title: HCT116 p53-/- ORC5 deletion, rep2 [ATACseq]

description: Library name: Sample8

data_processing:
Raw sequence data in fastq format were processed as follows: FastQC (v0.11.5) (Andrews, 2010) was used for quality control and sequence data were then mapped to human genome (hg38) using bowtie2 (v2.2.9) (Langdon, 2015). Sam files were converted into bam files using samtools (v1.12) (Li et al., 2009) and only high-quality reads (q-score ≥30) were retained for subsequent analyses. Bam files were then converted to bed files using samtools. Reads no longer than 150 bp were selected and used for ATAC-seq peak calling. Peak calling for ATAC-seq data was performed with MACS2 callpeak function (callpeak -g hs -B --SPMR -q 0.05 --keep-dup 1 -f BEDPE) (v2.1.4) (Zhang et al., 2008).
Assembly: hg38
Supplementary files format and content: BigWig files with pileup signals are generated by bdg2bw.
Supplementary files format and content: Bed files for peak summits are generated by MACS2 peak calling. ATAC_down are ATAC peaks that are down-regulated in ORC2 KO and rescued, ATAC_up are ATAC peaks that are up-regulated in ORC2 KO and rescued.

value: ORC5 deletion


title: HCT116 p53-/- WT, rep1 [ATACseq]-2

status: Public on Jun 05 2025

type: SRA

city: Birmingham

first: Zhangli

last: Su

state: Alabama

address: 720 20th Street South

department: Department of Genetics

country: USA

institute: University of Alabama

description: Library name: Sample1

library_source: genomic

data_processing:
Raw sequence data in fastq format were processed as follows: FastQC (v0.11.5) (Andrews, 2010) was used for quality control and sequence data were then mapped to human genome (hg38) using bowtie2 (v2.2.9) (Langdon, 2015). Sam files were converted into bam files using samtools (v1.12) (Li et al., 2009) and only high-quality reads (q-score ≥30) were retained for subsequent analyses. Bam files were then converted to bed files using samtools. Reads no longer than 150 bp were selected and used for ATAC-seq peak calling. Peak calling for ATAC-seq data was performed with MACS2 callpeak function (callpeak -g hs -B --SPMR -q 0.05 --keep-dup 1 -f BEDPE) (v2.1.4) (Zhang et al., 2008).
Assembly: hg38
Supplementary files format and content: BigWig files with pileup signals are generated by bdg2bw.

molecule: genomic DNA

organism: Homo sapiens

growth_protocol: HCT116 p53-/- cell (referred to as wild-type, RRID: CVCL_S744) was a generous gift from Fred Bunz (Johns Hopkins) (Bunz et al., 1998). ORC2B2 (referred to as ORC2-/-) was a clonal cell line that was established by CRISPR/Cas9 technology in the HCT116 p53-/- background (Shibata et al., 2016). ORC2 rescue cells were established by pLHCXORC2 cloning ORC2 with 3’UTR and 5’UTR and clonal selection. ORC1 or ORC5KO clones were established in HCT116 p53-/- cells using CRISPR/Cas9 technology (Shibata and Dutta, 2020; Shibata et al., 2016). All cell lines were maintained in McCoy’s 5A-modified medium (Corning, no. 10-050-CV) supplemented with 10% fetal bovine serum.

extract_protocol: ATAC-seq for cell lines was performed based on Omni-ATAC-seq protocol (Corces et al., 2017) with 50,000 cells. Nuclear pellet was subjected to transposition with Nextera DNA Sample Preparation Kit (Illumina, no. FC-121-1030) in the presence of 0.01% digitonin and 0.1% Tween-20 at 37 degree for 30 minutes.  The reaction was then cleaned up by DNA Clean and Concentrator-5 Kit (Zymo, no. D4014) and PCR amplified with NEBNext High-Fidelity 2X PCR Master Mix (NEB, no. M0541L) and Nextera Index kit (Illumina, no. 15055289). The resulting libraries were pooled and sequenced on Illumina NextSeq500, according to validated standard operating procedures established by the University of Virginia Genome And Technology Core, RRID: SCR_018883.

tag: cell line

tag: genotype

value: wild-type


title: 58176_209W

city: Duarte

first: Hsun

middle: Teresa

last: Ku

state: CA

address: 1500 E. Duarte Road

department: Translational Research and Cellular Therapeutics

institute: City of Hope

description: Library name: P209W

library_source: transcriptomic

data_processing:
RNA-Seq reads were trimmed to remove sequencing adapters using Trimmomatic and polyA tails using FASTP.
The processed reads were mapped to the human genome hg38 using STAR (v. 2.6.0.a), and gene expression levels were summarized by HTSeq-count v.0.11.1.
Gene expression raw counts were normalized using TMM normalization method and differential expression analysis was conducted using log likelihood ratio test implemented in “edgeR”.
Assembly: hg38
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

molecule: total RNA

source_name: Peripheral blood

extract_protocol:
RNA extraction, sequencing, and analysis RNA from 100,000 cells from each CAR T cell product was extracted with the miRNeasy Mini Kit (QIAGEN, 217004), and RNA quality was assessed using the Agilent 2100 Bioanalyzer according to the manufacturer’s instructions.
The libraries were prepared with SMART-Seq® Ultra Low Input RNA Kit for Sequencing – v4 (TaKaRa, Cat. 634888) according to the manufacturer's protocol. The final libraries were validated with the Agilent Bioanalyzer DNA High Sensitivity Kit and quantified with Qubit. Sequencing was performed on Illumina HiSeq 2500 with the single read mode of 51cycle.

tag: tissue

value: Peripheral blood

tag: cell type

value: T cells

value: Wild type

tag: treatment

value: With Rapamycin


title: KD_OP 2

city: Changsha

first: Zhang

middle: xiu

last: mei

address: tian ma road

country: China

institute: Haijun Tu

data_processing:
The image data measured by the high-throughput sequencer is converted into sequence data (reads) by Casava base recognition.
It mainly includes the removal of reads with adapter, the removal of reads containing n (n indicates that the base information cannot be determined), and the removal of low-quality reads (the base number with qphred < =20 accounts for more than 50% of the whole read length).
The raw gene expression matrix was imported into the R environment for further processing and analysis. Genes with low read counts (less than 50 reads in all eight libraries) were filtered out.
Reads were mapped to the worm reference genome (Wbcel235) using HISAT2. Uniquely mapped reads were summarised to Worm Base annotated genes using feature Counts.
Assembly: Wbcel235
Supplementary files format and content: CT_OP_1_1.fq and CT_OP_1_2.fq files include complete reads for each sample.

organism: Caenorhabditis elegans

source_name: whole body

growth_protocol: Transferring L4 stage worms, which were maintained in NGM plate at 20C, to new plate  at  25C.

extract_protocol:
RNA was harvested using TransZol  Up Plus RNA Kit(Thermo Fisher).
>=1ug total RNA was used for the construction of sequencing libraries. RNA libraries for RNA-seq were prepared using NEBNext® UltraTM RNA Library Prep Kit following manufacturer's protocols.

treatment_protocol: Using pathogenic bacterial PA14 to infect worms.

value: whole body

value: OP50 normal feeding


title: CT_PA 1

value: DCL569 + inx-14 RNAi

value: PA14 infection


city: Berkeley

first: Sharon

last: Greenblum

address: 1 Cyclotron Road

institute: DOE Joint Genome Institute

description: Library name: AT1G76880_F_vesca_Hawaii-4-F7_DAPi712F11-ORGi5034-96P220

data_processing:
Fastq files were quality filtered and adapters were trimmed using BBTools v38.96 bbduk.sh62 with parameters k=21 mink=11 ktrim=r tbo tpe qtrim=r trimq=6 maq=10, and then aligned to the corresponding reference genome using bowtie2 v2.4.2 and parameters --no-mixed --no-discordant. Bam files from negative control wells were merged using the samtools v1.15.1 merge command, to generate a single background file for each 96-well plate. The MACS3 v3.0.0a6 callpeak command was used to generate narrowPeak files, using the merged background as the control, with the parameters --call-summits --keep-dup 1 and –gsize with the total fasta genome size. Bigwig files were generated using deeptools v3.5.2 bamCoverage with parameters --extendReads --binSize 1 --ignoreDuplicates --maxFragmentLength 600 --normalizeUsing RPGC, and --effectiveGenomeSize with the total fasta genome assembly size of each species.
Assembly: Fragaria vesca Hawaii-4-F7: UCD/HAU via Phytozome v4.0.a2
Supplementary files format and content: narrowPeak are tab-delimited extended bed format files that contain peak regions identified by MACS3, using the matched negative controls on each 96 well plate to dentify regions that were enriched for by each transcription factor. The identified peaks represent putative transcription factor binding sites.
Supplementary files format and content: bigwig files show the genome coverage of each DAP-seq library. They can be used to compare coverage between different libraries and to view peaks in a genome browser. Note that they should be compared to the matched negative control libraries from the same plate.
Library strategy: DAP-seq

organism: Fragaria vesca

source_name: plant

growth_protocol: Various growth protocols and tissues were used for gDNA extraction depending on the plant species, however gDNA libraries were PCR amplified upstream of DAP-seq to remove condition/tissue-specific DNA modifications.

extract_protocol:
CTAB protocol for gDNA extraction
Genomic DNA fragment libraries were constructed with an average shearing size at 150 bp. Different species were labeled by unique Illumina i5 index adapters to enable multiplexing following the multiDAP method. Upstream of the DAP-seq assay, fragment libraries were amplified for 10 cycles to remove any DNA modifications. After performing the DAP-seq enrichment in 96-well plates with each well containing a single in vitro expressed transcription factor, the libraries were amplified with i7 index primers to attach a unique i7 adapter corresponding to each well.

value: plant

tag: tf id

tag: tf family

value: TRIHELIX

tag: multidap sample_id

tag: 96 well_plate_id

tag: tf source_species


title: MOLM13, MBD6 CLIP, azaC, rep3

city: Chicago

first: Boyang

last: Gao

state: IL

address: 929 E 57th Street

department: Chemistry

institute: University of Chicago

description: Library name: MOLM13, MBD6 CLIP, azaC, rep3

data_processing:
For RNA-seq and Nascent RNA-seq, adapters were trimmed by cutadapt -m 20 -a NNNAGATCGGAAGAGCACACGTCTGAACTCCAGTCA -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT -U 3. Reads after adapter trimming were uploaded. Samples were mapped by hisat2, and read numbers for each gene is quantified by featureCounts. Differential expression was computed using DESeq2 except for the case of MOLM13 RNA-seq with 5azaC treatment, where we used RUVSeq to account for the ERCC spike in. For the m5C MeRIP-seq, reads after adapter trimming and umi extract were uploaded. Samples were mapped by hisat2, deduped by umi_tools and peaks were called by macs3 callpeak. For CLIP-seq, adapters were trimmed by cutadapt -m 20 -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -A GATCGTCGGACTGTAGAACTCTGAACGTGTAGATCTCGGTGGTCGCCGTATCATT. Reads after adapter trimming were uploaded. Samples were mapped by hisat2, and deduplicated by picard MarkDuplicates.
Assembly: hg38, mm10
Supplementary files format and content: csv, DESeq2 or RUVSeq results of differential expression
Supplementary files format and content: txt, featureCounts results of read numbers for each annotated genes
Supplementary files format and content: bed, merged peak file from m5C MeRIP from two conditions
Supplementary files format and content: bw, averaged bigwig file

extract_protocol:
For RNA-seq, total RNA was harvested by TRIzol™ reagent. For nascent RNA-seq, EU labeled RNA was enriched following manufacturer's instructions with Click-iT™ Nascent RNA Capture Kit for gene expression analysis (Invitrogen™, C10365). After the final washing steps, RNA was eluted in 50 μL of 95% formamide supplemented with 2.5 mM EDTA by heating at 65°C for 5 mins, followed by 95°C for 5 mins. The supernatant was immediately harvested while still hot, and RNA was extracted using 1 mL TRIzol™ reagent. For m5C MeRIP, chromatin-associated RNA was purified. For MOLM13 cells, 0.02 million drosophila S2 cells were added to 20 million MOLM13 cells before proceeding with cellular fractionation. rRNA removal was carried out using RiboMinus Eukaryote System v2 (Invitrogen™, A15026). 2 μg ribo-depleted caRNA was then used for m5C immunoprecipitation. RNA was fragmented using 1× fragmentation buffer (NEB, E6186A) at 94°C for 2 mins, and 5% of the sample was saved as input. The RNA was heated to 72°C for 2 mins and then placed immediately on ice for denaturation. Next, the RNA was added to protein G beads conjugated with 2 μg anti-m5C antibody (Diagenode, MAb-081-100) in 300 μL IP buffer (10 mM Tris-HCl pH 7.5, 150 mM NaCl, 0.05% Triton X-100, 1 mM spermidine, 0.2 U/μL SUPERase•In™ RNase Inhibitor), and incubated with end-to-end rotation at 4°C for 2 hours. The beads were washed three times with IP buffer and eluted with buffer RLT (Qiagen, 79216). For CLIP-seq, 100 million cells were used for each replicate. Following the designated treatment, cells were crosslinked in PBS using 4500 J/m2 UV at 254 nm. Cells were lysed in 200 μL iCLIP lysis buffer (50 mM Tris-HCl pH 7.5, 100 mM NaCl, 1% NP-40 substitute, 0.1% SDS, 0.5% sodium deoxycholate, 100× proteinase inhibitor cocktail and 0.2 U/μL SUPERase•In™ RNase Inhibitor) at 4°C for 15 mins with end-to-end rotation. SDS were then added to reach a final concentration of 1% for protein release from chromatin. Samples were sonicated (35% amplitude, 2s on / 4s off cycles, 1 min on ice) and diluted 10-fold with SDS-free iCLIP lysis buffer to reduce SDS back to 0.1%. After centrifugation at 15,000 x g for 30 mins at 4°C, the supernatant was harvested and treated with 0.2 U/μL RNase T1 (Thermo Scientific™, EN0642) at 22°C for 15 mins, then quenched on ice for 5 mins. 2% of the lysate was saved as input and digested with 10 U/μL RNase T1 at 22°C for 10 mins, followed by proteinase K digestion, RNA purification and end repair. The remaining lysate was incubated overnight at 4°C with protein A beads conjugated to 30 μL MBD6 antibodies (gifted from Prof. Lu Wang) per sample. Beads were washed three times with CLIP wash buffer (50 mM Tris-HCl pH 7.5, 300 mM KCl, 0.05% NP-40, 1000× protein inhibitor cocktail and 0.2 U/μL SUPERase•In™ RNase Inhibitor), followed by digestion with 10 U/μL RNase T1 at 22°C for 10 mins. Beads were further washed for three times each with CLIP high salt buffer (50 mM Tris-HCl pH 7.5, 500 mM KCl, 0.05% NP-40, 100× protein inhibitor cocktail and 0.2 U/μL SUPERase•In™ RNase Inhibitor) and PNK buffer without DTT, and subjected to end-repair using T4 PNK (NEB, M0201L). After proteinase K digestion, RNA was purified for library preparation.
The purified RNA was constructed for library with SMARTer® Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian, with ribominus reactions supplied by the kit. For the m5C MeRIP-seq, customized adapters with umi was used for deduplication purpose. For CLIP-seq, libraries were constructed using the NEBNext® Small RNA Library Prep Set.


