title: PFCR27, ctrl, WT

description: 10x Genomics


title: WGBS data of PIAL1-ZF T2 plant in fwa background

status: Public on Jun 09 2023

type: SRA

city: Los Angeles

first: Zhenhui

last: Zhong

address: 610 Charles E Young Dr East

department: Department of Molecular, Cell and Developmental Biology

country: USA

institute: University of California, Los Angeles

library_source: genomic

data_processing:
For ChIP-seq analysis, raw reads were trimmed using trim_galore (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) and aligned to the TAIR10 reference genome with bowtie2 (v2.4.2) allowing zero mismatch and reporting one valid alignment for each read. The Samtools (v1.15) were used to convert sam files to bam files, sort bam files and remove duplicate reads. Track files in bigWig format were generated using bamCoverage of deeptools (v3.5.1) with RPKM normalization. Peaks were called with MACS2 (v2.1.2) and peaks frequently identified in previous ChIP-seq of Col-0 plant with M2 antibody for FLAG epitope were removed from analysis.
For RNA-seq analysis, the raw reads were aligned to the TAIR10 reference genome with bowtie2. Rsem-calculate-expression from RSEM with default settings was used to calculate expression levels. DEGs and DE-TEs were calculated with run_DE_analysis.pl from Trinity version 2.8.5 and log2 FC ≥ 1 and FDR < 0.05 were used as the cut off. RNA-seq track files in bigWig format were generated using bamCoverage of deeptools (v3.1.3) with RPKM normalization.
For WGBS analysis, the raw reads were aligned to both strands of the TAIR10 reference genome using BSMAP (v.2.74), allowing up to 2 mismatches and 1 best hit. Reads with more than 3 consecutives methylated CHH sites were removed, and the methylation level was calculated with the ratio of C/(C+T).
For BSPCR analysis, raw reads were aligned to both strands of the TAIR10 reference genome with BSMAP (v.2.90) allowing up to 2 mismatches and 1 best hit. After quality filtering, the methylation level of cytosines was calculated as the ratio of C/(C+T).
For ATAC-seq analysis, raw reads were adaptor-trimmed with trim_galore and mapped to the TAIR10 reference genome with Bowtie2 (-X 2000 -m 1). After removing duplicate reads and reads mapped to chloroplast and mitochondrial, ATAC-Seq open chromatin peaks of each replicate were called using MACS2 with parameters -p 0.01 --nomodel --shift -100 --extsize 200. Consensus peaks between replicates were identified with bedtools (version 2.26.0) intersect and differential accessible peaks were called with the R packge edgeR (version 3.30.0).
Assembly: tair10
Supplementary files format and content: .bw files are bigWig files of coverage tracks normalized with RPKM (for ChIP-seq and ATAC-seq), or methylation levels (for WGBS)
Supplementary files format and content: _methratio_type.txt files are tab-delimited text files containing methylation type and level at indicated chromosome positions.
Supplementary files format and content: .genes.results files are tab-delimited text files containing RNA-seq quantification data over genes and TEs.
Supplementary files format and content: .narrowPeak files are bed files containing position of called peaks for ChIP-seq.

molecule: genomic DNA

organism: Arabidopsis thaliana

source_name: rosette leaf tissue

growth_protocol: Arabidopsis plants of the Columbia-0 (Col-0) ecotype were used in this study. All plants were grown under green house condition (16 h light/8 h dark, 22C). For ChIP-seq and ATAC-seq, floral tissues were collected from about one-month-old plants. For BS-PCR and WGBS, rossette leaves were were collected from about one-month-old plants. For RNA-seq, twelve-day-old whole seedlings grown on half MS plates were collected.

extract_protocol:
Genomic DNA for WGBS was extracted with DNeasy Plant Mini Kit (QIAGEN). Genomic DNA for BS-PCR-seq was extracted with CTAB method. RNA was extracted with Direct-zol RNA MiniPrep kit (Zymo Research).
ChIP-seq library preparation: 15 ml of unopened flower buds were collected for each ChIP and flash-frozen in liquid nitrogen. The flower tissue was ground to fine powder with Retsch homogenizer in liquid nitrogen and resuspended in nuclei extraction buffer (50 mM HEPES pH 8.0, 1 M sucrose, 5 mM KCl, 5 mM MgCl2, 0.6% Triton X-100, 0.4 mM PMSF, 5 mM benzamidine, cOmplete EDTA-free Protease Inhibitor Cocktail (Roche), 50uM MG132). For transgenic lines of MOM1-MYC and PIAL2-MYC, EGS was first added to resuspended lysate to 1.5 mM and the tissue lysate was incubated at room temperature for 10 min with rotation. Then the lysate was supplemented with formaldehyde at 1% and rotated at room temperature for another 10 min followed by adding glycine to stop crosslinking. For ChIP of all other proteins, crosslinking was performed by directly supplementing formaldehyde to 1% without adding EGS, then rotated at room temperature for 10 min followed by adding glycine to stop crosslinking. The crosslinked nuclei were isolated, lysed with Nuclei Lysis Buffer and diluted with ChIP Dilution Buffer. Then the lysate was sonicated for 22 min (30 s on/30s off) with Bioruptor Plus (Diagenode). After centrifugation, antibody for FLAG epitope (M2 monoclonal antibody, Sigma F1804, 10 ul per ChIP) or for MYC epitope (Cell Signaling, 71D10, 20 ul per ChIP) were added to the supernatant and incubated at 4 ℃ overnight with rotation. Then, Protein A and Protein G Dynabeads (Invitrogen) were added and incubated at 4 ℃ for 2 hours with rotation. After that, the beads were washed and eluted, and the eluted chromatin was reverse-crosslinked by adding 20 ul 5 M NaCl and incubating at 65 ℃ overnight followed by treatment of Proteinase K (Invitrogen) for 4 hours at 45 ℃. DNA was purified and precipitated with 3 M Sodium Acetate, GlycoBlue (Invitrogen) and ethanol at -20 ℃ overnight. After centrifugation, the precipitated DNA was washed with ice cold 70% ethanol, air dried and dissolved in 120 ul of H2O. ChIP-seq libraries were prepared with Ovation Ultra Low System V2 kit (NuGEN).
RNA-seq library preparation: Twelve-day old seedlings grown on half MS medium (Murashige and Skoog Basal Medium) were collected and flash-frozen in liquid nitrogen. RNA was extracted with Direct-zol RNA MiniPrep kit (Zymo Research) and 1ug of total RNA was used to prepare RNA-seq libraries with TruSeq Stranded mRNA kit (Illumina)
WGBS library preparation: Rosette leaves of about one-month-old Arabidopsis plants were collected for DNA extraction using DNeasy Plant Mini Kit (QIAGEN). 500 ng DNA was sheared with Covaris S2 (Covaris) into around 200bp at 4℃. The DNA fragments were used to perform end repair reaction using the Kapa Hyper Prep kit (Roche), and together with Illumina TruSeq DNA sgl Index Set A/B (Illumina) to perform adapter ligation. The ligation products were purified with AMPure beads (Beckman Coulter), and then converted with EpiTect Bisulfite kit (QIAGEN). The converted ligation products were used as templates, together with the primers from the Kapa Hyper Prep kit (Roche) and MyTaq Master mix (Bioline) to perform PCR. The PCR products were purified with AMPure beads (Beckman Coulter) and used for sequencing.
ATAC-seq library preparation: About 5 grams of unopened flower buds was collected and immediately transferred into ice-cold grinding buffer (300 mM sucrose, 20 mM Tris pH 8, 5 mM MgCl2, 5 mM KCl, 0.2% Triton X-100, 5 mM β-mercaptoethanol, and 35% glycerol). The samples were ground with Omni International General Laboratory Homogenizer on ice and then filtered through a two-layer Miracloth and a 40-µm nylon mesh Cell Strainer (Fisher). Samples were spin filtered for 10 min at 3,000 g, the supernatant was discarded, and the pellet was resuspended with 25 ml of grinding buffer using a Dounce homogenizer. The wash step was performed twice in total, and nuclei were resuspended in 0.5 ml of freezing buffer (50 mM Tris pH 8, 5 mM MgCl2, 20% glycerol, and 5 mM β-mercaptoethanol). Nuclei were subjected to a transposition reaction with Tn5 (Illumina). For the transposition reaction, 25 µl of 2x DMF (66 mM Tris-acetate pH 7.8, 132 mM K-Acetate, 20 mM Mg-Acetate, and 32% DMF) was mixed with 2.5 µl Tn5 and 22.5 µl nuclei suspension at 37°C for 30 min. Transposed DNA fragments were purified with ChIP DNA Clean & Concentrator Kit (Zymo). Libraries were prepared with Phusion High-Fidelity DNA Polymerase (NEB) in a system containing 12.5 µl 2x Phusion, 1.25 µl 10 mM Ad1 primer, 1.25 µl 10 mM Ad2 primer, 4 µl ddH2O, and 6 µl purified transposed DNA fragments.
BS-PCR library preparation: Rosette leaves of about one-month-old plants were collected and subject to DNA extraction with CTAB method followed by bisulfite DNA conversion using the EpiTect Bisulfite kit (QIAGEN) kit. Three regions of the FWA gene were amplified from the converted DNA with Pfu Turbo Cx (Agilent): Region 1 (chr4: 13038143-13038272), Region 2 (chr4: 13038356- 13038499) and Region3 (chr4: 13038568-13038695). Libraries were prepared with the purified PCR product by the Kapa DNA Hyper Kit (Roche) together with TruSeq DNA UD indexes for Illumina (Illumina) and were sequenced on Illumina iSeq 100 or HiSeq 4000 instruments.

tag: tissue

value: rosette leaf tissue

tag: cell line

tag: cell type

value: one month old

tag: genotype

value: PIAL1-ZF in fwa


title: iPSN-C9-3_6h

city: Shanghai

first: Xiaoyang

last: Dou

address: 320 Yue Yang Road

country: China

institute: CAS Center for Excellence in Molecular Cell Science, CAS

library_source: transcriptomic

data_processing:
Raw reads were trimmed with Trimmomatic-0.38 and aligned to human genome and transcriptome (hg38) and external RNA Control Consortium (ERCC) RNA spike-in control (Thermo Fisher Scientific) with ‘--rna-strandness RF’  parameters.
Reads on each GENCODE annotated gene were counted using HTSeq and then normalized to counts per million (CPM) using edgeR.
Assembly: hg38
Supplementary files format and content: read counts for each sample

molecule: polyA RNA

organism: Homo sapiens

source_name: iPSC-derived neuron

growth_protocol: iPSCs were maintained in mTeSR media on Matrigel, following the Cedars-Sinai Standard Operating Procedure (SOP, https://www.cedars-sinai.edu/content/dam/cedars-sinai/research/documents/biomanufacturing/complete-ipsc-culturing-protocol-rev-4-2020.pdf). iPSCs were differentiated into spinal neurons using the direct induced motor neuron protocol. All cells were maintained at 37°C with 5% CO2.

extract_protocol:
Total RNA was extracted from cells using TRIzol (Thermo Fisher).
RNAs were subjected to NEBNext Ultra II Directional RNA Library Prep (New England Biolabs) coupled with NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs).

value: iPSC-derived neuron

value: patient-derived

tag: treatment

value: actinomycin D treatment 6 hour


title: RPMI_8226_EPZ6438_72hr_MEN1

city: New York

first: Chao

last: Lu

state: New York

address: 1130 Saint Nicholas Ave

department: Genetics & Development

institute: Columbia University Medical Center

data_processing:
Basecalls performed using Illumina CASAVA version 1.7
For RNA-seq samples, reads of DLBCL cell lines were mapped to the human genome assembly hg38 using HISAT2 (v2.1.0). The mapped reads count of each gene was measured by featureCounts (v1.6.1). For CUT&Tag samples, reads were mapped to the human genome assembly hg38 using HISAT2 (v2.1.0). Potential PCR duplicates were removed by the function "MarkDuplicates" (parameter: REMOVE_DUPLICATES=true) of Picard (v2.23.1).
Assembly: hg38
Supplementary files format and content: For RNA-seq samples, tab-delimited text files include reads count values for each gene in each sample. For CUT&Tag samples, bigwig files normalized to count per million reads.
Library strategy: CUT&Tag

source_name: Cell line

extract_protocol:
CUT&Tag was performed as described previously (nature communications, 2019).
CUT&Tag was performed as described previously (nature communications, 2019).

