files_format_and_content: bigWig file
Supplementary_files_format_and_content: peak file

extract_protocol: ATAC-Seq Kit (Active Motif, catalog No.53150)


title: CNPP_96

value: Chernobyl Nuclear Power Plant


title: Fig5C rdr6 background nCasphi pUB10 ribozyme gR10 T1 plant 40

value: leaf tissue


title: Fig5C rdr6 background nCasphi pUB10 ribozyme gR10 T1 plant 43

value: 3-4 weeks


title: Rh4_PAX3-FOXO1-FKBP cells ATAC-seq_dTAG2hr_rep1


title: Fig5C rdr6 background nCasphi pUB10 ribozyme gR10 T1 plant 42


title: Fig5C rdr6 background nCasphi pUB10 ribozyme gR10 T1 plant 41


title: Rh4_PAX3-FOXO1-FKBP cells ATAC-seq_DMSO_rep2


title: Fig5C rdr6 background nCasphi pUB10 ribozyme gR10 T1 plant 38


title: CNPP_95


title: CNPP_64


title: Fig5C rdr6 background nCasphi pUB10 ribozyme gR10 T1 plant 37


title: Fig5C rdr6 background nCasphi pUB10 ribozyme gR10 T1 plant 36


title: Rh4_PAX3-FOXO1-FKBP cells ATAC-seq_DMSO_rep1


title: CNPP_63


title: Rh30_PAX3-FOXO1-FKBP_cells RNA-seq_dTAG72hr_rep1

data_processing:
Raw FASTQ data were trimmed by Trimmomatic (v0.32).
Paired end reads were aligned to a concatenated human hg19 using Bowtie2.
Differential analysis was performed using CuffDiff (v. 2.1.1)
Genome_build: hg19
Supplementary_files_format_and_content: raw counts

extract_protocol:
Total RNA was extracted using TRIzol.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: DMSO

