title: HiC_Setdb1KO_rep2

description:
This library was run on two lanes, each represented by a separate SRR ID.
HiC_Setdb1KO.hic
mESC_Setdb1KO_adj.txt.gz

data_processing:
Raw Hi-C sequencing data were processed using the “scHiC2” pipeline. Topologically associated domain (TAD) identification was performed using TopDom on the 100kb resolution iced maps using a window of 5 (ws=5). To optimize resolution and avoid over-segmentation TAD boundaries called on the 100kb bin maps were shifted to the closest boundary called on the 25kb bin maps using a window of 20 (ws=20). TADs overlap significance was calculated using R’s phyper function as follows: n_A=length of TADs overlapping with set1, n_B= length of TADs overlapping with set2, n_C= length of set1, n_A_B=length of TADs overlapping both set1 and set2.
Genome_build: mm10
Supplementary_files_format_and_content: Compressed HiC tracks

extract_protocol:
Hi-C-seq was performed as described in EpiTect Hi-C Kit from Qiagen.
Hi-C-seq was performed as described in EpiTect Hi-C Kit from Qiagen. Then Hi-C sequencing library is cleaned up with AMPure XP beads to remove remaining free Illumina adapter. Hi-C sequencing library is transferred into fresh tube. 1µL of library was used to run Agilent High Sensitivity DNA electrophoresis for checking DNA fragment size. Before sequencing, Hi-C libraries are quantified by qPCR. Libraries were sequenced 150bp paired-end with 1,2 billion reads of depth sequencing on NovaSeq 6000 Illumina machine at the MGX platforms.

tag: chip antibody

value: 5 days with 800 nM 4-hydroxytamoxifen (4-OHT)


title: 6_B.LS.V2

status: Public on Jan 25 2022

type: RNA

city: New York

first: Ana

last: Pavel

state: NY

address: One Gustave L. Levy Place

department: Dermatology

country: USA

institute: Icahn School of Medicine at Mount Sinai

description: Gene expression data from skin biopsy

hyb_protocol: Affymetrix Human U133Plus 2.0 gene arrays were used. Total RNA (50 ng) was reverse transcribed and amplified with Ovation Whole Blood Solution from NuGen (San Carlos, CA). The labeled target was fragmented and hybridized to probe gene arrays, using Encore Biotin Module from NuGen (San Carlos, CA). The chips were washed, stained with streptavidin-phycoerythrin, and scanned (HP GeneArray Scanner; Hewlett-Packard Company, Palo Alto, CA). On each chip, the human housekeeping genes β-actin and glyceraldehyde-3-phosphate dehydrogenase (GAPDH) served as controls. Suite 5.0 software normalized the expression level values using these controls.

scan_protocol: Hewlett-Packard GeneArray Scanner G2500A

data_processing: Quality control of Affymetrix chips was done using standard QC metrics and R packages. Expression measures were obtained using GC Robust Multi-array Average (GCRMA) algorithm. Batch effects corresponding to the hybridization date were detected by principal component analyses and adjusted using ComBat algorithm from R’s sva package. Probe sets with expression >3 in at least 15 samples were used for further analyses. Gene expression changes were modeled using mixed-effect models, with treatment, time and tissue type as a fixed interaction term, and a random effect for each patient. Fold changes (FCHs) for the comparisons of interest were estimated, and hypothesis testing was conducted with contrasts under the general framework of linear models in the R limma package. P-values were adjusted for multiple hypotheses using the Benjamini-Hochberg procedure, which controls the false discovery rate (FDR).