title: KD_OP 1


title: THP-1 cells, M1+HA4-1, Day1

city: Kizugawa

first: Eiko

last: Uno

state: Kyoto

address: 6-5-4 Kunimidai

country: Japan

institute: Rohto Pharmaceutical Co., Ltd.

description: Library name: Sample 7

data_processing:
The resulting reads were analyzed using CLC Genomics Workbench software (ver. 8.01, Qiagen, Venlo, The Netherlands).
Using the RNA-Seq Analysis tool in CLC Genomics Workbench, read counts were obtained for each gene ID and transcript ID. The counts were then normalized by gene length and read depth to calculate TPM (Transcripts Per Million) values. In the processed data file, the expression values represent TPM values.
Statistical differences were analyzed by multiple unpaired t-tests using Prism (version 10.0; GraphPad Software, Boston, MA, USA).
Gene pathway analysis was performed using Ingenuity Pathway Analysis (Qiagen, Venlo, The Netherlands).
The heat map displayed log2(TPM+1) values for each gene from the RNA-seq data created with Prism.
A volcano plot was produced with log2(fold change) on the x-axis and -log10(p-value) on the y-axis using Origin Pro 2023 (Northampton, MA).
Principal component analysis (PCA) was conducted using JMP Pro 18 (SAS Institute Cary, CA) to validate intragroup variance.
Assembly: Homo sapience GRCh37 (hg19) release-75
Supplementary files format and content: xlsx file include TPM values for each sample

source_name: skin

growth_protocol: The human acute monocytic leukemia cell line, THP-1, was obtained from the American Type Culture Collection (Manassas, VA, USA). THP-1 cells were maintained in RPMI-1640 medium fortified with 10% FBS, penicillin (100 IU/mL), streptomycin (100 μg/mL), and β-mercaptoethanol (50μM), and they were also grown in an incubator with 5% CO2 at 37°C.

extract_protocol:
Total RNA was extracted from macrophages and NHDF utilizing the Maxwell® RSC Instrument (Promega, Madison, WI, USA).
The mRNA was then purified using oligo dT beads (NEBNext Poly (A) mRNA Magnet Isolation Module, New England Biolabs, NEB, Ipswich, MA). Complementary DNA (cDNA) library preparation was performed using the NEBNext Ultra II RNA Library Prep Kit (NEB) along with NEBNextplex Oligos for Illumina according to a previously established method (9). Index sequences were incorporated into the fragments through PCR amplification. The cDNA libraries were combined in equal molecular amounts and sequenced on an Illumina Next-seq DNA sequencer, employing a 75-bp single-end cycle sequencing kit (Illumina, San Diego, CA).

treatment_protocol: THP-1 cells were differentiated into M0 macrophages by treating them with 5 ng/mL phorbol 12-myristate 13-acetate (PMA) for 72 hours. For M1 polarization, M0 macrophages received treatment with 10 ng/mL lipopolysaccharide (LPS) and 20 ng/mL interferon-γ (IFN-γ) for 24 hours. The impact of HA4 was evaluated during M1 polarization, conducted with and without 0.1% (w/v) or 1% (w/v) HA4 added for 24 h at initiation. RNA extraction was performed 24 hours after the last stimulation for M1  group macrophages.

value: skin

value: Macrophages

value: WT

value: Macrophage differentiation

tag: time


description: Library name: AL2G32420.t2_F_vesca_Hawaii-4-F7_DAPi712F10-ORGi5034-96P247

value: MYBRELATED


title: HCT116 p53-/- ORC2 rescue, rep2 [ATACseq]

description: Library name: Sample6

value: ORC2 rescue


title: MOLM13, MBD6 CLIP, azaC, rep2

description: Library name: MOLM13, MBD6 CLIP, azaC, rep2


title: CT_OP 2


description: Library name: AT4G14770_F_vesca_Hawaii-4-F7_DAPi712F10-ORGi5034-96P220

value: CPP


title: MOLM13, MBD6 CLIP, azaC, rep1

description: Library name: MOLM13, MBD6 CLIP, azaC, rep1


description: Library name: Carub.0008s0039.1_F_vesca_Hawaii-4-F7_DAPi712F09-ORGi5034-96P247


description: Library name: AT1G18330_F_vesca_Hawaii-4-F7_DAPi712G01-ORGi5034-96P220


title: HCT116 p53-/- ORC2 rescue, rep1 [ATACseq]

description: Library name: Sample5


description: Library name: LOC_Os09g25060.1_F_vesca_Hawaii-4-F7_DAPi712F11-ORGi5034-96P247

value: WRKY


title: HCT116 p53-/- ORC2 deletion, rep2 [ATACseq]

description: Library name: Sample4

value: ORC2 deletion


title: 58177_209WO

description: Library name: P209WO

value: Peripheral blood

value: T cells

value: Wild type

value: Without Rapamycin


description: Library name: AT3G50060_F_vesca_Hawaii-4-F7_DAPi712G02-ORGi5034-96P220

value: MYB


title: MOLM13, MBD6 CLIP, Ctrl, rep2

description: Library name: MOLM13, MBD6 CLIP, Ctrl, rep2

value: Ctrl


description: Library name: AT2G45480_F_vesca_Hawaii-4-F7_DAPi712F09-ORGi5034-96P220

value: plant

value: GRF


title: HCT116 p53-/- ORC2 deletion, rep1 [ATACseq]

description: Library name: Sample3


title: MOLM13, MBD6 CLIP, Ctrl, rep3

description: Library name: MOLM13, MBD6 CLIP, Ctrl, rep3


title: MOLM13, MBD6 CLIP, Ctrl, rep1

description: Library name: MOLM13, MBD6 CLIP, Ctrl, rep1


title: HCT116 p53-/- WT, rep2 [ATACseq]

description: Library name: Sample2

value: wild-type


description: Library name: AT2G02820_F_vesca_Hawaii-4-F7_DAPi712F08-ORGi5034-96P220


description: Library name: XP_013586407.1_F_vesca_Hawaii-4-F7_DAPi712F07-ORGi5034-96P247

value: BZIP


title: HCT116 p53-/- ORC5 deletion, rep1 [ATACseq]

description: Library name: Sample7

value: ORC5 deletion


title: HCT116 p53-/- WT, rep1 [ATACseq]

description: Library name: Sample1


title: MOLM13, CLIP input, 5azaC, rep2

description: Library name: MOLM13, CLIP input, 5azaC, rep2


title: MOLM13, CLIP input, 5azaC, rep3

description: Library name: MOLM13, CLIP input, 5azaC, rep3


title: HCT116 p53-/- ORC2 rescue CTCF rep 2 [CUT&RUN]

data_processing:
Raw sequence data in fastq format were processed as follows: FastQC (v0.11.5) (Andrews, 2010) was used for quality control and sequence data were then mapped to human genome (hg38) using bowtie2 (v2.2.9) (Langdon, 2015). Sam files were converted into bam files using samtools (v1.12) (Li et al., 2009) and only high-quality reads (q-score ≥30) were retained for subsequent analyses. Bam files were then converted to bed files using samtools. Peak calling for CTCF was performed with MACS2 (callpeak -g hs -B --SPMR -q 0.05 --keep-dup 1 -f BAMPE).
Assembly: hg38
Supplementary files format and content: BigWig files with pileup signals are generated by bdg2bw.
Supplementary files format and content: Bed files for peak summits are generated by MACS2 peak calling. CTCF-up are CTCF peaks that are unique in ORC2 KO samples, CTCF-down are CTCF peaks that are absent in ORC2 KO samples.
Library strategy: CUT&RUN

extract_protocol: CUT&RUN Assay Kit (cell signaling technology, no. 86652) was used to perform cut&run according to the manufacturer's instructions. Anti-CTCF (cell signaling technology, no. 3418) was used.


description: Library name: Control_TF_DNA_S_lycopersicum_Heinz-1706-BG_DAPi712H01-ORGi5039-96P247

data_processing:
Fastq files were quality filtered and adapters were trimmed using BBTools v38.96 bbduk.sh62 with parameters k=21 mink=11 ktrim=r tbo tpe qtrim=r trimq=6 maq=10, and then aligned to the corresponding reference genome using bowtie2 v2.4.2 and parameters --no-mixed --no-discordant. Bam files from negative control wells were merged using the samtools v1.15.1 merge command, to generate a single background file for each 96-well plate. The MACS3 v3.0.0a6 callpeak command was used to generate narrowPeak files, using the merged background as the control, with the parameters --call-summits --keep-dup 1 and –gsize with the total fasta genome size. Bigwig files were generated using deeptools v3.5.2 bamCoverage with parameters --extendReads --binSize 1 --ignoreDuplicates --maxFragmentLength 600 --normalizeUsing RPGC, and --effectiveGenomeSize with the total fasta genome assembly size of each species.
Assembly: Solanum lycopersicum Heinz-1706-BG:: SGN/ITAG via Phytozome ITAG4.0
Supplementary files format and content: narrowPeak are tab-delimited extended bed format files that contain peak regions identified by MACS3, using the matched negative controls on each 96 well plate to dentify regions that were enriched for by each transcription factor. The identified peaks represent putative transcription factor binding sites.
Supplementary files format and content: bigwig files show the genome coverage of each DAP-seq library. They can be used to compare coverage between different libraries and to view peaks in a genome browser. Note that they should be compared to the matched negative control libraries from the same plate.
Library strategy: DAP-seq

organism: Solanum lycopersicum


description: Library name: Control_TF_DNA_S_lycopersicum_Heinz-1706-BG_DAPi712A12-ORGi5039-96P247


title: CT_OP 1

value: whole body

value: OP50 normal feeding


description: Library name: Control_TF_DNA_S_lycopersicum_Heinz-1706-BG_DAPi712H12-ORGi5039-96P247


description: Library name: Control_TF_DNA_S_lycopersicum_Heinz-1706-BG_DAPi712A01-ORGi5039-96P247


title: MOLM13, CLIP input, 5azaC, rep1

description: Library name: MOLM13, CLIP input, 5azaC, rep1


title: HCT116 p53-/- ORC2 rescue CTCF rep 1 [CUT&RUN]

value: ORC2 rescue


description: Library name: AT2G45420_F_vesca_Hawaii-4-F7_DAPi712F06-ORGi5034-96P220


description: Library name: Control_TF_DNA_S_lycopersicum_Heinz-1706-BG_DAPi712H12-ORGi5039-96P220


description: Library name: AT2G01060_F_vesca_Hawaii-4-F7_DAPi712F05-ORGi5034-96P220


description: Library name: Control_TF_DNA_S_lycopersicum_Heinz-1706-BG_DAPi712H01-ORGi5039-96P220


title: MOLM13, CLIP input, Ctrl, rep3

description: Library name: MOLM13, CLIP input, Ctrl, rep3


description: Library name: Control_TF_DNA_S_lycopersicum_Heinz-1706-BG_DAPi712A12-ORGi5039-96P220


title: HCT116 p53-/- ORC2 deletion CTCF rep 2 [CUT&RUN]


title: MOLM13, CLIP input, Ctrl, rep2

description: Library name: MOLM13, CLIP input, Ctrl, rep2


description: Library name: Control_TF_DNA_S_lycopersicum_Heinz-1706-BG_DAPi712A01-ORGi5039-96P220


description: Library name: AT4G25480_F_vesca_Hawaii-4-F7_DAPi712F04-ORGi5034-96P220


description: Library name: Solyc08g079120.3.1_F_vesca_Hawaii-4-F7_DAPi712F03-ORGi5034-96P247

value: NAC


title: HCT116 p53-/- ORC2 deletion CTCF rep 1 [CUT&RUN]


description: Library name: AT1G33240_F_vesca_Hawaii-4-F7_DAPi712F03-ORGi5034-96P220

value: TRIHELIX


description: Library name: AT5G52830_F_vesca_Hawaii-4-F7_DAPi712F07-ORGi5034-96P220

value: WRKY


title: SKM1, caRNA m5C MeRIP, 5azaC, rep3

description: Library name: SKM1, caRNA m5C MeRIP, 5azaC, rep3

molecule: nuclear RNA


title: MOLM13, CLIP input, Ctrl, rep1

description: Library name: MOLM13, CLIP input, Ctrl, rep1


title: HCT116 p53-/- ORC2 deletion IgG rep 2 [CUT&RUN]

value: ORC2 deletion


description: Library name: AT4G31800_F_vesca_Hawaii-4-F7_DAPi712F02-ORGi5034-96P220


title: HCT116 p53-/- ORC2 deletion IgG rep 1 [CUT&RUN]


description: Library name: AT2G46270_S_lycopersicum_Heinz-1706-BG_DAPi712H11-ORGi5039-96P220


title: SKM1, caRNA m5C MeRIP, 5azaC, rep2

description: Library name: SKM1, caRNA m5C MeRIP, 5azaC, rep2


title: SKM1, caRNA m5C MeRIP, 5azaC, rep1

description: Library name: SKM1, caRNA m5C MeRIP, 5azaC, rep1


title: HCT116 p53-/- WT CTCF rep 2 [CUT&RUN]


description: Library name: AT5G47390_F_vesca_Hawaii-4-F7_DAPi712F01-ORGi5034-96P220

value: MYBRELATED


title: SKM1, caRNA m5C MeRIP, Ctrl, rep3

description: Library name: SKM1, caRNA m5C MeRIP, Ctrl, rep3


title: HCT116 p53-/- ORC2 rescue IgG rep 2 [CUT&RUN]


title: HCT116 p53-/- WT CTCF rep 1 [CUT&RUN]


description: Library name: AT2G47070_S_lycopersicum_Heinz-1706-BG_DAPi712H10-ORGi5039-96P220

value: SBP


description: Library name: Solyc04g078640.3.1_F_vesca_Hawaii-4-F7_DAPi712F01-ORGi5034-96P247


description: Library name: Solyc05g007180.3.1_F_vesca_Hawaii-4-F7_DAPi712E12-ORGi5034-96P247

value: HOMEOBOX


title: SKM1, caRNA m5C MeRIP, Ctrl, rep2

description: Library name: SKM1, caRNA m5C MeRIP, Ctrl, rep2


description: Library name: Solyc08g078340.3.1_S_lycopersicum_Heinz-1706-BG_DAPi712H09-ORGi5039-96P247