value: MM cell line

value: Treated by EPZ6438


title: PFCR36, ctrl, WT

city: Bologna

first: Chiara

last: Cabrelle

address: Via Irnerio, 49

country: Italy

institute: University of Bologna

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
Raw 10x Genomics reads from 16 samples (n=4 3xTg-AD and WT mice with and without histories of repeated alcohol intoxication) were aligned on the Mus musculus genome version mm10 (downloaded on 13 August 2021) using Cell Ranger v.6.1.1 based on the STAR aligner.
Assembly: mm10
Supplementary files format and content: Tab-separated values file with rawcounts

molecule: total RNA

organism: Mus musculus

source_name: Prefrontal cortex

extract_protocol:
Male 3xTg-AD mice were sacrificed under deep isoflurane anesthesia and freshly dissected brain regions were snap-frozen and processed for snRNA-Seq by Singulomics (New York City, NY) using the 10x Genomics Chromium gene expression platform.
Chromium Next GEM Single Cell 3ʹ Kit v3.1 (dual index)
snRNA-seq

value: control

value: Prefrontal cortex

tag: strain

tag: age

value: 22 weeks


title: iPSN-C9-3_0h

value: actinomycin D treatment 0 hour


title: WGBS data of PHD1-ZF T2 plant in fwa background

value: PHD1-ZF in fwa


title: PFCR21, AD, 3xTg-AD

description: 10x Genomics


title: PFCR26, ctrl, WT

description: 10x Genomics


title: iPSN-C9-1_6h


title: MM.1S_DMSO_MLL1

value: Treated by DMSO


title: RPMI_8226_EPZ6438_72hr_H3K27me3_spikein


title: iPSN-C9-4_0h


title: WGBS data of MOM2-ZF T2 plant in fwa background

value: MOM2-ZF in fwa


title: iPSN-C9-1_3h

value: actinomycin D treatment 3 hour


title: WGBS data of MOM1-ZF T2 plant in fwa background

value: MOM1-ZF in fwa


title: PFCR18, alcohol, WT

description: 10x Genomics

value: alcohol


title: MM.1S_DMSO_H3K27me3_spikein


title: MM.1S_EPZ6438_72hr_MLL1


title: PFCR14, AD, 3xTg-AD

description: 10x Genomics


title: RNA-seq data of pial2-1 replicate 3

source_name: whole seedling

value: whole seedling

value: 12 day old


title: iPSN-C9-1_0h

value: iPSC-derived neuron


title: iPSN-Ctrl-4_IP_YTHDF2-RIP

data_processing:
Raw reads were trimmed with Trimmomatic-0.39, then aligned to human genome and transcriptome (hg38) using HISAT (version 2.1.0) with ‘--rna-strandness RF’ parameters. Reads on each GENCODE annotated gene were counted using HTSeq and then differentially expressed genes were called using DESeq2 package.
Reads on each GENCODE annotated gene were counted using HTSeq and then differentially expressed genes were called using DESeq2 package.
Assembly: hg38
Supplementary files format and content: read counts for each sample

extract_protocol:
Total RNA was extracted from cells using TRIzol (Thermo Fisher). Protein-RNA complexes were isolated with YTHDF2 antibody-coated protein G beads. After washing, 1ml TRIZOL was added to the beads to elute the RNAs.
RNAs recovered from RIP and input were subjected to NEBNext Ultra II Directional RNA Library Prep (New England Biolabs) coupled with NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs).

value: Non-neurologic control


title: PFCR17, alcohol, WT

description: 10x Genomics


title: RNA-seq data of pial2-1 replicate 1


title: MM.1S_DMSO_MEN1


title: PFCR13, AD, 3xTg-AD

description: 10x Genomics


title: iPSN-Ctrl-5_IP_YTHDF2-RIP


title: iPSN-Ctrl-3_IP_YTHDF2-RIP


title: RNA-seq data of pial2-1 replicate 2


title: MM.1S_EPZ6438_72hr_MEN1


title: PFCR12, AD, 3xTg-AD

description: 10x Genomics


title: MM.1S_EPZ6438_72hr_H3K27me3_spikein


title: RNA-seq data of pial1pial2double replicate 3

value: pial1pial2 double mutant


title: RNA-seq data of pial1pial2double replicate 1


title: Farage_VTP50469_MEN1

value: DLBCL cell line

value: Farage

value: Treated by VTP50469


title: iPSN-Ctrl-1_IP_YTHDF2-RIP


title: PFCR6, alcohol, WT

description: 10x Genomics

value: Prefrontal cortex


title: iPSN-Ctrl-2_IP_YTHDF2-RIP


title: RNA-seq data of pial1pial2double replicate 2


title: PFCR7, alcohol, WT

description: 10x Genomics

value: 22 weeks


title: Farage_VTP50469_MLL1


title: iPSN-Ctrl-5_Input_YTHDF2-RIP


title: iPSN-Ctrl-4_Input_YTHDF2-RIP


title: RNA-seq data of pial1-2 replicate 3


title: t672_2_sgKdm6a RPP

city: Boston

first: Leslie

last: Duplaquet

state: Massachusetts

address: 360 Longwood Ave

department: Medical Oncology

institute: DFCI

data_processing:
Sequencing reads were mapped to the mm10 genome by STAR. Statistics for differentially expressed genes were calculated by DESeq2.
Assembly: mm10
Supplementary files format and content: FPKM and read count

source_name: mouse small cell lung cancer (SCLC) tumor

growth_protocol: SCLC tumors were harvested at necropsy and were flash-frozen

extract_protocol:
RNA was extracted using RNeasy mini kit (Qiagen #74106) including a DNase digestion step according to the manufacturer’s instructions and RNA sequencing was performed
The libraries for RNA-seq are prepared using NEBNext Ultra II non-stranded kit.  Paired end 150bp sequencing was performed on Novaseq6000 sequencer using S4 flow cell.

treatment_protocol: No treatment

value: mouse small cell lung cancer tumor cells

tag: mouse background

value: pure congenic Lox-stop-lox (LSL) Cas9 BL6J mice

value: sgKdm6a RPP


title: PFCR4, AD_alcohol, 3xTg-AD

description: 10x Genomics


title: Farage_VTP50469_H3K27me3_spikein


title: RNA-seq data of pial1-2 replicate 2


title: Farage_ctr_H3K27me3_spikein

value: Treated by DMSO


title: t672_1_sgKdm6a RPP

value: mouse small cell lung cancer (SCLC) tumor


title: t651R_sgKdm6a RPP


title: t651L_sgKdm6a RPP


title: iPSN-Ctrl-3_Input_YTHDF2-RIP


title: RNA-seq data of phd1-4 replicate 3


title: iPSN-Ctrl-1_Input_YTHDF2-RIP


title: RNA-seq data of phd1-4 replicate 2


title: K422_VTP50469_MEN1


title: K422_VTP50469_MLL1


title: RNA-seq data of pial1-2 replicate 1


title: K422_EPZ6438_72hr_MLL1

value: Treated by EPZ6438


title: differentiated Ribo-Seq2

city: Callaghan

first: Dylan

last: Kiltschewskij

state: NSW

address: Room MS616, Level 6, Medical Sciences Building, University Drive

department: School of Biomedical Sciences and Pharmacy

country: Australia

institute: The University of Newcastle

description: ribo.cpm.txt

data_processing:
Bcl files were demultiplexed and converted to fastq format using 'Bcl2fastq' version 2.2. Lane data for each sample were merged.
Using 'Cutadapt' version 1.14, low quality 3 prime nucleotides (Phred33 < 28), single 5´ nucleotides and reads < 25 or > 40nt were removed. Reads aligning to abundant non-coding RNAs (rRNA, miRNA, tRNA, snoRNA, snRNA) were discarded using Bowtie2 (2.2.6)
Reads were mapped to the hg19 reference genome using 'TopHat2' version 2.2.1, and reads aligning to features were counted with 'HTSeq' version 0.9.1.
Differential expression was calculated using 'EdgeR' version 3.8
Genome_build: hg19
Supplementary_files_format_and_content:  ribo.cpm.txt (Tab delimited text file containing normalized counts per million for each gene.)

source_name: Neuronally differentiated SH-SY5Y

growth_protocol: SH-SY5Y neuronal differentiation was induced via sequential treatment with all-trans retinoic acid (ATRA, Sigma-Aldrich, St. Louis, MO, USA) and brain-derived neurotrophic factor (BDNF, Life Technologies, Carlsbad, CA, USA). One day prior to differentiation (day -1), cells were seeded into T75 culture flasks at a density of 25,000 cells/cm2 in standard culture medium. The next day (day 0), standard medium was replaced with ATRA-supplemented medium (10µM) and cells were protected from light exposure, with ATRA medium replaced on day 2. On day 5, ATRA medium was aspirated, cells were washed 3 times with standard culture medium, then returned to standard culturing conditions in BDNF-supplemented (50ng/mL), serum-free medium. BDNF medium was replaced on days 7, 9 and 11, after which the methods were continues as described on day 12.

extract_protocol:
Enrichment of ribosome protected RNA was performed via the Illumina TruSeq Ribo Profile Kit (H/M/R), with minor amendments. Translational activity was firstly suspended by incubating cells with warm culture medium supplemented with 0.1mg/ml cycloheximide (CHX) for 1 min. Cells were harvested on ice with 800µl mammalian lysis buffer (containing 0.1mg/ml CHX and 25U Turbo DNase I (ThermoFisher)) and ribosome foot-printing was conducted by adding 150U RNase I (Invitrogen) to 300µl clarified lysate for 45 min. Reactions were halted with 6µl Superase Inhibitor (ThermoFisher) and ribosome protected RNAs were enriched via size exclusion chromatography using MicroSpin S400 HR columns (GE Healthcare)
Ribosome profiling (Ribo-Seq) library preparation was conducted as per the TruSeq Ribo Profile Kit (Illumina). Briefly, ribosomal RNA was depleted using the Ribo-Zero rRNA Removal kit (Illumina) and ribosome protected RNA fragments (RPFs) were size selected (25–33nt) via 12% denaturing PAGE. RPFs were next subjected to end repair, 3´ adapter ligation and reverse transcription (50°C, 30 min), after which cDNA was size selected (70-100nt) via 10% denaturing PAGE. cDNA was then circularised and amplified via 12 PCR cycles, with libraries subjected to 101 cycles of single end sequencing via a NovaSeq6000 Instrument.

value: Neuronally differentiated SH-SY5Y

tag: passages

tag: molecule type

value: Ribosome protected RNA


title: t656_sgKdm6a RPP


title: differentiated Ribo-Seq1

description: ribo.cpm.txt


title: RNA-seq data of phd1-2 replicate 2

value: whole seedling

value: 12 day old


title: K422_VTP50469_H3K27me3_spikein


title: t236R_sgKdm6a RPP


title: K422_EPZ6438_72hr_MEN1


title: RNA-seq data of phd1-4 replicate 1


title: undifferentiated Ribo-Seq3

description: ribo.cpm.txt

growth_protocol: Standard culturing conditions: SH-SY5Y neuroblastoma cells were grown and sustained in Dulbecco’s Modified Eagle’s Medium (DMEM, HyClone, Logan UT, USA) supplemented with 10% heat-inactivated fetal bovine serum (Bovogen Biologicals, Essendon, VIC, Australia), 2% HEPES (Gibco, Carlsbad, CA, USA) and 1% L-glutamine (Invitrogen, Carlsbad, CA, USA). Cultures were maintained at 37°C in a 95% oxygen, 5% carbon dioxide, 90% humidity atmosphere and passaged regularly by washing with phosphate buffered saline (PBS, Gibco) and trypsinisation (0.1% trypsin-EDTA in PBS, Gibco).


title: iPSN-Ctrl-2_Input_YTHDF2-RIP

value: iPSC-derived neuron

value: Non-neurologic control


title: undifferentiated Ribo-Seq2

description: ribo.cpm.txt


title: K422_EPZ6438_72hr_H3K27me3_spikein

value: DLBCL cell line


title: RNA-seq data of phd1-2 replicate 1


title: t645_sgControl RPP

value: sgControl RPP


title: K422_ctr_MLL1


title: t236L_sgKdm6a RPP


title: undifferentiated Ribo-Seq1

description: ribo.cpm.txt


title: RNA-seq data of morchex replicate 3

value: morchex


title: t542_sgControl RPP


title: RNA-seq data of morchex replicate 2


title: WGBS_51L_Y3_luminal

city: Duarte

first: Dustin

middle: E

last: Schones

state: CA

address: 1500 E Duarte Rd.

institute: City of Hope

data_processing:
Raw sequencing reads were adapter trimmed and hard trimmed 8 bp from both ends using Trim Galore v0.4.5.
Trimmed reads were aligned to the human reference genome hg19 using Bismark v0.19.1 with the --bowtie1 option.
PCR duplicates were removed using Bismark. Methpipe v3.4.3 was used to determine the methylation status of individual CpG sites.
Genome_build: hg19
Supplementary_files_format_and_content: Bed format, columns: chr, CpG site, strand, cytosine context, methylation level (0 to 1), coverage

source_name: Mammary luminal epithelial cells

growth_protocol: Cells were grown in M87A medium with cholera toxin and oxytocin at 0.5 ng/ml and 0.1nM, respectively. Cells were stained with anti-human CD133-PE (Biolegend, clone 7) and anti-human CD271 (Biolegend, clone ME20.4) by following standard flow cytometry protocol. Luminal epithelial cells were enriched with Aria III (Becton Dickinson) as CD133+/CD271- fractions.

extract_protocol:
Quick-DNA Microprep kit (Zymo Research) was used to extract DNA.
Genomic DNA was bisulfite converted using the Zymo EZ DNA methylation kit (Zymo Research). Library preparation was done using TruSeq DNA Methylation Kit with 75ng of bisulfite converted DNA as per manufacturer’s recommendations.