value: 500nM dTAG

tag: time point


title: Fig5C rdr6 background nCasphi pUB10 ribozyme gR10 T1 plant 34


title: Chern_City_70

value: Mixed Breed


title: Fig5C rdr6 background nCasphi pUB10 ribozyme gR10 T1 plant 32


title: Rh30_PAX3-FOXO1-FKBP_cells RNA-seq_dTAG72hr_rep2


title: Fig5C rdr6 background nCasphi pUB10 ribozyme gR10 T1 plant 33


title: Rh30_PAX3-FOXO1-FKBP_cells RNA-seq_dTAG24hr_rep2


title: Fig5C rdr6 background nCasphi pUB10 ribozyme gR10 T1 plant 30


title: Fig5C rdr6 background nCasphi pUB10 ribozyme gR10 T1 plant 31


title: CNPP_94


title: Fig5C rdr6 background nCasphi pUB10 ribozyme gR10 T1 plant 39


title: Fig5C rdr6 background nCasphi pUB10 ribozyme gR10 T1 plant 29


title: Rh30_PAX3-FOXO1-FKBP_cells RNA-seq_dTAG24hr_rep1


title: Fig5C rdr6 background nCasphi pUB10 ribozyme gR10 T1 plant 28


title: Fig5C rdr6 background nCasphi pUB10 ribozyme gR10 T1 plant 35


title: CNPP_93


title: CNPP_92


title: Rh30_PAX3-FOXO1-FKBP_cells RNA-seq_dTAG6hr_rep2


title: Fig5C rdr6 background nCasphi pUB10 ribozyme gR10 T1 plant 26


title: CNPP_62


title: Rh30_PAX3-FOXO1-FKBP_cells RNA-seq_dTAG6hr_rep1


title: Fig5C rdr6 background nCasphi pUB10 ribozyme gR10 T1 plant 25


title: CNPP_91


title: Fig5C rdr6 background nCasphi pUB10 ribozyme gR10 T1 plant 24


title: Rh30_PAX3-FOXO1-FKBP_cells RNA-seq_dTAG2hr_rep2


title: CNPP_90


title: Rh30_PAX3-FOXO1-FKBP_cells RNA-seq_dTAG2hr_rep1


title: CNPP_61


title: Fig5C rdr6 background nCasphi pUB10 ribozyme gR10 T1 plant 22


title: Fig5C rdr6 background nCasphi pUB10 ribozyme gR10 T1 plant 23


title: Fig5C rdr6 background nCasphi pUB10 ribozyme gR10 T1 plant 21


title: Fig5C rdr6 background nCasphi pUB10 ribozyme gR10 T1 plant 20


title: Chern_City_69

value: Chernobyl City


title: Fig5C rdr6 background nCasphi pUB10 ribozyme gR10 T1 plant 19


title: Rh30_PAX3-FOXO1-FKBP_cells RNA-seq_DMSO_rep2


title: Chern_City_68


title: Fig5C rdr6 background nCasphi pUB10 ribozyme gR10 T1 plant 27


title: Rh30_PAX3-FOXO1-FKBP_cells RNA-seq_DMSO_rep1


title: Fig5C rdr6 background nCasphi pUB10 ribozyme gR10 T1 plant 18


title: Fig5C rdr6 background nCasphi pUB10 ribozyme gR10 T1 plant 17


title: Fig5C rdr6 background nCasphi pUB10 ribozyme gR10 T1 plant 16


title: Chern_City_67


title: Fig5C rdr6 background nCasphi pUB10 ribozyme gR10 T1 plant 15


title: Fig5C rdr6 background nCasphi pUB10 ribozyme gR10 T1 plant 14


title: Rh30_FOXO1-FKBP_cells RNA-seq_dTAG72hr_rep2


title: Chern_City_153


title: Fig5C rdr6 background nCasphi pUB10 ribozyme gR10 T1 plant 12


title: Fig5C rdr6 background nCasphi pUB10 ribozyme gR10 T1 plant 13


title: Fig5C rdr6 background nCasphi pUB10 ribozyme gR10 T1 plant 10


title: Rh30_FOXO1-FKBP_cells RNA-seq_dTAG24hr_rep2


title: Fig5C rdr6 background nCasphi pUB10 ribozyme gR10 T1 plant 11


title: Rh30_FOXO1-FKBP_cells RNA-seq_dTAG24hr_rep1


title: Fig5C rdr6 background nCasphi pUB10 ribozyme gR10 T1 plant 09


title: Fig5C rdr6 background nCasphi pUB10 ribozyme gR10 T1 plant 08


title: Fig5C rdr6 background nCasphi pUB10 ribozyme gR10 T1 plant 07


title: Rh30_FOXO1-FKBP_cells RNA-seq_dTAG6hr_rep2


title: Fig5C rdr6 background nCasphi pUB10 ribozyme gR10 T1 plant 06


title: Chern_City_151


title: Chern_City_150


title: Rh30_FOXO1-FKBP_cells RNA-seq_dTAG6hr_rep1


title: Fig5C rdr6 background nCasphi pUB10 ribozyme gR10 T1 plant 03


title: Fig5C rdr6 background nCasphi pUB10 ribozyme gR10 T1 plant 04


title: Rh30_FOXO1-FKBP_cells RNA-seq_dTAG72hr_rep1


title: Fig5C rdr6 background nCasphi pUB10 ribozyme gR10 T1 plant 01


title: Chern_City_149


title: Fig5C rdr6 background nCasphi CmYLCVp ribozyme gR10 T1 plant 54


title: Fig5C rdr6 background nCasphi CmYLCVp ribozyme gR10 T1 plant 53


title: CNPP_88


title: Chern_City_152


title: CNPP_89


title: Rh30_FOXO1-FKBP_cells RNA-seq_DMSO_rep2


title: Fig5C rdr6 background nCasphi CmYLCVp ribozyme gR10 T1 plant 52


title: CNPP_87


title: Fig5C rdr6 background nCasphi CmYLCVp ribozyme gR10 T1 plant 51


title: Fig5C rdr6 background nCasphi pUB10 ribozyme gR10 T1 plant 05


title: Rh30_FOXO1-FKBP_cells RNA-seq_DMSO_rep1


title: CNPP_86


title: Rh30_FOXO1-FKBP_cells RNA-seq_dTAG2hr_rep1


title: CNPP_85


title: Rh30_PAX3-FOXO1-FKBP_clone12 cells RNA-seq_rep4


title: Fig5C rdr6 background nCasphi CmYLCVp ribozyme gR10 T1 plant 50


title: Rh30_FOXO1-FKBP_cells RNA-seq_dTAG2hr_rep2


title: Fig5C rdr6 background nCasphi CmYLCVp ribozyme gR10 T1 plant 49


title: Fig5C rdr6 background nCasphi pUB10 ribozyme gR10 T1 plant 02


title: Fig5C rdr6 background nCasphi CmYLCVp ribozyme gR10 T1 plant 48


title: Fig5C rdr6 background nCasphi CmYLCVp ribozyme gR10 T1 plant 47


title: Rh30_PAX3-FOXO1-FKBP_clone12 cells RNA-seq_rep3


title: Chern_City_154


title: Fig5C rdr6 background nCasphi CmYLCVp ribozyme gR10 T1 plant 45


title: Fig5C rdr6 background nCasphi CmYLCVp ribozyme gR10 T1 plant 46


title: CNPP_84


title: Rh30_PAX3-FOXO1-FKBP_clone11 cells RNA-seq_rep2


title: Fig5C rdr6 background nCasphi CmYLCVp ribozyme gR10 T1 plant 44


title: Rh30_PAX3-FOXO1-FKBP_clone11 cells RNA-seq_rep1


title: CNPP_83


title: Rh30_PAX3-FOXO1-FKBP_clone10 cells RNA-seq_rep2


title: Rh30_PAX3-FOXO1-FKBP_clone10 cells RNA-seq_rep1


title: Fig5C rdr6 background nCasphi CmYLCVp ribozyme gR10 T1 plant 41


title: Fig5C rdr6 background nCasphi CmYLCVp ribozyme gR10 T1 plant 38


title: Fig5C rdr6 background nCasphi CmYLCVp ribozyme gR10 T1 plant 39


title: Fig5C rdr6 background nCasphi CmYLCVp ribozyme gR10 T1 plant 40


title: CNPP_80


title: Chern_City_148


title: CNPP_81


title: Rh30_PAX3-FOXO1-FKBP_clone4 cells RNA-seq_rep1


title: Fig5C rdr6 background nCasphi CmYLCVp ribozyme gR10 T1 plant 35


title: Fig5C rdr6 background nCasphi CmYLCVp ribozyme gR10 T1 plant 36


title: CNPP_79


title: Fig5C rdr6 background nCasphi CmYLCVp ribozyme gR10 T1 plant 33


title: Rh30_parental cells RNA-seq_rep2


title: CNPP_78


title: Fig5C rdr6 background nCasphi CmYLCVp ribozyme gR10 T1 plant 32


title: Rh30_PAX3-FOXO1-FKBP_clone4 cells RNA-seq_rep2


title: Fig5C rdr6 background nCasphi CmYLCVp ribozyme gR10 T1 plant 31


title: Fig5C rdr6 background nCasphi CmYLCVp ribozyme gR10 T1 plant 34


title: Rh30_parental cells RNA-seq_rep1


title: Fig5C rdr6 background nCasphi CmYLCVp ribozyme gR10 T1 plant 43


title: 81 Rec7_7 met

city: Olomouc

first: Maciej

last: Majka

state: Please select a region, state or province.

address: Šlechtitelů 31

country: Czech Republic

institute: Institute of Experimental Botany AS CR

description:
AB 3730xL Genetic Analyzer
Rec7 part 7

data_processing:
Geneious Prime version 2020.2.4
Bisulfate sequencing reads obtained for forward and reverse primers were aligned and trimmed.
Assembly: Wheat Chinese Spring IWGSC RefSeq v1.0 genome assembly (2018)
Supplementary files format and content: FASTA format text files.

organism: Triticum aestivum

source_name: Second leaf

extract_protocol:
DNA was extracted from 100 mg lyophilized leaf segments disrupted with two 5 mm glass beads in sealed 96-well 2ml plates. Lysis was performed in 1 ml of lysis buffer at 65°C for 45 min. Subsequently, plates were centrifuged at 1300 × g for 10 min at 4°C. DNA purification was done at a Biomek® NXP automated workstation. A 100 µl of lysate was transferred to a new PCR plate and mixed with 70 µl of isopropanol and 5 µl of Agencourt® Genfind® v2 magnetic beads and incubated for 5 min at RT. Subsequent steps comprised 5 min incubation at the magnet, supernatant discarding, and three-time wash with 100 µl of 70% ethanol. Elution was done in 100 µl of H20 with 10 min incubation at RT and 10 min incubation at the magnet. Eluted DNA was transferred to a new PCR plate.
DNA methylation in the regions with recombination events was determined using the EZ DNA Methylation-Gold Kit (Zymo Research, USA). 400 ng of genomic DNA was bisulfite converted and purified according to the manufacturer's instruction (ver. 1.0.1). For amplification of the bisulfite converted DNA, a set of new primers was designed.
For amplification and sequencing of the Hotspot region part 1 after CT-conversion we used: Hot1_Met_F 5’-TTGTGTGTGTAGTTAGGTATAAAAAGT-3’ and Hot1_Met _R 5’-ACTTCTTCTCCATACATCCTAATC-3’
For amplification and sequencing of the Hotspot region part 2 after CT-conversion we used: Hot2_Met_F 5’- TTGTTTATTTTTTTTATTTAGTGT -3’ and Hot2_Met _R 5’-AAACRAATACCAAAATTTTTCATTCTCTAT-3’
For amplification and sequencing of the Hotspot region part 3 after CT-conversion we used: Hot3_Met_F 5’- TTAAATTTTTAAAGAAGATAAAGAGAG -3’ and Hot3_Met _R 5’- ATATTCCTCCATCACCATCACACTAC -3’
For amplification and sequencing of the Hotspot region part 4 after CT-conversion we used: Hot4_Met_F 5’- TAATAAGATGYGTTGGGTAGAGGTG -3’ and Hot4_Met _R 5’- CTTCTAAACRCCATTAAAAACTTCATTA -3’
For amplification and sequencing of the Rec7 region part 1 after CT-conversion we used: Rec7_1F_Met 5’- GAATGTTATTTGTTAGTAGA -3’ and Rec7_1R_Met 5’- AAACTAAAAACTTTAAAACTTATCAT -3’
For amplification and sequencing of the Rec7 region part 2 after CT-conversion we used: Rec7_2F_Met 5’- TAGTATGAAATATGATATGTTTTT -3’ and Rec7_2R_Met 5’- ATAAATACAACTCAACCAAC -3’
For amplification and sequencing of the Rec7 region part 3 after CT-conversion we used: Rec7_3F_Met 5’- AAAGATAGTAATAGAAGTAATAAGT -3’ and Rec7_3R_Met 5’- TAAAACCTTACAATCCAACA -3’
For amplification and sequencing of the Rec7 region part 4 after CT-conversion we used: Rec7_4F2_Met 5’- TTTGAGTTGTTGTTATAATT -3’ and Rec7_4R4_Met 5’- CTTCACCAACRACTCCAA -3’
For amplification and sequencing of the Rec7 region part 5 after CT-conversion we used: Rec7_5F4_Met 5’- ATTTAATAAAGTTTAGAGTTYG -3’ and Rec7_5R3_Met 5’- ACACCCRCCATACCTTAA -3’
For amplification and sequencing of the Rec7 region part 6 after CT-conversion we used: Rec7_6F_Met 5’- TTTGTTAAAAATTAAGGTATGG -3’ and Rec7_6R_Met 5’- ATATTTTCATACCTAAATCACATAAA -3’
For amplification and sequencing of the Rec7 region part 7 after CT-conversion we used: Rec7_7F_Met 5’- TGAAGAAAATTTTGAAAAATATGAA -3’ and Rec7_7R_Met 5’- ATTCCRACAATTTATTTTTA -3’