description: Library name: AL2G28980.t1_S_lycopersicum_Heinz-1706-BG_DAPi712H11-ORGi5039-96P247


description: Library name: XP_013634112.1_S_lycopersicum_Heinz-1706-BG_DAPi712H08-ORGi5039-96P247


description: Library name: Carub.0002s1959.1_S_lycopersicum_Heinz-1706-BG_DAPi712H10-ORGi5039-96P247


title: HCT116 p53-/- WT IgG rep 1 [CUT&RUN]


description: Library name: AT1G52880_F_vesca_Hawaii-4-F7_DAPi712E12-ORGi5034-96P220


title: SKM1, caRNA m5C MeRIP, Ctrl, rep1

description: Library name: SKM1, caRNA m5C MeRIP, Ctrl, rep1


description: Library name: AT5G17300_S_lycopersicum_Heinz-1706-BG_DAPi712H08-ORGi5039-96P220


description: Library name: LOC_Os01g17260.2_S_lycopersicum_Heinz-1706-BG_DAPi712H07-ORGi5039-96P247


title: SKM1, caRNA input, 5azaC, rep3

description: Library name: SKM1, caRNA input, 5azaC, rep3


title: SKM1, caRNA input, 5azaC, rep2

description: Library name: SKM1, caRNA input, 5azaC, rep2


description: Library name: Carub.0002s2670.1_F_vesca_Hawaii-4-F7_DAPi712E11-ORGi5034-96P247


title: HCT116 p53-/- ORC5 deletion, rep2 [RNAseq]

description: Library name: Sample11

data_processing:
Raw sequence data in fastq format were processed as follows: FastQC (v0.11.5) (Andrews, 2010) was used for quality control and sequence data were then mapped to human genome (hg38) using hisat2 version 2.2.1 (Kim et al., 2019) (hisat2 -t -p 20 -5 20 -3 80). Sam files were converted into bam files using samtools (v1.12) (Li et al., 2009)and only high-quality reads (q-score ≥30) were retained for subsequent analyses. HTSeq version 2.0.5 (Putri et al., 2022) was used to calculate the readscount for every gene using command htseq-count -f bam -r name -s no. The reference genome is hg38 ncbiRefSeq. Differential gene analysis was performed using DESeq2 version 1.42.0 (Love et al., 2014).
Assembly: hg38
Supplementary files format and content: ORC2_KO_down.txt are genes that are down-regulated in ORC2 KO and rescued. ORC2_KO_up.txt are genes that are up-regulated in ORC2 KO and rescued.

molecule: polyA RNA

extract_protocol:
RNA-seq libraries were prepared as previously(Su et al., 2022). Total RNAs (1 μg) were poly-A selected by NEBNext poly(A) mRNA Magnetic Isolation Module (NEB #E7490) and followed by NEBNext UltraII Directional RNA Kit (NEB #7765). The resulting libraries were pooled and sequenced as paired-end reads on Illumina HiSeq2000 (Novogene) or NextSeq (UVA GATC core facility, RRID: SCR_018883) with >20 million reads per sample.
polyA RNA-seq


description: Library name: AT5G18560_S_lycopersicum_Heinz-1706-BG_DAPi712H07-ORGi5039-96P220


title: HCT116 p53-/- ORC5 deletion, rep1 [RNAseq]

description: Library name: Sample10


title: HCT116 p53-/- WT IgG rep 2 [CUT&RUN]


title: SKM1, caRNA input, 5azaC, rep1

description: Library name: SKM1, caRNA input, 5azaC, rep1


description: Library name: AT4G17980_F_vesca_Hawaii-4-F7_DAPi712E10-ORGi5034-96P220


title: HCT116 p53-/- ORC2 rescue, rep3 [RNAseq]

description: Library name: Sample9


description: Library name: AL4G45550.t1_S_lycopersicum_Heinz-1706-BG_DAPi712H06-ORGi5039-96P247


description: Library name: Solyc10g005080.3.1_F_vesca_Hawaii-4-F7_DAPi712E10-ORGi5034-96P247


description: Library name: AT3G50410_S_lycopersicum_Heinz-1706-BG_DAPi712H06-ORGi5039-96P220


title: HCT116 p53-/- ORC2 rescue, rep2 [RNAseq]

description: Library name: Sample8


description: Library name: XP_013615900.1_F_vesca_Hawaii-4-F7_DAPi712E09-ORGi5034-96P247


title: SKM1, caRNA input, Ctrl, rep2

description: Library name: SKM1, caRNA input, Ctrl, rep2


description: Library name: AT5G14960_F_vesca_Hawaii-4-F7_DAPi712E08-ORGi5034-96P220


title: HCT116 p53-/- ORC5 deletion, rep3 [RNAseq]

description: Library name: Sample12


description: Library name: AT1G01060_S_lycopersicum_Heinz-1706-BG_DAPi712H05-ORGi5039-96P220


title: SKM1, caRNA input, Ctrl, rep1

description: Library name: SKM1, caRNA input, Ctrl, rep1


title: HCT116 p53-/- ORC2 rescue, rep1 [RNAseq]

description: Library name: Sample7


title: HCT116 p53-/- ORC2 deletion, rep3 [RNAseq]

description: Library name: Sample6


description: Library name: AL3G23910.t2_F_vesca_Hawaii-4-F7_DAPi712E07-ORGi5034-96P247


description: Library name: Solyc01g102340.3.1_S_lycopersicum_Heinz-1706-BG_DAPi712H04-ORGi5039-96P247

value: MYB


title: HCT116 p53-/- ORC2 deletion, rep2 [RNAseq]

description: Library name: Sample5


description: Library name: AT5G56110_F_vesca_Hawaii-4-F7_DAPi712E06-ORGi5034-96P220


title: MOLM13, caRNA m5C MeRIP, 5azaC, rep2

description: Library name: MOLM13, caRNA m5C MeRIP, 5azaC, rep2


description: Library name: AT2G18550_F_vesca_Hawaii-4-F7_DAPi712E07-ORGi5034-96P220


title: MOLM13, caRNA m5C MeRIP, 5azaC, rep1

description: Library name: MOLM13, caRNA m5C MeRIP, 5azaC, rep1


description: Library name: AT3G60530_F_vesca_Hawaii-4-F7_DAPi712E05-ORGi5034-96P220


title: HCT116 p53-/- ORC2 deletion, rep1 [RNAseq]

description: Library name: Sample4


description: Library name: XP_013629448.1_S_lycopersicum_Heinz-1706-BG_DAPi712H03-ORGi5039-96P247


description: Library name: AT5G62020_F_vesca_Hawaii-4-F7_DAPi712E04-ORGi5034-96P220

value: HSF


title: MOLM13, caRNA m5C MeRIP, 5azaC, rep3

description: Library name: MOLM13, caRNA m5C MeRIP, 5azaC, rep3


description: Library name: AT2G22430_S_lycopersicum_Heinz-1706-BG_DAPi712H02-ORGi5039-96P220

value: plant


title: HCT116 p53-/- WT, rep2 [RNAseq]

description: Library name: Sample2


description: Library name: AT2G30250_S_lycopersicum_Heinz-1706-BG_DAPi712H03-ORGi5039-96P220


title: MOLM13, caRNA m5C MeRIP, Ctrl, rep3

description: Library name: MOLM13, caRNA m5C MeRIP, Ctrl, rep3

value: Ctrl


title: SKM1, caRNA input, Ctrl, rep3

description: Library name: SKM1, caRNA input, Ctrl, rep3


title: MOLM13, caRNA m5C MeRIP, Ctrl, rep2

description: Library name: MOLM13, caRNA m5C MeRIP, Ctrl, rep2


title: HCT116 p53-/- WT, rep1 [RNAseq]

description: Library name: Sample1

value: wild-type


description: Library name: XP_013609718.1_S_lycopersicum_Heinz-1706-BG_DAPi712G12-ORGi5039-96P247


description: Library name: LOC_Os02g42970.1_F_vesca_Hawaii-4-F7_DAPi712E03-ORGi5034-96P247


description: Library name: AT3G02940_S_lycopersicum_Heinz-1706-BG_DAPi712H04-ORGi5039-96P220


description: Library name: AT5G64750_F_vesca_Hawaii-4-F7_DAPi712E03-ORGi5034-96P220


title: MOLM13, caRNA input, 5azaC, rep3

description: Library name: MOLM13, caRNA input, 5azaC, rep3


description: Library name: Solyc03g116890.3.1_S_lycopersicum_Heinz-1706-BG_DAPi712G11-ORGi5039-96P247


title: HCT116 p53-/- ORC1 deletion, rep2 [RNAseq]

description: Library name: Sample5

data_processing:
Raw sequence data in fastq format were processed as follows: FastQC (v0.11.5) (Andrews, 2010) was used for quality control and sequence data were then mapped to human genome (hg38) using hisat2 version 2.2.1 (Kim et al., 2019) (hisat2 -t -p 20 -5 20 -3 80). Sam files were converted into bam files using samtools (v1.12) (Li et al., 2009)and only high-quality reads (q-score ≥30) were retained for subsequent analyses. HTSeq version 2.0.5 (Putri et al., 2022) was used to calculate the readscount for every gene using command htseq-count -f bam -r name -s no. The reference genome is hg38 ncbiRefSeq. Differential gene analysis was performed using DESeq2 version 1.42.0 (Love et al., 2014).
Assembly: hg38
Supplementary files format and content: DEseq2 output

value: ORC1 deletion


description: Library name: LOC_Os06g07030.1_F_vesca_Hawaii-4-F7_DAPi712E01-ORGi5034-96P247


description: Library name: AT5G09410_S_lycopersicum_Heinz-1706-BG_DAPi712G11-ORGi5039-96P220

value: CAMTA


title: MOLM13, caRNA input, 5azaC, rep2

description: Library name: MOLM13, caRNA input, 5azaC, rep2


title: HCT116 p53-/- WT, rep3 [RNAseq]

description: Library name: Sample3


title: MOLM13, caRNA input, 5azaC, rep1

description: Library name: MOLM13, caRNA input, 5azaC, rep1


description: Library name: LOC_Os10g26500.1_F_vesca_Hawaii-4-F7_DAPi712D12-ORGi5034-96P247


description: Library name: XP_013589913.1_S_lycopersicum_Heinz-1706-BG_DAPi712G10-ORGi5039-96P247


title: HCT116 p53-/- WT, rep3, control [RNAseq]

description: Library name: Sample3


description: Library name: AT5G45300_S_lycopersicum_Heinz-1706-BG_DAPi712G10-ORGi5039-96P220


title: MOLM13, caRNA input, Ctrl, rep3

description: Library name: MOLM13, caRNA input, Ctrl, rep3


description: Library name: AT1G13260_F_vesca_Hawaii-4-F7_DAPi712E01-ORGi5034-96P220

value: RAV


title: MOLM13, caRNA input, Ctrl, rep2

description: Library name: MOLM13, caRNA input, Ctrl, rep2


description: Library name: AT5G11260_F_vesca_Hawaii-4-F7_DAPi712D12-ORGi5034-96P220

value: BZIP


description: Library name: AT1G20980_F_vesca_Hawaii-4-F7_DAPi712E11-ORGi5034-96P220


title: MOLM13, caRNA m5C MeRIP, Ctrl, rep1

description: Library name: MOLM13, caRNA m5C MeRIP, Ctrl, rep1


description: Library name: LOC_Os10g41200.1_S_lycopersicum_Heinz-1706-BG_DAPi712G09-ORGi5039-96P247


description: Library name: XP_013587997.1_F_vesca_Hawaii-4-F7_DAPi712D11-ORGi5034-96P247


description: Library name: AT1G72740_S_lycopersicum_Heinz-1706-BG_DAPi712G09-ORGi5039-96P220


title: DGM-13747 (mRNA-seq)

city: New York

first: Yael

last: Strulovici-Barel

state: NY

address: 1300 York Avenue

department: Department of Genetic Medicine

institute: Weill Cornell Medical College

data_processing:
data was analyzed using Tuxedo pipeline software.
HiSeq Control Software (Illumina) was used to perform image analysis, base calling and sequence analysis on HiSeq generated sequence images resulting in fastq files.
Expression analysis was performed using Bowtie (v0.12.8.0, http://bowtie-bio.sourceforge.net), Tophat (v2.0.4, http://tophat.cbcb.umd.edu) and Cufflinks (v2.0.2, http://cufflinks.cbcb.umd.edu)
To correct for transcript length and depth of coverage raw paired-end sequenced reads were converted into fragments per kilobase of exon per million fragments sequenced (FPKM) resulting in the fpkm_tracking files.
Resultant fragments were aligned (mapped) to the reference genome build UCSC hg19 using Bowtie
Non-aligned reads were segmented using Tophat and re-aligned to the genome, aligning reads that span introns and determining junction splice sites. Cufflinks assembled reads into transcripts and assembled reads merged using Cuffmerge; the reads generated from a transcript are directly proportional to the transcripts relative abundance. For the analysis, Tophat (which automatically runs Bowtie) was run for each read pair in a given lane
For each read pair, Tophat produced one file which contained all reads mapped to the human_g1k_v37 genome and RefSeq (http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/refGene.txt.gz) transcriptome
This process was carried out independently for each sample lane. Before running Cufflinks, Samtools (v0.1.18.0, http://samtools.sourceforge.net) was used to merge each sample's independent Tophat results into one file. This file contains all the aligned reads for each read pair. Finally Cufflinks was run on the merged Tophat output to produce a file with FPKM values for each sample
Genome_build: UCSC hg19
Supplementary_files_format_and_content: fpkm_tracking files are text files that include the RefSeq gene ID and location, the FPKM value, high and low confidence and status.

source_name: oral biopsy

extract_protocol:
Total RNA from oral biopsies of nonsmokers and electroic cigarette vapers was extracted with TRIzol with subsequent RNA clean-up using the RNeasy MinElute RNA pu-rification kit to remove residual DNA
The TruSeq RNA Sample Prep Kit (Illumina, San Diego, CA) was utilized as per protocol to generate cDNA that was then purified with QIA-quick PCR purification kit (Qiagen, Valencia, CA)
Samples were loaded onto an Illumina flowcell for paired-end 101 x 2 sequencing reactions using the Illumina HiSeq 2000, using a single flow cell with 4 samples multiplexed per lane of flow cell.
HiSeq Control Software (Illumina) was used to perform image analysis, base calling and sequence analysis on HiSeq generated sequence images.