value: Mammary luminal epithelial cells

tag: facs sort group


title: K422_ctr_MEN1


title: t535_sgControl RPP


title: RNA-seq data of phd1-2 replicate 3


title: K422_ctr_H3K27me3_spikein


title: WGBS_356E_Y5_luminal


title: t18_222_sgControl RPP


title: t18_227_sgControl RPP


title: WGBS_429ER_O5_luminal


title: RNA-seq data of morc6-3 replicate 3


title: t18_221_sgControl RPP


title: WGBS_124_Y4_luminal


title: Episcreen_K562_Day14

data_processing:
Basecalls performed using Illumina CASAVA version 1.7
For RNA-seq samples, reads of DLBCL cell lines were mapped to the human genome assembly hg38 using HISAT2 (v2.1.0). The mapped reads count of each gene was measured by featureCounts (v1.6.1). For CUT&Tag samples, reads were mapped to the human genome assembly hg38 using HISAT2 (v2.1.0). Potential PCR duplicates were removed by the function "MarkDuplicates" (parameter: REMOVE_DUPLICATES=true) of Picard (v2.23.1).
Assembly: hg38
Supplementary files format and content: For RNA-seq samples, tab-delimited text files include reads count values for each gene in each sample. For CUT&Tag samples, bigwig files normalized to count per million reads.
Library strategy: CRISPR screen

extract_protocol:
CRISPR-Cas9 knockout screen screen was performed as described previously (nature cell biology, 2022).
CRISPR-Cas9 knockout screen screen was performed as described previously (nature cell biology, 2022).

value: CML cell line

value: untreated


title: Episcreen_K562_Day0


title: RNA-seq data of morc6-3 replicate 2


title: WGBS_237_O3_luminal


title: Episcreen_K422_Day0


title: NEJ146-D

city: Memphis

first: Xiang

last: Chen

state: TN

address: 262 Danny Thomas Place

department: Computational Biology

institute: St.Jude Children's Research Hospital

description:
tissue-NEJ146
Splash frozen the tumor tissue, mounted on OCT, Cryosectioned and placed on Visium Gene expression slide. Cryosection, H&E, cDNA and Library was prepared following Visium Gene expression reagents and slide  from 10X Genomics.

data_processing:
Library strategy: Spatial -RNASeq
Cell Ranger 6.0 used to generate Fastq, end count, web summary  and matrix files that used further analyzes.

source_name: liver tissue

extract_protocol:
Splash frozen the tumor tissue, mounted on OCT, Cryosectioned and placed on Visium Gene expression slide. 4 adjacent section were collected from NEJ146.
Cryosection, H&E, cDNA and Library was prepared following Visium Gene expression reagents and slide  from 10X Genomics.

value: hepatoblastoma

tag: tissue preparation

value: 10um Frozen section from the tumor


title: Episcreen_K422_Day14


title: RNA-seq data of morc6-3 replicate 1


title: BMP Distal 3

type: RNA

city: Stanford

first: Hirotsugu

last: Maekawa

address: 240 Pasteur Dr

institute: Stanford university

description: Gene expression data from Control Proximal 18

hyb_protocol: Samples were hybridized to the arrays with the GeneChip Hybridization Wash and Stain Kit. The arrays were washed and stained on the GeneChip Fluidics Station 450.

scan_protocol: The arrays were scanned with the GeneChip Scanner 3000 7G.

data_processing: Analysis was performed using Transcriptome Analysis Console 4.0 software. Data were normalized with MAS 5.0 algorithm.

label: bitotin

organism: Rattus norvegicus

source_name: soft tissue

label_protocol: Samples were fragmented and labeled with the GeneChip WT Terminal Labeling and Controls kit.

growth_protocol: Not applicalble

extract_protocol: RNA samples were extracted fromt tissue samples with QIAzol and QIAGEN Rneasy Universal kit.

treatment_protocol: Tissue samples were placed in QIAzol and disrupted by tissue homogenizer.

tag: gender

value: Male


title: RNA-seq data of mom2-2 replicate 2


title: K422_VTP2

data_processing:
Basecalls performed using Illumina CASAVA version 1.7
For RNA-seq samples, reads of DLBCL cell lines were mapped to the human genome assembly hg38 using HISAT2 (v2.1.0). The mapped reads count of each gene was measured by featureCounts (v1.6.1). For CUT&Tag samples, reads were mapped to the human genome assembly hg38 using HISAT2 (v2.1.0). Potential PCR duplicates were removed by the function "MarkDuplicates" (parameter: REMOVE_DUPLICATES=true) of Picard (v2.23.1).
Assembly: hg38
Supplementary files format and content: For RNA-seq samples, tab-delimited text files include reads count values for each gene in each sample. For CUT&Tag samples, bigwig files normalized to count per million reads.

extract_protocol:
Total RNA was extracted from cell pellets using the AllPrep DNA/RNA/miRNA Universal Kit (Qiagen) according to instructions from the manufacturer.
Library preparation was performed with ribosomal RNA depletion according to instructions from the manufacturer (NEB) to achieve greater coverage of mRNA and other long non-coding transcripts.

value: Treated by VTP50469


title: WGBS_029_O4_luminal


title: NEJ146-C


title: RNA-seq data of morchex replicate 1


title: NEJ146-B


title: BMP Distal 2

description: Gene expression data from Control Proximal 17


title: RNA-seq data of mom2-2 replicate 1


title: K422_EPZ2

value: Treated by EPZ6438


title: BMP Distal 1

description: Gene expression data from Control Proximal 16


title: NEJ146-A


title: K422_VTP1


title: BMP Proximal 3

description: Gene expression data from Control Proximal 15


title: K422_EPZ1


title: Mouse model of Heptablastoma, NEJ146-1

data_processing:
Cell Ranger 6.0 used to generate Fastq, end count and matrix files that used further analyses.
Genome_build: mm9
Supplementary_files_format_and_content: Cell Ranger output files (barcodes, features, matrix)

extract_protocol:
Tumor mass was dissociated by using a modified two-step collagenase procedure (Li et al., 2010)
cDNA and Library was prepared following 3' Single cell Expression V3 from 10X Genomics.
ScRNASeq

tag: disease state

value: mouse model of Heptablastoma

value: Single Cells_NEJ146


title: RNA-seq data of mom2-1 replicate 3

value: whole seedling


title: RNA-seq data of mom2-2 replicate 3

value: 12 day old


title: BMP Proximal 2

description: Gene expression data from Control Proximal 14


title: K422_CTR2

value: Treated by DMSO


title: BMP Proximal 1

description: Gene expression data from Control Proximal 13


title: RNA_embryo_inhib_rep2

city: New Haven

first: Bluma

middle: J

last: Lesch

state: CT

address: 333 Cedar Street

department: Genetics

institute: Yale University

data_processing:
Data were aligned and assembled with STAR (Dobin et al., 2013) using default parameters and mouse genome assembly mm10. Read counts from STAR alignments were generated using HTSeq (Anders et al., 2014).
mm10
See data processing associated with each sample
Genome_build: mm10
Supplementary_files_format_and_content: ChIP-seq: .bed files of peaks; RNA-seq: .txt files of read counts by gene

source_name: 8-cell embryo

extract_protocol:
Total RNA was prepared using the RNeasy Micro kit (Qiagen #74004) according to the manufacturer’s instructions. 30-35 mouse embryos at 56 hours post fertilization were disrupted in 75 ul Buffer RLT, and RNA was eluted in 12ul RNase-free water.
RNA-seq libraries were prepared SMARTer Stranded Total RNA-seq kit v3 – Pico Input (Takara Bio #634485) according to the manufacturers’ instructions.  Indexed libraries were quantitated by qPCR using the KAPA Library Quantification Kit (KAPA Biosystems #KK4854).

tag: ip antibody

value: wild type

value: Dot1L inhibitor (SGC0946)

value: B6D2F1 x Cast/EiJ


title: RNA_embryo_control_rep2

value: DMSO


title: Blank Distal 3

description: Gene expression data from Control Proximal 12


title: K422_Combo2

value: DLBCL cell line

value: Treated by EPZ6438 and VTP50469


title: RNA-seq data of mom1-3 replicate 3


title: RNA-seq data of mom2-1 replicate 1


title: RNA-seq data of mom1-3 replicate 2


title: Blank Distal 2

description: Gene expression data from Control Proximal 11


title: RNA-seq data of mom1-3 replicate 1


title: DHL10_VTP2


title: Blank Distal 1

description: Gene expression data from Control Proximal 10


title: RNA-seq data of mom1-2 replicate 3


title: DHL10_VTP1


title: Blank Proximal 3

description: Gene expression data from Control Proximal 9


title: RNA_mESCs_ko_rep1

data_processing:
Data were aligned and assembled with kallisto (Bray et al., 2016) or STAR (Dobin et al., 2013) using default parameters and mouse genome assembly mm10. Read counts from STAR alignments were generated using HTSeq (Anders et al., 2014).
mm10
See data processing associated with each sample
Genome_build: mm10
Supplementary_files_format_and_content: ChIP-seq: .bed files of peaks; RNA-seq: .txt files of read counts by gene

source_name: mESCs

extract_protocol:
Cell pellets were resuspended in 1 mL of TRIzol and cells were homogenized by drawing up and down in a 21G needle with 3 ml syringe. 200ul chloroform was added, then samples were vortexed and incubated briefly at room temperature and centrifuged at 12000xg, 15 min, 4C.  The aqueous phase was transferred to a gDNA eliminator column from the RNEasy Micro Plus kit (Qiagen), and total RNA was isolated according to manufacturer’s instructions.
RNA-seq libraries were prepared by ribosome depletion using the KAPA RNA Hyperprep Kit with RiboErase (Roche #08098140702) according to the manufacturer's instructions. Indexed libraries were quantitated by qPCR using the KAPA Library Quantification Kit (KAPA Biosystems #KK4854).

value: Dot1L KO


title: RNA_mESCs_ko_rep2


title: RNA-seq data of mom1-2 replicate 2


title: RNA-seq data of mom2-1 replicate 2


title: Blank Proximal 2

description: Gene expression data from Control Proximal 8


title: K422_CTR1


title: DHL10_EPZ2


title: RNA_embryo_inhib_rep1


title: RNA-seq data of mom1-2 replicate 1


title: Blank Proximal 1

description: Gene expression data from Control Proximal 7


title: DHL10_EPZ1


title: RNA-seq data of aipp3-2 replicate 3


title: RNA_mESCs_wt_rep2


title: RNA_mESCs_wt_rep1

data_processing:
Data were aligned and assembled with kallisto (Bray et al., 2016) using default parameters and mouse genome assembly mm10.
mm10
See data processing associated with each sample
Genome_build: mm10
Supplementary_files_format_and_content: ChIP-seq: .bed files of peaks; RNA-seq: .txt files of read counts by gene


title: K422_Combo1


title: RNA_embryo_control_rep1


title: DHL10_CTR2


title: Control Distal 3

description: Gene expression data from Control Proximal 6


title: H3K79me3_input_ko_rep2

data_processing:
Data were filtered for high-quality reads using the fastq_quality_filter tool from FASTX-Toolkit (Hannon, 2010) with parameters -q 20 -p 80 and aligned to the mm10 genome assembly using Bowtie2 with –end-to-end --fast parameters. Peaks were called using MACS2 with default parameters.
mm10
See data processing associated with each sample
Genome_build: mm10
Supplementary_files_format_and_content: ChIP-seq: .bed files of peaks; RNA-seq: .txt files of read counts by gene

extract_protocol:
Cells were cross-linked for ChIP-seq with 1% formaldehyde at room temperature for 10 min. The formaldehyde was quenched with 2.5M glycine at room temperature for 5 minutes. Fixed cells were spun down at 6000xg for 3 minutes at 4°C. Cells were washed with cold PBS twice and resuspended in 100ul ChIP lysis buffer (1% SDS, 10mM EDTA, 50mM Tri-HCl at pH 8.1) before being snap frozen in liquid nitrogen. Immunoprecipitation was carried out as previously described (Lesch et al, Nat Gen 2016).
DNA integrity and fragment size were confirmed on a BioAnalyzer.  Approximately 5-10ng of DNA was end-repaired, A-tailed, adapter-ligated, and PCR enriched (8-10 cycles) using the KAPA Hyper Library Preparation kit (KAPA Biosystems, #KK8504).


title: Control Distal 2

description: Gene expression data from Control Proximal 5


title: H3K79me3_ChIP_ko_rep2

value: Abcam, ab2621


title: Control Distal 1

description: Gene expression data from Control Proximal 4


title: DHL10_Combo2


title: H3K79me3_input_ko_rep1


title: Control Proximal 3

description: Gene expression data from Control Proximal 3


title: RNA_mESCs_wt_rep3


title: K422_MI503_MLL1

data_processing:
Library strategy: CUT&Tag
Basecalls performed using Illumina CASAVA version 1.7
For RNA-seq samples, reads of DLBCL cell lines were mapped to the human genome assembly hg38 using HISAT2 (v2.1.0). The mapped reads count of each gene was measured by featureCounts (v1.6.1). For CUT&Tag samples, reads were mapped to the human genome assembly hg38 using HISAT2 (v2.1.0). Potential PCR duplicates were removed by the function "MarkDuplicates" (parameter: REMOVE_DUPLICATES=true) of Picard (v2.23.1).
Genome_build: hg38
Supplementary_files_format_and_content: For RNA-seq samples, tab-delimited text files include reads count values for each gene in each sample. For CUT&Tag samples, bigwig files normalized to count per million reads.

