title: 4CMusD-Dac1J_Dac1J129sv_E12.5_FLHL_Rep3

data_processing:
*library strategy: 4C
Raw sequencing reads were pre-processed, mapped to a corresponding reference using BWA and normalized as reported previously
4C-seq data  were generated from mapped, filtered and deduplicated read pairs
Assembly: mm10
Supplementary files format and content: bedgraph

growth_protocol: Limbs from E12.5 mouse embryos were dissected in PBS, a single cell suspension was made using Trypsin, samples were fixed in 2% PFA, snap frozen, and stored at -80 °C.

extract_protocol: Snap frozen samples were first digested using DpnII, religated using the T4 DNA ligase (Thermo Fisher Scientific). The chimeric chromatin products were then decrosslinked overnight. RNase A treated chromatin was then precipiated.The precipiated chromatin was sheared using a Covaris sonicator (duty cycle: 10%; intensity: 5; cycles per burst: 200; time: 6 cycles of 60 s each; set mode: frequency sweeping; temperature: 4–7 °C). Adaptors were added to the sheared DNA and amplified according to the manufacturer’s instructions for Illumina sequencing (Agilent). The library was hybridized to the custom-designed SureSelect beads and indexed for sequencing following the manufacturer’s instructions (Agilent).

treatment_protocol: The 4C protocol was performed as decribed in (Formation of new chromatin domains determines pathogenecity of genomic duplications. Franke et al., Nature 2016).


title: 1_isotype control, heGDH

status: Public on Mar 15 2025

type: SRA

city: Epalinges

first: Julia

last: Esser-von Bieren

state: non

address: Chemin des Boveresses 155

country: Switzerland

institute: UNIL

library_source: genomic

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

molecule: genomic DNA

organism: Homo sapiens

source_name: MDM stimulated with heGDH

growth_protocol: CD14+ monocytes + TGFb1, GM-CSF

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

treatment_protocol: untreated or heGDH (5 µg/ml)

tag: tissue

value: blood

tag: cell type

value: monocyte derived macrophages

tag: treatment

value: heGDH


title: dual-AAV split-ePE3-367,1e12, tail-vein injection,liver,rep3,off target site 8

city: Hangzhou

first: Lijia

last: Ma

state: Zhejiang

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

department: School of Life Sciences

country: China

institute: Westlake university

description:
Library name: SP3R3liverot8
rep3,off target site 8
sPE_sep_processed_date.xls

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

organism: Mus musculus

source_name: liver

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

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

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

value: liver

tag: genotype

value: WT


title: dual-AAV split-ePE3-367,1e12, tail-vein injection,liver,rep2,off target site 8

description:
Library name: SP3R2liverot8
rep2,off target site 8
sPE_sep_processed_date.xls


title: Subject4_Day7_BM

city: Nijmegen

first: Hendrik

middle: G

last: Stunnenberg

state: Gelderland

address: Geert Grooteplein 28

department: Molecular Biology

country: Netherlands

institute: Radboud University

description: Bone marrow mononuclear cells were isolated one week (7 days) after in vivo LPS challenge (LPS-induced systemic inflammation) and scRNA-seq libraries were prepared using 10X single cell 3' (v3.1) method.

library_source: transcriptomic single cell

data_processing:
Sequencing data were mapped to hg38 reference genome and gene/cell count matrix was generated using cellRanger software with default parameters.
Assembly: hg38
Supplementary files format and content: tar.gz, Gene/single-cell Count Matrix obtained from CellRanger

molecule: total RNA

source_name: Adult Human Bone Marrow

growth_protocol: Bone marrow mononuclear cells were isolated from bone marrow aspirates and cryopreserved until library preparation step.

extract_protocol:
Single-cell RNA-seq libraries were prepared using Chromium (10X) single cell 3' V3 kit following manufacturer's protocol.
Chromium (10X) Single-cell 3' v3

treatment_protocol: No treatment

value: Bone Marrow Mononuclear Hematopoietic Cells

tag: protocol


title: 4CMusD-Dac1J_Dac1J129sv_E12.5_FLHL_Rep2

city: Berlin

first: Juliane

last: Glaser

address: Ihnestrasse 63-73

department: Development and Disease

country: Germany

institute: Max Planck Institute for Molecular Genetics

source_name: limbs

value: limbs

tag: developmental stage

tag: strain


title: Subject4_4h_BM

description: Bone marrow mononuclear cells were isolated 4 hours after in vivo LPS challenge (LPS-induced systemic inflammation) and scRNA-seq libraries were prepared using 10X single cell 3' (v3.1) method.


title: dual-AAV split-ePE3-367,2e12, tail-vein injection,liver,rep3,off target site 8

description:
Library name: SP4R3liverot8
rep3,off target site 8
sPE_sep_processed_date.xls


title: 4CMusD-Dac1J_Dac1J129sv_E12.5_FLHL_Rep1


title: dual-AAV split-ePE3-367,2e12, tail-vein injection,liver,rep3,off target site 7

description:
Library name: SP4R3liverot7
rep3,off target site 7
sPE_sep_processed_date.xls


title: dual-AAV split-ePE3-367,1e12, tail-vein injection,liver,rep1,off target site 8

description:
Library name: SP3R1liverot8
rep1,off target site 8
sPE_sep_processed_date.xls


title: 4CMusD-Dac1J_Dac1JBl6_E12.5_FLHL_Rep3


title: dual-AAV split-ePE3-367,2e12, tail-vein injection,liver,rep2,off target site 7

description:
Library name: SP4R2liverot7
rep2,off target site 7
sPE_sep_processed_date.xls


title: Subject4_Day0_BM

description: Bone marrow mononuclear cells were isolated from healthy volunteer on day 0, before in vivo LPS challenge (LPS-induced systemic inflammation) and scRNA-seq libraries were prepared using 10X single cell 3' (v3.1) method.


title: 4CMusD-Dac1J_Dac1JBl6_E12.5_FLHL_Rep2


title: Subject2_Day7_BM

value: isolated one week (7 days) after in vivo LPS challenge (LPS-induced systemic inflammation) and scRNA-seq libraries were prepared using 10X single cell 3' (v3.1) method.


title: 2_ H3K27ac, control

source_name: unstimulated MDM

value: control


title: dual-AAV split-ePE3-367,2e12, tail-vein injection,liver,rep1,off target site 7

description:
Library name: SP4R1liverot7
rep1,off target site 7
sPE_sep_processed_date.xls


title: 4CMusD-Dac1J_Dac1JBl6_E12.5_FLHL_Rep1


title: Subject2_4h_BM

value: isolated 4 hours after in vivo LPS challenge (LPS-induced systemic inflammation) and scRNA-seq libraries were prepared using 10X single cell 3' (v3.1) method.


title: dual-AAV split-ePE3-367,1e12, tail-vein injection,liver,rep3,off target site 7

description:
Library name: SP3R3liverot7
rep3,off target site 7
sPE_sep_processed_date.xls


title: AHCC+LPS (205659810031_R06C01)

type: genomic

city: ottawa

first: Hamed

last: Yasavoli Sharahi

state: ontario

address: 451 Smyth Rd

country: Canada

institute: university of ottawa

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridized to Infinium MouseMethylation285 BeadChip (Illumina) using standard Illumina protocol

scan_protocol: Illumina iScan System

data_processing:
Sesame R package
processed value definition: Average Beta

label: biotin

source_name: Mammary Gland

label_protocol: Standard Illumina Protocol

extract_protocol: Tissue DNA extraction was carried out using the Gentra Puregene Tissue Kit (33g) (Qiagen, Toronto, Canada) according to the manufacturer’s instructions. The extracted DNA was subsequently diluted with DNA rehydration solution, provided with the kit, to a final concentration of 20 ng/µl and stored at -20ºC.

value: Mammary Gland

value: AHCC+LPS


title: Diff_MK, Barcode-derived cDNA

city: Chicago

first: Rui

last: Yi

state: IL

address: 303 E. Chicago Avenue

country: USA

institute: Northwestern University

library_source: other

data_processing:
For scRNAseq, raw reads were aligned to mouse genome build mm10 using cellranger v6.1.2.
For lineage tracing barcode sequencing, barcodes were assigned to cells using Cite-seq Count.
Assembly: refdata-gex-mm10-2020-A
Supplementary files format and content: Filtered feature-barcode matrix from cellranger output with cell barcode as column name and gene feature as row name for scRNAseq libraries.
Supplementary files format and content: Feature-barcode matrix were generated from Cite-seq Count for barcode-derived libaries.

molecule: other

source_name: MK

growth_protocol: Mouse keratinocytes were maintained in E low medium supplemented with 15% fetal bovine serum plus antibiotics.

extract_protocol:
Mouse keratinocytes were trypsinzed and GFP positive lineage tracing barcode labelled cells were sorted using flow cytometry and then loaded onto 10x Genomics controller.
scRNAseq libraries were constructed using 10x Genomics Single Cell 3' v3 protocol; barcode-derived libraries were constructed following the CITEseq protocol.
scRNA-seq combined with lineage tracing barcode sequencing

tag: cell line

value: MK

value: Mouse keratinocyte

value: Dox


title: Subject2_Day0_BM

value: isolated from healthy volunteer on day 0, before in vivo LPS challenge (LPS-induced systemic inflammation) and scRNA-seq libraries were prepared using 10X single cell 3' (v3.1) method.


title: dual-AAV split-ePE3-367,1e12, tail-vein injection,liver,rep2,off target site 7

description:
Library name: SP3R2liverot7
rep2,off target site 7
sPE_sep_processed_date.xls


title: Subject1_Day7_BM


title: Diff_MK, mRNA-derived cDNA

molecule: polyA RNA


title: AHCC+LPS (205659810031_R05C02)


title: dual-AAV split-ePE3-367,1e12, tail-vein injection,liver,rep1,off target site 7

description:
Library name: SP3R1liverot7
rep1,off target site 7
sPE_sep_processed_date.xls


title: LPS (205659810031_R05C01)

value: LPS


title: MK, Barcode-derived cNDA


title: Subject1_4h_BM


title: Subject1_Day0_BM


title: Control (205659810031_R04C01)

value: Control


title: MK, mRNA-derived cDNA


title: dual-AAV split-ePE3-367,2e12, tail-vein injection,liver,rep3,off target site 6

description:
Library name: SP4R3liverot6
rep3,off target site 6
sPE_sep_processed_date.xls


title: dual-AAV split-ePE3-367,2e12, tail-vein injection,liver,rep2,off target site 6

description:
Library name: SP4R2liverot6
rep2,off target site 6
sPE_sep_processed_date.xls


title: chicken abd. fat, HS_3

city: Minamiminowa, Kamiina

first: Yukako

last: Tokutake

state: Nagano

country: Japan

institute: Shinshu University

description: Library name: cfat-HS-8

library_source: transcriptomic

data_processing:
Analyze the quality control of the sequenced raw reads. Overall reads quality, total bases, total reads, GC (%) and basic statistics are calculated.
In order to reduce biases in analysis, artifacts such as low quality reads, adaptor sequence, contaminant DNA, or PCR duplicates are removed.
Trimmed reads are mapped to reference genome with HISAT2 version 2.1.0, Bowtie2 2.3.4.1, splice-aware aligner.
Transcript is assembled by StringTie version 2.1.3b with aligned reads.
Expression profiles are represented as read count and normalization values which are calculated based on transcript length and depth of coverage. Normalization values are provided as FPKM (Fragments Per Kilobase of transcript per Million Mapped reads) / RPKM (Reads Per Kilobase of transcript per Million mapped reads) and TPM(Transcripts Per Kilobase Million).
In groups with different conditions, genes or transcripts that express differentially are filtered out through statistical hypothesis testing.
Assembly: GRCg6a
Supplementary files format and content: Excel file includes read counts for each Sample

organism: Gallus gallus

source_name: Abdominal fat

growth_protocol: Newly hatched male broiler chicks (Ross strain; Gallus domesticus) were housed in an electrically heated battery cage. At 14 days of age,  chicks were allocated to two treatments with 12 chickens in a completely randomized design. All chickens were transferred into individual wire cages in environmentally controlled chambers and housed at an optimum temperature (22.0 °C ± 0.5, humidity 50% ± 0.5). The chickens were housed under 24-h light conditions throughout the experimental period. All chicks were fed the same experimental diet until end of experiment.

extract_protocol:
Total RNA was extracted by TRIzol reagent (Thermo Fisher Scientific, inc.) and purified with QIAquick PCR Purification Kit (Qiagen).
RNA libraries for RNA-seq were prepared using TruSeq Stranded mRNA Library Prep Kit following manufacturer's protocols.

treatment_protocol: At 21 days of age, control and heat-stressed group chickens were exposed to thermoneutral condition (22.0 °C ± 0.5, humidity 50% ± 0.5) or heat stress condition (32.0 °C ± 0.5, humidity 50% ± 0.5) until 35 days of age.