value: Second leaf

value: Line 8.1


title: CNPP_82


title: Fig5C rdr6 background nCasphi CmYLCVp ribozyme gR10 T1 plant 42


title: CNPP_77


title: Fig5C rdr6 background nCasphi CmYLCVp ribozyme gR10 T1 plant 29


title: CNPP_76


title: Fig5C rdr6 background nCasphi CmYLCVp ribozyme gR10 T1 plant 30


title: Fig5C rdr6 background nCasphi CmYLCVp ribozyme gR10 T1 plant 37


title: CNPP_75


title: Fig5C rdr6 background nCasphi CmYLCVp ribozyme gR10 T1 plant 27


title: Rh30_PAX3-FOXO1-FKBP cells CUT&RUN_CDK8_dTAG4hr_rep1

data_processing:
Library strategy: CUT&RUN
Raw FASTQ data were trimmed by Trimmomatic (v0.32).
Paired end reads were aligned to a concatenated human and E.coli genome (hg19 and ecK12MG1655) using Bowtie2.
Peaks were called using Genrich (v. 0.6.1).
Differential analysis was performed using DiffBind and DESeq2.
BigWig files were generated and normalized using the DESeq2 size factors using Deeptools.
Genome_build: hg19 and ecK12MG1655
Supplementary_files_format_and_content: bigWig file
Supplementary_files_format_and_content: peak file

value: anti-CDK8 (Santa Cruz, sc-13155)


title: Fig5C rdr6 background nCasphi CmYLCVp ribozyme gR10 T1 plant 28


title: CNPP_74


title: 81 Rec7_6 met

description:
AB 3730xL Genetic Analyzer
Rec7 part 6


title: Rh30_PAX3-FOXO1-FKBP cells CUT&RUN_CDK8_dTAG2hr_rep2


title: 81 Rec7_5 met

description:
AB 3730xL Genetic Analyzer
Rec7 part 5


title: 81 Rec7_4 met

description:
AB 3730xL Genetic Analyzer
Rec7 part 4


title: CNPP_73


title: Fig5C rdr6 background nCasphi CmYLCVp ribozyme gR10 T1 plant 26


title: Rh30_PAX3-FOXO1-FKBP cells CUT&RUN_CDK8_DMSO_rep1


title: CNPP_72


title: Rh30_PAX3-FOXO1-FKBP cells CUT&RUN_CDK8_dTAG4hr_rep2


title: CNPP_71


title: 81 Rec7_1 met

description:
AB 3730xL Genetic Analyzer
Rec7 part 1


title: Rh30_PAX3-FOXO1-FKBP cells CUT&RUN_SPT16_dTAG4hr_rep2

value: anti-SPT16 (Cell Signaling, D7I2K #12191)


title: Fig5C rdr6 background nCasphi CmYLCVp ribozyme gR10 T1 plant 23


title: CNPP_69


title: Rh30_PAX3-FOXO1-FKBP cells CUT&RUN_SPT16_dTAG4hr_rep1


title: Fig5C rdr6 background nCasphi CmYLCVp ribozyme gR10 T1 plant 24


title: Rh30_PAX3-FOXO1-FKBP cells CUT&RUN_CDK8_dTAG2hr_rep1


title: CNPP_70


title: Fig5C rdr6 background nCasphi CmYLCVp ribozyme gR10 T1 plant 22


title: 81 Hot4 met

description:
AB 3730xL Genetic Analyzer
H1 part 4


title: 81 Hot3 met

description:
AB 3730xL Genetic Analyzer
H1 part 3


title: CNPP_68


title: 81 Rec7_3 met

description:
AB 3730xL Genetic Analyzer
Rec7 part 3


title: Rh30_PAX3-FOXO1-FKBP cells CUT&RUN_CDK8_DMSO_rep2


title: Rh30_PAX3-FOXO1-FKBP cells CUT&RUN_SPT16_dTAG2hr_rep2


title: Fig5C rdr6 background nCasphi CmYLCVp ribozyme gR10 T1 plant 21


title: Fig5C rdr6 background nCasphi CmYLCVp ribozyme gR10 T1 plant 20


title: CNPP_67


title: 81 Rec7_2 met

description:
AB 3730xL Genetic Analyzer
Rec7 part 2


title: Fig5C rdr6 background nCasphi CmYLCVp ribozyme gR10 T1 plant 19


title: Fig5C rdr6 background nCasphi CmYLCVp ribozyme gR10 T1 plant 25


title: Rh30_PAX3-FOXO1-FKBP cells CUT&RUN_SPT16_DMSO_rep2


title: Fig5C rdr6 background nCasphi CmYLCVp ribozyme gR10 T1 plant 18


title: 81 Hot1 met

description:
AB 3730xL Genetic Analyzer
H1 part 1


title: 81 Hot2 met

description:
AB 3730xL Genetic Analyzer
H1 part 2


title: Rh30_PAX3-FOXO1-FKBP cells CUT&RUN_SPT16_DMSO_rep1


title: Chern_City_146


title: CS Rec7_7 met

description:
AB 3730xL Genetic Analyzer
Rec7 part 7

value: Chinese Spring


title: Fig5C rdr6 background nCasphi CmYLCVp ribozyme gR10 T1 plant 17


title: CS Rec7_6 met

description:
AB 3730xL Genetic Analyzer
Rec7 part 6


title: Rh30_PAX3-FOXO1-FKBP cells CUT&RUN_ARID1A_dTAG4hr_rep2

value: anti-ARID1A (Cell Signaling, (D2A8U) #12354)


title: Chern_City_145


title: Chern_City_144


title: Rh30_PAX3-FOXO1-FKBP cells CUT&RUN_SPT16_dTAG2hr_rep1


title: Chern_City_143


title: Rh30_PAX3-FOXO1-FKBP cells CUT&RUN_ARID1A_dTAG2hr_rep2


title: Fig5C rdr6 background nCasphi CmYLCVp ribozyme gR10 T1 plant 15


title: Chern_City_147


title: Fig5C rdr6 background nCasphi CmYLCVp ribozyme gR10 T1 plant 14


title: CS Rec7_4 met

description:
AB 3730xL Genetic Analyzer
Rec7 part 4


title: Fig5C rdr6 background nCasphi CmYLCVp ribozyme gR10 T1 plant 16


title: CS Rec7_5 met

description:
AB 3730xL Genetic Analyzer
Rec7 part 5


title: Rh30_PAX3-FOXO1-FKBP cells CUT&RUN_ARID1A_dTAG2hr_rep1


title: CS Rec7_3 met

description:
AB 3730xL Genetic Analyzer
Rec7 part 3


title: Chern_City_133


title: Rh30_PAX3-FOXO1-FKBP cells CUT&RUN_ARID1A_DMSO_rep2


title: Rh30_PAX3-FOXO1-FKBP cells CUT&RUN_ARID1A_DMSO_rep1


title: Chern_City_132


title: CS Rec7_1 met

description:
AB 3730xL Genetic Analyzer
Rec7 part 1


title: CS Hot4 met

description:
AB 3730xL Genetic Analyzer
H1 part 4


title: Fig5C rdr6 background nCasphi CmYLCVp ribozyme gR10 T1 plant 13


title: Fig5C rdr6 background nCasphi CmYLCVp ribozyme gR10 T1 plant 12


title: Rh30_PAX3-FOXO1-FKBP cells CUT&RUN_PAX3_dTAG4hr_rep2

value: anti-PAX3 (Abcam, ab69856)