tag: smoking status

value: e cig vaper

value: oral biopsy


title: MOLM13, caRNA input, Ctrl, rep1

description: Library name: MOLM13, caRNA input, Ctrl, rep1


description: Library name: AT3G18990_F_vesca_Hawaii-4-F7_DAPi712D11-ORGi5034-96P220


title: HCT116 p53-/- ORC1 deletion, rep1 [RNAseq]

description: Library name: Sample4


title: SKM1, nascent RNA, 16hr 5azaC, rep3

description: Library name: SKM1, nascent RNA, 16hr 5azaC, rep3

value: 16hr 5azaC


title: DGM-13723 (mRNA-seq)


title: HCT116 p53-/- WT, rep2, control [RNAseq]

description: Library name: Sample2


title: SKM1, nascent RNA, 16hr 5azaC, rep2

description: Library name: SKM1, nascent RNA, 16hr 5azaC, rep2


title: DGM-13708 (mRNA-seq)


description: Library name: LOC_Os08g06110.3_F_vesca_Hawaii-4-F7_DAPi712D10-ORGi5034-96P247


title: HCT116 p53-/- WT, rep1, control [RNAseq]

description: Library name: Sample1


description: Library name: AL8G10650.t1_F_vesca_Hawaii-4-F7_DAPi712D09-ORGi5034-96P247


description: Library name: Carub.0003s1161.1.p_S_lycopersicum_Heinz-1706-BG_DAPi712G07-ORGi5039-96P247


title: SKM1, nascent RNA, 16hr 5azaC, rep1

description: Library name: SKM1, nascent RNA, 16hr 5azaC, rep1


title: DGM-13704 (mRNA-seq)


description: Library name: Carub.0008s0285.1_F_vesca_Hawaii-4-F7_DAPi712D08-ORGi5034-96P247


title: SKM1, nascent RNA, 8hr 5azaC, rep3

description: Library name: SKM1, nascent RNA, 8hr 5azaC, rep3

value: 8hr 5azaC


title: DGM-13681 (mRNA-seq)


description: Library name: AT5G03150_F_vesca_Hawaii-4-F7_DAPi712D08-ORGi5034-96P220


title: SKM1, nascent RNA, 8hr 5azaC, rep1

description: Library name: SKM1, nascent RNA, 8hr 5azaC, rep1


title: SKM1, nascent RNA, 8hr 5azaC, rep2

description: Library name: SKM1, nascent RNA, 8hr 5azaC, rep2


title: DGM-13680 (mRNA-seq)


description: Library name: AT1G69180_S_lycopersicum_Heinz-1706-BG_DAPi712G05-ORGi5039-96P220


description: Library name: AL4G38490.t1_S_lycopersicum_Heinz-1706-BG_DAPi712G08-ORGi5039-96P247


description: Library name: AT1G74480_F_vesca_Hawaii-4-F7_DAPi712D07-ORGi5034-96P220

value: RWPRK


title: DGM-13675 (mRNA-seq)


description: Library name: Solyc01g095460.3.1_F_vesca_Hawaii-4-F7_DAPi712D07-ORGi5034-96P247


title: DGM-13666 (mRNA-seq)


title: SKM1, nascent RNA, 4hr 5azaC, rep3

description: Library name: SKM1, nascent RNA, 4hr 5azaC, rep3

value: 4hr 5azaC


description: Library name: LOC_Os01g18240.1_S_lycopersicum_Heinz-1706-BG_DAPi712G04-ORGi5039-96P247


description: Library name: AT3G57920_F_vesca_Hawaii-4-F7_DAPi712D06-ORGi5034-96P220

value: SBP


description: Library name: AT1G46768_S_lycopersicum_Heinz-1706-BG_DAPi712G04-ORGi5039-96P220


description: Library name: AT2G01940_S_lycopersicum_Heinz-1706-BG_DAPi712G08-ORGi5039-96P220


title: DGM-13662 (mRNA-seq)


description: Library name: AT1G80840_S_lycopersicum_Heinz-1706-BG_DAPi712G03-ORGi5039-96P220

value: WRKY


title: DGM-13663 (mRNA-seq)


title: SKM1, nascent RNA, 4hr 5azaC, rep2

description: Library name: SKM1, nascent RNA, 4hr 5azaC, rep2


description: Library name: AT5G02320_S_lycopersicum_Heinz-1706-BG_DAPi712G06-ORGi5039-96P220

value: MYB


title: SKM1, nascent RNA, 4hr 5azaC, rep1

description: Library name: SKM1, nascent RNA, 4hr 5azaC, rep1


description: Library name: LOC_Os02g33430.1_F_vesca_Hawaii-4-F7_DAPi712D05-ORGi5034-96P247


description: Library name: AT5G19790_S_lycopersicum_Heinz-1706-BG_DAPi712G07-ORGi5039-96P220


description: Library name: AT2G01930_F_vesca_Hawaii-4-F7_DAPi712D05-ORGi5034-96P220

value: BBRBPC


title: DGM-13655 (mRNA-seq)


description: Library name: Carub.0001s1194.1_F_vesca_Hawaii-4-F7_DAPi712D03-ORGi5034-96P247

value: plant

value: NAC


description: Library name: AT3G50060_S_lycopersicum_Heinz-1706-BG_DAPi712G02-ORGi5039-96P220


title: SKM1, nascent RNA, 0hr 5azaC, rep3

description: Library name: SKM1, nascent RNA, 0hr 5azaC, rep3

value: 0hr 5azaC


title: DGM-13645 (mRNA-seq)


title: SKM1, nascent RNA, 0hr 5azaC, rep2

description: Library name: SKM1, nascent RNA, 0hr 5azaC, rep2


title: DGM-13644 (mRNA-seq)


title: DGM-13626 (mRNA-seq)


description: Library name: AT5G65410_F_vesca_Hawaii-4-F7_DAPi712D03-ORGi5034-96P220

value: ZFHD


description: Library name: AT1G18330_S_lycopersicum_Heinz-1706-BG_DAPi712G01-ORGi5039-96P220

value: MYBRELATED


title: MOLM13, nascent RNA, 16hr 5azaC, rep3

description: Library name: MOLM13, nascent RNA, 16hr 5azaC, rep3


title: MOLM13, nascent RNA, 16hr 5azaC, rep2

description: Library name: MOLM13, nascent RNA, 16hr 5azaC, rep2


description: Library name: AT1G76880_S_lycopersicum_Heinz-1706-BG_DAPi712F11-ORGi5039-96P220

value: TRIHELIX


description: Library name: Carub.0002s1646.1_F_vesca_Hawaii-4-F7_DAPi712C12-ORGi5034-96P247

value: HOMEOBOX


title: SKM1, nascent RNA, 0hr 5azaC, rep1

description: Library name: SKM1, nascent RNA, 0hr 5azaC, rep1


description: Library name: AT3G50260_F_vesca_Hawaii-4-F7_DAPi712D02-ORGi5034-96P220


title: MOLM13, nascent RNA, 16hr 5azaC, rep1

description: Library name: MOLM13, nascent RNA, 16hr 5azaC, rep1


description: Library name: AT1G12260_F_vesca_Hawaii-4-F7_DAPi712C12-ORGi5034-96P220


title: DGM-13563 (mRNA-seq)

value: e cig vaper


description: Library name: Carub.0008s0039.1_S_lycopersicum_Heinz-1706-BG_DAPi712F09-ORGi5039-96P247


description: Library name: AT2G45480_S_lycopersicum_Heinz-1706-BG_DAPi712F09-ORGi5039-96P220

value: GRF


description: Library name: AL2G32420.t2_S_lycopersicum_Heinz-1706-BG_DAPi712F10-ORGi5039-96P247


description: Library name: AT4G14770_S_lycopersicum_Heinz-1706-BG_DAPi712F10-ORGi5039-96P220

value: CPP


title: DGM-13506 (mRNA-seq)

value: oral biopsy


title: DGM-13493 (mRNA-seq)

value: nonsmoker


description: Library name: LOC_Os09g25060.1_S_lycopersicum_Heinz-1706-BG_DAPi712F11-ORGi5039-96P247


description: Library name: Carub.0001s3581.1.p_F_vesca_Hawaii-4-F7_DAPi712D01-ORGi5034-96P247


title: DGM-13624 (mRNA-seq)


title: MOLM13, nascent RNA, 8hr 5azaC, rep3

description: Library name: MOLM13, nascent RNA, 8hr 5azaC, rep3

value: 8hr 5azaC


title: DGM-13489 (mRNA-seq)


description: Library name: AT2G02820_S_lycopersicum_Heinz-1706-BG_DAPi712F08-ORGi5039-96P220


title: MOLM13, nascent RNA, 8hr 5azaC, rep1

description: Library name: MOLM13, nascent RNA, 8hr 5azaC, rep1


title: DGM-13484 (mRNA-seq)


description: Library name: Carub.0001s0116.1_F_vesca_Hawaii-4-F7_DAPi712C10-ORGi5034-96P247


title: MOLM13, nascent RNA, 4hr 5azaC, rep3

description: Library name: MOLM13, nascent RNA, 4hr 5azaC, rep3

value: 4hr 5azaC


description: Library name: XP_013586407.1_S_lycopersicum_Heinz-1706-BG_DAPi712F07-ORGi5039-96P247

value: BZIP


description: Library name: AL2G40550.t1_F_vesca_Hawaii-4-F7_DAPi712C11-ORGi5034-96P247

value: WRKY


title: MOLM13, nascent RNA, 4hr 5azaC, rep2

description: Library name: MOLM13, nascent RNA, 4hr 5azaC, rep2


description: Library name: AT5G52830_S_lycopersicum_Heinz-1706-BG_DAPi712F07-ORGi5039-96P220


title: DGM-13478 (mRNA-seq)


description: Library name: AT1G76420_F_vesca_Hawaii-4-F7_DAPi712C09-ORGi5034-96P220


description: Library name: AT2G45420_S_lycopersicum_Heinz-1706-BG_DAPi712F06-ORGi5039-96P220


title: DGM-13476 (mRNA-seq)


title: MOLM13, nascent RNA, 8hr 5azaC, rep2

description: Library name: MOLM13, nascent RNA, 8hr 5azaC, rep2


description: Library name: XP_013613838.1_F_vesca_Hawaii-4-F7_DAPi712C08-ORGi5034-96P247


title: MOLM13, nascent RNA, 4hr 5azaC, rep1

description: Library name: MOLM13, nascent RNA, 4hr 5azaC, rep1


title: DGM-13470 (mRNA-seq)


title: MOLM13, nascent RNA, 0hr 5azaC, rep3

description: Library name: MOLM13, nascent RNA, 0hr 5azaC, rep3


description: Library name: AT4G00730_F_vesca_Hawaii-4-F7_DAPi712C11-ORGi5034-96P220


description: Library name: AT4G25480_S_lycopersicum_Heinz-1706-BG_DAPi712F04-ORGi5039-96P220


title: MOLM13, nascent RNA, 0hr 5azaC, rep2

description: Library name: MOLM13, nascent RNA, 0hr 5azaC, rep2


description: Library name: AT5G60130_F_vesca_Hawaii-4-F7_DAPi712C07-ORGi5034-96P220


title: DGM-13469 (mRNA-seq)


description: Library name: Solyc06g048630.3.1_F_vesca_Hawaii-4-F7_DAPi712C09-ORGi5034-96P247


description: Library name: AT5G62470_F_vesca_Hawaii-4-F7_DAPi712C08-ORGi5034-96P220

value: MYB


title: DGM-13458 (mRNA-seq)


title: MOLM13, nascent RNA, 0hr 5azaC, rep1

description: Library name: MOLM13, nascent RNA, 0hr 5azaC, rep1


description: Library name: AT2G01060_S_lycopersicum_Heinz-1706-BG_DAPi712F05-ORGi5039-96P220

value: plant


description: Library name: LOC_Os01g46970.1_F_vesca_Hawaii-4-F7_DAPi712C07-ORGi5034-96P247


title: DGM-13445 (mRNA-seq)


description: Library name: AT4G31800_S_lycopersicum_Heinz-1706-BG_DAPi712F02-ORGi5039-96P220


description: Library name: Solyc08g079120.3.1_S_lycopersicum_Heinz-1706-BG_DAPi712F03-ORGi5039-96P247

value: NAC


title: K562, tetshIKZF1, RNA, Dox, 5azaC, rep3

description:
Library name: K562, tetshIKZF1, RNA, Dox, 5azaC, rep3
Geneid Chr Start End Strand Length Num

value: Dox, 5azaC


description: Library name: AT1G33240_S_lycopersicum_Heinz-1706-BG_DAPi712F03-ORGi5039-96P220


description: Library name: Solyc04g078640.3.1_S_lycopersicum_Heinz-1706-BG_DAPi712F01-ORGi5039-96P247


title: K562, tetshIKZF1, RNA, Dox, 5azaC, rep1

description:
Library name: K562, tetshIKZF1, RNA, Dox, 5azaC, rep1
Geneid Chr Start End Strand Length Num


title: DGM-13432 (mRNA-seq)


description: Library name: Solyc08g068320.3.1_F_vesca_Hawaii-4-F7_DAPi712C04-ORGi5034-96P247


description: Library name: AT3G27010_F_vesca_Hawaii-4-F7_DAPi712C04-ORGi5034-96P220

value: TCP


description: Library name: AT5G47390_S_lycopersicum_Heinz-1706-BG_DAPi712F01-ORGi5039-96P220

value: MYBRELATED


title: DGM-13430 (mRNA-seq)


title: DGM-13451 (mRNA-seq)


title: DGM-13418 (mRNA-seq)


title: K562, tetshIKZF1, RNA, Dox, Ctrl, rep3

description:
Library name: K562, tetshIKZF1, RNA, Dox, Ctrl, rep3
Geneid Chr Start End Strand Length Num

value: Dox, Ctrl


description: Library name: XP_013602769.1_F_vesca_Hawaii-4-F7_DAPi712C03-ORGi5034-96P247


title: K562, tetshIKZF1, RNA, Dox, Ctrl, rep2

description:
Library name: K562, tetshIKZF1, RNA, Dox, Ctrl, rep2
Geneid Chr Start End Strand Length Num


description: Library name: AT5G03790_F_vesca_Hawaii-4-F7_DAPi712C06-ORGi5034-96P220

value: HOMEOBOX


title: DGM-13409 (mRNA-seq)


description: Library name: Solyc05g007180.3.1_S_lycopersicum_Heinz-1706-BG_DAPi712E12-ORGi5039-96P247


description: Library name: Carub.0002s2670.1_S_lycopersicum_Heinz-1706-BG_DAPi712E11-ORGi5039-96P247


title: K562, tetshIKZF1, RNA, Dox, 5azaC, rep2

description:
Library name: K562, tetshIKZF1, RNA, Dox, 5azaC, rep2
Geneid Chr Start End Strand Length Num


title: DGM-13407 (mRNA-seq)


description:
Library name: K562, tetshIKZF1, RNA, Ctrl, 5azaC, rep3
Geneid Chr Start End Strand Length Num

value: Ctrl, 5azaC


description:
Library name: K562, tetshIKZF1, RNA, Ctrl, 5azaC, rep2
Geneid Chr Start End Strand Length Num