value: Abdominal fat

value: Heat stress (32 ℃)


title: chicken abd. fat, TN_2

description: Library name: cfat-TN-10

value: Thermoneutral (22 ℃)


title: LPS (205659810027_R06C02)


title: dual-AAV split-ePE3-367,1e12, tail-vein injection,liver,rep2,off target site 6

description:
Library name: SP3R2liverot6
rep2,off target site 6
sPE_sep_processed_date.xls

value: liver

value: WT


title: chicken abd. fat, TN_3

description: Library name: cfat-TN-12


title: Subject3_24h_exvivo_4h_LPS

description: Monocytes, 24 hours after in vivo LPS challenge (LPS-SI) were isolated from PBMC by CD14 positive selection. Thereafter, isolated monocytes were ex vivo (re)stimulated with LPS (10ng/ml) for 4 hours and then RNA-seq analysis performed on rRNA-depleted total RNA.

data_processing:
To infer gene expression levels, RNA-seq reads were aligned to the hg38 human reference transcriptome using STAR alignment tool. Genes with fewer than 50 reads on average in all samples were excluded from downstream analysis.
Utilizing DESeq2 libraries normalized and differentially expressed genes determined. Genes with more than two-fold change between at least two time points and less that 0.05 padj value were designated as significant differentially expressed genes.
Assembly: hg38
Supplementary files format and content: xlsx, Raw Count table of Gene Expression from all samples

source_name: Adult Human Peripheral Blood

growth_protocol: After isolation from PBMC using CD14 positive selection, monocytes were either analyzed by RNA-seq straightaway or ex vivo LPS-stimulated (10ng/ml) medium for 4hours and then analyzed by RNA-seq.

extract_protocol:
Total RNA was extracted from monocytes using the QIAGEN RNeasy RNA extraction kit (QIAGEN, Netherlands), using on-column DNaseI treatment.
Ribosomal RNA removal and library preparation for next generation RNA-sequencing was achieved utilizing KAPA RNA HyperPrep Kit with RiboErase (Roche), following the manufacturer’s protocol. The integrity and quality of prepared libraries were assessed using Agilent 2100 Bioanalyzer. Sequencing was performed using Illumina NextSeq 500 machine in a paired end sequencing fashion.

treatment_protocol: 4 hours of ex vivo LPS (10ng/ml) treatment for designated conditions.

value: Monocyte


title: Subject3_24h

description: Monocytes, 24 hours after in vivo LPS challenge (LPS-SI) were isolated from PBMC by CD14 positive selection. Thereafter (without any culturing) RNA-seq analysis performed on rRNA-depleted total RNA.


title: AHCC+LPS (205659810027_R06C01)


title: dual-AAV split-ePE3-367,1e12, tail-vein injection,liver,rep1,off target site 6

description:
Library name: SP3R1liverot6
rep1,off target site 6
sPE_sep_processed_date.xls


title: AHCC (205659810027_R04C02)

value: AHCC


title: Subject3_8h_exvivo_4h_LPS

description: Monocytes, 8 hours after in vivo LPS challenge (LPS-SI) were isolated from PBMC by CD14 positive selection. Thereafter, isolated monocytes were ex vivo (re)stimulated with LPS (10ng/ml) for 4 hours and then RNA-seq analysis performed on rRNA-depleted total RNA.


title: chicken abd. fat, HS_2

description: Library name: cfat-HS-7


title: dual-AAV split-ePE3-367,2e12, tail-vein injection,liver,rep1,off target site 6

description:
Library name: SP4R1liverot6
rep1,off target site 6
sPE_sep_processed_date.xls


title: LPS (205659810031_R03C01)


title: chicken abd. fat, TN_1

description: Library name: cfat-TN-7


title: dual-AAV split-ePE3-367,2e12, tail-vein injection,liver,rep3,off target site 5

description:
Library name: SP4R3liverot5
rep3,off target site 5
sPE_sep_processed_date.xls


title: LPS (205659810027_R04C01)


title: Subject3_8h

description: Monocytes, 8 hours after in vivo LPS challenge (LPS-SI) were isolated from PBMC by CD14 positive selection. Thereafter (without any culturing) RNA-seq analysis performed on rRNA-depleted total RNA.


title: Subject3_7d_exvivo_4h_LPS

description: Monocytes, one week (7 days) after in vivo LPS challenge (LPS-SI) were isolated from PBMC by CD14 positive selection. Thereafter, isolated monocytes were ex vivo (re)stimulated with LPS (10ng/ml) for 4 hours and then RNA-seq analysis performed on rRNA-depleted total RNA.


title: dual-AAV split-ePE3-367,2e12, tail-vein injection,liver,rep2,off target site 5

description:
Library name: SP4R2liverot5
rep2,off target site 5
sPE_sep_processed_date.xls


title: Subject3_4h_exvivo_4h_LPS

description: Monocytes, 4 hours after in vivo LPS challenge (LPS-SI) were isolated from PBMC by CD14 positive selection. Thereafter, isolated monocytes were ex vivo (re)stimulated with LPS (10ng/ml) for 4 hours and then RNA-seq analysis performed on rRNA-depleted total RNA.


title: AHCC (205659810027_R03C01)


title: dual-AAV split-ePE3-367,2e12, tail-vein injection,liver,rep1,off target site 5

description:
Library name: SP4R1liverot5
rep1,off target site 5
sPE_sep_processed_date.xls


title: Subject3_4h

description: Monocytes, 4 hours after in vivo LPS challenge (LPS-SI) were isolated from PBMC by CD14 positive selection. Thereafter (without any culturing) RNA-seq analysis performed on rRNA-depleted total RNA.


title: dual-AAV split-ePE3-367,1e12, tail-vein injection,liver,rep3,off target site 5

description:
Library name: SP3R3liverot5
rep3,off target site 5
sPE_sep_processed_date.xls


title: slpifq_6h_L_FR_2

city: Rishon LeZion,

first: Yogev

last: Burko

address: 68 HaMaccabim Rd.,

department: Plant Biology

country: Israel

institute: Volcani Institute

description:
The two fasq files from two different runs were merged and aligned to the genome with STAR
HTSeqcounts_WT_pif8a_pifq_6h.csv
Normalized_CPM_WT_pif8a_pifq_6h.csv
LOG2_Fold_Change_relative_to_21WL_WT_pif8a_pifq_6h.xlsx

data_processing:
base calling was done by RTA 1.17.20 (Illumina, CA)
demultiplexing was done by CASAVA 1.8.2 (Illumina, CA)
Sequenced reads were trimmed for adaptor sequence, then aligned (two fastq files for each sample) to the SL4.0 genome using STAR (v2.7.9a) with default parameters except --alignIntronMax 2000 and --outFilterMismatchNmax 10.
Mapped reads were counted by HTSeq (v0.13.5) with default parameters except "-m intersection-strict -s reverse" and differential expression was determined using edgeR (v3.40.2). The wild-type (time course) analysis and the comparison between wild-type, slpif8a, and slpifq were conducted separately.
Assembly: Tomato SL4.0 / ITAG4.0
Supplementary files format and content: HTSeqcounts_WT_3h_6h_24h.csv : csv files include counts for each gene in each sample of WT based on HtseqCount
Supplementary files format and content: HTSeqcounts_WT_pif8a_pifq_6h.csv : csv files include counts for each gene in each sample of WT, slpif8a and slpifq at 6h based on HtseqCount
Supplementary files format and content: Normalized_CPM_WT_3h_6h_24h.csv: csv files include normalized counts per million reads mapped  (cpm) generated using edgeR for WT at 3h, 6h, and 24h
Supplementary files format and content: Normalized_CPM_WT_pif8a_pifq_6h.csv: csv files include normalized counts per million reads mapped  (cpm) generated using edgeR for WT, pif8a and pifq at  6h
Supplementary files format and content: LOG2_Fold_Change_relative_to_21WL_WT_3h_6h_24h.xlsx: xlsx file includes Log2 Fold Change with FDR between 24FR and 24WL wild-type, at the same time point and same tissue.
Supplementary files format and content: LOG2_Fold_Change_relative_to_21WL_WT_pif8a_pifq_6h.xlsx: xlsx file includes Log2 Fold Change with FDR between 24FR and 24WL at 6h in each genotype and same tissue.

organism: Solanum lycopersicum

source_name: First Leaf

growth_protocol: Tomato plants were germinated on standard growing soil in a growth chamber in a long day (LD) white light (LED) at a constant 24°C (24WL, ~200 µmol m−2 s−1)

extract_protocol:
Total RNA was isolated from hypocotyl, epicotyl, cotyledons and first leaf separately, using the RNeasy Micro Kit (Qiagen). Tissue were collected from 4 seedlings per sample and directly snap-frozen in liquid nitrogen.
Stranded mRNA-seq libraries were prepared using the Illumina TruSeq Stranded mRNA Library Prep Kit according to the manufacturer's instructions

treatment_protocol: Plants were grown for 12 days in a long day (LD) white light at constant 24°C (24WL, ~200 µmol m−2 s−1) and either kept in the same condition or moved after 2 hours of light to 24 °C supplemented with far-red light (24FR, ~200 µmol m−2 s−1, R/FR= 0.6) for 3, 6 or 24 hours. Wild-type samples were also collected after 3 hours and 24 hours.

value: First Leaf

value: slpifq

tag: background

tag: time

value: White light + Far-red


title: Control (205659810027_R02C01)

value: Mammary Gland


title: Subject3_Baseline_exvivo_4h_LPS

description: Monocytes from healthy volunteer PBMC (before in vivo LPS challenge) isolated by CD14 positive selection. Thereafter, isolated monocytes were ex vivo (re)stimulated with LPS (10ng/ml) for 4 hours and then RNA-seq analysis performed on rRNA-depleted total RNA.


title: Subject3_Baseline

description: Monocytes from healthy volunteer PBMC (before in vivo LPS challenge) isolated by CD14 positive selection. Thereafter (without any culturing) RNA-seq analysis performed on rRNA-depleted total RNA.


title: slpifq_6h_L_WL_3

value: White light


title: slpifq_6h_L_FR_1


title: dual-AAV split-ePE3-367,1e12, tail-vein injection,liver,rep2,off target site 5

description:
Library name: SP3R2liverot5
rep2,off target site 5
sPE_sep_processed_date.xls


title: AHCC+LPS (205659810025_R05C02)

value: AHCC+LPS


title: slpifq_6h_L_FR_3


title: Sample2_24_3_2022

city: Cairo

first: Amal

last: Mohamed

address: El-Bohooth

department: Human Cytogenetics

country: Egypt

institute: National Research Centre

description:
Imprinting Disorder
Hybridization to SNP

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions

scan_protocol: We use Affymetrix fluidic station for wash and stain microchips.We used Affymetrix scanner 3000

data_processing:
We use ChAS software to analyse the generated cell files
SNP call, Loss of heterozygozity, copy number variance

label: Biotin

source_name: Blood Sample

label_protocol: As per manufacturer (Affymetrix)

extract_protocol: Genomic DNA was extracted from peripheral blood using the Qiagen DNA Blood Mini Kit. DNA quality and quantity was assessed using a Nano Quant instrumentation

tag: tag

value: ImpDis


title: slpifq_6h_L_WL_1


title: Subject2_7d_exvivo_4h_LPS

value: one week (7 days) after in vivo LPS challenge (LPS-SI) were isolated from PBMC by CD14 positive selection. Thereafter, isolated monocytes were ex vivo (re)stimulated with LPS (10ng/ml) for 4 hours


title: AHCC+LPS (205659810025_R05C01)


title: dual-AAV split-ePE3-367,1e12, tail-vein injection,liver,rep1,off target site 5

description:
Library name: SP3R1liverot5
rep1,off target site 5
sPE_sep_processed_date.xls


title: Subject3_7d

description: Monocytes, one week (7 days) after in vivo LPS challenge (LPS-SI) were isolated from PBMC by CD14 positive selection. Thereafter (without any culturing) RNA-seq analysis performed on rRNA-depleted total RNA.


title: Control (205659810031_R02C01)


title: Sample5_24_3_2022


title: Subject2_7d

value: one week (7 days) after in vivo LPS challenge (LPS-SI) were isolated from PBMC by CD14 positive selection. Thereafter (without any culturing) RNA-seq analysis performed on rRNA-depleted total RNA.


title: AHCC (205659810025_R04C02)


title: Sample3_24_3_2022


title: dual-AAV split-ePE3-367,2e12, tail-vein injection,liver,rep2,off target site 4

description:
Library name: SP4R2liverot4
rep2,off target site 4
sPE_sep_processed_date.xls


title: slpifq_6h_h_FR_3

source_name: Hypocotyl

value: Hypocotyl


title: Control (205659810025_R03C01)

value: Control


title: Sample1_24_3_2022


title: Sample2_5_8_2021


title: Sample 1_30_9_2021


title: Subject2_24h_exvivo_4h_LPS

description: Monocytes, 24 hours after in vivo LPS challenge (LPS-SI) were isolated from PBMC by CD14 positive selection. Thereafter, isolated monocytes were ex vivo (re)stimulated with LPS (10ng/ml) for 4 hours and then RNA-seq analysis performed on rRNA-depleted total RNA.


title: chicken abd. fat, HS_1

description: Library name: cfat-HS-5

value: Abdominal fat

value: Heat stress (32 ℃)


title: Control (205659810025_R02C02)


title: LPS (205659810025_R01C02)

value: LPS


title: dual-AAV split-ePE3-367,1e12, tail-vein injection,liver,rep3,off target site 4

description:
Library name: SP3R3liverot4
rep3,off target site 4
sPE_sep_processed_date.xls

value: liver

value: WT


title: slpifq_6h_h_FR_1


title: Subject2_24h

description: Monocytes, 24 hours after in vivo LPS challenge (LPS-SI) were isolated from PBMC by CD14 positive selection. Thereafter (without any culturing) RNA-seq analysis performed on rRNA-depleted total RNA.