title: Fig5C rdr6 background nCasphi CmYLCVp ribozyme gR10 T1 plant 11


title: Chern_City_131


title: Fig5C rdr6 background nCasphi CmYLCVp ribozyme gR10 T1 plant 10


title: Rh30_PAX3-FOXO1-FKBP cells CUT&RUN_ARID1A_dTAG4hr_rep1

value: 500nM dTAG47


title: Chern_City_130


title: Rh30_PAX3-FOXO1-FKBP cells CUT&RUN_PAX3_dTAG4hr_rep1


title: CS Hot3 met

description:
AB 3730xL Genetic Analyzer
H1 part 3


title: CS Hot2 met

description:
AB 3730xL Genetic Analyzer
H1 part 2


title: Rh30_PAX3-FOXO1-FKBP cells CUT&RUN_PAX3_dTAG2hr_rep2


title: CS Rec7_2 met

description:
AB 3730xL Genetic Analyzer
Rec7 part 2


title: Chern_City_141


title: CS Hot1 met

description:
AB 3730xL Genetic Analyzer
H1 part 1


title: Fig5C rdr6 background nCasphi CmYLCVp ribozyme gR10 T1 plant 08


title: Rh30_PAX3-FOXO1-FKBP cells CUT&RUN_PAX3_dTAG2hr_rep1


title: Fig5C rdr6 background nCasphi CmYLCVp ribozyme gR10 T1 plant 09


title: Rh30_PAX3-FOXO1-FKBP cells CUT&RUN_PAX3_DMSO_rep2


title: Chern_City_140


title: Chern_City_139


title: Rh30_PAX3-FOXO1-FKBP cells CUT&RUN_PAX3_DMSO_rep1


title: Chern_City_138


title: Fig5C rdr6 background nCasphi CmYLCVp ribozyme gR10 T1 plant 07


title: Fig5C rdr6 background nCasphi CmYLCVp ribozyme gR10 T1 plant 06


title: ATAC-seq on Patient #73

city: London

first: Cameron

last: Osborne

address: Guy's Hospital Campus

department: Medical and Molecular Genetics

country: United Kingdom

institute: King's College London

data_processing:
Reads were trimmed of adapters and low-quality reads using Trimmomatic and aligned to the hg19 genome using Bowtie2. PCR duplicates were removed using Samtools and blacklisted reads were removed. Peaks were called using Macs2 peak caller, with a q-value threshold of 0.01.
Assembly: hg19
Supplementary files format and content: Macs2 called narrow peak files for each sample is provided

source_name: PBMCs

extract_protocol: PBMC's were isolated and ATAC-seq was performed using the ATAC-seq kits from Active motif - based on the protocol by Corces et al. Nature 2017. https://www.activemotif.com/catalog/1301/atac-seq-kit

tag: subject status

value: Acute Promyelocytic Leukemia (APL) patient

value: PBMCs


title: sci-Plex D28 individuals (snRNA-seq)

city: Seattle

first: Amy

middle: Moreda

last: Tresenrider

state: WA

address: 3720 15th Ave NE

department: Genome Sciences

institute: University of Washington

description: Note, d28_d78_d185_sci_unfiltered_gene_metadata.csv and d28_individuals_unfiltered_gene_metadata.csv are the same.

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were performed using the Brotman Baty sci-RNA-seq demultiplexing and processing pipelines (https://github.com/bbi-lab/bbi-dmux; https://github.com/bbi-lab/bbi-sci).   The output of the pipeline was further analyzed using Monocle3
Assembly: GRCh38
Supplementary files format and content: Count Matrix (RDS file), Cell Metadata (comma separated values- .csv), Gene Metadata (comma separated values- .csv), Monocle3 cds object (RDS file)

molecule: nuclear RNA

source_name: ES cell line-derived retinal organoid

growth_protocol: hECSs were differentiated into EBs and then organoids following the protocol from Fligor et al. (2020). Differentiation of retinal organoids from human pluripotent stem cells. Methods Cell Biol. 159, 279–302.

extract_protocol:
An individual organoid was  added to each well of  a 96-well v-bottom plate. The organoids were washed in dPBS and resuspended in 100 uL accutase at 37C. Every 5-10 minutes the samples were pipetted up and down  until minimal cell clusters were observed by bright phase microscopy (30-45 minutes). The accutase was deactivated with 20 uL of FBS.
The library was prepared following the sci-RNA-seq3 protocol from (Srivatsan et al., 2020) which had been modified from (Cao et al., 2019). A reverse transcription reaction with barcoded RT primers captured 3'-polyAdenylated transcripts. Nuclei were pooled, diluted, and a second barcode was added through a ligation reaction. Nuclei were again pooled and then diluted into 96-well plates where second strand synthesis was followed by tagmentation. PCR was performed with barcoded primers and the library was size-selected. The unique combination of barcodes in the RT, ligation, and PCR steps enable the reconstruction of individual cells in silico.
single Cell RNA sequencing library containing hash molecules denoting where a nucleus originated from and the transcriptome measured for each cell

treatment_protocol: When indicated BMP4 (1.5 nM) was added on Day 6 and diluted by half every 2 days until Day 12. Signaling factor modulators (CHIR99021: 3 uM, SU5402: 1 uM, SAG: 1 uM) were added on Day 14 and 16.  Conditions: None; SAG; BMP4 ; BMP4, CHIR99021; BMP4, SU5402; BMP4, CHIR99021, SU5402; BMP4, CHIR99021, SU5402, SAG

value: ES cell line-derived retinal organoid

tag: cell line

value: WA09 (H9) hESC with NRL-GFP

value: 28 days

tag: fraction

value: nuclear polyA RNA


title: sci-Plex D63 individuals (snRNA-seq)

treatment_protocol: When indicated BMP4 (1.5 nM) was added on Day 6 and diluted by half every 2 days until Day 12. Signaling factor modulators (CHIR99021: 3 uM, SU5402: 1 uM) were added on Day 14 and 16.  Conditions: BMP4 ; BMP4, CHIR99021; BMP4, CHIR99021, SU5402

value: 63 days


title: Chern_City_137

value: Whole Blood

value: Mixed Breed


title: Fig5C rdr6 background nCasphi CmYLCVp ribozyme gR10 T1 plant 05

value: leaf tissue

value: 3-4 weeks


title: Chern_City_142

value: Chernobyl City


title: ATAC-seq on Patient #74


title: Rh30_PAX3-FOXO1-FKBP cells CUT&RUN_HEB_dTAG4hr_rep2

value: anti-HEB (Santa Cruz, sc-357)


title: Rh30_PAX3-FOXO1-FKBP cells CUT&RUN_HEB_dTAG4hr_rep1


title: Chern_City_135


title: Fig5C rdr6 background nCasphi CmYLCVp ribozyme gR10 T1 plant 04


title: Rh30_PAX3-FOXO1-FKBP cells CUT&RUN_HEB_dTAG2hr_rep2


title: Chern_City_136


title: Fig5C rdr6 background nCasphi CmYLCVp ribozyme gR10 T1 plant 03


title: Rh30_PAX3-FOXO1-FKBP cells CUT&RUN_HEB_dTAG2hr_rep1


title: Fig5C rdr6 background nCasphi CmYLCVp ribozyme gR10 T1 plant 02


title: Chern_City_134


title: Fig5C rdr6 background nCasphi CmYLCVp ribozyme gR10 T1 plant 01


title: Regro 7.5Gy

type: RNA

city: Seoul

first: YI NA

last: YOON

address: 75, Nowon-ro, Nowon-gu

country: South Korea

institute: korea institute of radiological and medical sciences

description:
GPL0013
Intratumoral CD45+ cells isolated from CT26 cancer cells implanted on BALB/c mice.
RNA from CD45 positive cells in tumor
To isolate intratumoral and splenic CD45+ cells, an EasySep™ Mouse CD45+ Cell Isolation Kit (StemCell Technologies, Vancouver, Canada) was used, according to the manufacturer’s instructions. Single cell samples of tumor tissues were resuspended in phosphate-buffered saline with 5% fetal bovine serum (FBS) and 1 mM ethylenediaminetetraacetic acid (fluorescence-activated cell sorting [FACS] buffer) for magnetic labeling. Cells were incubated for 8 min at room temperature with a CD45-positive selection cocktail and tetrameric antibody complexes. Tubes containing the mixture were placed in EasySep™ magnetic for 5 min, and the supernatant was discarded. Finally, magnetically labeled CD45+ cells were resuspended in FACS buffer. Using the MasterPureTM Complete RNA Purification Kit (Lucigen, MA, USA), RNA was isolated from the sorted intratumoral CD45+ cells. NanoString analysis was performed using an nCounter Analysis System (NanoString Technologies, WA, USA).

hyb_protocol: Probes and target transcripts were hybridized overnight at 65°C for at least 16 hours.

scan_protocol: Hybridized RNA was then diluted in molecular grade water and loaded into nCounter SPRINT cartridge (NanoString), placed into nCounter SPRINT Profiler, and quantified.

data_processing:
Data quality was assessed with the help of QC plots using R package NanoString nSolver software. All samples were imported and analyzed using R package NanoString nSolver software. Data was normalized using quantile normalization after background subtraction of geom-mean.
PD-1_PD-L1_axis.csv: Raw data extracted from nSolver (NanoString software).
PD-1_PD-L1_axis_normalized.csv: Normalized values based on endogeneous housekeeping genes. Data was extracted from nSolver.