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: Skin biopsy

label_protocol: Ovation WB Reagent (Nugen)

extract_protocol: Skin biopsies were stored in RNAlater® (Invitrogen) until further processing. RNA was extracted (Covance Genomics Lab).

tag: tissue

value: Skin biopsy

tag: tissue disease state

value: LS

tag: week

tag: treatment


title: 335_01

type: SRA

city: SHANGHAI

first: XIANGYU

last: ZHOU

state: SHANGHAI

address: Shanghai First Maternity and Infant Hospital

country: China

institute: Tongji University

library_source: transcriptomic

data_processing:
The expression level of each transcript was calculated according to fragments per kilobase of exon per million mapped reads (FPKM)
Genome_build: GRCh38.p13
Supplementary_files_format_and_content: xls (fpkm, reads count)

source_name: 293T cell line

growth_protocol: Human 293T cells are seeded in the 6-well plates

extract_protocol:
RNA extracted from cell transfected with corresponding plasimids (EHHADH WT and mutants)
Transcriptome libraries were prepared using a TruSeq RNA Sample Preparation kit (Illumina) and then sequenced using the Illumina HiSeq 2000
TruSeq RNA Sample Preparation kit (Illumina)

treatment_protocol: no additional treatment

tag: cell line background

tag: genotype/variation

value: Ehhadh  K335R overexpression


title: HiC_Setdb1KO_rep1

city: Montpellier

first: Amandine

last: BARRAL

state: Hérault

address: 141 rue de la cardonille

country: France

institute: IGH - CNRS

library_source: genomic

molecule: genomic DNA

organism: Mus musculus

source_name: Mouse embryonic stem cells

growth_protocol: Mouse embryonic stem cells and derivates were grown on gelatin coated dishes in DMEM containing 15% (v/v) fetal bovine serum, Penicillin streptomycin (10 000U/mL), 2mM L-Glutamine, 1X MEM Non-Essential Amino Acids, 10mM 2-Mercaptoethanol and 2mL of homemade Leukemia Inhibitory Factor (LIF) at 37°C with 5% C02. Setdb1 was knocked down by treating cells for 5 days with 800 nM 4-hydroxytamoxifen (4-OHT) in culture medium.

tag: strain


title: iDART_SMART-seq APOBEC1-YTH Cell 124

city: Durham

first: Matthew

last: Tegowski

state: NC

address: 153 Research Dr.

department: Biochemistry

institute: Duke University

data_processing:
Alignment to hg38 and UMI deduplication using Cell Ranger 3.1.0 (10x Genomics scRNA-seq samples only)
SMART-seq2 and bulk RNAseq samples: Trimming of adaptor sequences (Flexbar 3.0.3)
SMART-seq2 and bulk RNAseq samples:  Alignment using STAR 2.7.5c, and deduplication using SAMtools (1.11) fixmate and markdup
All samples: Identification of m6A sites using Bullseye
All samples: Expression normalization and integrated clustering of cells using Seurat (3.2.1)
Genome_build: hg38
Supplementary_files_format_and_content: Bed files for bulk RNAare a list of m6A sites identified within each replicate using Bullseye. High confidence m6A sites in paper were a result of keeping only these sites that occur in at least 2 of 3 APOBEC1-YTH replicates
Supplementary_files_format_and_content: a bed file consisting of APOBEC1-mediated C-to-U editing sites identified by downstream analysis

molecule: polyA RNA

source_name: Kidney

growth_protocol: HEK293T cells expressing APOBEC1-YTH or APOBEC1-YTHmut (iDART cells) were cultured in DMEM +10% FBS with penicillin/streptomycin.