value: Monocyte


title: dual-AAV split-ePE3-367,1e12, tail-vein injection,liver,rep3,off target site 6

description:
Library name: SP3R3liverot6
rep3,off target site 6
sPE_sep_processed_date.xls


title: Subject2_8h

description: Monocytes, 8 hours after in vivo LPS challenge (LPS-SI) were isolated from PBMC by CD14 positive selection. Thereafter (without any culturing) RNA-seq analysis performed on rRNA-depleted total RNA.


title: slpifq_6h_L_WL_2

value: First Leaf


title: AHCC (205659810025_R01C01)

value: AHCC


title: Subject2_4h_exvivo_4h_LPS

description: Monocytes, 4 hours after in vivo LPS challenge (LPS-SI) were isolated from PBMC by CD14 positive selection. Thereafter, isolated monocytes were ex vivo (re)stimulated with LPS (10ng/ml) for 4 hours and then RNA-seq analysis performed on rRNA-depleted total RNA.


title: 8 14-7-2021

description:
Imprinting Disorder
Hybridization to SNP array


title: slpifq_6h_h_WL_3

value: slpifq


title: Subject2_8h_exvivo_4h_LPS

description: Monocytes, 8 hours after in vivo LPS challenge (LPS-SI) were isolated from PBMC by CD14 positive selection. Thereafter, isolated monocytes were ex vivo (re)stimulated with LPS (10ng/ml) for 4 hours and then RNA-seq analysis performed on rRNA-depleted total RNA.


title: dual-AAV split-ePE3-367,2e12, tail-vein injection,liver,rep3,off target site 3

description:
Library name: SP4R3liverot3
rep3,off target site 3
sPE_sep_processed_date.xls


title: slpifq_6h_h_WL_2

description:
The two fasq files from two different runs were merged and aligned to the genome with STAR
HTSeqcounts_WT_pif8a_pifq_6h.csv
Normalized_CPM_WT_pif8a_pifq_6h.csv
LOG2_Fold_Change_relative_to_21WL_WT_pif8a_pifq_6h.xlsx


title: 367 V2 plasmids lipo 3000 transfection at VEGFA site rep3

description:
Library name: splitPE27-30
rep3
sPE_sep_processed_date.xls

source_name: HEK293T cell

value: HEK293T cell

value: human embryonic kidney cells


title: dual-AAV split-ePE3-367,1e12, tail-vein injection,liver,rep2,off target site 4

description:
Library name: SP3R2liverot4
rep2,off target site 4
sPE_sep_processed_date.xls


title: 8-1-8-2021


title: slpifq_6h_h_WL_1

value: White light


title: Sample10_4_7_2021

value: ImpDis


title: 367 V2 plasmids lipo 3000 transfection at VEGFA site rep2

description:
Library name: splitPE27-29
rep2
sPE_sep_processed_date.xls


title: dual-AAV split-ePE3-367,1e12, tail-vein injection,liver,rep1,off target site 4

description:
Library name: SP3R1liverot4
rep1,off target site 4
sPE_sep_processed_date.xls


title: Subject2_4h

description: Monocytes, 4 hours after in vivo LPS challenge (LPS-SI) were isolated from PBMC by CD14 positive selection. Thereafter (without any culturing) RNA-seq analysis performed on rRNA-depleted total RNA.


title: Sample1_1_8_2021

description:
Imprinting Disorder
Hybridization to SNP


title: dual-AAV split-ePE3-367,2e12, tail-vein injection,liver,rep1,off target site 3

description:
Library name: SP4R1liverot3
rep1,off target site 3
sPE_sep_processed_date.xls


title: dual-AAV split-ePE3-367,2e12, tail-vein injection,liver,rep2,off target site 3

description:
Library name: SP4R2liverot3
rep2,off target site 3
sPE_sep_processed_date.xls


title: Sample3_1_8_2021


title: slpifq_6h_E_FR_3

source_name: Epicotyl

value: Epicotyl

value: White light + Far-red


title: 9-14-7-2021

description:
Imprinting Disorder
Hybridization to SNP Cy


title: Subject2_Baseline

description: Monocytes from healthy volunteer PBMC (before in vivo LPS challenge) isolated by CD14 positive selection. Thereafter (without any culturing) RNA-seq analysis performed on rRNA-depleted total RNA.


title: 367 V1 plasmids lipo 3000 transfection at VEGFA site rep3

description:
Library name: splitPE27-27
rep3
sPE_sep_processed_date.xls


title: dual-AAV split-ePE3-367,1e12, tail-vein injection,liver,rep3,off target site 3

description:
Library name: SP3R3liverot3
rep3,off target site 3
sPE_sep_processed_date.xls


title: Subject1_7d_exvivo_4h_LPS

description: Monocytes, one week (7 days) after in vivo LPS challenge (LPS-SI) were isolated from PBMC by CD14 positive selection. Thereafter, isolated monocytes were ex vivo (re)stimulated with LPS (10ng/ml) for 4 hours and then RNA-seq analysis performed on rRNA-depleted total RNA.


title: 367 V1 plasmids lipo 3000 transfection at VEGFA site rep2

description:
Library name: splitPE27-26
rep2
sPE_sep_processed_date.xls


title: slpifq_6h_E_FR_2


title: Subject1_7d

description: Monocytes, one week (7 days) after in vivo LPS challenge (LPS-SI) were isolated from PBMC by CD14 positive selection. Thereafter (without any culturing) RNA-seq analysis performed on rRNA-depleted total RNA.


title: slpifq_6h_E_FR_1


title: dual-AAV split-ePE3-367,1e12, tail-vein injection,liver,rep2,off target site 3

description:
Library name: SP3R2liverot3
rep2,off target site 3
sPE_sep_processed_date.xls


title: dual-AAV split-ePE3-367,2e12, tail-vein injection,liver,rep1,off target site 4

description:
Library name: SP4R1liverot4
rep1,off target site 4
sPE_sep_processed_date.xls


title: slpifq_6h_E_WL_3

description:
The two fasq files from two different runs were merged and aligned to the genome with STAR
HTSeqcounts_WT_pif8a_pifq_6h.csv
Normalized_CPM_WT_pif8a_pifq_6h.csv
LOG2_Fold_Change_relative_to_21WL_WT_pif8a_pifq_6h.xlsx


title: dual-AAV split-ePE3-367,1e12, tail-vein injection,liver,rep1,off target site 3

description:
Library name: SP3R1liverot3
rep1,off target site 3
sPE_sep_processed_date.xls


title: 367 V1 plasmids lipo 3000 transfection at VEGFA site rep1

description:
Library name: splitPE27-25
rep1
sPE_sep_processed_date.xls


title: Subject1_24h_exvivo_4h_LPS

description: Monocytes, 24 hours after in vivo LPS challenge (LPS-SI) were isolated from PBMC by CD14 positive selection. Thereafter, isolated monocytes were ex vivo (re)stimulated with LPS (10ng/ml) for 4 hours and then RNA-seq analysis performed on rRNA-depleted total RNA.


title: Subject2_Baseline_exvivo_4h_LPS

description: Monocytes from healthy volunteer PBMC (before in vivo LPS challenge) isolated by CD14 positive selection. Thereafter, isolated monocytes were ex vivo (re)stimulated with LPS (10ng/ml) for 4 hours and then RNA-seq analysis performed on rRNA-depleted total RNA.


title: 367 V2 plasmids lipo 3000 transfection at VEGFA site rep1

description:
Library name: splitPE27-28
rep1
sPE_sep_processed_date.xls


title: 367 V4 plasmids lipo 3000 transfection at VEGFA site rep3

description:
Library name: splitPE27-24
rep3
sPE_sep_processed_date.xls


title: slpifq_6h_E_WL_1


title: Subject1_24h

description: Monocytes, 24 hours after in vivo LPS challenge (LPS-SI) were isolated from PBMC by CD14 positive selection. Thereafter (without any culturing) RNA-seq analysis performed on rRNA-depleted total RNA.


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

description:
Library name: SP4R3liverot2
rep3,off target site 2
sPE_sep_processed_date.xls


title: Subject1_8h_exvivo_4h_LPS

description: Monocytes, 8 hours after in vivo LPS challenge (LPS-SI) were isolated from PBMC by CD14 positive selection. Thereafter, isolated monocytes were ex vivo (re)stimulated with LPS (10ng/ml) for 4 hours and then RNA-seq analysis performed on rRNA-depleted total RNA.


title: slpifq_6h_C_FR_3

source_name: Cotyledons

value: Cotyledons


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

description:
Library name: SP4R2liverot2
rep2,off target site 2
sPE_sep_processed_date.xls


title: 367 V4 plasmids lipo 3000 transfection at VEGFA site rep1

description:
Library name: splitPE27-22
rep1
sPE_sep_processed_date.xls


title: 367 V4 plasmids lipo 3000 transfection at VEGFA site rep2

description:
Library name: splitPE27-23
rep2
sPE_sep_processed_date.xls


title: slpifq_6h_C_FR_2


title: Subject1_8h

description: Monocytes, 8 hours after in vivo LPS challenge (LPS-SI) were isolated from PBMC by CD14 positive selection. Thereafter (without any culturing) RNA-seq analysis performed on rRNA-depleted total RNA.


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

description:
Library name: SP4R1liverot2
rep1,off target site 2
sPE_sep_processed_date.xls


title: Subject1_4h_exvivo_4h_LPS

description: Monocytes, 4 hours after in vivo LPS challenge (LPS-SI) were isolated from PBMC by CD14 positive selection. Thereafter, isolated monocytes were ex vivo (re)stimulated with LPS (10ng/ml) for 4 hours and then RNA-seq analysis performed on rRNA-depleted total RNA.


title: dual-AAV split-ePE3-367,1e12, tail-vein injection,liver,rep3,off target site 2

description:
Library name: SP3R3liverot2
rep3,off target site 2
sPE_sep_processed_date.xls


title: 367 V3 plasmids lipo 3000 transfection at VEGFA site rep2

description:
Library name: splitPE27-20
rep2
sPE_sep_processed_date.xls


title: Control (205659810027_R01C02)

value: Mammary Gland

value: Control


title: Subject1_4h

description: Monocytes, 4 hours after in vivo LPS challenge (LPS-SI) were isolated from PBMC by CD14 positive selection. Thereafter (without any culturing) RNA-seq analysis performed on rRNA-depleted total RNA.


title: dual-AAV split-ePE3-367,1e12, tail-vein injection,liver,rep2,off target site 2

description:
Library name: SP3R2liverot2
rep2,off target site 2
sPE_sep_processed_date.xls


title: 367 V3 plasmids lipo 3000 transfection at VEGFA site rep3

description:
Library name: splitPE27-21
rep3
sPE_sep_processed_date.xls


title: slpifq_6h_C_WL_3

description:
The two fasq files from two different runs were merged and aligned to the genome with STAR
HTSeqcounts_WT_pif8a_pifq_6h.csv
Normalized_CPM_WT_pif8a_pifq_6h.csv
LOG2_Fold_Change_relative_to_21WL_WT_pif8a_pifq_6h.xlsx


title: 367 V3 plasmids lipo 3000 transfection at VEGFA site rep1

description:
Library name: splitPE27-19
rep1
sPE_sep_processed_date.xls


title: slpifq_6h_C_WL_2


title: slpifq_6h_E_WL_2


title: dual-AAV split-ePE3-367,1e12, tail-vein injection,liver,rep1,off target site 2

description:
Library name: SP3R1liverot2
rep1,off target site 2
sPE_sep_processed_date.xls


title: split-PE-367 plasmids lipo 3000 transfection at VEGFA site rep3

description:
Library name: splitPE27-18
rep3
sPE_sep_processed_date.xls


title: dual-AAV split-ePE3-367,2e12, tail-vein injection,liver,rep3,off target site 1

description:
Library name: SP4R3liverot1
rep3,off target site 1
sPE_sep_processed_date.xls


title: Subject1_Baseline_exvivo_4h_LPS

description: Monocytes from healthy volunteer PBMC (before in vivo LPS challenge) isolated by CD14 positive selection. Thereafter, isolated monocytes were ex vivo (re)stimulated with LPS (10ng/ml) for 4 hours and then RNA-seq analysis performed on rRNA-depleted total RNA.


title: slpifq_6h_C_WL_1


title: Subject1_Baseline

description: Monocytes from healthy volunteer PBMC (before in vivo LPS challenge) isolated by CD14 positive selection. Thereafter (without any culturing) RNA-seq analysis performed on rRNA-depleted total RNA.