label: codeset probes

organism: Mus musculus

source_name: CD45+ cells sorted from tumor mass

label_protocol: nCounter gene expression assays (NanoString Technologies) were performed for the NanoString innate immunology mouse panel. Samples were labelled with panel-specific codeset probes.

extract_protocol: To isolate intratumoral and splenic CD45+ cells, an EasySep™ Mouse CD45+ Cell Isolation Kit (StemCell Technologies, Vancouver, Canada) was used, according to the manufacturer’s instructions. Using the MasterPureTM Complete RNA Purification Kit (Lucigen, MA, USA), RNA was isolated from the sorted intratumoral CD45+ cells.

value: tumor

value: tumor infiltrating leukocytes

tag: phase

value: Regrowth, RT


title: Regro 2Gy

description:
GPL0012
Intratumoral CD45+ cells isolated from CT26 cancer cells implanted on BALB/c mice.
RNA from CD45 positive cells in tumor
To isolate intratumoral and splenic CD45+ cells, an EasySep™ Mouse CD45+ Cell Isolation Kit (StemCell Technologies, Vancouver, Canada) was used, according to the manufacturer’s instructions. Single cell samples of tumor tissues were resuspended in phosphate-buffered saline with 5% fetal bovine serum (FBS) and 1 mM ethylenediaminetetraacetic acid (fluorescence-activated cell sorting [FACS] buffer) for magnetic labeling. Cells were incubated for 8 min at room temperature with a CD45-positive selection cocktail and tetrameric antibody complexes. Tubes containing the mixture were placed in EasySep™ magnetic for 5 min, and the supernatant was discarded. Finally, magnetically labeled CD45+ cells were resuspended in FACS buffer. Using the MasterPureTM Complete RNA Purification Kit (Lucigen, MA, USA), RNA was isolated from the sorted intratumoral CD45+ cells. NanoString analysis was performed using an nCounter Analysis System (NanoString Technologies, WA, USA).


title: Regro 0Gy

description:
GPL0011
Intratumoral CD45+ cells isolated from CT26 cancer cells implanted on BALB/c mice.
RNA from CD45 positive cells in tumor
To isolate intratumoral and splenic CD45+ cells, an EasySep™ Mouse CD45+ Cell Isolation Kit (StemCell Technologies, Vancouver, Canada) was used, according to the manufacturer’s instructions. Single cell samples of tumor tissues were resuspended in phosphate-buffered saline with 5% fetal bovine serum (FBS) and 1 mM ethylenediaminetetraacetic acid (fluorescence-activated cell sorting [FACS] buffer) for magnetic labeling. Cells were incubated for 8 min at room temperature with a CD45-positive selection cocktail and tetrameric antibody complexes. Tubes containing the mixture were placed in EasySep™ magnetic for 5 min, and the supernatant was discarded. Finally, magnetically labeled CD45+ cells were resuspended in FACS buffer. Using the MasterPureTM Complete RNA Purification Kit (Lucigen, MA, USA), RNA was isolated from the sorted intratumoral CD45+ cells. NanoString analysis was performed using an nCounter Analysis System (NanoString Technologies, WA, USA).

value: Regrowth


title: Chern_City_66


title: Rh30_PAX3-FOXO1-FKBP cells CUT&RUN_HEB_DMSO_rep1

value: DMSO


title: Chern_City_63


title: Chern_City_62


title: Chern_City_65


title: Fig5AandSupFig3A 23 Celsius incubated rdr6 background version2 WTcasphi U6gR10 T1 plant 20


title: Chern_City_61


title: Fig5AandSupFig3A 23 Celsius incubated rdr6 background version2 WTcasphi U6gR10 T1 plant 19


title: Chern_City_64


title: Rh30_PAX3-FOXO1-FKBP cells CUT&RUN_RUNX1_dTAG2hr_rep1

value: 500nM dTAG47

value: anti-RUNX1 (Santa Cruz, sc-365644)


title: Fig5AandSupFig3A 23 Celsius incubated rdr6 background version2 WTcasphi U6gR10 T1 plant 21


title: Fig5AandSupFig3A 23 Celsius incubated rdr6 background version2 WTcasphi U6gR10 T1 plant 23


title: Rh30_PAX3-FOXO1-FKBP cells CUT&RUN_RUNX1_dTAG2hr_rep2


title: Fig5AandSupFig3A 23 Celsius incubated rdr6 background version2 WTcasphi U6gR10 T1 plant 18


title: Fig5AandSupFig3A 23 Celsius incubated rdr6 background version2 WTcasphi U6gR10 T1 plant 22


title: Nadir 7.5Gy

description:
GPL0010
Intratumoral CD45+ cells isolated from CT26 cancer cells implanted on BALB/c mice.
RNA from CD45 positive cells in tumor
To isolate intratumoral and splenic CD45+ cells, an EasySep™ Mouse CD45+ Cell Isolation Kit (StemCell Technologies, Vancouver, Canada) was used, according to the manufacturer’s instructions. Single cell samples of tumor tissues were resuspended in phosphate-buffered saline with 5% fetal bovine serum (FBS) and 1 mM ethylenediaminetetraacetic acid (fluorescence-activated cell sorting [FACS] buffer) for magnetic labeling. Cells were incubated for 8 min at room temperature with a CD45-positive selection cocktail and tetrameric antibody complexes. Tubes containing the mixture were placed in EasySep™ magnetic for 5 min, and the supernatant was discarded. Finally, magnetically labeled CD45+ cells were resuspended in FACS buffer. Using the MasterPureTM Complete RNA Purification Kit (Lucigen, MA, USA), RNA was isolated from the sorted intratumoral CD45+ cells. NanoString analysis was performed using an nCounter Analysis System (NanoString Technologies, WA, USA).

value: Nadir, RT


title: Rh30_PAX3-FOXO1-FKBP cells CUT&RUN_RUNX1_dTAG4hr_rep2


title: Rh30_PAX3-FOXO1-FKBP cells CUT&RUN_RUNX1_dTAG4hr_rep1


title: Nadir 2Gy

description:
GPL0009
Intratumoral CD45+ cells isolated from CT26 cancer cells implanted on BALB/c mice.
RNA from CD45 positive cells in tumor
To isolate intratumoral and splenic CD45+ cells, an EasySep™ Mouse CD45+ Cell Isolation Kit (StemCell Technologies, Vancouver, Canada) was used, according to the manufacturer’s instructions. Single cell samples of tumor tissues were resuspended in phosphate-buffered saline with 5% fetal bovine serum (FBS) and 1 mM ethylenediaminetetraacetic acid (fluorescence-activated cell sorting [FACS] buffer) for magnetic labeling. Cells were incubated for 8 min at room temperature with a CD45-positive selection cocktail and tetrameric antibody complexes. Tubes containing the mixture were placed in EasySep™ magnetic for 5 min, and the supernatant was discarded. Finally, magnetically labeled CD45+ cells were resuspended in FACS buffer. Using the MasterPureTM Complete RNA Purification Kit (Lucigen, MA, USA), RNA was isolated from the sorted intratumoral CD45+ cells. NanoString analysis was performed using an nCounter Analysis System (NanoString Technologies, WA, USA).


title: Nadir 0Gy

description:
GPL0008
Intratumoral CD45+ cells isolated from CT26 cancer cells implanted on BALB/c mice.
RNA from CD45 positive cells in tumor
To isolate intratumoral and splenic CD45+ cells, an EasySep™ Mouse CD45+ Cell Isolation Kit (StemCell Technologies, Vancouver, Canada) was used, according to the manufacturer’s instructions. Single cell samples of tumor tissues were resuspended in phosphate-buffered saline with 5% fetal bovine serum (FBS) and 1 mM ethylenediaminetetraacetic acid (fluorescence-activated cell sorting [FACS] buffer) for magnetic labeling. Cells were incubated for 8 min at room temperature with a CD45-positive selection cocktail and tetrameric antibody complexes. Tubes containing the mixture were placed in EasySep™ magnetic for 5 min, and the supernatant was discarded. Finally, magnetically labeled CD45+ cells were resuspended in FACS buffer. Using the MasterPureTM Complete RNA Purification Kit (Lucigen, MA, USA), RNA was isolated from the sorted intratumoral CD45+ cells. NanoString analysis was performed using an nCounter Analysis System (NanoString Technologies, WA, USA).