extract_protocol:
SMART-seq2 cells: Single cells were sorted using a FACS Aria II (BD) directly into lysis buffer provided with the SMART-seq HT Kit (Takara, Cat. 634438). The SMART-seq HT Kit was then used for reverse transcription and cDNA amplification. Sequencing libraries were constructed from cDNA using the Nextera XT kit (Illumina, FC-131-1096) and dual Nextera-compatible CDI indexes from IDT. Samples were pooled and sequenced targeting 5,000,000 reads/library (150bp paried-end) on a Novaseq6000 using the S4 flowcell.   10X Genomics cells: A single cell suspension was prepared according to manufacturer's instruction for Chromium v3 3' end sequencing (10x Genomics, Manual Part #CG00053). Samples were sequenced targeting 80,000 reads per cell on a Novaseq6000 using the S1 flowcell.  Bulk RNA-seq: Trizol was used to extract total RNA from iDART cells. The UltraII Directional RNA Library Prep Kit (NEB, E7760) with NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB, 7490) was used to generate sequencing libraries using 900ng of input RNA. The samples were sequenced targeting ~30 million reads (50bp paired-end sequencing) per sample on a Novaseq6000 using the S1 flowcell.
SMART-seq2 scRNA-seq: cDNA libraries were generated using the SMART-seq HT Kit (Takara, Cat. 634438). Final libraries were prepared using Nextera XT DNA Library Prep Kit (Illumina, FC-131-1096).   10x scRNA-seq: Libraries were generated from a single cell suspension using the 10x Genomics NextGEM Single Cell 3' Kit, v3.1 chemistry (10x Genomics)  Bulk-RNA seq: The UltraII Directional RNA Library Prep Kit (NEB, E7760) with NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB, 7490) was used to generate sequencing libraries using 900ng of input RNA.

treatment_protocol: When cells were 60-70% confluent, iDART cells were treated with 1µg/µL doxycycline for 24 hours for bulk RNA-seq, 10x Genomics scRNA-seq, and SMART-seq2 scRNA-seq

tag: cell line

value: HEK293T Cells

tag: transgene

value: 1microg/mL doxycycline; 24 hours


title: HiC_WT_rep2

description:
This library was run on two lanes, each represented by a separate SRR ID.
HiC_WT.hic, WT_TADs_HiC.txt
mESC_WT_adj.txt.gz


title: 329_03

value: Ehhadh  K329R overexpression


title: iDART_SMART-seq APOBEC1-YTH Cell 123


title: 3_C.LS.V10

description: Gene expression data from skin biopsy


title: Ash1l_het rep2

city: Shanghai

first: Ji-Song

last: Guan

address: ShanghaiTech University, Shanghai, China

department: School of Life Science and Technology

institute: ShanghaiTech University

data_processing:
Illumina’s Casava bcl2fastqv2.19 software program used for base-calling.
FASTQ reads were quality checked with FastQC (Andrews, S.. FastQC A Quality Control tool for High Throughput Sequence Data).
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using Seqtk, then mapped to GRCm38 whole genome using Hisat2（version:2.0.4） with default parameters.
Gene counts were calculated with Stringtie（version:1.3.0）, and normalized with trimmed mean of M-values (TMM) method to calculate Fragments Per Kilobase of exon model per Million mapped fragments (FPKM).
Differential gene expression analyses were performed with edgeR.
Genome_build: GRCm38
Supplementary_files_format_and_content: Matrix table with raw gene counts and FPKM for every gene and every sample

source_name: dorsal striatum

extract_protocol:
Dorsal striatum in the brain (adult male mice aged 1 year) was removed and lysed using TRIzol reagent, RNA was extracted by isopropanol precipitation and diluted in RNase-free water.
Sequencing libraries were generated using VAHTS Stranded mRNA-seq Library Prep Kit for Illumina® (Vazyme) according to manufacturer's instructions.