title: split-PE-367 plasmids lipo 3000 transfection at VEGFA site rep2

description:
Library name: splitPE27-17
rep2
sPE_sep_processed_date.xls


title: slpif8a_6h_L_FR_3


title: dual-AAV split-ePE3-367,2e12, tail-vein injection,liver,rep2,off target site 1

description:
Library name: SP4R2liverot1
rep2,off target site 1
sPE_sep_processed_date.xls


title: split-PE-367 plasmids lipo 3000 transfection at VEGFA site rep1

description:
Library name: splitPE27-16
rep1
sPE_sep_processed_date.xls


title: Rb/p53/Max mutant Max addback_replicate_3

city: Seattle

first: Brian

last: Freie

state: WA

address: 1100 Fairview Ave N

department: Basic Sciences

institute: Fred Hutchinson Cancer Research Center

description: Library name: H7536-MAX-3

data_processing:
Image analysis and base calling were performed using Illumina's Real Time Analysis v1.18 software, followed by 'demultiplexing' of indexed reads and generation of FASTQ files, using Illumina's bcl2fastq v1.8.4.
For RNASeq analysis, low quality reads were filtered out prior to alignment to mm10 using TopHat v2.1.0.
Counts were generated from TopHat alignments at the gene-level  using the  “intersection-strict” overlap mode in HTSeq v0.6.1. Normalization and gene expression results were done using EdgeR.
Assembly: mm10
Supplementary files format and content: For RNA-seq data, EdgeR count tables with Log2Fold gene expression changes and adjusted p values.

source_name: cultured thyroid cells

growth_protocol: Mouse cell lines were isolated and grown in DMEM supplemented with penicillin (100 U/ml), streptomycin (100 μg/ml), and 10 % fetal bovine serum. Cells were maintained at 37°C in a humidified atmosphere containing 5 % CO2 and 95 % air.

extract_protocol:
Total RNA was extracted using Trizol, and Zymogenetics Direct-Zol Miniprep kit.
Ultra RNA Library Prep Kit for Illumina

treatment_protocol: Cells were grown in DMEM supplemented with penicillin (100 U/ml), streptomycin (100 μg/ml), and 10 % fetal bovine serum.

value: cultured thyroid cells

value: Rb/p53/Max mutant Max addback

value: cells transduced with Max expressing vector


title: slpif8a_6h_L_FR_2


title: dual-AAV split-ePE3-367,2e12, tail-vein injection,liver,rep1,off target site 1

description:
Library name: SP4R1liverot1
rep1,off target site 1
sPE_sep_processed_date.xls

value: liver

value: WT


title: 367 V2 plasmids lipo 3000 transfection at HEK3 site rep3

description:
Library name: splitPE27-15
rep3
sPE_sep_processed_date.xls


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

description:
Library name: SP3R3liverot1
rep3,off target site 1
sPE_sep_processed_date.xls


title: slpif8a_6h_L_FR_1

value: First Leaf


title: Rb/p53/Max mutant Max addback_replicate_1

description: Library name: H7536-MAX-1


title: slpifq_6h_C_FR_1


title: Rb/p53/Max mutant Max addback_replicate_2

description: Library name: H7536-MAX-2


title: slpif8a_6h_L_WL_3


title: 367 V2 plasmids lipo 3000 transfection at HEK3 site rep2

description:
Library name: splitPE27-14
rep2
sPE_sep_processed_date.xls


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

description:
Library name: SP3R1liverot1
rep1,off target site 1
sPE_sep_processed_date.xls


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

description:
Library name: SP3R2liverot1
rep2,off target site 1
sPE_sep_processed_date.xls


title: 367 V2 plasmids lipo 3000 transfection at HEK3 site rep1

description:
Library name: splitPE27-13
rep1
sPE_sep_processed_date.xls


title: dual-AAV split-ePE3-367,2e12, tail-vein injection,liver,rep3,off target site 4

description:
Library name: SP4R3liverot4
rep3,off target site 4
sPE_sep_processed_date.xls


title: slpif8a_6h_L_WL_2

description:
The two fasq files from two different runs were merged and aligned to the genome with STAR
HTSeqcounts_WT_pif8a_pifq_6h.csv
Normalized_CPM_WT_pif8a_pifq_6h.csv
LOG2_Fold_Change_relative_to_21WL_WT_pif8a_pifq_6h.xlsx


title: Rb/p53/Max mutant empty vector_replicate_2

description: Library name: H7536-EMPTY-2

value: Rb/p53/Max mutant empty vector

value: cells transduced with empty vector control


title: 367 V1 plasmids lipo 3000 transfection at HEK3 site rep3

description:
Library name: splitPE27-12
rep3
sPE_sep_processed_date.xls

value: HEK293T cell


title: Rb/p53/Max mutant empty vector_replicate_1

description: Library name: H7536-EMPTY-1


title: dual-AAV v3em PE3,2e12, tail-vein injection,lung,rep3,on target

description:
Library name: SP8R3lung
rep3,on target
sPE_sep_processed_date.xls

source_name: lung

value: lung


title: slpif8a_6h_L_WL_1

value: White light


title: dual-AAV v3em PE3,2e12, tail-vein injection,lung,rep2,on target

description:
Library name: SP8R2lung
rep2,on target
sPE_sep_processed_date.xls


title: slpif8a_6h_h_FR_3

value: Hypocotyl


title: slpif8a_6h_h_FR_2


title: RNASeq RPM thyroid cells replicate 4

description: Library name: RPM-H9468-thy-line

value: Rb/p53/Max mutant


title: 367 V1 plasmids lipo 3000 transfection at HEK3 site rep1

description:
Library name: splitPE27-10
rep1
sPE_sep_processed_date.xls

value: human embryonic kidney cells


title: dual-AAV v3em PE3,2e12, tail-vein injection,lung,rep1,on target

description:
Library name: SP8R1lung
rep1,on target
sPE_sep_processed_date.xls


title: RNASeq RPM thyroid cells replicate 2

description: Library name: RPM-H7536-thy-line


title: dual-AAV v3em PE3,2e12, tail-vein injection,testis,rep2,on target

description:
Library name: SP8R2testis
rep2,on target
sPE_sep_processed_date.xls

source_name: testis

value: testis


title: dual-AAV v3em PE3,2e12, tail-vein injection,testis,rep3,on target

description:
Library name: SP8R3testis
rep3,on target
sPE_sep_processed_date.xls


title: Rb/p53/Max mutant empty vector_replicate_3

description: Library name: H7536-EMPTY-3


title: 367 V4 plasmids lipo 3000 transfection at HEK3 site rep1

description:
Library name: splitPE27-7
rep1
sPE_sep_processed_date.xls


title: slpif8a_6h_h_FR_1

value: White light + Far-red


title: 367 V4 plasmids lipo 3000 transfection at HEK3 site rep3

description:
Library name: splitPE27-9
rep3
sPE_sep_processed_date.xls


title: 367 V4 plasmids lipo 3000 transfection at HEK3 site rep2

description:
Library name: splitPE27-8
rep2
sPE_sep_processed_date.xls


title: RNASeq RPM thyroid cells replicate 1

description: Library name: RPM-H7533-thy-line


title: dual-AAV v3em PE3,2e12, tail-vein injection,testis,rep1,on target

description:
Library name: SP8R1testis
rep1,on target
sPE_sep_processed_date.xls


title: slpif8a_6h_h_WL_3


title: slpif8a_6h_h_WL_2


title: slpif8a_6h_h_WL_1


title: 367 V1 plasmids lipo 3000 transfection at HEK3 site rep2

description:
Library name: splitPE27-11
rep2
sPE_sep_processed_date.xls


title: RNASeq RP thyroid cells replicate 4

description: Library name: RP-H9939-thy-line

value: Rb/p53 mutant


title: dual-AAV v3em PE3,2e12, tail-vein injection,brain,rep3,on target

description:
Library name: SP8R3brain
rep3,on target
sPE_sep_processed_date.xls

source_name: brain

value: brain


title: slpif8a_6h_E_FR_3

value: Epicotyl


title: RNASeq RP thyroid cells replicate 2

description: Library name: RP-K2028-thy-line

value: cultured thyroid cells


title: 367 V3 plasmids lipo 3000 transfection at HEK3 site rep2

description:
Library name: splitPE27-5
rep2
sPE_sep_processed_date.xls


title: dual-AAV v3em PE3,2e12, tail-vein injection,brain,rep2,on target

description:
Library name: SP8R2brain
rep2,on target
sPE_sep_processed_date.xls


title: dual-AAV v3em PE3,2e12, tail-vein injection,brain,rep1,on target

description:
Library name: SP8R1brain
rep1,on target
sPE_sep_processed_date.xls


title: 367 V3 plasmids lipo 3000 transfection at HEK3 site rep1

description:
Library name: splitPE27-4
rep1
sPE_sep_processed_date.xls

value: 367 V3 plasmids lipo 3000 transfection at HEK3 site at HEK3 site


title: RNASeq RP thyroid cells replicate 3

description: Library name: RP-K2032-thy-line


title: slpif8a_6h_E_FR_2

description:
The two fasq files from two different runs were merged and aligned to the genome with STAR
HTSeqcounts_WT_pif8a_pifq_6h.csv
Normalized_CPM_WT_pif8a_pifq_6h.csv
LOG2_Fold_Change_relative_to_21WL_WT_pif8a_pifq_6h.xlsx


title: RNASeq RP thyroid cells replicate 1

description: Library name: RP-K2021-thy-line


title: RNASeq RPM thyroid cells replicate 3

description: Library name: RPM-H7691-thy-line


title: split-PE-367 plasmids lipo 3000 transfection at HEK3 site rep3

description:
Library name: splitPE27-3
rep3
sPE_sep_processed_date.xls

value: WT


title: dual-AAV v3em PE3,2e12, tail-vein injection,kidney,rep3,on target

description:
Library name: SP8R3kidney
rep3,on target
sPE_sep_processed_date.xls

source_name: kidney

value: kidney


title: slpif8a_6h_E_FR_1


title: RPM_H9468_Pol2

description: Library name: RPM_H9468_Pol2

data_processing:
Image analysis and base calling were performed using Illumina's Real Time Analysis v1.18 software, followed by 'demultiplexing' of indexed reads and generation of FASTQ files, using Illumina's bcl2fastq v1.8.4
Alignment was to mm10 with Bowtie 2,  reads >700bp filtered out
ChIPSeq data was aligned using Bowtie2. Bigwig files were produced using bedtools genomecov, and WigToBigWig scripts.
Assembly: mm10
Supplementary files format and content: Bigwig files are provided for ChIP-Seq data

growth_protocol: Mouse cell lines were isolated and grown in DMEM supplemented with penicillin (100 U/ml), streptomycin (100 μg/ml), and 10 % fetal bovine serum.

extract_protocol:
For ChIP-Seq formaldehyde cross-linking was used, followed by Micrococcal nuclease treatment, sonication, and Chromatin IP with specific or control antibodies.
for ChIP-Seq, libraries were prepared using the Kapa system, 25x25 paired-end sequencing was performed on an Illumina HiSeq 2500 instrument.


title: dual-AAV v3em PE3,2e12, tail-vein injection,kidney,rep2,on target

description:
Library name: SP8R2kidney
rep2,on target
sPE_sep_processed_date.xls


title: 367 V3 plasmids lipo 3000 transfection at HEK3 site rep3

description:
Library name: splitPE27-6
rep3
sPE_sep_processed_date.xls


title: slpif8a_6h_E_WL_3


title: slpif8a_6h_E_WL_2


title: dual-AAV v3em PE3,2e12, tail-vein injection,kidney,rep1,on target

description:
Library name: SP8R1kidney
rep1,on target
sPE_sep_processed_date.xls


title: split-PE-367 plasmids lipo 3000 transfection at HEK3 site rep1

description:
Library name: splitPE27-1
rep1
sPE_sep_processed_date.xls


title: split-PE-367 plasmids lipo 3000 transfection at RNF2 site- molar ratio 15:1 rep3

description:
Library name: splitPE27-48
molar ratio 15:1 rep3
sPE_sep_processed_date.xls


title: RPM_H7533_Pol2

description: Library name: RPM_H7533_Pol2


title: dual-AAV v3em PE3,2e12, tail-vein injection,heart,rep3,on target

description:
Library name: SP8R3heart
rep3,on target
sPE_sep_processed_date.xls

source_name: heart

value: heart


title: slpif8a_6h_E_WL_1


title: RP_K2032_Pol2

description: Library name: RP_K2032-Pol2


title: split-PE-367 plasmids lipo 3000 transfection at RNF2 site- molar ratio 15:1 rep2

description:
Library name: splitPE28-38
molar ratio 15:1 rep2
sPE_sep_processed_date.xls


title: slpif8a_6h_C_FR_3

value: Cotyledons


title: dual-AAV v3em PE3,2e12, tail-vein injection,heart,rep2,on target

description:
Library name: SP8R2heart
rep2,on target
sPE_sep_processed_date.xls


title: RP_K2028_Pol2

description: Library name: RP_K2028_Pol2


title: split-PE-367 plasmids lipo 3000 transfection at RNF2 site- molar ratio 15:1 rep1

description:
Library name: splitPE28-37
molar ratio 15:1 rep1
sPE_sep_processed_date.xls

value: HEK293T cell


title: split-PE-367 plasmids lipo 3000 transfection at RNF2 site- molar ratio 15:15 rep6

description:
Library name: splitPE28-36
molar ratio 15:15 rep6
sPE_sep_processed_date.xls