value: Nadir


title: Chern_City_60


title: Post2 7.5Gy

description:
GPL0007
Intratumoral CD45+ cells isolated from CT26 cancer cells implanted on BALB/c mice.
RNA from CD45 positive cells in tumor
To isolate intratumoral and splenic CD45+ cells, an EasySep™ Mouse CD45+ Cell Isolation Kit (StemCell Technologies, Vancouver, Canada) was used, according to the manufacturer’s instructions. Single cell samples of tumor tissues were resuspended in phosphate-buffered saline with 5% fetal bovine serum (FBS) and 1 mM ethylenediaminetetraacetic acid (fluorescence-activated cell sorting [FACS] buffer) for magnetic labeling. Cells were incubated for 8 min at room temperature with a CD45-positive selection cocktail and tetrameric antibody complexes. Tubes containing the mixture were placed in EasySep™ magnetic for 5 min, and the supernatant was discarded. Finally, magnetically labeled CD45+ cells were resuspended in FACS buffer. Using the MasterPureTM Complete RNA Purification Kit (Lucigen, MA, USA), RNA was isolated from the sorted intratumoral CD45+ cells. NanoString analysis was performed using an nCounter Analysis System (NanoString Technologies, WA, USA).

value: PostRT2, RT


title: Post2 2Gy

description:
GPL0006
Intratumoral CD45+ cells isolated from CT26 cancer cells implanted on BALB/c mice.
RNA from CD45 positive cells in tumor
To isolate intratumoral and splenic CD45+ cells, an EasySep™ Mouse CD45+ Cell Isolation Kit (StemCell Technologies, Vancouver, Canada) was used, according to the manufacturer’s instructions. Single cell samples of tumor tissues were resuspended in phosphate-buffered saline with 5% fetal bovine serum (FBS) and 1 mM ethylenediaminetetraacetic acid (fluorescence-activated cell sorting [FACS] buffer) for magnetic labeling. Cells were incubated for 8 min at room temperature with a CD45-positive selection cocktail and tetrameric antibody complexes. Tubes containing the mixture were placed in EasySep™ magnetic for 5 min, and the supernatant was discarded. Finally, magnetically labeled CD45+ cells were resuspended in FACS buffer. Using the MasterPureTM Complete RNA Purification Kit (Lucigen, MA, USA), RNA was isolated from the sorted intratumoral CD45+ cells. NanoString analysis was performed using an nCounter Analysis System (NanoString Technologies, WA, USA).


title: Post2 0Gy

description:
GPL0005
Intratumoral CD45+ cells isolated from CT26 cancer cells implanted on BALB/c mice.
RNA from CD45 positive cells in tumor
To isolate intratumoral and splenic CD45+ cells, an EasySep™ Mouse CD45+ Cell Isolation Kit (StemCell Technologies, Vancouver, Canada) was used, according to the manufacturer’s instructions. Single cell samples of tumor tissues were resuspended in phosphate-buffered saline with 5% fetal bovine serum (FBS) and 1 mM ethylenediaminetetraacetic acid (fluorescence-activated cell sorting [FACS] buffer) for magnetic labeling. Cells were incubated for 8 min at room temperature with a CD45-positive selection cocktail and tetrameric antibody complexes. Tubes containing the mixture were placed in EasySep™ magnetic for 5 min, and the supernatant was discarded. Finally, magnetically labeled CD45+ cells were resuspended in FACS buffer. Using the MasterPureTM Complete RNA Purification Kit (Lucigen, MA, USA), RNA was isolated from the sorted intratumoral CD45+ cells. NanoString analysis was performed using an nCounter Analysis System (NanoString Technologies, WA, USA).


title: Rh30_PAX3-FOXO1-FKBP cells CUT&RUN_RUNX1_DMSO_rep2


title: Rh30_PAX3-FOXO1-FKBP cells CUT&RUN_HEB_DMSO_rep2


title: Chern_City_59


title: Fig5AandSupFig3A 23 Celsius incubated rdr6 background version2 WTcasphi U6gR10 T1 plant 17


title: Rh30_PAX3-FOXO1-FKBP cells CUT&RUN_RUNX1_DMSO_rep1


title: Post1 7.5Gy

description:
GPL0004
Intratumoral CD45+ cells isolated from CT26 cancer cells implanted on BALB/c mice.
RNA from CD45 positive cells in tumor
To isolate intratumoral and splenic CD45+ cells, an EasySep™ Mouse CD45+ Cell Isolation Kit (StemCell Technologies, Vancouver, Canada) was used, according to the manufacturer’s instructions. Single cell samples of tumor tissues were resuspended in phosphate-buffered saline with 5% fetal bovine serum (FBS) and 1 mM ethylenediaminetetraacetic acid (fluorescence-activated cell sorting [FACS] buffer) for magnetic labeling. Cells were incubated for 8 min at room temperature with a CD45-positive selection cocktail and tetrameric antibody complexes. Tubes containing the mixture were placed in EasySep™ magnetic for 5 min, and the supernatant was discarded. Finally, magnetically labeled CD45+ cells were resuspended in FACS buffer. Using the MasterPureTM Complete RNA Purification Kit (Lucigen, MA, USA), RNA was isolated from the sorted intratumoral CD45+ cells. NanoString analysis was performed using an nCounter Analysis System (NanoString Technologies, WA, USA).

value: PostRT1, RT


title: Chern_City_58

value: Whole Blood


title: Rh30_PAX3-FOXO1-FKBP cells CUT&RUN_MYOD_dTAG4hr_rep1

value: anti-MYOD (Santa Cruz, sc-377460)


title: Post1 2Gy

description:
GPL0003
Intratumoral CD45+ cells isolated from CT26 cancer cells implanted on BALB/c mice.
RNA from CD45 positive cells in tumor
To isolate intratumoral and splenic CD45+ cells, an EasySep™ Mouse CD45+ Cell Isolation Kit (StemCell Technologies, Vancouver, Canada) was used, according to the manufacturer’s instructions. Single cell samples of tumor tissues were resuspended in phosphate-buffered saline with 5% fetal bovine serum (FBS) and 1 mM ethylenediaminetetraacetic acid (fluorescence-activated cell sorting [FACS] buffer) for magnetic labeling. Cells were incubated for 8 min at room temperature with a CD45-positive selection cocktail and tetrameric antibody complexes. Tubes containing the mixture were placed in EasySep™ magnetic for 5 min, and the supernatant was discarded. Finally, magnetically labeled CD45+ cells were resuspended in FACS buffer. Using the MasterPureTM Complete RNA Purification Kit (Lucigen, MA, USA), RNA was isolated from the sorted intratumoral CD45+ cells. NanoString analysis was performed using an nCounter Analysis System (NanoString Technologies, WA, USA).


title: Rh30_PAX3-FOXO1-FKBP cells CUT&RUN_MYOD_dTAG2hr_rep2


title: Fig5AandSupFig3A 23 Celsius incubated rdr6 background version2 WTcasphi U6gR10 T1 plant 16

value: leaf tissue


title: 170_RAW_Cuttag_shKDM1A_H3K9ac_rp1

first: Zhiqiang

last: Huang

state: Jiangsu

address: Hankou 22

department: Medical School

institute: Nanjing University

description: CUT&Tag

data_processing:
Library strategy: Cut&Tag
Cut and Tag raw files (fastq, paired-end) were aligned to the NCBI37/mm9 version of the mouse reference genome, using Bowtie2 with default parameters. Peaks were called by MACS2. HOMER was then used for the tag directories construction from SAM files, duplicated reads removal, peak calling, peaks annotation, raw tag counts extraction and Bed file generation. Only peaks with fold enrichment over input tag count and local tag count > 4 and fdr< 0.001 (default -F -L -C -fdr) are kept.
Genome_build: mm9
Supplementary_files_format_and_content: Bedgraph files contain the genomic coordinates and p-value of each peak. The differential expression files were further provided.

growth_protocol: WT RAW264.7 cells were maintained normal 10% FBS DMEM medium.

extract_protocol: The Cut and Tag Library preparation was performed through the manufacturer's introduction (Steven Henikoff lab,Bench top CUT&Tag V.3 ).