value: brain

tag: age


title: 329_02


title: iDART_SMART-seq APOBEC1-YTH Cell 122


title: 329_01


title: iDART_SMART-seq APOBEC1-YTH Cell 121


title: WT_03

value: Ehhadh WT overexpression


title: iDART_SMART-seq APOBEC1-YTH Cell 120


title: RNAseq_Setd2KO_rep3

description: processed data file: FC_RNAseqSetd2KO.txt

data_processing:
Quality controls of RNA-seq Fastq files were performed by FastQC. RNA-seq reads were mapped to the mm10 reference genome using STAR with --library-type fr-firststrand option. BigWig files are generated using Deeptools bamCoverage with --bs 50 and --normalizeUsing RPKM options. To obtain strand specific bigwig files, the --filterRNAstrand option was used. Fastq reads were mapped to Refseq genes using STAR with --library-type fr-firststrand and --quantMode Transcriptome SAM GeneCounts options to obtain read count files.  This was then input processed by deseq2. An adjusted p-value < 0.01 and a base mean > 2 were used as cut-off values for significant differential expression.
Genome_build: mm10
Supplementary_files_format_and_content: bw files correpond RPKM-normalized bigwig binary files (50bp bins), which can be visualized using the Integrative Genomics Viewer (IGV) software.

extract_protocol:
RNAs were extracted with Trizol following the manufacturer’s recommendations
1µg RNA was used for library preparation. RNA-seq library preparation was performed as described in TruSeq Stranded Total RNA Sample Preparation kit from Illumina with few adaptations. RNA Clean XP beads and AMPureXP beads are air-dry for 7min. 1uL of libraries were used to determine concentration by Qubit DNA HS assay kit and to run Agilent High Sensitivity DNA Electrophoresis to check DNA fragment size. Before sequencing, RNA-seq libraries were quantified by qPCR. Libraries were sequenced 100bp single-reads with 30 million reads of depth sequencing on NovaSeq 6000 Illumina machine at the MGX platforms.

tag: cell type

value: Mouse embryonic stem cells

tag: spike-in

value: ERCC RNA spike-in Mix


title: 335_02


title: TBX3 #2 Replicate 2

city: Cape Town

first: Victoria

last: Damerell

state: Western Cape

address: Anzio Road

department: Human Biology

country: South Africa

institute: University of Cape Town

hyb_protocol: 5.5 µg of each sample was used for fragmentation and labelling, followed by hybridization on the Clariom S array in an Affymetrix GeneChip® Hybridisation Oven-645 rotating at 60 rpm at 45 °C for 16 h.

scan_protocol: Hybridised chips were washed and stained using GeneChip™ Hybridization, Wash and Stain Kit in an Affymetrix GeneChip® Fluidics Station-450Dx before scanning using an Affymetrix GeneChip® Scanner-7G.

data_processing: From each scanned chip, the Affymetrix system generates a CEL file which has intensity values for all probes present on it. The CEL files were imported into the Affymetrix Transcriptome Analysis Console (TAC) v4.0.2 software for differential gene expression analysis.

source_name: Mesenchymal stem cell

label_protocol: A total of 5 ng RNA from each sample was used to synthesize first strand cDNA, followed by 3' adaptor and double stranded cDNA (ds-cDNA) using the Clariom S array (IVT) Pico kit according to the manufacturer’s protocol. The ds-cDNA was used to synthesize cRNA by in vitro transcription for 14 h at 40 °C and the cRNA was purified using purification beads on a magnetic stand. A total of 20 µg purified cRNA was used for 2nd-cycle ds-cDNA synthesis followed by RNA hydrolysis and ds-cDNA purification as described above.

growth_protocol: MSCs were maintained under standard culture conditions (37 °C, 5% CO2, 65% humidity) in Dulbecco’s Modified Eagle Medium GlutaMax™ culture medium (DMEM, Gibco, Life Technologies/Thermo Fisher Scientific, USA) supplemented with 20% fetal bovine serum (FBS, Gibco, USA) and 1% penicillin and streptomycin (pen/strep, Gibco, USA).

extract_protocol: Total RNA was extracted using the High Pure RNA Isolation Kit (Roche, Germany) according to the manufacturer’s instructions.

treatment_protocol: MSCs were genetically engineered to overexpress TBX3 using a lentiviral transduction system.