title: dual-AAV v3em PE3,2e12, tail-vein injection,heart,rep1,on target

description:
Library name: SP8R1heart
rep1,on target
sPE_sep_processed_date.xls


title: RP_K2021_Pol2

description: Library name: RP_K2021_Pol2


title: slpif8a_6h_C_FR_2


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

description:
Library name: SP8R3liver
rep3,on target
sPE_sep_processed_date.xls

source_name: liver

value: liver


title: RPM_H9468_MLX

description: Library name: RPM_H9468_MLX


title: slpifq_6h_h_FR_2

value: slpifq


title: split-PE-367 plasmids lipo 3000 transfection at RNF2 site- molar ratio 15:15 rep5

description:
Library name: splitPE28-35
molar ratio 15:15 rep5
sPE_sep_processed_date.xls


title: split-PE-367 plasmids lipo 3000 transfection at HEK3 site rep2

description:
Library name: splitPE27-2
rep2
sPE_sep_processed_date.xls


title: slpif8a_6h_C_FR_1

description:
The two fasq files from two different runs were merged and aligned to the genome with STAR
HTSeqcounts_WT_pif8a_pifq_6h.csv
Normalized_CPM_WT_pif8a_pifq_6h.csv
LOG2_Fold_Change_relative_to_21WL_WT_pif8a_pifq_6h.xlsx


title: slpif8a_6h_C_WL_3

value: White light


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

description:
Library name: SP8R2liver
rep2,on target
sPE_sep_processed_date.xls


title: RPM_H7691_Pol2

description: Library name: RPM_H7691_Pol2

value: Rb/p53/Max mutant


title: RPM_H7691_MLX

description: Library name: RPM_H7691_MLX


title: split-PE-367 plasmids lipo 3000 transfection at RNF2 site- molar ratio 15:15 rep4

description:
Library name: splitPE28-34
molar ratio 15:15 rep4
sPE_sep_processed_date.xls

value: human embryonic kidney cells


title: dual-AAV v3em PE3,1e12, tail-vein injection,lung,rep3,on target

description:
Library name: SP7R3lung
rep3,on target
sPE_sep_processed_date.xls

value: lung


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

description:
Library name: SP8R1liver
rep1,on target
sPE_sep_processed_date.xls


title: split-PE-367 plasmids lipo 3000 transfection at RNF2 site- molar ratio 1:15 rep3

description:
Library name: splitPE28-33
molar ratio 1:15 rep3
sPE_sep_processed_date.xls


title: slpif8a_6h_C_WL_1


title: RP_K2032_MLX

description: Library name: RP_K2032_MLX


title: RPM_H7533_MLX

description: Library name: RPM_H7533_MLX


title: slpif8a_6h_C_WL_2


title: split-PE-367 plasmids lipo 3000 transfection at RNF2 site- molar ratio 1:15 rep2

description:
Library name: splitPE28-32
molar ratio 1:15 rep2
sPE_sep_processed_date.xls


title: RP_K2028_MLX

description: Library name: RP_K2028_MLX


title: WT_6h_L_FR_3

description:
The two fasq files from two different runs were merged and aligned to the genome with STAR
HTSeqcounts_WT_3h_6h_24h.csv
HTSeqcounts_WT_pif8a_pifq_6h.csv
Normalized_CPM_WT_3h_6h_24h.csv
Normalized_CPM_WT_pif8a_pifq_6h.csv
LOG2_Fold_Change_relative_to_21WL_WT_3h_6h_24h.xlsx
LOG2_Fold_Change_relative_to_21WL_WT_pif8a_pifq_6h.xlsx

value: First Leaf

value: White light + Far-red


title: dual-AAV v3em PE3,1e12, tail-vein injection,lung,rep2,on target

description:
Library name: SP7R2lung
rep2,on target
sPE_sep_processed_date.xls


title: WT_6h_L_FR_2


title: dual-AAV v3em PE3,1e12, tail-vein injection,lung,rep1,on target

description:
Library name: SP7R1lung
rep1,on target
sPE_sep_processed_date.xls


title: split-PE-367 plasmids lipo 3000 transfection at EMX1 site- molar ratio 15:1 rep3

description:
Library name: splitPE28-39
molar ratio 15:1 rep3
sPE_sep_processed_date.xls


title: RP_K2021_MLX

description: Library name: RP_K2021_MLX

value: Rb/p53 mutant


title: dual-AAV v3em PE3,1e12, tail-vein injection,testis,rep3,on target

description:
Library name: SP7R3testis
rep3,on target
sPE_sep_processed_date.xls

value: testis


title: RPM_H9468_MNT

description: Library name: RPM_H9468_MNT

value: cultured thyroid cells


title: dual-AAV v3em PE3,1e12, tail-vein injection,testis,rep2,on target

description:
Library name: SP7R2testis
rep2,on target
sPE_sep_processed_date.xls


title: split-PE-367 plasmids lipo 3000 transfection at EMX1 site- molar ratio 15:1 rep2

description:
Library name: splitPE27-47
molar ratio 15:1 rep2
sPE_sep_processed_date.xls


title: WT_6h_L_FR_1


title: dual-AAV v3em PE3,1e12, tail-vein injection,testis,rep1,on target

description:
Library name: SP7R1testis
rep1,on target
sPE_sep_processed_date.xls


title: WT_6h_L_WL_3


title: RPM_H7691_MNT

description: Library name: RPM_H7691_MNT


title: WT_6h_L_WL_2


title: split-PE-367 plasmids lipo 3000 transfection at RNF2 site- molar ratio 1:15 rep1

description:
Library name: splitPE28-31
molar ratio 1:15 rep1
sPE_sep_processed_date.xls


title: split-PE-367 plasmids lipo 3000 transfection at EMX1 site- molar ratio 15:15 rep6

description:
Library name: splitPE27-45
molar ratio 15:15 rep6
sPE_sep_processed_date.xls


title: split-PE-367 plasmids lipo 3000 transfection at EMX1 site- molar ratio 15:1 rep1

description:
Library name: splitPE27-46
molar ratio 15:1 rep1
sPE_sep_processed_date.xls


title: dual-AAV v3em PE3,1e12, tail-vein injection,brain,rep3,on target

description:
Library name: SP7R3brain
rep3,on target
sPE_sep_processed_date.xls

value: brain


title: split-PE-367 plasmids lipo 3000 transfection at EMX1 site- molar ratio 15:15 rep5

description:
Library name: splitPE27-44
molar ratio 15:15 rep5
sPE_sep_processed_date.xls

value: WT


title: dual-AAV v3em PE3,1e12, tail-vein injection,brain,rep2,on target

description:
Library name: SP7R2brain
rep2,on target
sPE_sep_processed_date.xls


title: RP_K2032_MNT

description: Library name: RP_K2032-MNT


title: WT_6h_h_FR_3

value: Hypocotyl


title: WT_6h_L_WL_1


title: dual-AAV v3em PE3,1e12, tail-vein injection,brain,rep1,on target

description:
Library name: SP7R1brain
rep1,on target
sPE_sep_processed_date.xls


title: WT_6h_h_FR_2


title: RP_K2028_MNT

description: Library name: RP_K2028_MNT


title: split-PE-367 plasmids lipo 3000 transfection at EMX1 site- molar ratio 1:15 rep3

description:
Library name: splitPE27-42
molar ratio 1:15 rep3
sPE_sep_processed_date.xls


title: RP_K2021_MNT

description: Library name: RP_K2021_MNT


title: WT_6h_h_FR_1


title: dual-AAV v3em PE3,1e12, tail-vein injection,kidney,rep2,on target

description:
Library name: SP7R2kidney
rep2,on target
sPE_sep_processed_date.xls

value: kidney


title: split-PE-367 plasmids lipo 3000 transfection at EMX1 site- molar ratio 1:15 rep2

description:
Library name: splitPE27-41
molar ratio 1:15 rep2
sPE_sep_processed_date.xls


title: split-PE-367 plasmids lipo 3000 transfection at EMX1 site- molar ratio 1:15 rep1

description:
Library name: splitPE27-40
molar ratio 1:15 rep1
sPE_sep_processed_date.xls


title: WT_6h_h_WL_3

description:
The two fasq files from two different runs were merged and aligned to the genome with STAR
HTSeqcounts_WT_3h_6h_24h.csv
HTSeqcounts_WT_pif8a_pifq_6h.csv
Normalized_CPM_WT_3h_6h_24h.csv
Normalized_CPM_WT_pif8a_pifq_6h.csv
LOG2_Fold_Change_relative_to_21WL_WT_3h_6h_24h.xlsx
LOG2_Fold_Change_relative_to_21WL_WT_pif8a_pifq_6h.xlsx


title: RPM_H7533_MNT

description: Library name: RPM_H7533_MNT


title: RPM_H9468_MAX

description: Library name: RPM_H9468_MAX


title: RPM_H7691_MAX

description: Library name: RPM_H7691_MAX


title: dual-AAV v3em PE3,1e12, tail-vein injection,heart,rep3,on target

description:
Library name: SP7R3heart
rep3,on target
sPE_sep_processed_date.xls

value: heart


title: split-PE-367 plasmids lipo 3000 transfection at HEK3 site- molar ratio 15:1 rep3

description:
Library name: splitPE27-57
molar ratio 15:1 rep3
sPE_sep_processed_date.xls

value: HEK293T cell


title: RPM_H7533_MAX

description: Library name: RPM_H7533_MAX


title: RP_K2032_MAX

description: Library name: RP_K2032_MAX


title: split-PE-367 plasmids lipo 3000 transfection at HEK3 site- molar ratio 15:1 rep2

description:
Library name: splitPE27-56
molar ratio 15:1 rep2
sPE_sep_processed_date.xls


title: dual-AAV v3em PE3,1e12, tail-vein injection,heart,rep2,on target

description:
Library name: SP7R2heart
rep2,on target
sPE_sep_processed_date.xls


title: split-PE-367 plasmids lipo 3000 transfection at EMX1 site- molar ratio 15:15 rep4

description:
Library name: splitPE27-43
molar ratio 15:15 rep4
sPE_sep_processed_date.xls


title: dual-AAV v3em PE3,1e12, tail-vein injection,kidney,rep1,on target

description:
Library name: SP7R1kidney
rep1,on target
sPE_sep_processed_date.xls


title: WT_6h_h_WL_1


title: split-PE-367 plasmids lipo 3000 transfection at HEK3 site- molar ratio 15:1 rep1

description:
Library name: splitPE27-55
molar ratio 15:1 rep1
sPE_sep_processed_date.xls


title: WT_6h_h_WL_2


title: dual-AAV v3em PE3,1e12, tail-vein injection,heart,rep1,on target

description:
Library name: SP7R1heart
rep1,on target
sPE_sep_processed_date.xls


title: WT_6h_E_FR_2

value: Epicotyl


title: RP_K2028_MAX

description: Library name: RP_K2028_MAX


title: WT_6h_E_FR_1


title: RP_K2021_MAX

description: Library name: RP_K2021_MAX


title: dual-AAV v3em PE3,1e12, tail-vein injection,kidney,rep3,on target

description:
Library name: SP7R3kidney
rep3,on target
sPE_sep_processed_date.xls


title: RPM_H9468_IgG

description: Library name: RPM_H9468_IgG


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

description:
Library name: SP7R3liver
rep3,on target
sPE_sep_processed_date.xls

value: liver


title: split-PE-367 plasmids lipo 3000 transfection at HEK3 site- molar ratio 15:15 rep5

description:
Library name: splitPE27-53
molar ratio 15:15 rep5
sPE_sep_processed_date.xls