value: Treated by MI503


title: Control Proximal 2

description: Gene expression data from Control Proximal 2

value: Male


title: H3K79me3_ChIP_ko_rep1


title: H3K79me3_input_wt_rep2


title: RNA-seq data of aipp3-1 replicate 3

data_processing:
For ChIP-seq analysis, raw reads were trimmed using trim_galore (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) and aligned to the TAIR10 reference genome with bowtie2 (v2.4.2) allowing zero mismatch and reporting one valid alignment for each read. The Samtools (v1.15) were used to convert sam files to bam files, sort bam files and remove duplicate reads. Track files in bigWig format were generated using bamCoverage of deeptools (v3.5.1) with RPKM normalization. Peaks were called with MACS2 (v2.1.2) and peaks frequently identified in previous ChIP-seq of Col-0 plant with M2 antibody for FLAG epitope were removed from analysis.
For RNA-seq analysis, the raw reads were aligned to the TAIR10 reference genome with bowtie2. Rsem-calculate-expression from RSEM with default settings was used to calculate expression levels. DEGs and DE-TEs were calculated with run_DE_analysis.pl from Trinity version 2.8.5 and log2 FC ≥ 1 and FDR < 0.05 were used as the cut off. RNA-seq track files in bigWig format were generated using bamCoverage of deeptools (v3.1.3) with RPKM normalization.
For WGBS analysis, the raw reads were aligned to both strands of the TAIR10 reference genome using BSMAP (v.2.74), allowing up to 2 mismatches and 1 best hit. Reads with more than 3 consecutives methylated CHH sites were removed, and the methylation level was calculated with the ratio of C/(C+T).
For BSPCR analysis, raw reads were aligned to both strands of the TAIR10 reference genome with BSMAP (v.2.90) allowing up to 2 mismatches and 1 best hit. After quality filtering, the methylation level of cytosines was calculated as the ratio of C/(C+T).
For ATAC-seq analysis, raw reads were adaptor-trimmed with trim_galore and mapped to the TAIR10 reference genome with Bowtie2 (-X 2000 -m 1). After removing duplicate reads and reads mapped to chloroplast and mitochondrial, ATAC-Seq open chromatin peaks of each replicate were called using MACS2 with parameters -p 0.01 --nomodel --shift -100 --extsize 200. Consensus peaks between replicates were identified with bedtools (version 2.26.0) intersect and differential accessible peaks were called with the R packge edgeR (version 3.30.0).
Assembly: tair10
Supplementary files format and content: .bw files are bigWig files of coverage tracks normalized with RPKM (for ChIP-seq and ATAC-seq), or methylation levels (for WGBS)
Supplementary files format and content: _methratio_type.txt files are tab-delimited text files containing methylation type and level at indicated chromosome positions.
Supplementary files format and content: .genes.results files are tab-delimited text files containing RNA-seq quantification data over genes and TEs.
Supplementary files format and content: .narrowPeak files are bed files containing position of called peaks for ChIP-seq.


title: RNA-seq data of aipp3-1 replicate 1


title: RNA-seq data of aipp3-1 replicate 2


title: Control Proximal 1

description: Gene expression data from Control Proximal 1


title: K422_MI503_MEN1


title: H3K79me3_ChIP_wt_rep2


title: K422_DMSO_MLL1


title: DHL10_Combo1


title: RNA-seq data of aipp3-2 replicate 2


title: RNA-seq data of wild type (Col-0) control replicate 3


title: H3K79me3_input_wt_rep1


title: RNA-Seqoftobacco:Leaf [GDH88_Lc_1]

city: Guiyang

first: kai

last: pi

state: Guizhou

department: Key Laboratory for Tobacco Quality Research Guizhou Province

institute: Guizhou University

data_processing:
The raw paired end reads were trimmed and quality controlled by SeqPrep(https://github.com/jstjohn/SeqPrep) and Sickle (https://github.com/najoshi/sickle) with default parameters.
Then clean reads were separately aligned to reference genome（https://solgenomics.net/organism/Nicotiana_tabacum/genome） with orientation mode using HISAT2 (http://ccb.jhu.edu/software/hisat2/index.shtml)software.
The mapped reads of each sample were assembled by StringTie(https://ccb.jhu.edu/software/stringtie/index.shtml?t=example) .
RSEM (http://deweylab.github.io/RSEM/) establishes the maximum likelihood abundance estimation model based on the maximum expectation algorithm, and considers the paid end reads, the length of reads, the length distribution of fragments, and the quality value to distinguish which transcripts are different subtypes of the same gene. The results of expression quantification are expressed in TPM/FPKM. The homogenization process of TPM/FPKM makes the total expression amount in different samples consistent.
Assembly: Tobacco K326 Reference Genome（https://solgenomics.net/organism/Nicotiana_tabacum/genome）
Supplementary files format and content: all_ express.txt includes 15 transcriptome sequencing materials and 69500 gene expressions. The file can be opened in Excel for viewing.

organism: Nicotiana tabacum

source_name: Leaf

extract_protocol:
Total RNA was extracted from the tissue using TRIzol® Reagent (Plant RNA Purification Reagent for plant tissue) according the manufacturer’s instructions (Invitrogen) and genomic DNA was removed using DNase I (TaKara). Then RNA quality was determined by 2100 Bioanalyser (Agilent) andquantified using the ND-2000 (NanoDrop Technologies). Only high-quality RNA sample(OD260/280=1.8~2.2, OD260/230≥2.0, RIN≥6.5, 28S:18S≥1.0, >1μg) was used to construct sequencing library.
RNA-seq transcriptome librariy was prepared following TruSeqTM RNA sample preparation Kit from Illumina (San Diego, CA) using 1μg of total RNA. After quantified by TBS380, paired-end RNA-seq sequencing library was sequenced with the Illumina HiSeq xten/NovaSeq 6000 sequencer (2 × 150bp read length)

value: Leaf

value: After topping


title: K422_DMSO_MEN1


title: RNA-Seqoftobacco:Root [Hongda_Ra_1]

source_name: Root

value: Root

value: Hongda


title: DHL10_CTR1


title: RNA-seq data of aipp3-2 replicate 1

extract_protocol:
Genomic DNA for WGBS was extracted with DNeasy Plant Mini Kit (QIAGEN). Genomic DNA for BS-PCR-seq was extracted with CTAB method. RNA was extracted with Direct-zol RNA MiniPrep kit (Zymo Research).
ChIP-seq library preparation: 15 ml of unopened flower buds were collected for each ChIP and flash-frozen in liquid nitrogen. The flower tissue was ground to fine powder with Retsch homogenizer in liquid nitrogen and resuspended in nuclei extraction buffer (50 mM HEPES pH 8.0, 1 M sucrose, 5 mM KCl, 5 mM MgCl2, 0.6% Triton X-100, 0.4 mM PMSF, 5 mM benzamidine, cOmplete EDTA-free Protease Inhibitor Cocktail (Roche), 50uM MG132). For transgenic lines of MOM1-MYC and PIAL2-MYC, EGS was first added to resuspended lysate to 1.5 mM and the tissue lysate was incubated at room temperature for 10 min with rotation. Then the lysate was supplemented with formaldehyde at 1% and rotated at room temperature for another 10 min followed by adding glycine to stop crosslinking. For ChIP of all other proteins, crosslinking was performed by directly supplementing formaldehyde to 1% without adding EGS, then rotated at room temperature for 10 min followed by adding glycine to stop crosslinking. The crosslinked nuclei were isolated, lysed with Nuclei Lysis Buffer and diluted with ChIP Dilution Buffer. Then the lysate was sonicated for 22 min (30 s on/30s off) with Bioruptor Plus (Diagenode). After centrifugation, antibody for FLAG epitope (M2 monoclonal antibody, Sigma F1804, 10 ul per ChIP) or for MYC epitope (Cell Signaling, 71D10, 20 ul per ChIP) were added to the supernatant and incubated at 4 ℃ overnight with rotation. Then, Protein A and Protein G Dynabeads (Invitrogen) were added and incubated at 4 ℃ for 2 hours with rotation. After that, the beads were washed and eluted, and the eluted chromatin was reverse-crosslinked by adding 20 ul 5 M NaCl and incubating at 65 ℃ overnight followed by treatment of Proteinase K (Invitrogen) for 4 hours at 45 ℃. DNA was purified and precipitated with 3 M Sodium Acetate, GlycoBlue (Invitrogen) and ethanol at -20 ℃ overnight. After centrifugation, the precipitated DNA was washed with ice cold 70% ethanol, air dried and dissolved in 120 ul of H2O. ChIP-seq libraries were prepared with Ovation Ultra Low System V2 kit (NuGEN).
RNA-seq library preparation: Twelve-day old seedlings grown on half MS medium (Murashige and Skoog Basal Medium) were collected and flash-frozen in liquid nitrogen. RNA was extracted with Direct-zol RNA MiniPrep kit (Zymo Research) and 1ug of total RNA was used to prepare RNA-seq libraries with TruSeq Stranded mRNA kit (Illumina)
WGBS library preparation: Rosette leaves of about one-month-old Arabidopsis plants were collected for DNA extraction using DNeasy Plant Mini Kit (QIAGEN). 500 ng DNA was sheared with Covaris S2 (Covaris) into around 200bp at 4℃. The DNA fragments were used to perform end repair reaction using the Kapa Hyper Prep kit (Roche), and together with Illumina TruSeq DNA sgl Index Set A/B (Illumina) to perform adapter ligation. The ligation products were purified with AMPure beads (Beckman Coulter), and then converted with EpiTect Bisulfite kit (QIAGEN). The converted ligation products were used as templates, together with the primers from the Kapa Hyper Prep kit (Roche) and MyTaq Master mix (Bioline) to perform PCR. The PCR products were purified with AMPure beads (Beckman Coulter) and used for sequencing.
ATAC-seq library preparation: About 5 grams of unopened flower buds was collected and immediately transferred into ice-cold grinding buffer (300 mM sucrose, 20 mM Tris pH 8, 5 mM MgCl2, 5 mM KCl, 0.2% Triton X-100, 5 mM β-mercaptoethanol, and 35% glycerol). The samples were ground with Omni International General Laboratory Homogenizer on ice and then filtered through a two-layer Miracloth and a 40-µm nylon mesh Cell Strainer (Fisher). Samples were spin filtered for 10 min at 3,000 g, the supernatant was discarded, and the pellet was resuspended with 25 ml of grinding buffer using a Dounce homogenizer. The wash step was performed twice in total, and nuclei were resuspended in 0.5 ml of freezing buffer (50 mM Tris pH 8, 5 mM MgCl2, 20% glycerol, and 5 mM β-mercaptoethanol). Nuclei were subjected to a transposition reaction with Tn5 (Illumina). For the transposition reaction, 25 µl of 2x DMF (66 mM Tris-acetate pH 7.8, 132 mM K-Acetate, 20 mM Mg-Acetate, and 32% DMF) was mixed with 2.5 µl Tn5 and 22.5 µl nuclei suspension at 37°C for 30 min. Transposed DNA fragments were purified with ChIP DNA Clean & Concentrator Kit (Zymo). Libraries were prepared with Phusion High-Fidelity DNA Polymerase (NEB) in a system containing 12.5 µl 2x Phusion, 1.25 µl 10 mM Ad1 primer, 1.25 µl 10 mM Ad2 primer, 4 µl ddH2O, and 6 µl purified transposed DNA fragments.
BS-PCR library preparation: Rosette leaves of about one-month-old plants were collected and subject to DNA extraction with CTAB method followed by bisulfite DNA conversion using the EpiTect Bisulfite kit (QIAGEN) kit. Three regions of the FWA gene were amplified from the converted DNA with Pfu Turbo Cx (Agilent): Region 1 (chr4: 13038143-13038272), Region 2 (chr4: 13038356- 13038499) and Region3 (chr4: 13038568-13038695). Libraries were prepared with the purified PCR product by the Kapa DNA Hyper Kit (Roche) together with TruSeq DNA UD indexes for Illumina (Illumina) and were sequenced on Illumina iSeq 100 or HiSeq 4000 instruments.