value: Adipose derived MSCs

tag: transduced with


title: 37_B.LS.V7

description: Gene expression data from skin biopsy


title: iDART_SMART-seq APOBEC1-YTH Cell 119


title: RNAseq_Setd2KO_rep1


title: TBX3 #2 Replicate 3


title: WT_01


title: HDAC9 NKL54 ChIP rep2

city: Udine

first: Emiliano

last: Dalla

state: UD

address: Piazzale Kolbe 4

department: Department of Medicine

country: Italy

institute: Università degli Studi di Udine

description: HDAC9 bound regions in NKL54 treated cells

data_processing:
Basecalls performed using the ShortRead R/Biocoductor package
ChIP-seq reads were aligned to the hg38 genome assembly using bowtie2 version 2.3.4.3 with default configuration for unpaired reads
Duplicate reads were flagged using samtools but no duplicates were removed
peaks were called using MACS2 version 2.1.1 with the following setting: ChIP threshold (0.2), Enrichment Fold (2.5), Rescue Fold (3). ChIP-seq replicates were compared using the Irreproducibility Discovery Rate (IDR) framework, with MACS2 narrow peaks as input and applying the following settings: --input-file-type narrowPeak, --rank signal.value, --output-file-type narrowPeak.
Genome_build: hg38
Supplementary_files_format_and_content: Coverage tracks were generated using the bamCoverage (deepTools) tool, taking an alignment of reads as input (BAM file) and generating a coverage track (bigWig) as output, applying the following parameters: --outFileFormat bigwig --binSize 50 -p 10 --normalizeUsing RPKM

growth_protocol: SK-UT-1 cells were grown in DMEM supplemented with 10% FBS, 2mM L-glutamine and penicillin–streptomycin (Euroclone, Milan, Italy). For each ChIP, 3.2*10^6 cells were used.

extract_protocol:
Lysates were obtained with a two-step protocol (nuclei were obtained with an hypotonic buffer (20mM TRIS-HCl pH8; 85 mM KCl; 0.5% NP-40), and nuclear membrane was lysed with Lysis buffer (10mM TRIS pH7.5; 1% NP-40, 0.5% Na-deossicholate; 0.1% SDS); then lysates were clarified from sonicated nuclei (30', medium power, Bioruptor Diagenode) and histone-DNA complexes were isolated with protein A/antibodies (2μg of anti-H3K27ac (Abcam ab4729) , 2.5 μg of anti-MEF2D (BD Bioscience), 4μg of anti-HDAC4 (Paroni et al, 2004) and anti-HDAC9 (home-made antibody) antibodies or control IgG. Washes were performed in LOW SALT IMMUNE COMPLEX WASH BUFFER (0.1% SDS, 1% TRITON, 20mM Tris-HCl pH8, 150 mM NaCl), HIGH SALT WASH BUFFER (0.1% SDS, 1% TRITON, 2mM EDTA, 20mM Tris-HCl pH8, 500 mM NaCl), LiCl Immune Complex Wash Buffer (0.25M LiCl, 1% NP40, 0.2% Na-deossicolato, 1mM EDTA, 10Mm Tris-HCl pH8) and TE. RNA was digested with RNAseA (2μg). DNA was de-crosslinked and purified with Zymo DNA columns.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, 5 μg of DNA were used. DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on Illumina NextSseq550 following the manufacturer's protocols.
TruSeq ChIP Library

treatment_protocol: Cells were seeded in 200 mm plate three days before the ChIP. 14h before the harvesting, cells were DMSO or NKL54 (5µM) treated. At the moment of the ChIP, cross-linking was performed for 15' with 1% formaldeyde (Fisher Scientific, Schwerte, Germany) and then blocked with 125 mM Glycine (Sigma-Aldrich, Darmstadt, Germany).