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

description:
Library name: SP7R2liver
rep2,on target
sPE_sep_processed_date.xls


title: WT_6h_E_WL_3

value: White light


title: RPM_H7691_IgG

description: Library name: RPM_H7691_IgG

value: Rb/p53/Max mutant


title: split-PE-367 plasmids lipo 3000 transfection at HEK3 site- molar ratio 15:15 rep4

description:
Library name: splitPE27-52
molar ratio 15:15 rep4
sPE_sep_processed_date.xls

value: human embryonic kidney cells


title: WT_6h_E_WL_2


title: RPM_H7533_IgG

description: Library name: RPM_H7533_IgG


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

description:
Library name: SP7R1liver
rep1,on target
sPE_sep_processed_date.xls


title: WT_6h_E_FR_3


title: WT_6h_C_FR_3

value: Cotyledons


title: WT_6h_C_FR_1


title: dual-AAV v3em PE3,2e11, tail-vein injection,liver,rep2,on target

description:
Library name: SP6R2liver
rep2,on target
sPE_sep_processed_date.xls


title: split-PE-367 plasmids lipo 3000 transfection at HEK3 site- molar ratio 15:0 rep3

description:
Library name: splitPE26-H21
molar ratio 15:0 rep3
sPE_sep_processed_date.xls


title: dual-AAV v3em PE3,1e11, tail-vein injection,liver,rep3,on target

description:
Library name: SP5R3liver
rep3,on target
sPE_sep_processed_date.xls


title: split-PE-367 plasmids lipo 3000 transfection at HEK3 site- molar ratio 15:0 rep2

description:
Library name: splitPE26-H20
molar ratio 15:0 rep2
sPE_sep_processed_date.xls


title: WT_6h_E_WL_1

description:
The two fasq files from two different runs were merged and aligned to the genome with STAR
HTSeqcounts_WT_3h_6h_24h.csv
HTSeqcounts_WT_pif8a_pifq_6h.csv
Normalized_CPM_WT_3h_6h_24h.csv
Normalized_CPM_WT_pif8a_pifq_6h.csv
LOG2_Fold_Change_relative_to_21WL_WT_3h_6h_24h.xlsx
LOG2_Fold_Change_relative_to_21WL_WT_pif8a_pifq_6h.xlsx


title: dual-AAV v3em PE3,2e11, tail-vein injection,liver,rep3,on target

description:
Library name: SP6R3liver
rep3,on target
sPE_sep_processed_date.xls


title: RP_K2028_IgG

description: Library name: RP_K2028_IgG


title: split-PE-367 plasmids lipo 3000 transfection at HEK3 site- molar ratio 15:15 rep6

description:
Library name: splitPE27-54
molar ratio 15:15 rep6
sPE_sep_processed_date.xls


title: dual-AAV v3em PE3,1e11, tail-vein injection,liver,rep2,on target

description:
Library name: SP5R2liver
rep2,on target
sPE_sep_processed_date.xls


title: RP_K2032_IgG

description: Library name: RP_K2032_IgG


title: split-PE-367 plasmids lipo 3000 transfection at HEK3 site- molar ratio 1:15 rep3

description:
Library name: splitPE27-51
molar ratio 1:15 rep3
sPE_sep_processed_date.xls


title: split-PE-367 plasmids lipo 3000 transfection at HEK3 site- molar ratio 1:15 rep2

description:
Library name: splitPE27-50
molar ratio 1:15 rep2
sPE_sep_processed_date.xls


title: dual-AAV v3em PE3,1e11, tail-vein injection,liver,rep1,on target

description:
Library name: SP5R1liver
rep1,on target
sPE_sep_processed_date.xls


title: WT_6h_C_WL_2


title: split-PE-367 plasmids lipo 3000 transfection at HEK3 site- molar ratio 15:0 rep1

description:
Library name: splitPE26-H19
molar ratio 15:0 rep1
sPE_sep_processed_date.xls


title: dual-AAV split-ePE3-367,2e12, tail-vein injection,lung,rep3,on target

description:
Library name: SP4R3lung
rep3,on target
sPE_sep_processed_date.xls

value: lung


title: WT_6h_C_WL_3


title: split-PE-367 plasmids lipo 3000 transfection at HEK3 site- molar ratio 15:5 rep3

description:
Library name: splitPE26-H18
molar ratio 15:5 rep3
sPE_sep_processed_date.xls


title: cHiC_Dac1J129sv_E11.5_hearts_Rep1

description:
L35
cHic_Dac1J129sv_E11.5_hearts_merged_Dac1Jmm10_enriched_MAPQ30.hic

data_processing:
*library strategy: capture-HiC
Raw sequencing reads were processed with the HiCUP pipeline v0.6.1 (no size selection, Nofill: 1, Format: Sanger) using Bowtie2 v2.3.4.1 for mapping short reads. Replicates were then merged by combining their bam files.
Juicer tools v1.7.6 was used to generate binned contact maps and to normalize maps by Knights and Ruiz (KR) matrix balancing.
As an additional filtering step, read-pairs with genomic distances ≤ 10 kb were removed. Afterwards, cHi-C maps were generated with the Juicer tools ‘pre’ command using a custom chrom.sizes file containing only the length of the genomic region of interest (4.75 Mb) and requesting a MAPQ≥30.
Assembly: mm10
Supplementary files format and content: hic file

source_name: hearts

extract_protocol:
The capture HiC protocol was performed as decribed in (Formation of new chromatin domains determines pathogenecity of genomic duplications. Franke et al., Nature 2016).
Snap frozen samples were first digested using DpnII, religated using the T4 DNA ligase (Thermo Fisher Scientific). The chimeric chromatin products were then decrosslinked overnight. RNase A treated chromatin was then precipiated.The precipiated chromatin was sheared using a Covaris sonicator (duty cycle: 10%; intensity: 5; cycles per burst: 200; time: 6 cycles of 60 s each; set mode: frequency sweeping; temperature: 4–7 °C). Adaptors were added to the sheared DNA and amplified according to the manufacturer’s instructions for Illumina sequencing (Agilent). The library was hybridized to the custom-designed SureSelect beads and indexed for sequencing following the manufacturer’s instructions (Agilent).

treatment_protocol: Hearts from e11.5 mouse embryos were dissected in PBS, a single cell suspension was made using Trypsin, samples were fixed in 2% PFA, snap frozen, and stored at -80 °C.

value: hearts


title: cHiC_5LTR-LacZ_E11.5_FLHL_Rep2

data_processing:
*library strategy: Capture-HiC
Raw sequencing reads were processed with the HiCUP pipeline v0.6.1 (no size selection, Nofill: 1, Format: Sanger) using Bowtie2 v2.3.4.1 for mapping short reads. Replicates were then merged by combining their bam files.
Juicer tools v1.7.6 was used to generate binned contact maps and to normalize maps by Knights and Ruiz (KR) matrix balancing.
As an additional filtering step, read-pairs with genomic distances ≤ 10 kb were removed. Afterwards, cHi-C maps were generated with the Juicer tools ‘pre’ command using a custom chrom.sizes file containing only the length of the genomic region of interest (4.75 Mb) and requesting a MAPQ≥30.
Assembly: mm10

source_name: limbs

treatment_protocol: Limbs from e11.5 mouse embryos were dissected in PBS, a single cell suspension was made using Trypsin, samples were fixed in 2% PFA, snap frozen, and stored at -80 °C.

value: limbs


title: WT_6h_C_WL_1


title: dual-AAV v3em PE3,2e11, tail-vein injection,liver,rep1,on target

description:
Library name: SP6R1liver
rep1,on target
sPE_sep_processed_date.xls


title: cHiC_Dac1J129sv_E11.5_hearts_Rep2

description:
L36
cHic_Dac1J129sv_E11.5_hearts_merged_Dac1Jmm10_enriched_MAPQ30.hic


title: WT_6h_C_FR_2

value: White light + Far-red


title: RP_K2021_IgG

description: Library name: RP_K2021_IgG

value: cultured thyroid cells

value: Rb/p53 mutant


title: split-PE-367 plasmids lipo 3000 transfection at HEK3 site- molar ratio 1:15 rep1

description:
Library name: splitPE27-49
molar ratio 1:15 rep1
sPE_sep_processed_date.xls

value: WT


title: WT_3h_L_FR_2

description:
The two fasq files from two different runs were merged and aligned to the genome with STAR
HTSeqcounts_WT_3h_6h_24h.csv
Normalized_CPM_WT_3h_6h_24h.csv
LOG2_Fold_Change_relative_to_21WL_WT_3h_6h_24h.xlsx

value: First Leaf


title: cHiC_5LTR-LacZ_E11.5_FLHL_Rep1


title: cHiC_5LTR-LacZ_E11.5_FLHL_Rep3


title: split-PE-367 plasmids lipo 3000 transfection at HEK3 site- molar ratio 15:5 rep2

description:
Library name: splitPE26-H17
molar ratio 15:5 rep2
sPE_sep_processed_date.xls


title: cHiC_Dac1J129sv_E11.5_FLHL_techRep1


title: cHiC_Dac1J129sv_E11.5_FLHL_techRep2


title: dual-AAV split-ePE3-367,2e12, tail-vein injection,lung,rep1,on target

description:
Library name: SP4R1lung
rep1,on target
sPE_sep_processed_date.xls


title: WT_3h_L_FR_3


title: WT_3h_L_FR_1


title: WT_3h_L_WL_3


title: dual-AAV split-ePE3-367,2e12, tail-vein injection,testis,rep3,on target

description:
Library name: SP4R3testis
rep3,on target
sPE_sep_processed_date.xls

value: testis


title: split-PE-367 plasmids lipo 3000 transfection at HEK3 site- molar ratio 15:7.5 rep3

description:
Library name: splitPE26-H15
molar ratio 15:7.5 rep3
sPE_sep_processed_date.xls


title: dual-AAV split-ePE3-367,2e12, tail-vein injection,testis,rep2,on target

description:
Library name: SP4R2testis
rep2,on target
sPE_sep_processed_date.xls


title: dual-AAV split-ePE3-367,2e12, tail-vein injection,lung,rep2,on target

description:
Library name: SP4R2lung
rep2,on target
sPE_sep_processed_date.xls


title: split-PE-367 plasmids lipo 3000 transfection at HEK3 site- molar ratio 15:15 rep3

description:
Library name: splitPE26-H12
molar ratio 15:15 rep3
sPE_sep_processed_date.xls


title: cHiC_Dac1J129sv_E11.5_FLHL_Re2


title: WT_3h_L_WL_2


title: cHiC_Dac1J129sv_E11.5_FLHL_Rep1


title: split-PE-367 plasmids lipo 3000 transfection at HEK3 site- molar ratio 15:5 rep1

description:
Library name: splitPE26-H16
molar ratio 15:5 rep1
sPE_sep_processed_date.xls


title: split-PE-367 plasmids lipo 3000 transfection at HEK3 site- molar ratio 15:7.5 rep1

description:
Library name: splitPE26-H13
molar ratio 15:7.5 rep1
sPE_sep_processed_date.xls


title: dual-AAV split-ePE3-367,2e12, tail-vein injection,brain,rep3,on target

description:
Library name: SP4R3brain
rep3,on target
sPE_sep_processed_date.xls

value: brain


title: dual-AAV split-ePE3-367,2e12, tail-vein injection,testis,rep1,on target

description:
Library name: SP4R1testis
rep1,on target
sPE_sep_processed_date.xls


title: split-PE-367 plasmids lipo 3000 transfection at HEK3 site- molar ratio 15:7.5 rep2

description:
Library name: splitPE26-H14
molar ratio 15:7.5 rep2
sPE_sep_processed_date.xls

value: HEK293T cell


title: WT_3h_L_WL_1


title: cHiC_Dac1JBl6_E11.5_FLHL_techRep2


title: WT_3h_h_FR_3

value: Hypocotyl


title: split-PE-367 plasmids lipo 3000 transfection at HEK3 site- molar ratio 15:15 rep2

description:
Library name: splitPE26-H11
molar ratio 15:15 rep2
sPE_sep_processed_date.xls


title: cHiC_Dac1JBl6_E11.5_FLHL_techRep1


title: split-PE-367 plasmids lipo 3000 transfection at HEK3 site- molar ratio 15:15 rep1

description:
Library name: splitPE26-H10
molar ratio 15:15 rep1
sPE_sep_processed_date.xls


title: dual-AAV split-ePE3-367,2e12, tail-vein injection,brain,rep2,on target

description:
Library name: SP4R2brain
rep2,on target
sPE_sep_processed_date.xls


title: dual-AAV split-ePE3-367,2e12, tail-vein injection,brain,rep1,on target

description:
Library name: SP4R1brain
rep1,on target
sPE_sep_processed_date.xls


title: dual-AAV split-ePE3-367,2e12, tail-vein injection,kidney,rep3,on target

description:
Library name: SP4R3kidney
rep3,on target
sPE_sep_processed_date.xls

value: kidney


title: split-PE-367 plasmids lipo 3000 transfection at HEK3 site- molar ratio 7.5:15 rep2

description:
Library name: splitPE26-H8
molar ratio 7.5:15 rep2
sPE_sep_processed_date.xls


title: split-PE-367 plasmids lipo 3000 transfection at HEK3 site- molar ratio 7.5:15 rep3

description:
Library name: splitPE26-H9
molar ratio 7.5:15 rep3
sPE_sep_processed_date.xls


title: dual-AAV split-ePE3-367,2e12, tail-vein injection,kidney,rep2,on target

description:
Library name: SP4R2kidney
rep2,on target
sPE_sep_processed_date.xls


title: cHiC_Dac1JBl6_E11.5_FLHL_Rep1


title: dual-AAV split-ePE3-367,2e12, tail-vein injection,kidney,rep1,on target

description:
Library name: SP4R1kidney
rep1,on target
sPE_sep_processed_date.xls


title: WT_3h_h_FR_2

description:
The two fasq files from two different runs were merged and aligned to the genome with STAR
HTSeqcounts_WT_3h_6h_24h.csv
Normalized_CPM_WT_3h_6h_24h.csv
LOG2_Fold_Change_relative_to_21WL_WT_3h_6h_24h.xlsx


title: WT_3h_h_FR_1


title: split-PE-367 plasmids lipo 3000 transfection at HEK3 site- molar ratio 7.5:15 rep1

description:
Library name: splitPE26-H7
molar ratio 7.5:15 rep1
sPE_sep_processed_date.xls


title: cHiC_Dac1JBl6_E11.5_FLHL_Rep2


title: WT_3h_h_WL_3

value: White light


title: dual-AAV split-ePE3-367,2e12, tail-vein injection,heart,rep3,on target

description:
Library name: SP4R3heart
rep3,on target
sPE_sep_processed_date.xls

value: heart


title: split-PE-367 plasmids lipo 3000 transfection at HEK3 site- molar ratio 5:15 rep3

description:
Library name: splitPE26-H6
molar ratio 5:15 rep3
sPE_sep_processed_date.xls