value: whole seedling


title: RNA-seq data of wild type (Col-0) control replicate 1

value: 12 day old


title: RNA-Seqoftobacco:Leaf [V×G88_Lc_1]


title: K422_MLL1

value: untreated


title: H3K79me3_ChIP_wt_rep1

value: wild type


title: H3K79me2_input_ko_rep2


title: RNA-Seqoftobacco:Leaf [Va116_Lc_1]


title: RNA-seq data of nrpe1-11 replicate 3


title: K422_MEN1


title: RNA-seq data of nrpe1-11 replicate 2


title: RNA-Seqoftobacco:Leaf [Basma_Lc_1]

value: Basma


title: RNA-seq data of wild type (Col-0) control replicate 2


title: H3K79me2_ChIP_ko_rep2

value: Abcam, ab3594


title: RNA-Seqoftobacco:Leaf [H×B_Lc_1]

value: HxB


title: H3K79me2_input_ko_rep1


title: RNA-seq data of nrpe1-11 replicate 1


title: H3K79me2_ChIP_ko_rep1


title: K422_IgG

value: DLBCL cell line


title: RNA-Seqoftobacco:Leaf [Hongda_Lc_1]


title: Farage_MI503_MEN1

value: Farage


title: H3K79me2_input_wt_rep2


title: RNA-seq data of wild type (Col-0) control (for nrpe1-11) replicate 2


title: H3K79me2_ChIP_wt_rep2


title: RNA-Seqoftobacco:Leaf [GDH88_Lb_1]


title: RNA-seq data of wild type (Col-0) control (for nrpe1-11) replicate 3


title: RNA-Seqoftobacco:Leaf [V×G88_Lb_1]


title: RNA-seq data of wild type (Col-0) control (for nrpe1-11) replicate 1


title: Farage_MI503_MLL1


title: Farage_DMSO_MLL1

value: Treated by DMSO


title: ChIP-seq data of wild type plants as control for PIAL2-myc replicate 2

source_name: floral tissue

value: floral tissue

value: one month old

value: anti-myc (cell Signaling 71D10)


title: RNA-Seqoftobacco:Leaf [Va116_Lb_1]

value: Leaf


title: H3K79me2_input_wt_rep1


title: Farage_DMSO_MEN1


title: H3K79me2_ChIP_wt_rep1


title: K422_H3K27me3


title: ChIP-seq data of wild type plants as control for PIAL2-myc replicate 1


title: Farage_MLL1


title: RNA-Seqoftobacco:Leaf [Basma_Lb_1]

value: After topping


title: ChIP-seq data of wild type plants as control for PHD3 replicate 2 with myc epitope


title: RNA-Seqoftobacco:Leaf [H×B_Lb_1]


title: ChIP-seq data of wild type plants as control for PHD3 replicate 1 with flag epitope

value: anti-flag (M2 monoclonal, sigma F1804)


title: Farage_H3K27me3


title: ChIP-seq data of wild type plants as control for PHD1-flag replicate 2


title: Farage_IgG


title: RNA-Seqoftobacco:Leaf [Hongda_Lb_1]

value: Hongda


title: RNA-Seqoftobacco:Leaf [GDH88_La_1]


title: NPC-Con3

city: Palo Alto

first: Liana

middle: Nicole

last: Bonanno

state: California

address: 3801 Miranda Ave, Bldg 100 Rm D3-111

department: Neurology

institute: Stanford University

data_processing:
The quality of fastq files was assessed using FASTQC (v 0.11.4)
Reads were trimmed to 75bp using fastX toolkit (v 0.0.14)
Trimmed reads were mapped to mouse mm9 reference genome using STAR (v 2.5.1b). Raw read counts were generated with STAR using the GeneCounts function.
Differential expression in RNA-Seq was analyzed using the R DESeq2 package
Differential expression in RNA-Seq was analyzed using the R DESeq2 package. Read counts were used as input and normalized using built-in algorithms in DESeq2.
Genome_build: mm9
Supplementary_files_format_and_content: comma separated value file of normalized read counts from DESeq2 software

source_name: Microglia

extract_protocol:
All procedures were carried out at 4°C. Mice were perfused, cerebella were chopped and homogenized using a Dounce homogenizer in 2ml cold Medium A (HBSS+ 15mM HEPES+0.05% glucose+ 1:500 DnaseI), filtered through 100µm cell strainer, rinsed with 5ml Medium A and centrifuged at 340g for 5 mins. For myelin removal, the precipitate was resuspended in 25% standard isotonic percoll (25% Percoll in PBS, diluted with Medium A) and centrifuged at 950g for 20 mins. CD11b+Tmem119+ microglia (~20,000 per sample) were FACS sorted into 500µl RLT buffer (Qiagen) and stored on -80°C.
RNA was extracted from isolated microglia using RNeasy Plus Micro kit (Qiagen) and the quality assessed by Agilent 2100 Bioanalyzer (Stanford PAN facility). About 1ng RNA was converted to cDNA and amplified for 12 cycles using SMART-seq v4 Ultra Low input RNA kit for sequencing (Takara Bio USA, Inc.) according to manufacturer’s instructions. Amplified cDNA was then purified by immobilization on AMPure XP beads. Purified cDNA was normalized and tagmented for 5 mins using Nextera XT DNA library prep kit (Illumina). Unique indexes were then added to each sample, which were then amplified for 12 cycles. cDNA was purified using AMPure XP beads and quality assessed by Advanced Analytical Fragment Analyzer (Stanford PAN facility). Samples were then normalized and pooled together and sequenced on Illumina Novaseq 6000 (Novogene Corporation Inc.) to obtain 150bp paired-end reads.

value: microglia

value: 9 week

value: Control


title: NPC-Con5


title: NPC-Con4


title: ChIP-seq data of wild type plants as control for PHD1-flag replicate 1


title: SUDHL5-MI503-2

data_processing:
Basecalls performed using Illumina CASAVA version 1.7
For RNA-seq samples, reads of DLBCL cell lines were mapped to the human genome assembly hg38 using HISAT2 (v2.1.0). The mapped reads count of each gene was measured by featureCounts (v1.6.1). For CUT&Tag samples, reads were mapped to the human genome assembly hg38 using HISAT2 (v2.1.0). Potential PCR duplicates were removed by the function "MarkDuplicates" (parameter: REMOVE_DUPLICATES=true) of Picard (v2.23.1).
Genome_build: hg38
Supplementary_files_format_and_content: For RNA-seq samples, tab-delimited text files include reads count values for each gene in each sample. For CUT&Tag samples, bigwig files normalized to count per million reads.

value: Treated by MI503


title: RNA-Seqoftobacco:Leaf [V×G88_La_1]


title: SUDHL5-MI503-1


title: RNA-Seqoftobacco:Leaf [Va116_La_1]


title: NPC-Con1


title: ChIP-seq data of wild type plants as control for MORC6-myc replicate 1


title: ChIP-seq data of wild type plants as control for MORC6-myc replicate 2


title: RNA-Seqoftobacco:Leaf [Basma_La_1]

value: Basma


title: NPC-PLX5


title: SUDHL5-DMSO-2


title: SUDHL5-DMSO-1


title: RNA-Seqoftobacco:Leaf [H×B_La_1]


title: Farage_MEN1

extract_protocol:
CUT&Tag was performed as described previously (nature communications, 2019).
CUT&Tag was performed as described previously (nature communications, 2019).

value: untreated


title: ChIP-seq data of wild type plants as control for MOM1-myc replicate 2


title: FARAGE-MI503-2


title: RNA-Seqoftobacco:Leaf [Hongda_La_1]


title: NPC-Con2


title: FARAGE-MI503-1


title: RNA-Seqoftobacco:Stalk [GDH88_Sc_1]

source_name: Stalk

value: Stalk


title: ChIP-seq data of wild type plants as control for AIPP3flag replicate 2


title: RNA-Seqoftobacco:Stalk [V×G88_Sc_1]


title: NPC-PLX1


title: FARAGE-DMSO-2

value: DLBCL cell line


title: NPC-9C


title: FARAGE-DMSO-1

value: Farage


title: RNA-Seqoftobacco:Stalk [Basma_Sc_1]


title: RNA-Seqoftobacco:Stalk [Va116_Sc_1]


title: DB-MI503-1

value: DB


title: NPC-PLX3


title: ChIP-seq data of PIAL2-myc replicate 2

value: floral tissue


title: ChIP-seq data of wild type plants as control for MOM1-myc replicate 1

value: one month old


title: NPC-PLX4


title: ChIP-seq data of PHD3 replicate1 with flag epitope tagged transgenic plants


title: ChIP-seq data of PIAL2-myc replicate 1

value: anti-myc (cell Signaling 71D10)


title: RNA-Seqoftobacco:Stalk [Hongda_Sc_1]


title: RNA-Seqoftobacco:Stalk [H×B_Sc_1]

value: HxB


title: DB-DMSO-2

value: Treated by DMSO


title: NPC-PLX2


title: ChIP-seq data of wild type plants as control for AIPP3flag replicate 1

value: anti-flag (M2 monoclonal, sigma F1804)


title: NPC-9A


title: ChIP-seq data of PHD1-flag replicate2


title: NPC-6C

value: 6 week


title: DB-MI503-2


title: DB-DMSO-1


title: RNA-Seqoftobacco:Stalk [GDH88_Sb_1]

value: After topping


title: RNA-Seqoftobacco:Stalk [V×G88_Sb_1]


title: NPC-9B

value: microglia

value: 9 week


title: K422-MI503-1

value: Treated by MI503


title: K422-MI503-2


title: RNA-Seqoftobacco:Stalk [Va116_Sb_1]


title: NPC-6B


title: ChIP-seq data of MORC6-myc replicate 2


title: NPC-6D


title: RNA-Seqoftobacco:Stalk [Basma_Sb_1]

value: Basma


title: NPC-3D

value: 3 week


title: RNA-Seqoftobacco:Stalk [H×B_Sb_1]

value: Stalk


title: NPC-6A


title: ChIP-seq data of PHD3 replicate2 with myc epitope tagged transgenic plants


title: ChIP-seq data of MORC6-myc replicate 1


title: K422-DMSO-2

value: DLBCL cell line


title: NPC-3B


title: K422-DMSO-1


title: ChIP-seq data of MOM1-myc replicate 2


title: RNA-Seqoftobacco:Stalk [Hongda_Sb_1]

value: Hongda


title: ChIP-seq data of AIPP3-flag replicate 2


title: NPC-3C


title: differentiated miRNA-Seq3

description: mirna.cpm.txt

data_processing:
Bcl files were demultiplexed and converted to fastq format using 'Bcl2fastq' version 2.2, with automatic adapter trimming disabled. Lane data for each sample were merged.
Using 'Cutadapt' version 1.14, sequencing adapters were trimmed, low quality 3 prime nucleotides (Phred33 < 28) were removed. Reads aligning to mature and precursor tRNAs (gtRNAdb, v2.0) were identified and removed using 'Bowtie2' version 2.2.6.
Unaligned reads were retained and aligned to the reference genome (GRCh38, NCBI, used for compatability with miRBase) using Bowtie2. Reads aligning to mature miRNAs (miRBase release 22) were counted with 'HTSeq' version 0.9.1.
Differential expression was calculated using 'EdgeR' version 3.8
Genome_build: hg19
Supplementary_files_format_and_content:  mirna.cpm.txt (Tab delimited text file containing normalized counts per million for each mature miRNA.)

extract_protocol:
Total RNA was extracted from all groups by harvesting cells in 1mL TRIzol reagent (ThermoFisher, Waltham, MA, USA), as per the manufacturer’s instructions, with RNA precipitated at –30°C overnight to increase yield.
For small RNA sequencing, libraries were produced from 1µg of total RNA using the Illumina TruSeq Small RNA Library Preparation Kit, according to the manufacturer’s instructions. Firstly, adapters were ligated to RNAs, prior to reverse transcription, amplification via 11 PCR cycles and quantification via Agilent High Sensitivity DNA kit. Based on estimated small RNA concentrations, samples were pooled in equimolar ratios and volumes, and small RNAs between ~20–33nt were purified via 6% native PAGE. After eluting the combined PCR amplicon from gel fragments, cDNA was ethanol precipitated, quantified, denatured and diluted to a final concentration of 3pM. The resultant library was then subjected to 76 cycles of single end sequencing using the Illumina NextSeq500.

value: Neuronally differentiated SH-SY5Y

value: small RNA


title: differentiated miRNA-Seq2

description: mirna.cpm.txt


title: ChIP-seq data of PHD1-flag replicate1

value: floral tissue

value: one month old


title: differentiated miRNA-Seq1

description: mirna.cpm.txt


title: NPC-1D

value: 1 week


title: RNA-Seqoftobacco:Stalk [GDH88_Sa_1]


title: BS-PCR data of miniMOM1-ZF T2 plant without transgene

source_name: rosette leaf tissue

value: rosette leaf tissue

value: miniMOM1-ZF transgene free segragate plant


title: ChIP-seq data of AIPP3-flag replicate 1

value: anti-flag (M2 monoclonal, sigma F1804)


title: NPC-1C


title: RNA-Seqoftobacco:Stalk [Va116_Sa_1]

value: After topping


title: undifferentiated miRNA-Seq3

description: mirna.cpm.txt


title: undifferentiated miRNA-Seq2

description: mirna.cpm.txt


title: BS-PCR data of miniMOM1-ZF T2 plant with transgene

value: miniMOM1-ZF with transgene


title: RNA-Seqoftobacco:Stalk [Basma_Sa_1]


title: NPC-1B

value: microglia


title: NPC-1A


title: ChIP-seq data of MOM1-myc replicate 1

value: anti-myc (cell Signaling 71D10)


title: BS-PCR data of PIAL2-ZF T2 plant without transgene

value: PIAL2-ZF transgene free segragate plant


title: NPC-3A

value: 3 week


title: RNA-Seqoftobacco:Stalk [H×B_Sa_1]

value: Stalk

value: HxB


title: BS-PCR data of fwa control plant

value: fwa


title: undifferentiated miRNA-Seq1

description: mirna.cpm.txt

value: Neuronally differentiated SH-SY5Y


title: WT-9D

value: balb/c

value: 9 week


title: WT-9C


title: differentiated PAT-Seq2

description:
apa.dexseq.txt
polya.length.tail.tools_revised.csv

data_processing:
Demultiplexed fastq files were analysed using the 'tail-tools' version 0.4.1 package, which automates genome alignment, identification of adenylation sites, read-counting, poly(A) tail length estimation and differential tail length analysis. Firstly, adapter sequences and poly(A) tails were trimmed from fastq-formatted reads. Poly(A) tails were identified by calling a run of consecutive “A” residues extending to the 3´ end or the adapter sequence, with an error rate of 1 in 5 bases and Phred33 quality score > 10 allowed.
Reads were then aligned to the reference genome (hg19, UCSC) using Bowtie2, during which reads were identified as polyadenylated if a non-templated run of ≥ 4 consecutive “A” residues was detected. For genes with at least 10 poly(A) reads, average tail length was calculated for downstream analysis.
Differential analysis of tail length between experimental conditions was then determined using a custom modification of the limma voom statistical pipeline to account for depth-associated variation in tail length estimations.
Alternative polyadenylation analysis was conducted with DEXSeq version 1.32.0.
Genome_build: hg19
Supplementary_files_format_and_content:  polya.length.tail.tools_revised.csv (Comma separated values containing poly(A) tail counts and gene counts for each gene product.)
Supplementary_files_format_and_content:  apa.dexseq.txt (Tab-delimited text file containing differential expression analysis of alternative polyadenylation sites and normalized counts for each site.)