value: Leiomyosarcoma cells

tag: passages

value: below 20

value: HDAC9 (Di Giorgio et al, 2019 PMID 31754707)


title: RNAseq_Setdb1KO_rep3

description: processed data file: FC_RNAseqSetdb1KO.txt


title: iDART_SMART-seq APOBEC1-YTH Cell 118


title: HiC_WT_rep1


title: RNAseq_Setdb1KO_rep2


title: 472335_ERF_S48

description: SK-UT-1 TMP-195 5uM  24h round 3

data_processing:
Illumina Casava1.7 software used for basecalling.
Transcripts were quantified from raw reads with salmon (v 1.4.0) on the human transcriptome GRCh38 (Ensembl 100). Quantifications were summarized to gene level with tximeta (1.6.3).
Differential expression analysis was performed with DESeq2 package (v 1.28.1) using the Wald test for significance testing and independent filtering. Genes were considered differentially expressed if the adjusted p value <0.05 and abs(log2(FoldChange)) >1.
Genome_build: GRCh38 (Ensembl 100)
Supplementary_files_format_and_content: tab-delimited text file includes TPM values for each Sample and quantified gene
Supplementary_files_format_and_content: tab-delimited text file with raw gene counts for every gene and every sample

growth_protocol: SK-UT-1 cells were grown in DMEM supplemented with 10% FBS, 2mM L-glutamine and penicillin–streptomycin (Euroclone, Milan, Italy). For each experiment, 0.8*10^5 cells were seeded.

extract_protocol:
SK-UT-1 cells were lysed using Tri Reagent (Molecular Research Center). Total RNA was treated with DNAse I (NEB #T2010) and purified with RNA Clean & Concentrator (Zymo Research),  following manufacturer's instructions.
Libraries were constructed by TruSeq Stranded Total RNA, following manufacturer's instuctions.
Coding RNA plus multiple forms of non-coding RNA were preserved, while cytoplasmic rRNA was depleted.

treatment_protocol: Cells were seeded in 60 mm plate 24h before thetreatment. DMSO and HDACI were added in the medium and cells were treated for the indicated time, as specified in sample description.

value: TMP-195 5uM

tag: time

tag: replicate

value: round 3


title: iDART_SMART-seq APOBEC1-YTH Cell 117


title: RNAseq_Setdb1KO_rep1

value: 5 days with 800 nM 4-hydroxytamoxifen (4-OHT)


title: 472334_ERE_S44

description: SK-UT-1 TMP-195 5uM  6h round 3


title: TBX3 #1 Replicate 2


title: TBX3 #1 Replicate 1


title: TBX3 #2 Replicate 1


title: RNAseq_Setd2KO_rep2


title: EV #2 Replicate 3

value: empty vector


title: RNAseq_WT_rep3


title: 472333_ERD_S46

description: SK-UT-1 TMP-195 5uM  24h round 2

value: round 2


title: TBX3 #1 Replicate 3


title: RNAseq_WT_rep2


title: iDART_SMART-seq APOBEC1-YTH Cell 115


title: 472332_ERC_S43

description: SK-UT-1 TMP-195 5uM  24h round 1

value: round 1


title: WT_02


title: iDART_SMART-seq APOBEC1-YTH Cell 114

value: HEK293T Cells


title: EV #2 Replicate 1


title: RNAseq_WT_rep1


title: 472331_ERB_S44

description: SK-UT-1 TMP-195 5uM  6h round 2


title: CIDOP_Input_rep2

data_processing:
Quality controls of CIDOP-seq Fastq files were performed by FastQC. CIDOP-seq Fastq file reads were mapped to the mm10 reference genome using Bowtie2 with default parameters. To determine peaks, CIDOP-seq datasets were processed using MACS2 with --broad and --g mm options. BigWig files were generated using Deeptools bamCoverage with --bs 50 and --normalizeUsing RPKM options.
Genome_build: mm10
Supplementary_files_format_and_content: bw files correpond RPKM-normalized bigwig binary files (50bp bins), which can be visualized using the Integrative Genomics Viewer (IGV) software.