value: RAW 264.7 Macrophage

value: BALB/c

tag: genotype/variation

tag: chip antibody

tag: chip antibody vendor

value: Sigma

tag: chip antibody cat.


title: Chern_City_57

tag: location

value: Chernobyl City

tag: tissue

tag: breed

value: Mixed Breed


title: Rh30_PAX3-FOXO1-FKBP cells CUT&RUN_MYOD_DMSO_rep2


title: Chern_City_56


title: Chern_City_54


title: Fig5AandSupFig3A 23 Celsius incubated rdr6 background version2 WTcasphi U6gR10 T1 plant 13

tag: developmental stage

value: 3-4 weeks

tag: strain

tag: background genotype

tag: target locus


title: 171_RAW_Cuttag_shKDM1A_H3K9ac_rp2

description: CUT&Tag

tag: cell type


title: Rh30_PAX3-FOXO1-FKBP cells CUT&RUN_MYOD_dTAG2hr_rep1

tag: treatment

tag: antibody


title: CNPP_66

value: Chernobyl Nuclear Power Plant


title: Fig5AandSupFig3A 23 Celsius incubated rdr6 background version2 WTcasphi U6gR10 T1 plant 12


title: Fig5AandSupFig3A 23 Celsius incubated rdr6 background version2 WTcasphi U6gR10 T1 plant 11


title: Chern_City_53


title: Rh30_PAX3-FOXO1-FKBP cells CUT&RUN_MYOD_DMSO_rep1

value: DMSO


title: Fig5AandSupFig3A 23 Celsius incubated rdr6 background version2 WTcasphi U6gR10 T1 plant 14


title: Fig5AandSupFig3A 23 Celsius incubated rdr6 background version2 WTcasphi U6gR10 T1 plant 15


title: Chern_City_55


title: 168_RAW_Cuttag_shGFP_H3K9ac_rp1

description: CUT&Tag

value: shGFP


title: Fig5AandSupFig3A 23 Celsius incubated rdr6 background version2 WTcasphi U6gR10 T1 plant 10


title: PreRT

description:
GPL0001
Intratumoral CD45+ cells isolated from CT26 cancer cells implanted on BALB/c mice.
RNA from CD45 positive cells in tumor
To isolate intratumoral and splenic CD45+ cells, an EasySep™ Mouse CD45+ Cell Isolation Kit (StemCell Technologies, Vancouver, Canada) was used, according to the manufacturer’s instructions. Single cell samples of tumor tissues were resuspended in phosphate-buffered saline with 5% fetal bovine serum (FBS) and 1 mM ethylenediaminetetraacetic acid (fluorescence-activated cell sorting [FACS] buffer) for magnetic labeling. Cells were incubated for 8 min at room temperature with a CD45-positive selection cocktail and tetrameric antibody complexes. Tubes containing the mixture were placed in EasySep™ magnetic for 5 min, and the supernatant was discarded. Finally, magnetically labeled CD45+ cells were resuspended in FACS buffer. Using the MasterPureTM Complete RNA Purification Kit (Lucigen, MA, USA), RNA was isolated from the sorted intratumoral CD45+ cells. NanoString analysis was performed using an nCounter Analysis System (NanoString Technologies, WA, USA).

value: tumor

value: tumor infiltrating leukocytes

value: Non-irradiated

value: PreRT


title: Rh30_PAX3-FOXO1-FKBP cells CUT&RUN_MYOD_dTAG4hr_rep2

value: 500nM dTAG47


title: 167_RAW_Cuttag_CRISPR_GPS2_KO_H3K9ac_rp2

description: CUT&Tag

value: GPS2 KO


title: Rh30_PAX3-FOXO1-FKBP cells CUT&RUN_H3K4me3_dTAG4hr_rep1

value: anti-H3K4me3 (Abcam, ab12209)


title: Post1 0Gy

description:
GPL0002
Intratumoral CD45+ cells isolated from CT26 cancer cells implanted on BALB/c mice.
RNA from CD45 positive cells in tumor
To isolate intratumoral and splenic CD45+ cells, an EasySep™ Mouse CD45+ Cell Isolation Kit (StemCell Technologies, Vancouver, Canada) was used, according to the manufacturer’s instructions. Single cell samples of tumor tissues were resuspended in phosphate-buffered saline with 5% fetal bovine serum (FBS) and 1 mM ethylenediaminetetraacetic acid (fluorescence-activated cell sorting [FACS] buffer) for magnetic labeling. Cells were incubated for 8 min at room temperature with a CD45-positive selection cocktail and tetrameric antibody complexes. Tubes containing the mixture were placed in EasySep™ magnetic for 5 min, and the supernatant was discarded. Finally, magnetically labeled CD45+ cells were resuspended in FACS buffer. Using the MasterPureTM Complete RNA Purification Kit (Lucigen, MA, USA), RNA was isolated from the sorted intratumoral CD45+ cells. NanoString analysis was performed using an nCounter Analysis System (NanoString Technologies, WA, USA).


title: CNPP_10

value: Whole Blood


title: Rh30_PAX3-FOXO1-FKBP cells CUT&RUN_H3K4me3_dTAG2hr_rep2


title: CNPP_65


title: 169_RAW_Cuttag_shGFP_H3K9ac_rp2

description: CUT&Tag

value: RAW 264.7 Macrophage


title: Fig5AandSupFig3A 23 Celsius incubated rdr6 background version2 WTcasphi U6gR10 T1 plant 08

value: leaf tissue


title: Fig5AandSupFig3A 23 Celsius incubated rdr6 background version2 WTcasphi U6gR10 T1 plant 07


title: 166_RAW_Cuttag_CRISPR_GPS2_KO_H3K9ac_rp1

description: CUT&Tag

value: BALB/c

value: Sigma


title: Rh30_PAX3-FOXO1-FKBP cells CUT&RUN_H3K4me3_dTAG2hr_rep1


title: Rh30_PAX3-FOXO1-FKBP cells CUT&RUN_H3K4me3_DMSO_rep2


title: CNPP_9

value: Mixed Breed


title: 163_RAW_Cuttag_CRISPR_GPS2_KO_H3K9me3_rp2

description: CUT&Tag

value: Abcam


title: CNPP_8

value: Chernobyl Nuclear Power Plant


title: Fig5AandSupFig3A 23 Celsius incubated rdr6 background version2 WTcasphi U6gR10 T1 plant 06

value: 3-4 weeks


title: Rh30_PAX3-FOXO1-FKBP cells CUT&RUN_H3K4me3_DMSO_rep1

value: DMSO


title: 164_RAW_Cuttag_CRISPR_Con_H3K9ac_rp1

description: CUT&Tag

value: Control


title: Fig5AandSupFig3A 23 Celsius incubated rdr6 background version2 WTcasphi U6gR10 T1 plant 05


title: Fig5AandSupFig3A 23 Celsius incubated rdr6 background version2 WTcasphi U6gR10 T1 plant 03


title: Rh30_PAX3-FOXO1-FKBP cells CUT&RUN_BRD4_dTAG24hr_rep2

description: 5301-BRD4-dTAG24-merge.CPMnorm.bs20.bw, 5301_BRD4_counttable_raw.txt

value: anti-BRD4 (BETHYL, #A301-985A50)


title: CNPP_7


title: Rh30_PAX3-FOXO1-FKBP cells CUT&RUN_BRD4_dTAG24hr_rep1


title: Fig5AandSupFig3A 23 Celsius incubated rdr6 background version2 WTcasphi U6gR10 T1 plant 04


title: 161_RAW_Cuttag_CRISPR_Con_H3K9me3_rp2

description: CUT&Tag


title: CNPP_6


title: 162_RAW_Cuttag_CRISPR_GPS2_KO_H3K9me3_rp1

description: CUT&Tag


title: CNPP_5


title: Fig5AandSupFig3A 23 Celsius incubated rdr6 background version2 WTcasphi U6gR10 T1 plant 09


title: 165_RAW_Cuttag_CRISPR_Con_H3K9ac_rp2

description: CUT&Tag


title: Rh30_PAX3-FOXO1-FKBP cells CUT&RUN_BRD4_dTAG4hr_rep2

description: 5301-BRD4-dTAG4-merge.CPMnorm.bs20.bw, 5301_BRD4_counttable_raw.txt


title: 160_RAW_Cuttag_CRISPR_Con_H3K9me3_rp1

description: CUT&Tag


title: 159_RAW_Cuttag_shSMRT_KDM1A

description: CUT&Tag

value: shSMRT


title: CNPP_3


title: Fig5AandSupFig3A 23 Celsius incubated rdr6 background version2 WTcasphi U6gR10 T1 plant 02