title: K562, tetshIKZF1, RNA, Dox, Ctrl, rep1

description:
Library name: K562, tetshIKZF1, RNA, Dox, Ctrl, rep1
Geneid Chr Start End Strand Length Num


description: Library name: AT1G27730_F_vesca_Hawaii-4-F7_DAPi712C01-ORGi5034-96P220


description: Library name: AT2G40620_F_vesca_Hawaii-4-F7_DAPi712B12-ORGi5034-96P220


description: Library name: Solyc10g005080.3.1_S_lycopersicum_Heinz-1706-BG_DAPi712E10-ORGi5039-96P247


description: Library name: AT1G69690_F_vesca_Hawaii-4-F7_DAPi712C02-ORGi5034-96P220


description: Library name: AT1G52880_S_lycopersicum_Heinz-1706-BG_DAPi712E12-ORGi5039-96P220


title: DGM-13367 (mRNA-seq)


description:
Library name: K562, tetshIKZF1, RNA, Ctrl, 5azaC, rep1
Geneid Chr Start End Strand Length Num


title: DGM-13387 (mRNA-seq)


description: Library name: Solyc07g040920.2.1_F_vesca_Hawaii-4-F7_DAPi712B11-ORGi5034-96P247


description: Library name: AT1G20980_S_lycopersicum_Heinz-1706-BG_DAPi712E11-ORGi5039-96P220

value: SBP


title: DGM-13362 (mRNA-seq)


description: Library name: AT4G17980_S_lycopersicum_Heinz-1706-BG_DAPi712E10-ORGi5039-96P220


title: K562, tetshIKZF1, RNA, Ctrl, Ctrl, rep3

description:
Library name: K562, tetshIKZF1, RNA, Ctrl, Ctrl, rep3
Geneid Chr Start End Strand Length Num

value: Ctrl, Ctrl


description: Library name: XP_013587350.1_F_vesca_Hawaii-4-F7_DAPi712B10-ORGi5034-96P247


description: Library name: XP_013615900.1_S_lycopersicum_Heinz-1706-BG_DAPi712E09-ORGi5039-96P247


title: DGM-13224 (mRNA-seq)

value: oral biopsy


description: Library name: XP_013589953.1_F_vesca_Hawaii-4-F7_DAPi712B12-ORGi5034-96P247


title: DGM-13206 (mRNA-seq)

value: nonsmoker


description: Library name: AT1G20910_F_vesca_Hawaii-4-F7_DAPi712B10-ORGi5034-96P220

value: ARID


description: Library name: LOC_Os03g21800.1_F_vesca_Hawaii-4-F7_DAPi712B09-ORGi5034-96P247


title: K562, tetshIKZF1, RNA, Ctrl, Ctrl, rep1

description:
Library name: K562, tetshIKZF1, RNA, Ctrl, Ctrl, rep1
Geneid Chr Start End Strand Length Num


title: DGM-12964 (mRNA-seq)

value: e cig vaper


title: MOLM13, tetshNSUN2, RNA, Dox, rep2

description:
Library name: MOLM13, tetshNSUN2, RNA, Dox, rep2
gene,baseMean,log2FoldChange,lfcSE,stat,pvalue,padj

value: Dox


description: Library name: AT1G79580_F_vesca_Hawaii-4-F7_DAPi712B09-ORGi5034-96P220


title: K562, tetshIKZF1, RNA, Ctrl, Ctrl, rep2

description:
Library name: K562, tetshIKZF1, RNA, Ctrl, Ctrl, rep2
Geneid Chr Start End Strand Length Num


description: Library name: AT5G56110_S_lycopersicum_Heinz-1706-BG_DAPi712E06-ORGi5039-96P220


description: Library name: AL8G13510.t2_F_vesca_Hawaii-4-F7_DAPi712B08-ORGi5034-96P247


description: Library name: AT2G18550_S_lycopersicum_Heinz-1706-BG_DAPi712E07-ORGi5039-96P220


description: Library name: AT5G14960_S_lycopersicum_Heinz-1706-BG_DAPi712E08-ORGi5039-96P220


title: MOLM13, tetshNSUN2, RNA, Dox, rep3

description:
Library name: MOLM13, tetshNSUN2, RNA, Dox, rep3
gene,baseMean,log2FoldChange,lfcSE,stat,pvalue,padj


title: MOLM13, tetshNSUN2, RNA, Dox, rep1

description:
Library name: MOLM13, tetshNSUN2, RNA, Dox, rep1
gene,baseMean,log2FoldChange,lfcSE,stat,pvalue,padj


description: Library name: AL3G23910.t2_S_lycopersicum_Heinz-1706-BG_DAPi712E07-ORGi5039-96P247

value: BZIP


description: Library name: XP_013631649.1_F_vesca_Hawaii-4-F7_DAPi712B05-ORGi5034-96P247


title: DGM-10123 (mRNA-seq)


description: Library name: AT3G60530_S_lycopersicum_Heinz-1706-BG_DAPi712E05-ORGi5039-96P220


title: DGM-12804 (mRNA-seq)


title: DGM-10500 (mRNA-seq)


title: MOLM13, tetshNSUN2, RNA, Ctrl, rep2

description:
Library name: MOLM13, tetshNSUN2, RNA, Ctrl, rep2
gene,baseMean,log2FoldChange,lfcSE,stat,pvalue,padj

value: Ctrl


description: Library name: AT4G25470_F_vesca_Hawaii-4-F7_DAPi712B06-ORGi5034-96P220

value: plant


description: Library name: Carub.0004s2898.1.p_F_vesca_Hawaii-4-F7_DAPi712B07-ORGi5034-96P247


description: Library name: AT5G62020_S_lycopersicum_Heinz-1706-BG_DAPi712E04-ORGi5039-96P220

value: HSF


title: DGM-01577 (mRNA-seq)


title: MOLM13, tetshNSUN2, RNA, Ctrl, rep1

description:
Library name: MOLM13, tetshNSUN2, RNA, Ctrl, rep1
gene,baseMean,log2FoldChange,lfcSE,stat,pvalue,padj


description: Library name: AT3G08500_F_vesca_Hawaii-4-F7_DAPi712B05-ORGi5034-96P220

value: MYB


description: Library name: LOC_Os02g42970.1_S_lycopersicum_Heinz-1706-BG_DAPi712E03-ORGi5039-96P247

value: NAC


description: Library name: AT5G64750_S_lycopersicum_Heinz-1706-BG_DAPi712E03-ORGi5039-96P220


title: DGM-01542 (mRNA-seq)


title: SKM1, RNA, 5azaC, rep3

description:
Library name: SKM1, RNA, 5azaC, rep3
gene,baseMean,log2FoldChange,lfcSE,stat,pvalue,padj


title: MOLM13, tetshNSUN2, RNA, Ctrl, rep3

description:
Library name: MOLM13, tetshNSUN2, RNA, Ctrl, rep3
gene,baseMean,log2FoldChange,lfcSE,stat,pvalue,padj


title: DGM-12941 (mRNA-seq)


title: SKM1, RNA, 5azaC, rep2

description:
Library name: SKM1, RNA, 5azaC, rep2
gene,baseMean,log2FoldChange,lfcSE,stat,pvalue,padj


description: Library name: AT1G13260_S_lycopersicum_Heinz-1706-BG_DAPi712E01-ORGi5039-96P220

value: RAV


description: Library name: LOC_Os06g07030.1_S_lycopersicum_Heinz-1706-BG_DAPi712E01-ORGi5039-96P247


title: DGM-00757 (mRNA-seq)


title: DGM-00926 (mRNA-seq)


description: Library name: AT3G56400_F_vesca_Hawaii-4-F7_DAPi712B02-ORGi5034-96P220

value: WRKY


description: Library name: AT1G29160_F_vesca_Hawaii-4-F7_DAPi712B04-ORGi5034-96P220


title: SKM1, RNA, 5azaC, rep1

description:
Library name: SKM1, RNA, 5azaC, rep1
gene,baseMean,log2FoldChange,lfcSE,stat,pvalue,padj


description: Library name: LOC_Os10g26500.1_S_lycopersicum_Heinz-1706-BG_DAPi712D12-ORGi5039-96P247

value: HOMEOBOX


title: DGM-00342 (mRNA-seq)


description: Library name: AL1G23550.t1_F_vesca_Hawaii-4-F7_DAPi712B03-ORGi5034-96P247


title: SKM1, RNA, Ctrl, rep3

description:
Library name: SKM1, RNA, Ctrl, rep3
gene,baseMean,log2FoldChange,lfcSE,stat,pvalue,padj


description: Library name: AT5G11260_S_lycopersicum_Heinz-1706-BG_DAPi712D12-ORGi5039-96P220


title: DGM-13723 (miRNA-seq)


description: Library name: AT5G67300_F_vesca_Hawaii-4-F7_DAPi712B01-ORGi5034-96P220


description: Library name: AL1G53260.t1_F_vesca_Hawaii-4-F7_DAPi712B01-ORGi5034-96P247


description: Library name: XP_013587997.1_S_lycopersicum_Heinz-1706-BG_DAPi712D11-ORGi5039-96P247


description: Library name: LOC_Os01g51154.1_F_vesca_Hawaii-4-F7_DAPi712A11-ORGi5034-96P247

value: MYBRELATED


title: DGM-13708 (miRNA-seq)


description: Library name: AL1G11460.t1_F_vesca_Hawaii-4-F7_DAPi712A10-ORGi5034-96P247


title: DGM-13704 (miRNA-seq)


description: Library name: AT3G18990_S_lycopersicum_Heinz-1706-BG_DAPi712D11-ORGi5039-96P220


title: MOLM13, RNA, 5azaC, rep3

description:
Library name: MOLM13, RNA, 5azaC, rep3
gene,baseMean,log2FoldChange,lfcSE,stat,pvalue,padj


title: DGM-13747 (miRNA-seq)


description: Library name: AL8G10650.t1_S_lycopersicum_Heinz-1706-BG_DAPi712D09-ORGi5039-96P247


title: SKM1, RNA, Ctrl, rep1

description:
Library name: SKM1, RNA, Ctrl, rep1
gene,baseMean,log2FoldChange,lfcSE,stat,pvalue,padj


title: MOLM13, RNA, 5azaC, rep2

description:
Library name: MOLM13, RNA, 5azaC, rep2
gene,baseMean,log2FoldChange,lfcSE,stat,pvalue,padj


description: Library name: Carub.0008s0285.1_S_lycopersicum_Heinz-1706-BG_DAPi712D08-ORGi5039-96P247


title: DGM-13681 (miRNA-seq)


title: SKM1, RNA, Ctrl, rep2

description:
Library name: SKM1, RNA, Ctrl, rep2
gene,baseMean,log2FoldChange,lfcSE,stat,pvalue,padj


description: Library name: Carub.0004s2291.1_F_vesca_Hawaii-4-F7_DAPi712A09-ORGi5034-96P247


title: DGM-13680 (miRNA-seq)


title: MOLM13, RNA, Ctrl, rep3

description:
Library name: MOLM13, RNA, Ctrl, rep3
gene,baseMean,log2FoldChange,lfcSE,stat,pvalue,padj


title: MOLM13, RNA, 5azaC, rep1

description:
Library name: MOLM13, RNA, 5azaC, rep1
gene,baseMean,log2FoldChange,lfcSE,stat,pvalue,padj


description: Library name: AT5G03150_S_lycopersicum_Heinz-1706-BG_DAPi712D08-ORGi5039-96P220


description: Library name: Solyc11g064950.3.1_F_vesca_Hawaii-4-F7_DAPi712A08-ORGi5034-96P247


title: MOLM13, RNA, Ctrl, rep2

description:
Library name: MOLM13, RNA, Ctrl, rep2
gene,baseMean,log2FoldChange,lfcSE,stat,pvalue,padj


description: Library name: XP_013631386.1_F_vesca_Hawaii-4-F7_DAPi712A07-ORGi5034-96P247


title: DGM-13675 (miRNA-seq)


description: Library name: AT1G74480_S_lycopersicum_Heinz-1706-BG_DAPi712D07-ORGi5039-96P220

value: RWPRK


description: Library name: Solyc01g095460.3.1_S_lycopersicum_Heinz-1706-BG_DAPi712D07-ORGi5039-96P247


description: Library name: AT4G25490_F_vesca_Hawaii-4-F7_DAPi712A08-ORGi5034-96P220


title: DGM-13663 (miRNA-seq)


title: MOLM13, RNA, Ctrl, rep1

description:
Library name: MOLM13, RNA, Ctrl, rep1
gene,baseMean,log2FoldChange,lfcSE,stat,pvalue,padj


description: Library name: LOC_Os08g06110.3_S_lycopersicum_Heinz-1706-BG_DAPi712D10-ORGi5039-96P247


title: SKM1, tetshNSUN2, SRSF2, Dox, rep2

description: Library name: SKM1, tetshNSUN2, SRSF2, Dox, rep2

data_processing:
Adapters were trimmed by cutadapt -m 20 T -A CTGTCTCTTATACACATCT. Reads after adapter trimming were uploaded. Samples were mapped by bowtie2 and deduplicated by picard MarkDuplicates. Peaks were called by macs3 callpeak. For histone modifications, broad peaks were identified using the parameters “--broad --broad-cutoff 0.01” was used. Differential peak analysis was conducted using DiffBind.
Assembly: hg38, mm10
Supplementary files format and content: bw, averaged bigwig file
Library strategy: CUT&Tag

extract_protocol:
CUT&Tag was performed using the CUT&Tag-IT Assay Kit (Active motif, 53160) following the manufacturer’s instructions. 0.2 million cells were used per sample. For 5-azaC-treated CUT&Tag profiling of H2AK119ub and H3K27ac, 4,000 drosophila nuclei (Active motif, 53168) were added as a spike-in control. Primary antibodies used included 1 μL H2AK119ub antibody (Cell Signaling Technology, 8240S), 1 μL H3K27ac antibody (Active motif, 39034) or 0.25 μL SRSF2 antibody (Abcam, ab11826).
Libraries were constructed according to the kit protocol and sequenced on the Illumina NovaSeqX platform with pair-end 150 bp reads.