value: human embryonic kidney cells


title: WT_3h_h_WL_1


title: SarcomatoidHigh63

city: Buffalo

first: Jianmin

last: Wang

state: NY

address: Elm and Carlton Streets

department: Bioinformatics and Biostatistics

institute: Roswell Park Comprehensive Cancer Center

data_processing:
Adapters were trimmed with Trimmomatic.
Sequenced reads were mapped to the hg19 reference genome using STAR
RSEM was used to quantify gene expression
Assembly: hg19
Supplementary files format and content: csv containing RSEM counts matrix

extract_protocol:
Cells were lysed using the QIAzol Lysis Reagent (Qiagen) and RNA was isolated by chloroform extraction and ethanol precipitation. RNA was evaluated with the Agilent 4200 TapeStation system
Libraries were prepared with the Illumina TruSeq Stranded mRNA Kit purified with AMPure XP beads (Beckman Coulter)

value: Primary Human

value: Tumor Tissue


title: WT_3h_h_WL_2


title: SarcomatoidHigh64


title: split-PE-367 plasmids lipo 3000 transfection at HEK3 site- molar ratio 5:15 rep1

description:
Library name: splitPE26-H4
molar ratio 5:15 rep1
sPE_sep_processed_date.xls


title: WT_3h_E_FR_3

value: Epicotyl


title: SarcomatoidHigh61


title: dual-AAV split-ePE3-367,2e12, tail-vein injection,heart,rep1,on target

description:
Library name: SP4R1heart
rep1,on target
sPE_sep_processed_date.xls


title: split-PE-367 plasmids lipo 3000 transfection at HEK3 site- molar ratio 5:15 rep2

description:
Library name: splitPE26-H5
molar ratio 5:15 rep2
sPE_sep_processed_date.xls


title: WT_3h_E_FR_2


title: split-PE-367 plasmids lipo 3000 transfection at HEK3 site- molar ratio 0:15 rep3

description:
Library name: splitPE26-H3
molar ratio 0:15 rep3
sPE_sep_processed_date.xls


title: WT_3h_E_FR_1


title: SarcomatoidHigh59


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

description:
Library name: SP4R2liver
rep2,on target
sPE_sep_processed_date.xls

value: liver


title: split-PE-367 plasmids lipo 3000 transfection at HEK3 site- molar ratio 0:15 rep2

description:
Library name: splitPE26-H2
molar ratio 0:15 rep2
sPE_sep_processed_date.xls


title: SarcomatoidHigh58


title: SarcomatoidHigh60


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

description:
Library name: SP4R3liver
rep3,on target
sPE_sep_processed_date.xls


title: WT_3h_E_WL_3


title: split-PE-367 plasmids lipo 3000 transfection at HEK3 site- molar ratio 0:15 rep1

description:
Library name: splitPE26-H1
molar ratio 0:15 rep1
sPE_sep_processed_date.xls


title: SarcomatoidLow62


title: dual-AAV split-ePE3-367,2e12, tail-vein injection,heart,rep2,on target

description:
Library name: SP4R2heart
rep2,on target
sPE_sep_processed_date.xls


title: WT_3h_E_WL_2


title: dual-AAV split-ePE3-367,1e12, tail-vein injection,lung,rep3,on target

description:
Library name: SP3R3lung
rep3,on target
sPE_sep_processed_date.xls

value: lung


title: SarcomatoidLow57


title: split-PE-367 plasmids lipo 3000 transfection at RNF2 site- molar ratio 15:0 rep1

description:
Library name: splitPE26-R19
molar ratio 15:0 rep1
sPE_sep_processed_date.xls


title: WT_3h_C_FR_3

value: Cotyledons

value: White light + Far-red


title: WT_3h_C_FR_2

value: WT


title: SarcomatoidLow56


title: SarcomatoidLow55


title: dual-AAV split-ePE3-367,1e12, tail-vein injection,lung,rep2,on target

description:
Library name: SP3R2lung
rep2,on target
sPE_sep_processed_date.xls


title: split-PE-367 plasmids lipo 3000 transfection at RNF2 site- molar ratio 15:5 rep3

description:
Library name: splitPE26-R18
molar ratio 15:5 rep3
sPE_sep_processed_date.xls


title: dual-AAV split-ePE3-367,1e12, tail-vein injection,testis,rep3,on target

description:
Library name: SP3R3testis
rep3,on target
sPE_sep_processed_date.xls


title: WT_3h_C_FR_1

description:
The two fasq files from two different runs were merged and aligned to the genome with STAR
HTSeqcounts_WT_3h_6h_24h.csv
Normalized_CPM_WT_3h_6h_24h.csv
LOG2_Fold_Change_relative_to_21WL_WT_3h_6h_24h.xlsx


title: SarcomatoidHigh53


title: dual-AAV split-ePE3-367,1e12, tail-vein injection,testis,rep2,on target

description:
Library name: SP3R2testis
rep2,on target
sPE_sep_processed_date.xls


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

description:
Library name: SP4R1liver
rep1,on target
sPE_sep_processed_date.xls


title: split-PE-367 plasmids lipo 3000 transfection at RNF2 site- molar ratio 15:0 rep2

description:
Library name: splitPE26-R20
molar ratio 15:0 rep2
sPE_sep_processed_date.xls


title: split-PE-367 plasmids lipo 3000 transfection at RNF2 site- molar ratio 15:0 rep3

description:
Library name: splitPE26-R21
molar ratio 15:0 rep3
sPE_sep_processed_date.xls


title: split-PE-367 plasmids lipo 3000 transfection at RNF2 site- molar ratio 15:5 rep2

description:
Library name: splitPE26-R17
molar ratio 15:5 rep2
sPE_sep_processed_date.xls


title: WT_3h_C_WL_3


title: WT_3h_C_WL_2


title: WT_3h_E_WL_1


title: SarcomatoidHigh52


title: split-PE-367 plasmids lipo 3000 transfection at RNF2 site- molar ratio 15:5 rep1

description:
Library name: splitPE26-R16
molar ratio 15:5 rep1
sPE_sep_processed_date.xls


title: split-PE-367 plasmids lipo 3000 transfection at RNF2 site- molar ratio 15:7.5 rep2

description:
Library name: splitPE26-R14
molar ratio 15:7.5 rep2
sPE_sep_processed_date.xls


title: SarcomatoidHigh54


title: WT_3h_C_WL_1


title: SarcomatoidLow51


title: split-PE-367 plasmids lipo 3000 transfection at RNF2 site- molar ratio 15:7.5 rep3

description:
Library name: splitPE26-R15
molar ratio 15:7.5 rep3
sPE_sep_processed_date.xls


title: dual-AAV split-ePE3-367,1e12, tail-vein injection,lung,rep1,on target

description:
Library name: SP3R1lung
rep1,on target
sPE_sep_processed_date.xls


title: dual-AAV split-ePE3-367,1e12, tail-vein injection,brain,rep3,on target

description:
Library name: SP3R3brain
rep3,on target
sPE_sep_processed_date.xls


title: WT_24h_L_FR_3

value: First Leaf


title: SarcomatoidLow50


title: dual-AAV split-ePE3-367,1e12, tail-vein injection,testis,rep1,on target

description:
Library name: SP3R1testis
rep1,on target
sPE_sep_processed_date.xls

value: testis


title: WT_24h_L_FR_2


title: SarcomatoidLow49


title: split-PE-367 plasmids lipo 3000 transfection at RNF2 site- molar ratio 15:15 rep3

description:
Library name: splitPE26-R12
molar ratio 15:15 rep3
sPE_sep_processed_date.xls


title: dual-AAV split-ePE3-367,1e12, tail-vein injection,brain,rep2,on target

description:
Library name: SP3R2brain
rep2,on target
sPE_sep_processed_date.xls

value: brain


title: dual-AAV split-ePE3-367,1e12, tail-vein injection,brain,rep1,on target

description:
Library name: SP3R1brain
rep1,on target
sPE_sep_processed_date.xls


title: SarcomatoidHigh48


title: WT_24h_L_FR_1


title: SarcomatoidHigh47


title: split-PE-367 plasmids lipo 3000 transfection at RNF2 site- molar ratio 15:15 rep2

description:
Library name: splitPE26-R11
molar ratio 15:15 rep2
sPE_sep_processed_date.xls

value: HEK293T cell


title: WT_24h_L_WL_3


title: dual-AAV split-ePE3-367,1e12, tail-vein injection,kidney,rep2,on target

description:
Library name: SP3R2kidney
rep2,on target
sPE_sep_processed_date.xls


title: split-PE-367 plasmids lipo 3000 transfection at RNF2 site- molar ratio 15:15 rep1

description:
Library name: splitPE26-R10
molar ratio 15:15 rep1
sPE_sep_processed_date.xls


title: SarcomatoidHigh46


title: SarcomatoidLow45


title: dual-AAV split-ePE3-367,1e12, tail-vein injection,heart,rep3,on target

description:
Library name: SP3R3heart
rep3,on target
sPE_sep_processed_date.xls


title: WT_24h_L_WL_2

description:
The two fasq files from two different runs were merged and aligned to the genome with STAR
HTSeqcounts_WT_3h_6h_24h.csv
Normalized_CPM_WT_3h_6h_24h.csv
LOG2_Fold_Change_relative_to_21WL_WT_3h_6h_24h.xlsx


title: WT_24h_L_WL_1


title: split-PE-367 plasmids lipo 3000 transfection at RNF2 site- molar ratio 15:7.5 rep1

description:
Library name: splitPE26-R13
molar ratio 15:7.5 rep1
sPE_sep_processed_date.xls


title: dual-AAV split-ePE3-367,1e12, tail-vein injection,heart,rep1,on target

description:
Library name: SP3R1heart
rep1,on target
sPE_sep_processed_date.xls


title: SarcomatoidHigh44


title: split-PE-367 plasmids lipo 3000 transfection at RNF2 site- molar ratio 7.5:15 rep3

description:
Library name: splitPE26-R9
molar ratio 7.5:15 rep3
sPE_sep_processed_date.xls


title: split-PE-367 plasmids lipo 3000 transfection at RNF2 site- molar ratio 7.5:15 rep2

description:
Library name: splitPE26-R8
molar ratio 7.5:15 rep2
sPE_sep_processed_date.xls


title: dual-AAV split-ePE3-367,1e12, tail-vein injection,kidney,rep1,on target

description:
Library name: SP3R1kidney
rep1,on target
sPE_sep_processed_date.xls


title: dual-AAV split-ePE3-367,1e12, tail-vein injection,kidney,rep3,on target

description:
Library name: SP3R3kidney
rep3,on target
sPE_sep_processed_date.xls


title: SarcomatoidHigh43


title: split-PE-367 plasmids lipo 3000 transfection at RNF2 site- molar ratio 5:15 rep3

description:
Library name: splitPE26-R6
molar ratio 5:15 rep3
sPE_sep_processed_date.xls


title: dual-AAV split-ePE3-367,1e12, tail-vein injection,heart,rep2,on target

description:
Library name: SP3R2heart
rep2,on target
sPE_sep_processed_date.xls


title: WT_24h_h_FR_2

value: Hypocotyl


title: split-PE-367 plasmids lipo 3000 transfection at RNF2 site- molar ratio 7.5:15 rep1

description:
Library name: splitPE26-R7
molar ratio 7.5:15 rep1
sPE_sep_processed_date.xls


title: SarcomatoidLow42

value: kidney


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

description:
Library name: SP3R3liver
rep3,on target
sPE_sep_processed_date.xls


title: SarcomatoidLow41


title: WT_24h_h_WL_3

value: White light


title: split-PE-367 plasmids lipo 3000 transfection at RNF2 site- molar ratio 5:15 rep2

description:
Library name: splitPE26-R5
molar ratio 5:15 rep2
sPE_sep_processed_date.xls