title: 158_RAW_Cuttag_shNCOR_KDM1A

description: CUT&Tag

value: shNCOR


title: Fig5AandSupFig3A 23 Celsius incubated rdr6 background version2 WTcasphi U6gR10 T1 plant 01


title: Rh30_PAX3-FOXO1-FKBP cells CUT&RUN_BRD4_dTAG4hr_rep1

value: 500nM dTAG47


title: Rh30_PAX3-FOXO1-FKBP cells CUT&RUN_BRD4_dTAG2hr_rep2

description: 5301-BRD4-dTAG2-merge.CPMnorm.bs20.bw, 5301_BRD4_counttable_raw.txt


title: 156_RAW_Cuttag_shSMRT_H3K9me3

description: CUT&Tag


title: 155_RAW_Cuttag_shNCOR_H3K9me3

description: CUT&Tag


title: CNPP_2


title: Rh30_PAX3-FOXO1-FKBP cells CUT&RUN_BRD4_DMSO_rep2

description: 5301-BRD4-dTAG0-merge.CPMnorm.bs20.bw, 5301_BRD4_counttable_raw.txt


title: Rh30_PAX3-FOXO1-FKBP cells CUT&RUN_BRD4_DMSO_rep1


title: CNPP_60


title: Rh30_PAX3-FOXO1-FKBP cells CUT&RUN_H3K4me3_dTAG4hr_rep2


title: CNPP_59


title: Fig5AandFig5C WT control plant1

value: wild type


title: CNPP_1


title: Fig5AandFig5C WT control plant2


title: CNPP_4


title: Rh30_PAX3-FOXO1-FKBP cells CUT&RUN_P3F_Xlink_dTAG24hr_rep2

value: Anti-HA (Cell Signaling, (C29F4) #3724)


title: 154_RAW_Cuttag_shGFP_H3K9me3

description: CUT&Tag

value: shGFP


title: Rh30_PAX3-FOXO1-FKBP cells CUT&RUN_BRD4_dTAG2hr_rep1


title: Fig5A rdr6 background version2 vcasphi U6gR10 T1 plant 48


title: Chern_City_52

value: Chernobyl City

value: Whole Blood


title: 153_ATACseq_RAW_shSMRT_rp3

data_processing:
ChIP-seq raw files (fastq or txt files, single-end) were aligned to the NCBI37/mm9 version of the mouse reference genome, using Bowtie2 with default parameters. HOMER were then used for the tag directories construction from SAM files, duplicated reads removal, peak calling, peaks annotation, raw tag counts extraction and Bed file generation. Only peaks with fold enrichment over input tag count and local tag count > 4 and fdr< 0.001 (default -F -L -C -fdr) are kept.
ATAC-seq raw files (fastq, paired-end) were aligned to the NCBI37/mm9 version of the mouse reference genome, using Bowtie2 with default parameters. Peaks were called by MACS2. HOMER was then used for the tag directories construction from SAM files, duplicated reads removal, peak calling, peaks annotation, raw tag counts extraction and Bed file generation. Only peaks with fold enrichment over input tag count and local tag count > 4 and fdr< 0.001 (default -F -L -C -fdr) are kept.
RNA-seq raw files (fastq, single-end) were aligned to the NCBI37/mm9 version of the mouse reference genome, using HISAT2 with default parameters. Read counts were imported by HOMER and analyzed using analyzeRepeats with the option rna and parameters -noadj -condenseGenes and -count exons for four replicates per condition. Differential gene expression was performed with DESeq2 using HOMER’s getDiffExpression.pl using default parameter. Transcripts with an adjusted p-value < 0.05 were considered as differentially expressed genes.
Cut and Tag raw files (fastq, paired-end) were aligned to the NCBI37/mm9 version of the mouse reference genome, using Bowtie2 with default parameters. Peaks were called by MACS2. HOMER was then used for the tag directories construction from SAM files, duplicated reads removal, peak calling, peaks annotation, raw tag counts extraction and Bed file generation. Only peaks with fold enrichment over input tag count and local tag count > 4 and fdr< 0.001 (default -F -L -C -fdr) are kept.
Genome_build: mm9
Supplementary_files_format_and_content: Bedgraph files contain the genomic coordinates and p-value of each peak. The differential expression files were further provided.

growth_protocol:
ChIP-Seq: WT RAW264.7 cells, lentivirus-medicated knockdown cells and GPS2 CRISPR KO cells were maintained normal 10% FBS DMEM medium.
ATAC-Seq: WT RAW264.7 cells were maintained normal 10% FBS DMEM medium.
RNA-Seq: BMDM cells were maintained normal 10% FBS DMEM medium supplement with 30% L929 medium for one week.
Cut&Tag: WT RAW264.7 cells were maintained normal 10% FBS DMEM medium.

extract_protocol:
ChIP-Seq: Fresh cells were crosslinked with 2 mM disuccinimidyl glutarate (DSG) for 30 min, followed by 1% formaldehyde for 10 min at room temperature. Nuclei were isolated, sonicated and incubated with magnetic bead-antibody complexes.
ChIP-Seq: ChIPed DNA was processed using Takara SMRTer ThruPLEX DNA-seq Kit. Briefly, DNA was end-repaired and ligated to stem-loop adaptors. Then DNA was PCR amplified with Illumina-compatible primers for 7-11 cycles and library fragments of 200 to 400 bp were selected using Ampure XP beads.
ATAC-Seq: WT RAW264.7 cells were seeded with triplicates in the 12 wells plates with 2×10^5 cells one day before the experiments. Cells were harvested with IL4 1h treatment, washed with PBS and then resuspended in lysis buffer. Cell nuclei were spined down and transferred into the transposition reaction buffer and incubated at 37 °C for 30 minutes using 105 cells. Genomic DNA was extracted using Qiagen MinElute PCR Purification Kit. ATAC-seq library was done with the protocol as previously reported (Buenrostro et al., 2015). The Purified ATAC-seq DNA library mix was sequenced on NextSeq 550 (Illumina, 35 SE reads, paired-end) in BEA Core Facility (Karolinska Institutet, Huddinge, Sweden).
ATAC-Seq: The ATAC-seq Library preparation was performed through the manufacturer's introduction.
RNA-Seq: 2×10^5 WT and GPS2 KO BMDM cells were seeded one day before the treatment. The next day the cells were treatment with IL4 6h and the total RNA was extracted from the manufacturer's introduction.
RNA-Seq: The RNA-seq library preparation was followed by the instructions of the NEB Next Ultra II RNA Library kit (NEB, E7770S).
Cut&Tag: 2×10^5 shGFP and shKDM1A RAW cells were seeded one day before.
Cut&Tag: The Cut and Tag Library preparation was performed through the manufacturer's introduction (Steven Henikoff lab,Bench top CUT&Tag V.3 ).

treatment_protocol:
ChIP-Seq: RAW264.7 cells were treated with or without LPS (100ng/ml) or IL4 (20ng/ml) treatment for indicated time.
ATAC-Seq: RAW264.7 cells were treated IL4 (20ng/ml) for 1h .
RNA-Seq: BMDM cells were treated with or without IL4 (20ng/ml) treatment for 6h.
Cut&Tag: No treatment

value: Macrophage

value: BALB/c

value: No antibody

value: No


title: Rh30_PAX3-FOXO1-FKBP cells CUT&RUN_P3F_Xlink_dTAG24hr_rep1


title: Fig5A rdr6 background version2 vcasphi U6gR10 T1 plant 47

value: leaf tissue


title: Fig5AandFig5C WT control plant3

value: 3-4 weeks


title: 157_RAW_Cuttag_shGFP_KDM1A

description: CUT&Tag

value: RAW 264.7 Macrophage

value: Abcam


title: Chern_City_51

data_processing: Image data was analyzed using GenomeStudio with GT module (Illumina).

value: Mixed Breed


title: 152_ATACseq_RAW_shSMRT_rp2

value: Control