title: DGM-13662 (miRNA-seq)


title: SKM1, tetshNSUN2, SRSF2, Dox, rep1

description: Library name: SKM1, tetshNSUN2, SRSF2, Dox, rep1


description: Library name: AT5G05550_F_vesca_Hawaii-4-F7_DAPi712A10-ORGi5034-96P220

value: TRIHELIX


title: DGM-13655 (miRNA-seq)

value: oral biopsy


description: Library name: AT3G12250_F_vesca_Hawaii-4-F7_DAPi712A07-ORGi5034-96P220


description: Library name: AT3G57920_S_lycopersicum_Heinz-1706-BG_DAPi712D06-ORGi5039-96P220

value: SBP


title: DGM-13644 (miRNA-seq)


title: SKM1, tetshNSUN2, SRSF2, Ctrl, rep2

description: Library name: SKM1, tetshNSUN2, SRSF2, Ctrl, rep2


description: Library name: AT2G01930_S_lycopersicum_Heinz-1706-BG_DAPi712D05-ORGi5039-96P220

value: BBRBPC


title: DGM-13624 (miRNA-seq)

value: e cig vaper


title: SKM1, tetshNSUN2, SRSF2, Ctrl, rep1

description: Library name: SKM1, tetshNSUN2, SRSF2, Ctrl, rep1


description: Library name: AT5G10030_F_vesca_Hawaii-4-F7_DAPi712A06-ORGi5034-96P220


description: Library name: AT1G49480_F_vesca_Hawaii-4-F7_DAPi712A04-ORGi5034-96P220

value: REM


title: SKM1, tetshNSUN2, H3K27ac, Dox, rep3

description: Library name: SKM1, tetshNSUN2, H3K27ac, Dox, rep3

value: Dox


description: Library name: LOC_Os02g33430.1_S_lycopersicum_Heinz-1706-BG_DAPi712D05-ORGi5039-96P247


title: DGM-13493 (miRNA-seq)

value: nonsmoker


title: SKM1, tetshNSUN2, H3K27ac, Dox, rep2

description: Library name: SKM1, tetshNSUN2, H3K27ac, Dox, rep2


description: Library name: AT5G65410_S_lycopersicum_Heinz-1706-BG_DAPi712D03-ORGi5039-96P220

value: plant

value: ZFHD


description: Library name: Carub.0001s1194.1_S_lycopersicum_Heinz-1706-BG_DAPi712D03-ORGi5039-96P247


title: SKM1, tetshNSUN2, H3K27ac, Dox, rep1

description: Library name: SKM1, tetshNSUN2, H3K27ac, Dox, rep1


description: Library name: AT1G69780_F_vesca_Hawaii-4-F7_DAPi712A03-ORGi5034-96P220


title: DGM-13484 (miRNA-seq)


title: DGM-13489 (miRNA-seq)


description: Library name: AT5G39760_F_vesca_Hawaii-4-F7_DAPi712A02-ORGi5034-96P220


description: Library name: LOC_Os08g37970.1_F_vesca_Hawaii-4-F7_DAPi712A06-ORGi5034-96P247

value: MYB


title: SKM1, tetshNSUN2, H3K27ac, Ctrl, rep3

description: Library name: SKM1, tetshNSUN2, H3K27ac, Ctrl, rep3

value: Ctrl


description: Library name: AT3G50260_S_lycopersicum_Heinz-1706-BG_DAPi712D02-ORGi5039-96P220


title: LK, RNA, 5azaC, rep3

description:
Library name: LK, RNA, 5azaC, rep3
gene,baseMean,log2FoldChange,lfcSE,stat,pvalue,padj

organism: Mus musculus

source_name: Bone marrow

value: Bone marrow

value: Lin(minus)Kit(plus)


description: Library name: Carub.0002s1646.1_S_lycopersicum_Heinz-1706-BG_DAPi712C12-ORGi5039-96P247

value: HOMEOBOX


title: LK, RNA, 5azaC, rep2

description:
Library name: LK, RNA, 5azaC, rep2
gene,baseMean,log2FoldChange,lfcSE,stat,pvalue,padj


title: DGM-13478 (miRNA-seq)


title: SKM1, tetshNSUN2, H3K27ac, Ctrl, rep2

description: Library name: SKM1, tetshNSUN2, H3K27ac, Ctrl, rep2


title: LK, RNA, 5azaC, rep1

description:
Library name: LK, RNA, 5azaC, rep1
gene,baseMean,log2FoldChange,lfcSE,stat,pvalue,padj


description: Library name: AT1G12260_S_lycopersicum_Heinz-1706-BG_DAPi712C12-ORGi5039-96P220

value: NAC


title: DGM-13506 (miRNA-seq)


title: SKM1, tetshNSUN2, H3K27ac, Ctrl, rep1

description: Library name: SKM1, tetshNSUN2, H3K27ac, Ctrl, rep1


title: DGM-13470 (miRNA-seq)


description: Library name: AL2G40550.t1_S_lycopersicum_Heinz-1706-BG_DAPi712C11-ORGi5039-96P247

value: WRKY


description: Library name: AT5G62940_F_vesca_Hawaii-4-F7_DAPi712A05-ORGi5034-96P220


title: DGM-13451 (miRNA-seq)


title: LK, RNA, Ctrl, rep3

description:
Library name: LK, RNA, Ctrl, rep3
gene,baseMean,log2FoldChange,lfcSE,stat,pvalue,padj


title: SKM1, SRSF2, 5azaC, rep2

description: Library name: SKM1, SRSF2, 5azaC, rep2


title: DGM-13469 (miRNA-seq)


description: Library name: AT4G00730_S_lycopersicum_Heinz-1706-BG_DAPi712C11-ORGi5039-96P220


description: Library name: Carub.0001s0116.1_S_lycopersicum_Heinz-1706-BG_DAPi712C10-ORGi5039-96P247

value: MYBRELATED


title: LK, RNA, Ctrl, rep1

description:
Library name: LK, RNA, Ctrl, rep1
gene,baseMean,log2FoldChange,lfcSE,stat,pvalue,padj


description: Library name: Solyc06g048630.3.1_S_lycopersicum_Heinz-1706-BG_DAPi712C09-ORGi5039-96P247

value: BZIP


title: SKM1, SRSF2, 5azaC, rep1

description: Library name: SKM1, SRSF2, 5azaC, rep1


title: DGM-13432 (miRNA-seq)

value: oral biopsy


title: DGM-13445 (miRNA-seq)


title: LK, H2AK119ub, 5azaC, rep3

description: Library name: LK, H2AK119ub, 5azaC, rep3


title: SKM1, SRSF2, Ctrl, rep2

description: Library name: SKM1, SRSF2, Ctrl, rep2


description: Library name: AT1G76420_S_lycopersicum_Heinz-1706-BG_DAPi712C09-ORGi5039-96P220


title: LK, H2AK119ub, 5azaC, rep2

description: Library name: LK, H2AK119ub, 5azaC, rep2


title: DGM-13430 (miRNA-seq)


title: SKM1, H3K27ac, 5azaC, rep3

description: Library name: SKM1, H3K27ac, 5azaC, rep3


description: Library name: XP_013613838.1_S_lycopersicum_Heinz-1706-BG_DAPi712C08-ORGi5039-96P247


title: DGM-13418 (miRNA-seq)


title: DGM-13409 (miRNA-seq)


title: LK, RNA, Ctrl, rep2

description:
Library name: LK, RNA, Ctrl, rep2
gene,baseMean,log2FoldChange,lfcSE,stat,pvalue,padj


title: LK, H2AK119ub, Ctrl, rep3

description: Library name: LK, H2AK119ub, Ctrl, rep3


title: DGM-13407 (miRNA-seq)


title: SKM1, SRSF2, Ctrl, rep1

description: Library name: SKM1, SRSF2, Ctrl, rep1


description: Library name: AT5G62470_S_lycopersicum_Heinz-1706-BG_DAPi712C08-ORGi5039-96P220


description: Library name: LOC_Os01g46970.1_S_lycopersicum_Heinz-1706-BG_DAPi712C07-ORGi5039-96P247


title: LK, H2AK119ub, Ctrl, rep2

description: Library name: LK, H2AK119ub, Ctrl, rep2


description: Library name: Carub.0001s3581.1.p_S_lycopersicum_Heinz-1706-BG_DAPi712D01-ORGi5039-96P247


title: SKM1, H3K27ac, 5azaC, rep1

description: Library name: SKM1, H3K27ac, 5azaC, rep1


title: LK, H2AK119ub, 5azaC, rep1

description: Library name: LK, H2AK119ub, 5azaC, rep1


title: SKM1, H3K27ac, Ctrl, rep2

description: Library name: SKM1, H3K27ac, Ctrl, rep2


title: DGM-13387 (miRNA-seq)


title: DGM-13367 (miRNA-seq)


description: Library name: AT5G03790_S_lycopersicum_Heinz-1706-BG_DAPi712C06-ORGi5039-96P220


title: LK, H2AK119ub, Ctrl, rep1

description: Library name: LK, H2AK119ub, Ctrl, rep1


title: SKM1, H3K27ac, Ctrl, rep3

description: Library name: SKM1, H3K27ac, Ctrl, rep3


title: DGM-13362 (miRNA-seq)


title: SKM1, H3K27ac, 5azaC, rep2

description: Library name: SKM1, H3K27ac, 5azaC, rep2


title: SET7KO-4

city: Zurich

first: Genome

last: Informatics

address: Winterthurerstrasse 190

department: Functional Genomics Center Zurich (FGCZ)

country: Switzerland

institute: ETH ZURICH / University of Zurich

description: Library name: WT4

data_processing:
RNA-seq reads were pseudoaligned with Kallisto using the genome build GENCODE Mus musculus GRCh39 Release M31
Assembly: GRCm39
Supplementary files format and content: Kallisto transcript text files

source_name: Heart

extract_protocol:
RNA was extracted using the QIAGEN Rneasy Mini kit (50) (Cat.No - 74104). 3 micro gram of RNA was send to FGCZ, Zurich for the library preparation and sequencing.
RNA was extracted using the QIAGEN RNA extraction kit following manufacturer’s protocol. Extracted RNA was prepared for sequencing using the Illumina Truseq mRNA Library assay following manufacturer’s protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Heart

value: cardiomyocytes

value: SETD7 c-SETD7-/-


description: Library name: Solyc08g068320.3.1_S_lycopersicum_Heinz-1706-BG_DAPi712C04-ORGi5039-96P247


title: SET7KO-3

description: Library name: WT3


title: MOLM13, H3K27ac, 5azaC, rep3

description: Library name: MOLM13, H3K27ac, 5azaC, rep3


description: Library name: XP_013602769.1_S_lycopersicum_Heinz-1706-BG_DAPi712C03-ORGi5039-96P247


title: SKM1, H3K27ac, Ctrl, rep1

description: Library name: SKM1, H3K27ac, Ctrl, rep1


title: SET7KO-2

description: Library name: WT2


title: MOLM13, H3K27ac, 5azaC, rep1

description: Library name: MOLM13, H3K27ac, 5azaC, rep1


title: SET7KO-1

description: Library name: WT1


description: Library name: AT3G27010_S_lycopersicum_Heinz-1706-BG_DAPi712C04-ORGi5039-96P220

value: TCP


title: MOLM13, H3K27ac, Ctrl, rep3

description: Library name: MOLM13, H3K27ac, Ctrl, rep3


title: DGM-12964 (miRNA-seq)

value: e cig vaper


description: Library name: AT1G69690_S_lycopersicum_Heinz-1706-BG_DAPi712C02-ORGi5039-96P220

value: plant


description: Library name: AT5G60130_S_lycopersicum_Heinz-1706-BG_DAPi712C07-ORGi5039-96P220


title: MOLM13, H3K27ac, Ctrl, rep2

description: Library name: MOLM13, H3K27ac, Ctrl, rep2


title: DGM-12941 (miRNA-seq)

value: nonsmoker


title: MOLM13, H3K27ac, Ctrl, rep1

description: Library name: MOLM13, H3K27ac, Ctrl, rep1


title: B6-ND3

description: Library name: ND3

value: SETD7 fl/fl


title: DGM-12804 (miRNA-seq)


title: DGM-13224 (miRNA-seq)


description: Library name: XP_013589953.1_S_lycopersicum_Heinz-1706-BG_DAPi712B12-ORGi5039-96P247


title: B6-ND4

description: Library name: ND4


title: MOLM13, H3K27ac, 5azaC, rep2

description: Library name: MOLM13, H3K27ac, 5azaC, rep2


title: B6-ND2

description: Library name: ND2


description: Library name: AT2G40620_S_lycopersicum_Heinz-1706-BG_DAPi712B12-ORGi5039-96P220


title: MOLM13, H2AK119ub, 5azaC, rep3

description: Library name: MOLM13, H2AK119ub, 5azaC, rep3


title: B6-ND1

description: Library name: ND1


title: DGM-10500 (miRNA-seq)


title: DGM-01577 (miRNA-seq)


description: Library name: XP_013587350.1_S_lycopersicum_Heinz-1706-BG_DAPi712B10-ORGi5039-96P247


title: MOLM13, H2AK119ub, 5azaC, rep1

description: Library name: MOLM13, H2AK119ub, 5azaC, rep1


title: MOLM13, H2AK119ub, 5azaC, rep2

description: Library name: MOLM13, H2AK119ub, 5azaC, rep2


title: DGM-01542 (miRNA-seq)


title: DGM-00757 (miRNA-seq)


title: DGM-13206 (miRNA-seq)


description: Library name: LOC_Os03g21800.1_S_lycopersicum_Heinz-1706-BG_DAPi712B09-ORGi5039-96P247


description: Library name: AT1G20910_S_lycopersicum_Heinz-1706-BG_DAPi712B10-ORGi5039-96P220

value: ARID


title: DGM-00926 (miRNA-seq)


title: B6-HFD2

description: Library name: HFD2


description: Library name: Solyc07g040920.2.1_S_lycopersicum_Heinz-1706-BG_DAPi712B11-ORGi5039-96P247


title: B6-HFD1

description: Library name: HFD1


title: MOLM13, H2AK119ub, Ctrl, rep2

description: Library name: MOLM13, H2AK119ub, Ctrl, rep2

value: Ctrl


description: Library name: AT1G79580_S_lycopersicum_Heinz-1706-BG_DAPi712B09-ORGi5039-96P220


title: MOLM13, H2AK119ub, Ctrl, rep1

description: Library name: MOLM13, H2AK119ub, Ctrl, rep1


title: DGM-00342 (miRNA-seq)


title: SET7KO-HFD4

description: Library name: HFD-KO4


title: B6-HFD4

description: Library name: HFD4


description: Library name: Carub.0004s2898.1.p_S_lycopersicum_Heinz-1706-BG_DAPi712B07-ORGi5039-96P247


title: 4T1p

city: Kfar Sava

first: Sapir

last: Levin

address: Adam Yekutiel 7

country: Israel

institute: Technion

description: Library name: Sample 1

library_source: transcriptomic single cell

data_processing:
Cellranger
Assembly: mm10
Supplementary files format and content: Compressed Matrix Market format (a sparse matrix format)
Supplementary files format and content: Tab-separated values, compressed with gzip.

source_name: mammary fat pad

extract_protocol:
GR-1⁺ cells were then isolated by positive selection using the EasySep Mouse PE Positive Selection Kit (BioLegend), according to the manufacturer’s instructions. Purified GR-1⁺ cells were washed in PBS containing 0.04% BSA to minimize cell clumping and resuspended at a concentration of 1,000 cells/µL in PBS. RNA was immediately extracted.
cells were processed using the 10x Genomics Chromium platform for single-cell sequencing. Library preparation was performed using the Chromium Single Cell 3′ Library & Gel Bead Kit v3 (10x Genomics).