extract_protocol:
Total RNA was extracted from all groups by harvesting cells in 1mL TRIzol reagent (ThermoFisher, Waltham, MA, USA), as per the manufacturer’s instructions, with RNA precipitated at –30°C overnight to increase yield.
Poly(A) tail sequencing (PAT-Seq) was conducted using 1µg of high quality RNA (RNA integrity number = 10 for all samples) as previously described (Harrison et al, 2015). Briefly, biotinylated ePAT primers (5´-Bio-CAGACGTGTGCTCTTCCGATCTTTTTTTTTTTTTTTTTT-3´; 100µM) were ligated to polyadenylated mRNAs and 3´ ends were extended using 5 units (U) of the Klenow fragment of DNA polymerase I (NEB, Ipswich, MA, USA). RNAs were then subjected to limited RNase T1 digestion (10U, Roche, Basel, Switzerland), with parameters optimised to produce ~250nt fragments, after which 3´ fragments were collected with streptavidin beads (NEB). Phosphorylation of 5´-ends was next performed with Poly Nucleotide Kinase (0.5U, NEB), prior to ligation of 5´ splinted linkers, reverse transcription and size selection (120–400bp) via 6% denaturing urea-polyacrylamide gel. To amplify all samples, 10µL of cDNA was subjected to 16 PCR cycles, with 2µL of ScriptSeq indexed reverse primers (50µM, Epicentre, Madison, WI, USA) included for sample indexing compatible with Illumina (San Diego, CA, USA) sequencing platforms. PAT-Seq libraries were subsequently normalized, pooled and sequenced on a single lane of an Illumina HiSeq 1500, with a total of 151 single ended cycles performed.

value: Poly(A) mRNA


title: RNA-Seqoftobacco:Stalk [V×G88_Sa_1]


title: differentiated PAT-Seq1


title: BS-PCR data of PIAL2-ZF T2 plant with transgene

value: one month old

value: PIAL2-ZF with transgene


title: WT-9B


title: RNA-Seqoftobacco:Root [GDH88_Rc_1]

value: Root


title: RNA-Seqoftobacco:Stalk [Hongda_Sa_1]

value: Hongda


title: BS-PCR data of PIAL1-ZF T2 plant without transgene

value: rosette leaf tissue

value: PIAL1-ZF transgene free segragate plant


title: WT-9A

value: microglia


title: BS-PCR data of PIAL1-ZF T2 plant with transgene

value: PIAL1-ZF with transgene


title: undifferentiated PAT-Seq3


title: RNA-Seqoftobacco:Root [Va116_Rc_1]

value: After topping


title: RNA-Seqoftobacco:Root [V×G88_Rc_1]


title: BS-PCR data of PHD1-ZF T2 plant without transgene

value: PHD1-ZF transgene free segragate plant


title: undifferentiated PAT-Seq2


title: WT-6D

value: 6 week


title: WT-6C


title: RNA-Seqoftobacco:Root [H×B_Rc_1]

value: HxB


title: undifferentiated PAT-Seq1


title: differentiated PAT-Seq3


title: RNA-Seqoftobacco:Root [Basma_Rc_1]

value: Basma


title: BS-PCR data of PHD1-ZF T2 plant with transgene

value: PHD1-ZF with transgene


title: BS-PCR data of MOM2-ZF T2 plant without transgene

value: MOM2-ZF transgene free segragate plant


title: WT-6B

value: balb/c


title: WT-6A


title: BS-PCR data of MOM2-ZF T2 plant with transgene

value: MOM2-ZF with transgene


title: RNA-Seqoftobacco:Root [Hongda_Rc_1]


title: differentiated RNA-Seq2

description: mrna.cpm.txt

data_processing:
Bcl files were demultiplexed and converted to fastq format using 'Bcl2fastq' version 2.2. Lane data for each sample were merged.
Using 'Cutadapt' version 1.14, sequencing adapters were trimmed, low quality 3 prime nucleotides (Phred33 < 28) were removed.
Reads were mapped to the hg19 reference genome using 'HISAT2' version 2.0.2, and reads aligning to features were counted with 'HTSeq' version 0.9.1.
Differential expression was calculated using 'EdgeR' version 3.8
Genome_build: hg19
Supplementary_files_format_and_content:  mrna.cpm.txt (Tab delimited text file containing normalized counts per million for each gene.)

extract_protocol:
Total RNA was extracted from all groups by harvesting cells in 1mL TRIzol reagent (ThermoFisher, Waltham, MA, USA), as per the manufacturer’s instructions, with RNA precipitated at –30°C overnight to increase yield.
For each sample, 1µg of high quality (RNA integrity number = 10 for all samples) total RNA was subjected to library preparation for mRNA sequencing using the TruSeq Stranded mRNA Kit (Illumina), as per the manufacturer’s instructions. Briefly, mRNA was denatured (65°C, 5 min) and ligated to oligo-dT magnetic beads (room temperature, 5 min), after which unbound RNA and non-specifically bound rRNA was discarded. mRNA was then heat fragmented (94°C, 8 min), following which reverse transcription and adapter ligation were performed as per the manufacturer’s instructions. Enrichment of cDNA fragments was subsequently conducted via 15 cycles of PCR, after which libraries were normalized, pooled and subjected to 151 cycles of sequencing using the NextSeq 500 system.

value: Neuronally differentiated SH-SY5Y

value: Poly(A) mRNA


title: differentiated RNA-Seq3

description: mrna.cpm.txt


title: RNA-Seqoftobacco:Root [GDH88_Rb_1]

value: Root


title: WT-3D

value: 3 week


title: RNA-Seqoftobacco:Root [V×G88_Rb_1]


title: BS-PCR data of MOM1-ZF T2 plant with transgene

value: rosette leaf tissue

value: one month old

value: MOM1-ZF with transgene


title: undifferentiated RNA-Seq3

description: mrna.cpm.txt


title: WT-3C

value: microglia


title: RNA-Seqoftobacco:Root [Va116_Rb_1]

value: After topping


title: differentiated RNA-Seq1

description: mrna.cpm.txt


title: WT-3B


title: undifferentiated RNA-Seq1

description: mrna.cpm.txt


title: RNA-Seqoftobacco:Root [H×B_Rb_1]


title: RNA-Seqoftobacco:Root [Basma_Rb_1]


title: BS-PCR data of AIPP3-ZF T2 line2 plant with transgene

value: AIPP3-ZF with transgene


title: iPSC_CB RNA-seq

city: Muenster

first: Hyun-Woo

last: Jeong

state: NRW

department: Dept. Tissue Morphogenesis

country: Germany

institute: Max-Planck-Institute for Molecular Biomedicine

data_processing:
illumina bcl2fastq (v2.19.1.403) used for basecalling and demultiplexing
Tophat (v2.1.1) used for alignment
HTSeq-count (v0.6.1) used for transcriptome abundance measurement
DESeq2(v1.20.0) used for differential gene expression analyses
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample

source_name: iPSC

extract_protocol:
Cultured samples were directly lysis into RLT plus buffer and total RNA were extracted using RNeasy plus Micro Kit (Qiagen)
Cells were directly lysis into RLT plus buffer and total RNA were extracted using RNeasy plus Micro Kit (Qiagen)
Cultured samples were directly lysis into RLT plus buffer and total RNA were extracted using RNeasy plus Micro Kit (Qiagen)
TruSeq Stranded Total RNA kit Gold (Illumina) or Whole transcriptome Ovation Solo RNA seq Library Preparation Kit (TECAN, NuGEN) was used for the library preparation of all samples

value: iPSC

tag: differentiation stage

value: Wild type iPSCs line


title: RNA-Seqoftobacco:Root [Hongda_Rb_1]

value: Hongda


title: WT-3A


title: BS-PCR data of AIPP3-ZF T2 line1 plant withwout transgene

value: AIPP3-ZF transgene free segragate plant


title: BS-PCR data of MOM1-ZF T2 plant without transgene

value: MOM1-ZF transgene free segragate plant


title: BS-PCR data of AIPP3-ZF T2 line2 plant withwout transgene


title: undifferentiated RNA-Seq2

description: mrna.cpm.txt


title: iPSC_LGMD2A RNA-seq


title: BS-PCR data of Col0 control plant


title: BS-PCR data of AIPP3-ZF T2 line1 plant with transgene


title: Org_8wk Rep2 RNA-seq

source_name: iPSC-derived organoid

extract_protocol:
Cultured samples were directly lysis into RLT plus buffer and total RNA were extracted using RNeasy plus Micro Kit (Qiagen)
Organoids were flash frozen on dry ice, and RNA was harvested using the RNAeasy Micro Kit from Qiagen. Whole transcriptome Illumina TruSeq Stranded Total RNA Library Prep Kit Gold (Illumina) was used for the constuction of libraries
Cultured samples were directly lysis into RLT plus buffer and total RNA were extracted using RNeasy plus Micro Kit (Qiagen)
TruSeq Stranded Total RNA kit Gold (Illumina) or Whole transcriptome Ovation Solo RNA seq Library Preparation Kit (TECAN, NuGEN) was used for the library preparation of all samples

value: iPSC-derived organoid


title: WT-1B

value: balb/c

value: 1 week


title: WT-1C


title: RNA-Seqoftobacco:Root [V×G88_Ra_1]


title: RNA-Seqoftobacco:Root [GDH88_Ra_1]


title: WT-1A


title: ATAC seq data of mom1-3 mutant replicate 2

value: floral tissue


title: RNA-Seqoftobacco:Root [Va116_Ra_1]

value: Root


title: Org_8wk Rep1 RNA-seq


title: Org_4wk Rep3 RNA-seq


title: sev1-3

city: shanghai

first: yanyong

last: cheng

address: 639 Zhizaoju Road

department: Department of Anesthesiology

institute: Shanghai Ninth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine

data_processing:
Basecalls performed using CASAVA version 1.8
Cellranger was utilized to calculate the raw counts and cell whitelist by default parameter
1. We applied the Seurat [https://satijalab.org/seurat/] package for cell normalization and cell filtering considering the MT percentage, minimum and maximum gene numbers under following criteria:   MT% < 20%;    Cell Gene Number < Median Gene Number * 2;   Cell Gene Number > 200.  PCA and tSNE analysis was used for the single cell to cell relation description. Graphcluster and K-mean was utilized for cell clustering and based on the marker gene achieved some cluster was combined. Wilcox rank sum test was then used for marker gene analysis.
Genome_build: mm10
Supplementary_files_format_and_content: TXT file contain counts for each sample

source_name: prefrontal cortex

growth_protocol: The animal studies were performed according to the guidelines and regulations of the Institute of Laboratory Animal Science, Peking Union Medical College and Chinese Academy of Medical Science (Peking, China).

extract_protocol:
prefrontal cortex were harvested , flash frozen on dry ice, and RNA was harvested using Trizol reagent.
Single Cell RNA sequencing library were generated using the 10x Genomics Chromium Platform and sequenced on the Illumina NovaSeq 6000.

treatment_protocol: Mus musculus of both sexes were exposed to about 3% sevoflurane inhalation anesthesia on post-natal day 6 and then sacrificed after exposure at post-natal day 6

value: prefrontal cortex

value: post natal day 6


title: RNA-Seqoftobacco:Root [Basma_Ra_1]

value: Basma


title: sev1-2


title: WT-1D


title: ATAC seq data of wild type (Col-0) replicate 1

value: one month old


title: ATAC seq data of wild type (Col-0) replicate 2


title: RNA-Seqoftobacco:Root [H×B_Ra_1]

value: HxB


title: Org_4wk Rep2 RNA-seq


title: sev1-1


title: Org_4wk Rep1 RNA-seq


title: aRBC_RNAseq_Rep2

status: Public on Jun 08 2023

city: Mexico City

first: Mayra

last: Furlan-Magaril

state: Mexico City

address: Circuito exterior s/n

department: Molecular Genetics

country: Mexico

institute: IFC-UNAM

data_processing:
RNA-seq reads were mapped to the GRCg6a genome using STAR (v2.7.2b), raw counts were obtained using featureCounts and FPKM were calculated.
Because RNA content in chicken erythrocytes is significantly lower than in the other cell types, raw counts and FPKM were normalized for the number of cells required to obtain 1 µg of RNA
Assembly: GRCg6a
Supplementary files format and content: Tab-delimited text file including FPKM values for each sample.