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

description:
Library name: SP3R2liver
rep2,on target
sPE_sep_processed_date.xls


title: SarcomatoidLow40


title: WT_24h_h_WL_2


title: WT_24h_h_FR_3


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

description:
Library name: SP3R1liver
rep1,on target
sPE_sep_processed_date.xls


title: SarcomatoidLow39


title: dual-AAV split-ePE3-367,2e11, tail-vein injection,liver,rep3,on target

description:
Library name: SP2R3liver
rep3,on target
sPE_sep_processed_date.xls


title: WT_24h_h_WL_1


title: SarcomatoidHigh38


title: WT_24h_h_FR_1


title: split-PE-367 plasmids lipo 3000 transfection at RNF2 site- molar ratio 0:15 rep3

description:
Library name: splitPE26-R3
molar ratio 0:15 rep3
sPE_sep_processed_date.xls


title: split-PE-367 plasmids lipo 3000 transfection at RNF2 site- molar ratio 0:15 rep1

description:
Library name: splitPE26-R1
molar ratio 0:15 rep1
sPE_sep_processed_date.xls


title: split-PE-367 plasmids lipo 3000 transfection at RNF2 site- molar ratio 0:15 rep2

description:
Library name: splitPE26-R2
molar ratio 0:15 rep2
sPE_sep_processed_date.xls


title: WT_24h_E_FR_2

description:
The two fasq files from two different runs were merged and aligned to the genome with STAR
HTSeqcounts_WT_3h_6h_24h.csv
Normalized_CPM_WT_3h_6h_24h.csv
LOG2_Fold_Change_relative_to_21WL_WT_3h_6h_24h.xlsx


title: split-PE-367 plasmids lipo 3000 transfection at EMX1 site- molar ratio 15:0 rep3

description:
Library name: splitPE26-E21
molar ratio 15:0 rep3
sPE_sep_processed_date.xls


title: dual-AAV split-ePE3-367,2e11, tail-vein injection,liver,rep2,on target

description:
Library name: SP2R2liver
rep2,on target
sPE_sep_processed_date.xls


title: SarcomatoidHigh35


title: SarcomatoidLow37


title: SarcomatoidHigh36


title: WT_24h_E_FR_3


title: dual-AAV split-ePE3-367,2e11, tail-vein injection,liver,rep1,on target

description:
Library name: SP2R1liver
rep1,on target
sPE_sep_processed_date.xls


title: split-PE-367 plasmids lipo 3000 transfection at EMX1 site- molar ratio 15:0 rep1

description:
Library name: splitPE26-E19
molar ratio 15:0 rep1
sPE_sep_processed_date.xls


title: WT_24h_E_FR_1


title: dual-AAV split-ePE3-367,1e11, tail-vein injection,liver,rep1,on target

description:
Library name: SP1R1liver
rep1,on target
sPE_sep_processed_date.xls


title: dual-AAV split-ePE3-367,1e11, tail-vein injection,liver,rep2,on target

description:
Library name: SP1R2liver
rep2,on target
sPE_sep_processed_date.xls


title: dual-AAV split-ePE3-367,1e11, tail-vein injection,liver,rep3,on target

description:
Library name: SP1R3liver
rep3,on target
sPE_sep_processed_date.xls


title: split-PE-367 plasmids lipo 3000 transfection at EMX1 site- molar ratio 15:0 rep2

description:
Library name: splitPE26-E20
molar ratio 15:0 rep2
sPE_sep_processed_date.xls


title: SarcomatoidHigh34


title: SarcomatoidHigh33


title: split-PE-367 plasmids lipo 3000 transfection at RNF2 site- molar ratio 5:15 rep1

description:
Library name: splitPE26-R4
molar ratio 5:15 rep1
sPE_sep_processed_date.xls


title: split-PE-367 plasmids lipo 3000 transfection at EMX1 site- molar ratio 15:5 rep3

description:
Library name: splitPE26-E18
molar ratio 15:5 rep3
sPE_sep_processed_date.xls


title: WT_24h_E_WL_1


title: SarcomatoidHigh32


title: split-PE-367 plasmids lipo 3000 transfection at Rosa26 site rep3

description:
Library name: splitPE28-18
rep3
sPE_sep_processed_date.xls

source_name: Hepa1-6 cell

value: Hepa1-6 cell

value: mouse hepatocellular carcinoma cells


title: split-PE-367 plasmids lipo 3000 transfection at EMX1 site- molar ratio 15:5 rep2

description:
Library name: splitPE26-E17
molar ratio 15:5 rep2
sPE_sep_processed_date.xls

value: human embryonic kidney cells


title: WT_24h_C_FR_3


title: split-PE-367 plasmids lipo 3000 transfection at Rosa26 site rep2

description:
Library name: splitPE28-17
rep2
sPE_sep_processed_date.xls


title: split-PE-367 plasmids lipo 3000 transfection at Rosa26 site rep1

description:
Library name: splitPE28-16
rep1
sPE_sep_processed_date.xls


title: split-PE-367 plasmids lipo 3000 transfection at EMX1 site- molar ratio 15:5 rep1

description:
Library name: splitPE26-E16
molar ratio 15:5 rep1
sPE_sep_processed_date.xls


title: split-PE-367 plasmids lipo 3000 transfection at EMX1 site- molar ratio 15:7.5 rep3

description:
Library name: splitPE26-E15
molar ratio 15:7.5 rep3
sPE_sep_processed_date.xls


title: WT_24h_E_WL_3

description:
The two fasq files from two different runs were merged and aligned to the genome with STAR
HTSeqcounts_WT_3h_6h_24h.csv
Normalized_CPM_WT_3h_6h_24h.csv
LOG2_Fold_Change_relative_to_21WL_WT_3h_6h_24h.xlsx


title: split-PE-367 plasmids lipo 3000 transfection at Hoxd13 site rep3

description:
Library name: splitPE28-15
rep3
sPE_sep_processed_date.xls


title: SarcomatoidHigh31

value: Primary Human

value: Tumor Tissue


title: WT_24h_C_FR_1


title: WT_24h_C_FR_2


title: split-PE-367 plasmids lipo 3000 transfection at EMX1 site- molar ratio 15:7.5 rep2

description:
Library name: splitPE26-E14
molar ratio 15:7.5 rep2
sPE_sep_processed_date.xls


title: SarcomatoidLow29


title: split-PE-367 plasmids lipo 3000 transfection at Hoxd13 site rep2

description:
Library name: splitPE28-14
rep2
sPE_sep_processed_date.xls


title: WT_24h_E_WL_2

value: Epicotyl


title: split-PE-367 plasmids lipo 3000 transfection at EMX1 site- molar ratio 15:15 rep3

description:
Library name: splitPE26-E12
molar ratio 15:15 rep3
sPE_sep_processed_date.xls


title: WT_24h_C_WL_1


title: WT_24h_C_WL_3


title: SarcomatoidHigh28


title: split-PE-367 plasmids lipo 3000 transfection at Hoxd13 site rep1

description:
Library name: splitPE28-13
rep1
sPE_sep_processed_date.xls


title: WT_24h_C_WL_2


title: split-PE-367 plasmids lipo 3000 transfection at EMX1 site- molar ratio 15:7.5 rep1

description:
Library name: splitPE26-E13
molar ratio 15:7.5 rep1
sPE_sep_processed_date.xls


title: SarcomatoidHighLow27


title: split-PE-367 plasmids lipo 3000 transfection at Dnmt1 site rep3

description:
Library name: splitPE28-12
rep3
sPE_sep_processed_date.xls


title: SarcomatoidLow26


title: split-PE-367 plasmids lipo 3000 transfection at Dnmt1 site rep2

description:
Library name: splitPE28-11
rep2
sPE_sep_processed_date.xls


title: split-PE-367 plasmids lipo 3000 transfection at EMX1 site- molar ratio 15:15 rep1

description:
Library name: splitPE26-E10
molar ratio 15:15 rep1
sPE_sep_processed_date.xls


title: s-LNv TRIBE-seq ADARcd experiment 2

city: New York

first: Daniel

last: Guzman Gundermann

address: 100 Washington Square E

institute: NYU

description:
merged_datasets_TRIBE-seq_Fig3.csv
ADARcd_exp2

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

organism: Drosophila melanogaster

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

value: adult LNvs

value: Pdf-RFP, Pdf-Gal4 / UAS-ADARcd ; tub-Gal80ts / Sp or TM6B

value: 30°C for 4 hours before dissections


title: SarcomatoidLow24


title: split-PE-367 plasmids lipo 3000 transfection at EMX1 site- molar ratio 7.5:15 rep3

description:
Library name: splitPE26-E9
molar ratio 7.5:15 rep3
sPE_sep_processed_date.xls

value: WT


title: split-PE-367 plasmids lipo 3000 transfection at EMX1 site- molar ratio 15:15 rep2

description:
Library name: splitPE26-E11
molar ratio 15:15 rep2
sPE_sep_processed_date.xls


title: s-LNv TRIBE-seq ADARcd experiment 1

description:
merged_datasets_TRIBE-seq_Fig3.csv
ADARcd_exp1


title: split-PE-367 plasmids lipo 3000 transfection at EMX1 site- molar ratio 7.5:15 rep2

description:
Library name: splitPE26-E8
molar ratio 7.5:15 rep2
sPE_sep_processed_date.xls


title: SarcomatoidLow23


title: SarcomatoidHigh25


title: s-LNv TRIBE-seq Fmr1-ADARcd experiment 2

description:
merged_datasets_TRIBE-seq_Fig3.csv
Fmr1-ADARcd_exp2

value: Pdf-RFP, Pdf-Gal4 / UAS-Fmr1-ADARcd ; tub-Gal80ts / +


title: SarcomatoidHigh21


title: SarcomatoidLow30


title: split-PE-367 plasmids lipo 3000 transfection at EMX1 site- molar ratio 5:15 rep3

description:
Library name: splitPE26-E6
molar ratio 5:15 rep3
sPE_sep_processed_date.xls


title: v3em PE3 plasmids lipo 3000 transfection at Rosa26 site rep3

description:
Library name: splitPE28-9
rep3
sPE_sep_processed_date.xls


title: s-LNv TRIBE-seq Fmr1-ADARcd experiment 1

description:
merged_datasets_TRIBE-seq_Fig3.csv
Fmr1-ADARcd_exp1


title: SarcomatoidLow20


title: L7A5KO_02_BM

city: Shanghai

first: LU

last: MENG

address: No.320 Yue Yang Road

department: Immunology

institute: Institute Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, China

description: SLC7A5 knockout (KO) mice by breeding SLC7A5fl/fl mice with CD19-Cre mice

data_processing:
Reads filtering under criteria removing reads with 20% of the base quality lower than 13
HISAT2.1.0 mapping to reference genome
count counting
Assembly: mm10
Supplementary files format and content: TXT file contain counts for each sample

source_name: bone marrow b cells

extract_protocol:
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.
mRNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: BM-B cells were obtained using the EasySep™ Mouse B Cell Isolation Kit

value: bone marrow


title: split-PE-367 plasmids lipo 3000 transfection at EMX1 site- molar ratio 5:15 rep2

description:
Library name: splitPE26-E5
molar ratio 5:15 rep2
sPE_sep_processed_date.xls


title: split-PE-367 plasmids lipo 3000 transfection at Dnmt1 site rep1

description:
Library name: splitPE28-10
rep1
sPE_sep_processed_date.xls


title: split-PE-367 plasmids lipo 3000 transfection at EMX1 site- molar ratio 7.5:15 rep1

description:
Library name: splitPE26-E7
molar ratio 7.5:15 rep1
sPE_sep_processed_date.xls


title: L7A5KO_03_BM


title: v3em PE3 plasmids lipo 3000 transfection at Hoxd13 site rep3

description:
Library name: splitPE28-6
rep3
sPE_sep_processed_date.xls


title: CTRL_03_BM


title: v3em PE3 plasmids lipo 3000 transfection at Rosa26 site rep1

description:
Library name: splitPE28-7
rep1
sPE_sep_processed_date.xls


title: v3em PE3 plasmids lipo 3000 transfection at Hoxd13 site rep2

description:
Library name: splitPE28-5
rep2
sPE_sep_processed_date.xls


title: v3em PE3 plasmids lipo 3000 transfection at Hoxd13 site rep1

description:
Library name: splitPE28-4
rep1
sPE_sep_processed_date.xls


title: v3em PE3 plasmids lipo 3000 transfection at Rosa26 site rep2

description:
Library name: splitPE28-8
rep2
sPE_sep_processed_date.xls


title: SarcomatoidLow22


title: split-PE-367 plasmids lipo 3000 transfection at EMX1 site- molar ratio 0:15 rep3

description:
Library name: splitPE26-E3
molar ratio 0:15 rep3
sPE_sep_processed_date.xls


title: 7day cut

city: Toon

first: Yuuki

last: Imai

state: Ehime

address: Shituskawa

department: Proteo-Science Center

institute: Ehime University

description: RNA was pooled from 11 independent mice.

data_processing:
Sequence data were mapped on the mouse genome (mm10) using Tophat and analyzed by Cufflinks.
Assembly: mm10

source_name: Achilles tendon

growth_protocol: Achilles tendons were harvested from 7-day and 6-mouth-old male Scx-EGFP mice treated with tenotomy or sham operations using surgical microscope. In tenotomy group, distal stumps of the Achilles tendons without surrounding connective tissue were selectively collected.

extract_protocol:
Total RNA was extracted with RNeasy Plus Mini Kit (Qiagen).The integrity of the isolated RNA was verified using the Bioanalyzer RNA6000 pico kit (Agilent Technologies).
Due to an RNA integrity value of the samples were less than 8, RNA-Seq libraries were prepared from 10ng of RNA using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina kit, NEBNext rRNA Depletion Kit (Human/Mouse/Rat) and NEBNext Multiplex Oligos for Illumina. Each library was sequenced on MiSeq (Illumina) with MiSeq Reagent kit V3 150 cycle (Illumina) by 75 base pair-end reads. Differentially expressed genes were determined by an exact test after normalization.

value: Scx-EGFP homo (C57BL/6 background)

tag: Sex

value: Male

value: 7-day neonatal mice were underwent Achilles tenotomy on the right hindlimbs. RNA was collected from uninjured Achilles tendons 5 days postoperatively.

value: Achilles tendon


title: 6month sham

description: RNA was pooled from 5 independent mice.

value: 6-month adult mice were underwent sham operation on the left hindlimbs. RNA was collected from uninjured Achilles tendons 5 days postoperatively.


title: v3em PE3 plasmids lipo 3000 transfection at Dnmt1 site rep3

description:
Library name: splitPE28-3
rep3
sPE_sep_processed_date.xls

value: Hepa1-6 cell


title: v3em PE3 plasmids lipo 3000 transfection at Dnmt1 site rep2

description:
Library name: splitPE28-2
rep2
sPE_sep_processed_date.xls

value: mouse hepatocellular carcinoma cells