value: mammary fat pad

value: Myeloid cells


title: SET7KO-HFD3

description: Library name: HFD-KO3


title: 4T1m

description: Library name: Sample 2


description: Library name: AT1G27730_S_lycopersicum_Heinz-1706-BG_DAPi712C01-ORGi5039-96P220


description: Library name: AL8G13510.t2_S_lycopersicum_Heinz-1706-BG_DAPi712B08-ORGi5039-96P247


title: T cells, ABE9 edited, pAKT/pS6 high, Donor 3

first: Zachary

last: Walsh

state: New York

address: 650 West 168th Street, Rm 1708

department: Hematology/Oncology

institute: Columbia University

description:
Library name: D3_ABE9_AKTS6hi
pAKT/pS6 screen (ABE9)

data_processing:
.bases files were converted to FASTQ and samples were demultiplexed using Element's Bases2Fastq platform.
FASTQ files were trimmed with Cutadapt with the input: CTTGTGGAAAGGACGAAACACCG.
sgRNA enrichment analysis was performed using MAGeCK. For each sample, MAGeCK’s ‘count’ command was used to determine the number of sequencing reads mapped to each sgRNA. Across all sequenced samples, the mean reads per sample was 5,613,368 (range 2,842,507 to 9,279,031), mean percent of reads mapping to the sgRNA dictionary was 89.5% (range 88.0% to 91.7%), and mean Gini index was 0.066 (range 0.040 to 0.097).
MAGeCK’s ‘test’ command with default parameters was used to determine enriched and depleted guides in “treated” versus “control” conditions. For the pAKT/pS6 screen, “control” was defined as the pAKT/pS6-negative sort bin and “treated” was defined as the pAKT/pS6-high sort bin. For the proliferation screen, “control” was defined as a sampling timepoint immediately post-base editing and “treated” was defined as a sampling timepoint 14 days after T cell re-expansion. sgRNAs with low coverage (defined as MAGeCK median normalized read count <30 in the control group) were filtered from downstream analyses. A two-sided MAGeCK P value cutoff rather than a log2(fold change) cutoff was used to score significance to incorporate consideration of both sgRNA effect size and read count. sgRNAs were scored as significant if the MAGeCK two-sided P value was < 0.05.
Assembly: The custom sgRNA dictionary file was used to map sgRNA read counts per sample in MAGeCK count.
Supplementary files format and content: Raw sgRNA count outputs form MAGeCK count for each sample.
Library strategy: CRISPR Screen

source_name: Primary Human T cells

growth_protocol: All T cell cultures were performed with OpTmizer SFM (Gibco #A1048501) supplemented with 1:40 OpTmizer Supplement (Gibco #A1048501), 1:100 GlutaMAX (Gibco #35050061), and 300 IU/ml IL-2 (Chiron) using a humidified incubator at 37 °C with 5% CO2.

extract_protocol:
For unfixed samples (proliferation screen), DNA was extracted from library-edited T cells using a DNeasy Blood & Tissue Kit (Qiagen, #69504) per to the manufacturer’s protocols with buffer AL, and eluted in 100 µl buffer EB (Qiagen, #19086) per 5e6 T cells. For fixed samples (pAKT/pS6 screen), DNA was extracted as above with the following modification: samples were incubated overnight at 65 °C in buffer AL and proteinase K with shaking at 1000 RPM.
Sample amplification and indexing PCR was performed with ExTaq polymerase (Takara Bio, #RR001A): for unfixed and unsorted samples, 10 µg gDNA input per 100 µl PCR with 24 cycles; for fixed samples, 1µg gDNA input per 100 µl PCR with 24 cycles. Each gDNA sample was split across 8 parallel PCRs and then products were pooled after PCR to minimize library skewing. Pooled PCR products for each sample were cleaned up with 1x SPRI, quantified by D5000 Tapestation (Agilent, #5067-5588), and then pooled targeting 1000x read coverage per sgRNA per library and sequenced with a CloudBreak Freestyle Kit (Element Biosciences, #860-00015), 75 bp Read 1, 8 bp Index 1 on an Element AVITI sequencer (Element Bioscience).

treatment_protocol: Proliferation screen: T cells were restimulated with Immunocult CD3/CD28/CD2 T cell activation cocktail and expanded in G-REX 6-well plates for 14 days. Every 2-4 days, IL-2 and media were refreshed. After 14 days, T cells were harvested for DNA extraction and sequencing. AKT/S6 Screen: A total of 100e6 library-edited T cells per donor were stimulated in 96-well plates (with crosslinked anti-CD3/CD28 antibodies) for 20 minutes with approximately 1e6 T cells per well, to ensure high library coverage. Cells were then fixed, permeabilized, and stained with anti-pAKT (pS473) and anti-pS6 (pS235/pS236). Cells were sorted using an MA-900 cell sorter (Sony) with the 100µm nozzle, binned into the top 15% and bottom 15% of pAKT/pS6 expression, and collected in FACS buffer. Following the sort, the DNA extraction protocol was immediately initiated.

value: Primary Human T cells

value: Base edited (PIK3CD/PIK3R1 library)

value: Transduced, edited (ABE9), acutely stimulated, pAKT/pS6-sorted

tag: batch

value: Day 11


title: T cells, ABE9 edited, pAKT/pS6 negative, Donor 3

description:
Library name: D3_ABE9_AKTS6neg
pAKT/pS6 screen (ABE9)


title: MOLM13, H2AK119ub, Ctrl, rep3

description: Library name: MOLM13, H2AK119ub, Ctrl, rep3


title: T cells, ABE9 edited, pAKT/pS6 high, Donor 2

description:
Library name: D2_ABE9_AKTS6hi
pAKT/pS6 screen (ABE9)


title: SET7KO-HFD1

description: Library name: HFD-KO1


title: T cells, ABE9 edited, pAKT/pS6 negative, Donor 2

description:
Library name: D2_ABE9_AKTS6neg
pAKT/pS6 screen (ABE9)


title: E12.5_SB_rep1, SB431542, 1 day

city: New Orleans

first: Qinghuang

last: Tang

state: LA

address: 2000 Percival Stern Hall

department: Cell and Molecular Biology

institute: Tulane University

description:
Library name: E12.5_SB_rep1
E12.5_SB.bw

data_processing:
Basecalls were performed using bcl-convert for Illumina NextSeq 500 and NovaSeq 6000 outputs.
The RNA-seq sequencing reads were mapped to the mm10 transcriptome using Salmon quant for quantification of gene expression at transcript level (Patro et al., 2017). Salmon quantification files were then imported into R with the tximport package (Soneson et al., 2015) to summarize gene-level expression.
RNA-seq reads were mapped to the mm10 transcriptome using Salmon quant (Patro et al., 2017), then imported into R with tximport (Soneson et al., 2015) for gene-level expression quantification.
Differentially expressed genes were identified using DESeq2 (Love et al., 2014).
For UCSC genome browser visualization, RNA-seq reads were aligned to the mouse reference genome (mm10) using Hisat2 (Kim et al., 2019), merged between replicates with samtools (Li et al., 2009), and converted to bigwig format using deepTools bamCoverage (Ramirez et al., 2016).
Assembly: mm10
Supplementary files format and content: Text files contain raw counts for each sample
Supplementary files format and content: BigWig files display RNA-seq read coverage signals for each group, showing RNA expression levels.

growth_protocol: The E12.5 and E13.5 molar tooth germs dissected from BRE-GFP mouse embryos were cultured in vitro in the DMEM supplemented with 10% FBS (Cytiva) and GlutaMAX™-1 (Gibco).

extract_protocol:
Total RNAs were extracted using the RNeasy Micro Plus Kit (Qiagen), quantified using a Qubit 2.0 Fluorometric Quantitation system (Life Technologies), and then subjected to RNA-seq library construction.
RNA-seq libraries were constructed using the SMARTer Universal Low Input RNA Kit (Takara Bio) and the TruSeq RNA Sample Preparation Kit v2 (Illumina) following the manufacturer's protocols.

treatment_protocol: The in vitro cultured molar tooth germs at indicated stages were treated with DMSO, SB431542 (Sigma-Aldrich) or SIS3 (Tocris Bioscience) for 1 day, and then were subjected to subsequent RNA-seq assays.

tag: library preparation

value: SMARTer Universal Low Input RNA Kit

value: BRE-GFP

value: 1 day


title: SET7KO-HFD2

description: Library name: HFD-KO2

value: Heart

value: cardiomyocytes

value: SETD7 c-SETD7-/-


description: Library name: AT3G08500_S_lycopersicum_Heinz-1706-BG_DAPi712B05-ORGi5039-96P220

value: plant

value: MYB


title: E12.5_SB_rep2, SB431542, 1 day

description:
Library name: E12.5_SB_rep2
E12.5_SB.bw


title: E12.5_con_rep1, DMSO, 1 day

description:
Library name: E12.5_con_rep1
E12.5 control datasets were used for identification of differentially expressed genes induced by either SIS3 or SB431542 treatments.
E12.5_con.bw

value: DMSO


title: SPF Lactation

city: La Jolla

first: Jingting

last: Yu

address: 10010 N Torrey Pines Rd

institute: Salk Institute for Biological Studies

description: Library name: SPF_Lact_S1

data_processing:
Raw data were demultiplxed with CellRanger and preprocessed with Seurat to generate the RDS files.
Assembly: mm10
Supplementary files format and content: Serat objects saved in RDS format (generated by R)

source_name: mammary gland

extract_protocol:
Mammary glands were isolated in 2% FBS DMEM, minced, treated with collagenase type 2 and digested at 37 degrees in a shaking water bath. The small intestines and colons were collected in 2% FBS RPMI and treated with 1mM DTT and 20mM EDTA at 37 degrees for 15 mins then minced and dissociated in collagenase type 2 with constant stirring at 37 for 40 minutes. Spleen and thymus were collected in 2% FBS RPMI and mechanically disrupted. All samples were filtered and washed in 2% FBS DMEM. All organs, other than spleen, underwent red blood cell lysis and additional washing to obtain a single cell suspension.
The libraries were prepared by following the official protocols using 10X 5' Immune Profiling Kit and Chromium Single Cell 3' Reagent Kit.

value: mammary gland

value: Epithelial cells and CD45+ cells enriched with TCRB+ cells

tag: library type

value: mRNA


title: SPF Nulliparous

description: Library name: SPF_Virgin_S2


title: Germfree Nulliparous

description: Library name: GF_Virgin_S4

value: germfree


title: E12.5_con_rep2, DMSO, 1 day

description:
Library name: E12.5_con_rep2
E12.5 control datasets were used for identification of differentially expressed genes induced by either SIS3 or SB431542 treatments.
E12.5_con.bw


title: T cells, ABE9 edited, pAKT/pS6 negative, Donor 1

description:
Library name: D1_ABE9_AKTS6neg
pAKT/pS6 screen (ABE9)

value: Primary Human T cells


description: Library name: AT1G29160_S_lycopersicum_Heinz-1706-BG_DAPi712B04-ORGi5039-96P220


title: E13.5_con_rep2, DMSO, 1 day

description: Library name: E13.5_con_rep2


description: Library name: AL1G23550.t1_S_lycopersicum_Heinz-1706-BG_DAPi712B03-ORGi5039-96P247

value: NAC


title: Germfree Lactation

description: Library name: GF_Lact_S3


description: Library name: AT3G56400_S_lycopersicum_Heinz-1706-BG_DAPi712B02-ORGi5039-96P220

value: WRKY


title: AJ2 Antibody

description: Library name: AJ2_CSP_S4

library_source: other

molecule: protein

source_name: multiple tissues

value: multiple tissues

value: CD3+  Tcell

value: Protein

tag: hashid

value: TotalSeq C1=Lactating thymus; C2=Virgin thymus; C3=Lactating spleen; C4=virgins spleen; C5=lactating small intestine; C6=virgins small intestine; C7=lactating colon; C8=virgin colon; C9=lactating mammary gland; C10=virgin mammary gland;


title: T cells, ABE9 edited, baseline, Donor 1

description:
Library name: D1_ABE9_baseline
Control for baseline sgRNA library distribution immediately post-editing (ABE9)

value: Base edited (PIK3CD/PIK3R1 library)

value: Transduced, edited (ABE9)

value: Day 4


title: E13.5_con_rep1, DMSO, 1 day

description: Library name: E13.5_con_rep1

value: SMARTer Universal Low Input RNA Kit

value: BRE-GFP

value: 1 day


title: MOG microglia TAM4

city: Bethesda

first: Anup

last: Dey

address: 9000 Rockville Pike

department: DDB

institute: NIH/NICHD

data_processing:
RNA-seq data was analyzed using CCBR pipeliner and RENEE (RNA sequencing analysis pipeline).
These pipelines allowed determination of sequence quality before and after adaptor trimming (Fastqc), adaptor trimming (Cutadapt), align reads against reference genome (STAR), convert STAR aligned bam file into forward and reverse strand bigwigs, suitable for genome track viewer,
Pipelines include quantification of gene expression (RSEM) and differential expression profiling (DESeq2, edgeR)
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes TPM values for each sample
Supplementary files format and content: BigWig files for each sample

source_name: Microglia

growth_protocol: Tamoxifen 2mg/mouse was injected intraperitoneally  at 7-8 weeks old female mice

extract_protocol:
10,000 to 40,000 Mononuclear cells were prepared from brain and spinal cord using percoll gradient. CD11b/CD45/TMEM119 postive microglia cells were FACS sorted. Total RNA was extracted using Trizol/chloroform. RNA was precipitated with isopropanol, washed with ETOH, dried and subjected for library preparation.
For library preparation from small input RNA, Smart-Seq v4 RNA-seq library kit was used  Nexttera XT-DNA library prep kit was used for Adaptor ligation and library normalization.