organism: Gallus gallus

source_name: Primary red blood cells from adult hens (28-38 weeks old)

growth_protocol: Primary fibroblasts and HD3 cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM; GIBCO) supplemented with 10% fetal bovine serum (Biowest), 2% chicken serum and penicillin/streptomycin (Invitrogen).

extract_protocol:
Total RNA was isolated using TRIzol (Invitrogen) following manufacturer's instructions. Libraries were prepared starting from 1 µg of RNA.
RNA-seq libraries were prepared A using the TruSeq Stranded Total RNA Ribo-Zero H/M/R Gold kit (Illumina) following manufacturer's instructions.

value: WT


title: aRBC_RNAseq_Rep3

value: Primary red blood cells from adult hens (28-38 weeks old)


title: aRBC_RNAseq_Rep1


title: eRBC_RNAseq_Rep3

source_name: Primary embryonic red blood cells (Embryonic day 10)


title: eRBC_RNAseq_Rep2

value: Primary embryonic red blood cells (Embryonic day 10)


title: Erythroblasts_RNAseq_Rep3

value: Chicken erythroblasts


title: Fibroblasts_RNAseq_Rep1

source_name: Primary fibroblasts

value: Primary fibroblasts


title: Fibroblasts_RNAseq_Rep2


title: eRBC_RNAseq_Rep1


title: Erythroblasts_RNAseq_Rep2


title: Erythroblasts_RNAseq_Rep1


title: Fibroblasts_RNAseq_Rep3


title: aRBC_Hic_Rep1

data_processing:
Hi-C experiments were processed following the HiC-Pro (v2.11.1) pipeline using the merge data from both replicates to generate .validPairs files with interacting regions.
.validPairs files were normalized to contain the same number of interacting pairs.
Assembly: GRCg6a
Supplementary files format and content: .validPairs files containing the interacting pairs for each sample. validPairs files can be used to generate Hi-C matrices with HiC-Pro.

extract_protocol:
10 x 106 cells were fixed with formaldehyde 2% for 10 minutes at room temperature. Chromatin was digested with MboI overnight and 5′ overhangs were filled with Biotin-14-dATP and religated in nuclei. DNA fragments were purified and shared to an average size of 500 bp using a Covaris machine.
Hi-C libraries were generated using the TruSeq Illumina system.


title: ATAC seq data of mom1-3 mutant replicate 1


title: eRBC_ATACseq_Rep2

data_processing:
ATAC-seq reads were mapped to the GRCg6a genome using Bowtie2 (v2.3.5). Duplicates and reads longer than 150 bp were removed with Samtools (v1.9).
Peaks were called with MACS2 (v2.1.2) with a significance level of 0.01 and the peaks conserved between two biological replicates were used for analysis
Assembly: GRCg6a
Supplementary files format and content: NarrowPeak file with the consensus accessible peaks shared between 2 biological replicates per cell type.

extract_protocol:
Nuclei extraction of 150,000 cells was treated with the Tn5 enzyme (Illumina) for 30 min. Following tagmentation, DNA was extracted using MinElute columns (Qiagen).
ATAC-seq libraries were amplified for 10 PCR cycles using the Nextera barcode system (Illumina).


title: eRBC_Hic_Rep1


title: eRBC_ATACseq_Rep1


title: Erythroblasts_Hic_Rep1


title: Erythroblasts_ATACseq_Rep1


title: Erythroblasts_ATACseq_Rep2


title: Nor, H3K9ac, patient 3, ChIP

city: Wenzhou

first: Chenghao

last: Li

state: Zhejiang

address: Wenzhou Medical University, Xueyuan Xi Road

institute: Wenzhou Medical University

data_processing:
chip-seq reads were alioned to the UCSC hg38 genome using Bowtie version 1.12.0nly uniquely mapping reads with at most two mismatches were retained.
ChIP-seq data were marked for duplicates using Picard (v1.128) and filtered for mapping quality using SAMtools
MACS2 (Version 2.1.1) with genomic DNA as input to define background, following all default parameters except -p 1e-9.
The BAM files were converted to BigWig format using deepTools
Assembly: hg38
Supplementary files format and content: bigwig

source_name: Nor

extract_protocol:
Fresh tissues obtained during surgery were collected and digested into single cells or small cell aggregates. Cells were crosslinked with 1% formaldehyde for 10 min in PBS at room temperature and terminated with 125 mM glycine. The fixed DNA was sheared to 100-600bp by the Covaris#M220 focused-ultrasonicator.
DNA was subjected to library preparation with NEBNext ChIP-seq Library Pre Reagent (NEB #E7370S, USA)

value: esophageal squamous cell carcinoma

tag: individual

value: patient 3

value: Nor

tag: Stage

value: Stage III

tag: chip antibody


title: LNC, H3K9ac, patient 3, ChIP

source_name: LNC

tag: tissue

value: LNC


title: Nor, input, patient 3, ChIP


title: EC, H3K9ac, patient 3, ChIP

source_name: EC

value: EC


title: LNC, input, patient 3, ChIP


title: EC, input, patient 3, ChIP


title: EC, H3K9ac, patient 1, ChIP

value: patient 1

value: Stage IV


title: EC, H3K9ac, patient 2, ChIP

value: patient 2


title: 900CTG_20CTG

city: Columbus

first: Camila

middle: F

last: Almeida

state: OH

address: 700 Children's Drive, RB2 WA3103

department: Center for Gene therapy

institute: Nationwide Children's Hospital

description:
FeatureCounts_V31genes_RawCounts_ENSG.tsv
modulize_3CTG_20CTG_junctions.tsv
modulize_NT_20CTG_junctions.tsv

data_processing:
The effective read length was extended using the FLASH tool (Magoč & Salzberg, 2011; PMID: 21903629) that merged overlapping paired-end reads
Extended read-pairs and non-extended forward reads were mapped using STAR v2.7.8c with options: --twopassMode Basic --alignSJDBoverhangMin 1 --alignSJoverhangMin 8 --outFilterMismatchNoverLmax 0.3 --outFilterMultimapNmax 10
Gene-level read counts were extracted from STAR output BAM files using featureCounts v.1.6.5 (PMID: 24227677) with parameters set to strand-specific read counting
The MAJIQ/Voila v2.4.dev3+g85d0781 software (Modeling Alternative Junction Inclusion Quantification) was used to detect and quantify splice variation from the filtered BAM alignment files (Vaquero-Garcia et al., 2016; PMID: 26829591)
Relative inclusion values (“percent selected index” or PSI) of splice junctions within LSVs were calculated using the MAJIQ psi command with parameters minreads = 2 and minpos = 1.
Pairwise delta PSI values (dPSI) were calculated for pairwise groups using the MAJIQ psi command with default parameters and max(PSI) >= 0.050.
The Voila modulize command used the --changing-between-group-dpsi 0.1 option and modules keeping modules if max(P(|dPSI|>=0.100) >= 0.950.
Assembly: GRCh37/hg19
Supplementary files format and content: tab-delimited MATRIX files include Ensemble Gene_ID columns and fragment count values for each sample
Supplementary files format and content: Voila modulize output files are tab separated value files where each line is a single LSV.

source_name: skin biopsy

extract_protocol:
Total RNA was extracted with TRIzol reagent (Fisher BioReagents, BP2805-25), followed by concentration and purification with Zymo kit, including DNase treatment to remove genomic DNA. RNA integrity was assessed with RNA 6000 Nano kit (Agilent, 5067-1511) in the 2100 Bioanalyzer. rRNA was depleted with NEB Next rRNA Depletion Kit (human, mouse, rat) (E #E6310X).
For RNA-seq (mRNA) libraries generation, 200 ng of total RNA was treated with NEBNext rRNA Depletion kit (New England Biolabs, E6310X) and fragmented for 10 minutes. NEBNext Ultra II Directional (stranded) RNA Library Prep (New England Biolabs, E7760L) and NEBNext Multiplex Oligos (New England Biolabs, E6442L) kits were used for cDNA synthesis and amplification for 11 PCR cycles. The concentration of cDNA libraries was determined on Qubit Fluorometer (Thermo Fisher).

tag: condition

value: myotonic dystrophy type 1

value: skin biopsy

tag: cell line

tag: cell type

value: transdifferentiated myotubes

tag: genotype

value: 900 CTG repeats in DMPK gene


title: 1450CTG_20CTG

value: 1450 CTG repeats in DMPK gene

tag: treatment


title: 900CTG_3'CTG

description:
FeatureCounts_V31genes_RawCounts_ENSG.tsv
modulize_3CTG_20CTG_junctions.tsv
modulize_NT_3CTG_junctions.tsv


title: LNC, H3K9ac, patient 1, ChIP


title: Nor, H3K9ac, patient 1, ChIP


title: 1150CTG_3'CTG

value: 1150 CTG repeats in DMPK gene


title: 1150CTG_20CTG


title: 1450CTG_3'CTG


title: 900CTG_NT

description:
FeatureCounts_V31genes_RawCounts_ENSG.tsv
modulize_NT_20CTG_junctions.tsv
modulize_NT_3CTG_junctions.tsv

value: untreated


title: 1450CTG_NT


title: 1150CTG_NT


title: melas_1_purified_rpe_per_atac

city: Iowa City

first: Nathaniel

middle: Kevin

last: Mullin

state: IA

address: 375 Newton Road

institute: University of Iowa

description:
10X Genomics Chromium Controller
ATAC library portion of multimodal experiment

data_processing:
library strategy: Multimodal scRNA-seq & mt-scATAC-seq
FASTQ files were generated from base calls with the bcl2fastq software (Illumina).
Sequencing reads were mapped to a modified GRCh38 reference genome that was generated by hard-masking nuclear regions that share homology with mitochondrial sequences, as described previously (Lareau et al., 2020). Mapping and quantification were carried out by Cell Ranger ARC (v2.0.0, 10X Genomics) using the ‘count’ function.
For gene expression libraries, cells were filtered with the Seurat (v3.1) subset function. Neural retina cells with nUMIs less than 100 (to remove cells with poor read quality) or greater than 4000 (to remove cells likely to be doublets) were removed. RPE/choroid cells with nUMIs less than 500 or greater than 4000 were removed. Neural retina cells with greater than 40% of reads originating from mitochondrial genes or 30% of reads originating from ribosomal genes were also removed.  RPE choroid cells with greater than 30% of reads originating from mitochondrial genes or 20% of reads originating from ribosomal genes were also removed.
For each of the gene expression libraries, reads were normalized with the Seurat (v3.1) NormalizeData function, and 2000 variable features were identified with the FindVariableFeatures command using the ‘vst’ method. Integration anchors from the first 30 dimensions of the canonical correlation analysis (CCA) were used to integrate gene expression data. Data scaling, principal component analysis, and clustering of the gene expression data were performed using Seurat (v3.1).
For ATAC libraries, cells were filtered with the Signac (v1.4.0) subset function. Neural retina cells with fewer than 500 peak region fragments or greater than 15,000 peak region fragments were removed. RPE/choroid cells with fewer than 750 peak region fragments or greater than 15,000 peak region fragments were removed. Cells with greater than 1000x mtDNA depth were also removed.
Term frequency inverse document frequency (TF-IDF) normalization and partial singular value decomposition were performed on each ATAC library using RunTFIDF() and RunSVD() (Signac) with default settings. Gene activities were computed using GeneActivity().
Integration anchors between ATAC datasets were identified using reciprocal LSI projection using  FindIntegrationAnchors() in Signac. Dimensions 2-30 from the CCA were used. LSI embeddings were integrated using IntegrateEmbeddings based on these anchors and using dimensions 1-30.
Gene expression and ATAC portions of the experiment were combined using WNN analysis (Seurat). Integrated ATAC and gene expression objects were subset to include only common cells (i.e., cells that passed both ATAC and gene expression quality control thresholds).
Following multimodal integration, cluster identities (i.e., cell type annotation) identified using the gene expression portion of the experiment with the TransferData() function in Seurat from the annotated neural retina or RPE/choroid scRNAseq data obtained in this study (Figure 1C, E). Transfer anchors between were identified using FindTransferAnchors with the following parameters: reduction = 'pca', dims = 1:30. Cells were annotated with a prediction score > 0.5.
Assembly: GRCh38
Supplementary files format and content: Processed expression data matrix files are provided in tab-delimited format for count(*_gex_count.csv) and processed/normalized (*_gex_normalized.csv) expression values. For processed/normalized files, log-normalized expression values (from GetAssayData(object = seurat_object)) were appended to relevant metadata (barcode, cluster label, and donor number from the manuscript). Each row represents a unique cell, and columns correspond to metadata and log normalized gene expression values. For count files, raw counts were obtained (from GetAssayData(object = seurat_object, slot = “counts”)) for each cell type in each cluster and appended to relevant metadata (barcode, cluster label, and donor number from the manuscript).
Supplementary files format and content: Processed peak matrix files are provided in tab-delimited format for count(*_atac_count.csv) and processed/normalized (*_atac_normalized.csv) activity values. For processed/normalized files, log-normalized peak values (from GetAssayData(object = seurat_object)) were appended to relevant metadata (barcode, cluster label, and donor number from the manuscript). Each row represents a unique cell, and columns correspond to metadata and log normalized peak values. For count files, raw peak accessibility levels were obtained (from GetAssayData(object = seurat_object, slot = “counts”)) for each cell type in each cluster and appended to relevant metadata (barcode, cluster label, and donor number from the manuscript).