treatment_protocol: For active immunization 11-12 weeks old Mice were immunized with MOG35-55/CFA and PTX following the instruction of Hooke laboratory (http://hooklabs.com)

value: Microglia

value: MOG immunized-Tamoxifen


description: Library name: AT4G25470_S_lycopersicum_Heinz-1706-BG_DAPi712B06-ORGi5039-96P220

value: plant


title: AJ2 V(D)J

description: Library name: AJ2_VDJ_S6

molecule: other

value: V(D)J


description: Library name: AT5G67300_S_lycopersicum_Heinz-1706-BG_DAPi712B01-ORGi5039-96P220

value: MYB


title: T cells, ABE8e edited, pAKT/pS6 high, Donor 3

description:
Library name: D3_ABE8e_AKTS6hi
pAKT/pS6 screen (ABE8e)

value: Primary Human T cells

value: Transduced, edited (ABE8e), acutely stimulated, pAKT/pS6-sorted

value: Day 11


title: AJ2 GEX

description: Library name: AJ2_GEX_S2

value: multiple tissues

value: CD3+  Tcell

value: mRNA


title: MOG microglia TAM2


title: T cells, ABE8e edited, pAKT/pS6 negative, Donor 3

description:
Library name: D3_ABE8e_AKTS6neg
pAKT/pS6 screen (ABE8e)

value: Base edited (PIK3CD/PIK3R1 library)


title: T cells, ABE9 edited, baseline, Donor 3

description:
Library name: D3_ABE9_baseline
Control for baseline sgRNA library distribution immediately post-editing (ABE9)

value: Transduced, edited (ABE9)


title: AJ1 Antibody

description: Library name: AJ1_CSP_S3

value: Protein

value: TotalSeq C1=Lactating thymus; C2=Virgin thymus; C3=Lactating spleen; C4=virgins spleen; C5=lactating small intestine; C6=virgins small intestine; C7=lactating colon; C8=virgin colon; C9=lactating mammary gland; C10=virgin mammary gland;


description: Library name: AL1G11460.t1_S_lycopersicum_Heinz-1706-BG_DAPi712A10-ORGi5039-96P247

value: MYBRELATED


title: MOG microglia TAM1


title: T cells, ABE8e edited, pAKT/pS6 negative, Donor 2

description:
Library name: D2_ABE8e_AKTS6neg
pAKT/pS6 screen (ABE8e)


title: T cells, ABE9 edited, baseline, Donor 2

description:
Library name: D2_ABE9_baseline
Control for baseline sgRNA library distribution immediately post-editing (ABE9)

value: Day 4


description: Library name: AL1G53260.t1_S_lycopersicum_Heinz-1706-BG_DAPi712B01-ORGi5039-96P247


title: T cells, ABE8e edited, pAKT/pS6 high, Donor 2

description:
Library name: D2_ABE8e_AKTS6hi
pAKT/pS6 screen (ABE8e)


title: MOG microglia WT4

value: Microglia

value: WT

value: MOG immunized


title: MOG microglia TAM3

value: MOG immunized-Tamoxifen


description: Library name: Carub.0004s2291.1_S_lycopersicum_Heinz-1706-BG_DAPi712A09-ORGi5039-96P247

value: plant

value: BZIP


title: T cells, ABE8e edited, pAKT/pS6 high, Donor 1

description:
Library name: D1_ABE8e_AKTS6hi
pAKT/pS6 screen (ABE8e)

value: Primary Human T cells

value: Transduced, edited (ABE8e), acutely stimulated, pAKT/pS6-sorted


description: Library name: XP_013631649.1_S_lycopersicum_Heinz-1706-BG_DAPi712B05-ORGi5039-96P247


title: Arabidopsis thaliana, H3.14 myc, Input, NaCl, biol rep 3

city: Madrid

first: Crisanto

last: Gutierrez

address: Nicolas Cabrera 1

department: Genome Dynamics and Function

country: Spain

institute: Centro de Biologia Molecular Severo Ochoa

data_processing:
ChIP-Seq raw reads were trimmed with Trimmomatic (v 0.39) to remove adapters and small sequences.
FastQC (v 0.11.9) was used to assess the quality control of the reads.
Trimmed reads were then aligned to the A. thaliana reference genome (TAIR10) using Bowtie2 (v 2.3.4.3) with default parameters.
Duplicate reads were removed with Picard MarkDuplicates (v 2.7.1)
Unmapped reads and unwanted regions (transposons, miRNA) were removed with SAMtools (v 1.9)
Narrow peaks were called with MACS2 (v 2.2.6, additional parameters -p 0.05 -s 150). DeepTools bamCompare (v 3.5.1) was used to normalize reads with CPM and against H3.
Assembly: Read pileup plots were generated with deepTools.
Supplementary files format and content: TAIR10
Supplementary files format and content: bam file for each sample

organism: Arabidopsis thaliana

source_name: Root tips

growth_protocol: Arabidopsis thaliana seedlings were grown in Murashige and Skoog (MS) with 1% sucrose and 1% agar medium. Seedlings were synchronized in long days (16h light 8h dark) at 22ºC.

extract_protocol:
Samples were fixed in 1% formaldehyde solution under vacuum (16% Formaldehyde (w/v), Methanol-free, ThermoFisher) for a total of 12 minutes. After nuclei extraction and lysis, soluble chromatin was incubated overnight at 4ºC with anti-myc. Conjugates were immunoprecipitated for 4 hours at 4ºC with protein G Dynabeads™ (ThermoFisher).
Libraries were generated using the Ovation® Ultralow V2 DNA-Seq Library Preparation Kit (Tecan), following manufacturer´s instructions. Total ChIPed DNA was resuspended in 10 µL of nuclease-free water and quantified by Qubit HS dsDNA assay (ThermoScientific) before the amplification step. 7 to 16 amplification cycles were used after taking in consideration ChIPed DNA concentration.

treatment_protocol: pHTR14::gHTR14::myc seedlings were treated with 140 mM NaCl during 4 hours 5 days after sowing.

value: Root tips

tag: ecotype

tag: chip antibody

value: 4 h 140 mM NaCl


title: MOG microglia WT2

tag: genotype


title: MOG microglia WT3

tag: tissue


title: T cells, ABE8e edited, pAKT/pS6 negative, Donor 1

description:
Library name: D1_ABE8e_AKTS6neg
pAKT/pS6 screen (ABE8e)

tag: cell type

value: Day 11


description: Library name: Solyc11g064950.3.1_S_lycopersicum_Heinz-1706-BG_DAPi712A08-ORGi5039-96P247


title: Arabidopsis thaliana, H3.14 myc, Input, NaCl, biol rep 2

tag: treatment


title: T cells, ABE8e edited, post re-expansion, Donor 3

description:
Library name: D3_ABE8e_reexpanded
Proliferation screen (two-weeks of T cell expansion) (ABE8e)

value: Base edited (PIK3CD/PIK3R1 library)

value: Transduced, edited (ABE8e), re-expanded

value: Day 18


title: Arabidopsis thaliana, H3.14 myc, Input, NaCl, biol rep 1


title: MOG microglia WT1


title: AJ1 V(D)J

description: Library name: AJ1_VDJ_S5

value: multiple tissues

value: CD3+  Tcell

value: V(D)J

value: TotalSeq C1=Lactating thymus; C2=Virgin thymus; C3=Lactating spleen; C4=virgins spleen; C5=lactating small intestine; C6=virgins small intestine; C7=lactating colon; C8=virgin colon; C9=lactating mammary gland; C10=virgin mammary gland;


title: Naïve microglia TAM4

value: Microglia

value: Tamoxifen


title: AJ1 GEX

description: Library name: AJ1_GEX_S1

value: mRNA


description: Library name: AT5G05550_S_lycopersicum_Heinz-1706-BG_DAPi712A10-ORGi5039-96P220

value: plant

tag: tf id

value: TRIHELIX


title: T cells, ABE8e edited, post re-expansion, Donor 2

description:
Library name: D2_ABE8e_reexpanded
Proliferation screen (two-weeks of T cell expansion) (ABE8e)

value: Primary Human T cells


description: Library name: LOC_Os01g51154.1_S_lycopersicum_Heinz-1706-BG_DAPi712A11-ORGi5039-96P247

tag: tf family

value: MYBRELATED


title: Arabidopsis thaliana, H3.14 myc, antimyc, NaCl, biol rep 3

value: Root tips

value: anti-myc


description: Library name: AT3G12250_S_lycopersicum_Heinz-1706-BG_DAPi712A07-ORGi5039-96P220

value: BZIP

tag: multidap sample_id


title: Naïve microglia TAM3


title: Arabidopsis thaliana, H3.14 myc, antimyc, NaCl, biol rep 2

value: 4 h 140 mM NaCl


title: T cells, ABE8e edited, post re-expansion, Donor 1

description:
Library name: D1_ABE8e_reexpanded
Proliferation screen (two-weeks of T cell expansion) (ABE8e)

value: Base edited (PIK3CD/PIK3R1 library)

value: Transduced, edited (ABE8e), re-expanded


title: Naïve microglia TAM2


description: Library name: LOC_Os08g37970.1_S_lycopersicum_Heinz-1706-BG_DAPi712A06-ORGi5039-96P247

value: MYB

tag: 96 well_plate_id


title: T cells, ABE8e edited, baseline, Donor 3

description:
Library name: D3_ABE8e_baseline
Control for baseline sgRNA library distribution immediately post-editing (ABE8e)

value: Transduced, edited (ABE8e)

value: Day 4


description: Library name: AT5G10030_S_lycopersicum_Heinz-1706-BG_DAPi712A06-ORGi5039-96P220

tag: tf source_species


title: Naïve microglia TAM1


title: brassica-mix,flower bud,rep2

description: Library name: OCUXB

data_processing:
Raw fastq files for each library were filtered using BBTools v38.96 bbduk.sh to remove read pairs with 31-mers in read 2 matching common ribosomal 31-mers. Filtered fastq files from 10X Chromium libraries were processed with Cellranger count v7.0.1, and filtered fastqs from BD Rhapsody libraries were processed with BD Rhapsody CWL pipeline (v2.2, available at bitbucket.org/CRSwDev/cwl) with default parameters. For libraries containing multiplexed species, combined-species reference genome and gene annotation files with species name preprended to the chromosome name were provided. Both processing workflows performed barcode identification, alignment, UMI de-duplication, gene aggregation, and final DGE matrix construction. Custom scripts were used to differentiate cell barcodes containing nuclei from each species (or multiple species in the case of doublets), as well as putatively empty droplets/wells and perform QC filtering. Demultiplexed libraries from the same species and tissue were integrated and clustered using Seurat v5.0 to create final atlases for a subset of species (available here as 14 Supplementary .RDS files).
Assembly: Arabidopsis thaliana Col-0 TAIR/Araport via Phytozome
Assembly: Arabidopsis lyrata MN47 Phytozome v2.1
Assembly: Brassica oleracea TO1000DH3 NCBI RefSeq GCF_000695525.1
Assembly: Capsella rubella Monte_Gargano Phytozome v1.1
Assembly: Sorghum bicolor RTx430 Phytozome v2.1
Assembly: Camelina sativa DH55 (via cruciferseq)
Assembly: Panicum hallii var. FIL2 Phytozome v3.2
Assembly: Brachypodium distachyon Bd21 Phytozome v3.2
Assembly: Thlaspi arvense MN106 NCBI GCA_911865555.2
Supplementary files format and content: Tab-separated values files and matrix files summarising transcript counts of each gene associated with each cell barcode (raw counts before any barcode filtering)

organism:
Arabidopsis thaliana
Brassica oleracea
Arabidopsis lyrata
Capsella rubella

source_name: flower bud

growth_protocol: Seeds from each species were surface sterilized before planting vertically on agar plates containing 3 mM Ca(NO3)2, 1.5 mM MgSO4, 1.25 mM NH4H2PO4, 1 mM KCl, 1x micronutrients (Murashige and Skoog Micronutrient Salts 100x, MSP18-10LT), in 0.8% agar with pH 5.7. Seedling root and shoot tissues from A. thaliana, A. lyrata, C. rubella, and B. oleracea were harvested at the 5-7 day old growth stage, and  root and shoot samples from S. bicolor were harvested from 3 day old seedlings. For mature leaves, we sampled the youngest fully expanded rosette leaf from plants grown in soil in a plant grow room or cold room. For floral buds, we sampled young buds on the main stem from plants grown in soil, where the petal was just emerging (~1 mm visible). Plant tissue samples were either processed immediately after harvest or flash frozen in liquid nitrogen.

extract_protocol:
Nuclei were isolated by chopping 20-100 mg fresh or frozen tissue for 3 minutes using a razor blade on a glass plate with 100-200 μl buffer in a cold room at 4°C. For multiplexed samples, tissues from different species were weighed separately before being combined and chopped together. The samples were then transferred to a 48-well filter plate. The filtered nuclei solution was centrifuged at 500x g for 10 minutes at 4°C to pellet the nuclei, after which the supernatant was discarded.
For profiling with 10X Chromium, the nuclei suspension was diluted to a concentration of 700-1000 nuclei/μl, then single nuclei were partitioned and barcoded using a Chromium system (10x Genomics) with the Chromium Next GEM Single Cell 3’ Reagent Kits v3.1 (Dual Index). Approximately 20,000 nuclei in total were loaded for single species samples, and up to 60,000 nuclei for multiplexed species samples. Library creation was carried out following the manufacturer’s protocol. For profiling with BD Rhapsody, the pooled nuclei suspension was diluted to a concentration of 600-900 total nuclei/μl, then single nuclei were partitioned and barcoded on a BD Rhapsody system (BD Rhapsody HT Xpress, BD Rhapsody Scanner), using the BD Rhapsody WTA V3 kit and cartridge, loading 50,000-150,000 total nuclei per lane. Library creation was carried out following the manufacturer’s protocol.

value: flower bud

tag: tissue condition

value: fresh

tag: platform

value: 10X Chromium

tag: number of_multiplexed_species


title: T cells, ABE8e edited, baseline, Donor 2

description:
Library name: D2_ABE8e_baseline
Control for baseline sgRNA library distribution immediately post-editing (ABE8e)

tag: batch


title: brassica-mix,flower bud,rep1

description: Library name: OCUXA


description: Library name: AT5G62940_S_lycopersicum_Heinz-1706-BG_DAPi712A05-ORGi5039-96P220


title: Naïve microglia WT4

value: Microglia

value: WT

value: No treatment


description: Library name: XP_013631386.1_S_lycopersicum_Heinz-1706-BG_DAPi712A07-ORGi5039-96P247

value: plant


title: Naïve microglia WT3


title: brassica-mix,leaf,rep2

description: Library name: OCHBN

source_name: leaf

value: leaf


title: B6-HFD3

description: Library name: HFD3

value: Heart

value: cardiomyocytes

value: SETD7 fl/fl


title: T cells, transduced unedited, Donor 2

description:
Library name: D2_U
Control for baseline sgRNA library distribution pre-editing; serves as baseline for ABE8e and ABE9 screens as the same donors/cells were edited with each editor

value: Primary Human T cells

value: Wild-type (unedited)

value: Transduced, unedited

value: Day 0


description: Library name: AT1G69780_S_lycopersicum_Heinz-1706-BG_DAPi712A03-ORGi5039-96P220

value: HOMEOBOX


title: T cells, transduced unedited, Donor 3

description:
Library name: D3_U
Control for baseline sgRNA library distribution pre-editing; serves as baseline for ABE8e and ABE9 screens as the same donors/cells were edited with each editor


description: Library name: AT5G39760_S_lycopersicum_Heinz-1706-BG_DAPi712A02-ORGi5039-96P220

value: ZFHD


title: Naïve microglia WT1