source_name: Purified RPE

extract_protocol:
Neural retina was dissected away from the underlying retinal pigment epithelium and choroid prior to tissue dissociation. RPE/choroid samples were dissociated mechanically using razor blades into one-millimeter pieces then dissociated enzymatically using collagenase on a shaker at 37˚C for 60 minutes. Purified RPE samples were harvested by mechanically scraping RPE from the underlying Bruch's membrane. Following isolation/dissociation, cells were cryopreserved in DMSO-based Recovery Cell Cryopreservation Media (Gibco). After overnight cooling at -80˚C, samples were transferred to liquid nitrogen (vapor phase) for long-term storage prior to encapsulation and library preparation.
Cells were prepared for multimodal profiling using the sample preparation modifications described previously (Mimitou et al., 2021). Briefly, cells were thawed and filtered through a 70µm cell strainer. Cells were then washed twice with dPBS-/- (Gibco). Cells were fixed with 1% formaldehyde (Sigma) in PBS-/- for 10 minutes at room temperature. Fixation was quenched with the addition of glycine (Research Products International) to a final concentration of 0.125M for 5 minutes at room temperature. Following fixation, cells were washed twice with ice-cold PBS-/-. Following the second wash, cells were resuspended in 100µL ice-cold Lysis Buffer (10 mM Tris-HCl pH 7.4 (Millipore-Sigma), 10 mM NaCl (Ambion/Invitrogen), 3 mM MgCl2 (Ambion/Invitrogen), 0.1% Nonidet-P40 substitute (Research Products International), 1% Fraction V BSA (Research Products International)) and incubated on ice for 2.5 minutes. Following incubation, 1mL of ice-cold Wash Buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 1% BSA) was added, and cells were pelleted at 500 x g for 5 minutes at 4˚C. Cells were resuspended in 10µL diluted Nuclei Buffer (10X Genomics) and counted using Trypan Blue (Gibco) with the Countess automated cell counter (Invitrogen).  Cells were then processing following the 10X Genomics Chromium Next GEM Single Cell Multiome ATAC + Gene Expression (Rev. E) without modification. Final libraries were quantified using the Qubit dsDNA HS Assay Kit and diluted to 3ng/µL. Library quality was checked using the Bioanalyzer system.

value: Purified RPE

value: m.3243A/m.3243G (heteroplasmic)


title: control_9_rpe_choroid_per_atac

source_name: RPE/choroid

value: RPE/choroid


title: control_3_purified_rpe_per_atac


title: control_3_purified_rpe_per_gex

description:
10X Genomics Chromium Controller
3' RNA library portion of multimodal experiment


title: control_2_rpe_choroid_per_atac


title: control_10_rpe_choroid_per_atac


title: LNC, H3K9ac, patient 2, ChIP

value: esophageal squamous cell carcinoma


title: melas_1_purified_rpe_per_gex


title: Nor, H3K9ac, patient 2, ChIP

value: Nor

value: Stage III


title: melas_1_rpe_choroid_per_atac_rep2

description:
10X Genomics Chromium Controller
ATAC library portion of multimodal experiment
melas_1_rpe_choroid_ATAC_counts.csv
melas_1_rpe_choroid_ATAC_normalized.csv


title: melas_1_rpe_choroid_per_atac_rep1


title: melas_1_retina_per_atac

source_name: neural retina

value: neural retina


title: control_2_rpe_choroid_per_gex


title: control_9_rpe_choroid_per_gex


title: control_10_retina_per_atac


title: control_9_retina_per_atac


title: melas_1_rpe_choroid_per_gex_rep1


title: control_9_retina_per_gex


title: control_10_rpe_choroid_per_gex


title: melas_1_retina_per_gex


title: DAA, Late-tx, subject 3, scRNAseq

city: Los Angeles

first: Ana

middle: C

last: Maretti-Mira

address: 1450 Biggy Street, NRT 3514

department: Medicine

institute: USC

description: 10x Genomics, kit 5' v2

data_processing:
Raw data processing: Cell by gene count matrices were generated by processing FASTQ files using the Cell Ranger count (version 5.0.1, 10X Genomics) pipeline with the GRCh38 (version refdata-gex-GRCh38-2020-A, 10X Genomics) human genome reference for each sample.
Gene expression data were processed using the R package Seurat (version 4) [PMID: 29608179]
We first, filtered the data for low quality cells by removing cells with 1) less than 500 reads, 2) less than 300 or greater than 2,000 genes detected, and 3) cells with greater than 10% of reads mapping to mitochondrial genes. We further filtered out cells with CD3 and CD8 expression less than 1.
Dextramer positivity was determined by the maximum expressing dextramer within each cell. To account for any background non-specific dextramer stating we removed any cell with a maximum dextramer read count less than 10 times higher than the sum of all other dextramer counts.
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Peripheral blood

extract_protocol:
PBMCs were thawed at room temperature in RPMI media and centrifuged at 350xg for 10min at 4˚C. Cells were washed with Washing Buffer (PBS, pH 7.4 + 5% FBS), centrifuged, and the cell pellet was resuspended in Stain Buffer (PBS, pH 7.4 + 5% FBS + 0.1g/L Herring sperm DNA). Then, we added 0.2 µl 100µM d-Biotin (Avidity LLC, Aurora, CO) per included dextramer and added 2µl of desired dCODE™ Dextramer®-PE reagents (Immudex, Denmark), including the negative control for allele and random dextramers. After 10 min of incubation in the dark, we added the antibody cocktail for CD8+ T cell staining (CD4-APC, CD3-FITC, CD8-V500, and CD56-V450) and incubated for 30 min at 4˚C in the dark. We sorted the CD3+ CD8+ Dextramer+ cells using BD FACSAria™ Fusion into 90% FBS solution at 4˚C. Sorted cells were centrifuged and resuspended in 50µl of PBS with 0.04% BSA for scRNAseq partitioning.
Library was performed according to the manufacter’s instructions (single cell 5’ v1.1 or v2 protocol, 10x Genomics). Briefly, cells were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: CD8+ T cells

value: Peripheral blood

tag: dextramer


title: DAA, Post-tx, subject 2, scRNAseq

description: 10x Genomics, kit 5' v2


title: DAA, Late-tx, subject 2, scRNAseq

description: 10x Genomics, kit 5' v2


title: DAA, Early-tx, subject 3, scRNAseq

description: 10x Genomics, kit 5' v2


title: DAA, Early-tx, subject 2, scRNAseq

description: 10x Genomics, kit 5' v2


title: DAA, Late-tx, subject 1, scRNAseq

description: 10x Genomics, kit 5' v2


title: DAA, Pre-tx, subject 1, scRNAseq

description: 10x Genomics, kit 5' v2


title: Chronic HCV, replicate 3, scRNAseq

description: 10x Genomics, kit 5' v1.1


title: melas_1_rpe_choroid_per_gex_rep2

description:
10X Genomics Chromium Controller
3' RNA library portion of multimodal experiment
melas_1_rpe_choroid_GEX_counts.csv
melas_1_rpe_choroid_GEX_normalized.csv


title: Chronic HCV, replicate 1, scRNAseq

description: 10x Genomics, kit 5' v1.1


title: DAA, Early-tx, subject 1, scRNAseq

description: 10x Genomics, kit 5' v2


title: Control, replicate 3, scRNAseq

description: 10x Genomics, kit 5' v1.1


title: Control, replicate 1, scRNAseq

description: 10x Genomics, kit 5' v1.1


title: DAA, Pre-tx, subject 3, scRNAseq

description: 10x Genomics, kit 5' v2


title: Resolved HCV, replicate 2, scRNAseq

description: 10x Genomics, kit 5' v1.1


title: DAA, Pre-tx, subject 2, scRNAseq

description: 10x Genomics, kit 5' v2


title: DAA, Post-tx, subject 3, scRNAseq

description: 10x Genomics, kit 5' v2


title: Chronic HCV, replicate 2, scRNAseq

description: 10x Genomics, kit 5' v1.1


title: Chronic HCV, replicate 4, scRNAseq

description: 10x Genomics, kit 5' v1.1


title: U2OS ASH1L knockout cells transfected with empty vector, 3H, biol rep1

city: Zurich

first: Michelle

last: Yancoskie

address: Winterthurerstr. 260

department: Vetsuisse Faculty

country: Switzerland

institute: Institute of Veterinary Pharmacology and Toxicology, University of Zurich

description:
ASH1LCTD_ALKO_3h_Rep1.broadPeak.gz
ASH1LCTD_ALKO_3h_Rep1.bw

data_processing:
Raw reads were trimmed to remove reads shorter than 99 base pairs and crop reads exceeding 101 bp, or for paired-end top-up reads, to crop to 149-151 bp (TrimGalore v.0.6.5), then aligned (bwa mem v.0.7.17-r1188) to the human reference genome build GCA hg38 lacking chrY but including non-canonical contigs.
Alignments were filtered to exclude reads with mapping quality scores below 30 (bedtools v.2.29.2), PCR and optical duplicates (Picard MarkDuplicates, v.2.23.8), ENCODE-blacklisted regions, non-canonical contigs, and unmapped or secondary alignments (and for paired-end top-up reads, unpaired reads) (samtools v.1.7).
Filtered alignments (with single-end reads and paired-end top-up alignments pooled for H3K36me2) were used to call peaks (macs2 v.2.2.7.1) from treatment (IP) over pooled control (input control for H3K36me2, empty vector-transfected ASH1L knockout cells for ASH1L-CTD ChIP-seq) tagAlign files, with default parameters and cutoff p-value of 1e-2; broad peaks were called for both H3K36me2 and ASH1L-CTD ChIP-seq. Peaks were used to verify replicabiity with idr (v.2.0.4.2). For H3K36me32, only robust peaks (those shared across both biological duplicates) were retained in downsteam analyses. For ASH1L-CTD ChIP-seq, only the top quartile (when peaks were rank ordered by signal strength) of robust (shared across at least two of three biological triplicates) were used in downstream analyses.
Fold enrichment (bigWig) tracks were generated of IP signal over input control.
Assembly: hg38
Supplementary files format and content: bigWig, broadPeak BED files

growth_protocol: Low glucose DMEM, 10% fetal calf serum. Cells were cultured at 37C at 5% CO2.

extract_protocol:
Non-UV or 3h-post UV cells were crosslinked with 1% formaldehyde for 10 minutes. Quenching and lysis was followed by sonication (BioRuptor Plus) for 20 cycles (30 sec on/off).
To remove UV-induced DNA lesions with the potential to inhibit sequencing, samples were incubated with PreCR Repair mix (New England BioLabs, M0309) for 15 min at 37°C, then re-purified, quantified by Qubit (Invitrogen, Q33238) and sent to the Functional Genomics Center Zurich for final library preparation with the NEB Next Ultra Kit (New England BioLabs, E7645). Libraries were sequenced as 100 bp single-end reads on a NovaSeq 6000 (Illumina). Topped up reads for the H3K36me2 experiment were sequenced as 150 bp paired-end reads (NovaSeq 6000).

treatment_protocol: Cells grown to 80-90% confluency were left untreated (non-UV) or were UV-C irradiated at 20 J/m2 and left to recover for 3h.

value: ASH1L knockout

value: 3h post UV

value: anti-FLAG (Sigma, F1804)


title: Resolved HCV, replicate 4, scRNAseq

description: 10x Genomics, kit 5' v1.1


title: U2OS ASH1L knockout cells transfected with empty vector, 3H, biol rep3

description:
ASH1LCTD_ALKO_3h_Rep3.broadPeak.gz
ASH1LCTD_ALKO_3h_Rep3.bw


title: control_10_retina_per_gex


title: U2OS ASH1L knockout cells transfected with ASH1L-CTD, 3H, biol rep3


title: U2OS ASH1L knockout cells transfected with ASH1L-CTD, 3H, biol rep1


title: Resolved HCV, replicate 3, scRNAseq

description: 10x Genomics, kit 5' v1.1


title: U2OS ASH1L knockout cells transfected with empty vector, no UV, biol rep3

description:
ASH1LCTD_ALKO_noUV_Rep3.broadPeak.gz
ASH1LCTD_ALKO_noUV_Rep3.bw

value: no UV


title: DAA, Post-tx, subject 1, scRNAseq

description: 10x Genomics, kit 5' v2


title: U2OS ASH1L knockout cells transfected with empty vector, no UV, biol rep2

description:
ASH1LCTD_ALKO_noUV_Rep2.broadPeak.gz
ASH1LCTD_ALKO_noUV_Rep2.bw


title: Resolved HCV, replicate 1, scRNAseq

description: 10x Genomics, kit 5' v1.1


title: U2OS ASH1L knockout cells transfected with ASH1L-CTD, no UV, biol rep3


title: Control, replicate 2, scRNAseq

description: 10x Genomics, kit 5' v1.1


title: U2OS ASH1L knockout cells transfected with empty vector, no UV, biol rep1

description:
ASH1LCTD_ALKO_noUV_Rep1.broadPeak.gz
ASH1LCTD_ALKO_noUV_Rep1.bw