extract_protocol:
CIDOP chromatin capture reaction was performed as described in Mausser et al 2017, Epigenetics & Chromtain with a few adaptations. For MNAse digestion, 64U of MNAse from NEB per µg of DNA was used with 1mM CaCl2. MNAse reaction was placed directly at 37°C and incubated for 5min to obtain 10% of dinucleosomes and 90% of mononucleosomes. MNase reaction was stopped by adding 2mM EDTA + 30mM NaCl then samples were centrifuged at 13000g for 10min at 4°C. For CIDOP reaction, 60µg pre-clear mononucleosome-DNA was used with 0,5µM HiMID recombinant peptide in 500µL DP Buffer (16.7mM Tris-HCl pH=8, 167mM NaCl, 1.1% TritonX-100, 1.2mM EDTA). CIDOP retaction was incubated O/N at 4°C on a rotating wheel. Next day, 40µL Glutathione Sepharose 4B beads was added per IP then incubate at 4°C for 2h on a rotating wheel. IP reactions were washed as described in Mausser’s protocole. For elution step, 100µL Elution Buffer and 3µL NEB Proteinase K were added and incubated at RT for 45min on a rotation wheel then 55°C for 1h. DNA was purified as described in Chromatin IP DNA purification Kit from Active Motif. For CIDOP-seq, CIDOP-DNA was eluted in 36µL with pre-warmed Elution Buffer then quantified with Qubit dsDNA HS Assay Kit. 1µL was also used to run Agilent High Sensitivity DNA electrophoresis to check DNA fragment size with majority of fragment at 150 nucleotides. 10ng of CIDOP-DNA was used for library preparation.
10ng CIDOP-DNA were used for library preparation. CIDOP-seq library preparation was performed as described in TruSeq ChIP Sample Preparation kit from Illumina with few adaptations. The Enrich DNA Fragment step is proceeded before Purify Ligation Products step. AMPure XP beads were air-dry 7min. 1µL library was diluted 1:10 in H20 to quantified library concentration by Qubit DNA HS assay quantification. Agilent High Sensitivity DNA Electrophoresis was run to check DNA fragment size. Before sequencing, ChIP-seq and CIDOP-seq libraries were quantified by qPCR. Libraries were sequenced 50bp or 100bp single-reads with 50 million reads of depth sequencing on NovaSeq 6000 Illumina machine at the MGX platforms.


title: 472330_ERA_S43

description: SK-UT-1 TMP-195 5uM  6h round 1


title: EV #1 Replicate 2


title: iDART_SMART-seq APOBEC1-YTH Cell 112

value: 1microg/mL doxycycline; 24 hours


title: CIDOP_Input_rep1


title: Sample 73_Acclimation_ABA_48_3

city: Geneva

first: Hongrui

last: Wang

address: 630 W. North Street

department: School of Integrative Plant Science, Horticulture section

institute: Cornell University

description: 11939_5751_124888_HFGFNBGXG_NSF022_H02_ABA_2018_A_3_5_1_TACCTT_R1

data_processing:
FastQC for quality control
BBDuk for removing adaptors and poly-A following the pipeline suggested by the manufacturer (https://www.lexogen.com/quantseq-data-analysis/)
STAR for gene level quantification using ‘-quantMode GeneCounts’
Low count gene filterig based on 'total gene count greater than sample number'
DESeq2 for variance stabilization transformation and gene expression normalization
WGCNA for gene co-expression analysis, noise gene filtering, module eigengene visualization and contrast generation
GSEA for pathway enrichment analysis
Genome_build: Vitis vinifera 12X.v2 genome with VCost.v3 annotation
Supplementary_files_format_and_content: Two matrix tables with raw gene counts for every gene and every sample without any filtering

organism: Vitis vinifera

growth_protocol: In the acclimation experiment, two-year-old, self-rooted ‘Cabernet Franc’ grapevines were potted-grown in greenhouse the Ohio Agricultural Research and Development Center (OARDC, Wooster, OH, USA). In the greenhouse, temperature was set at 22 °C/19 °C (day/night), lighting was maintained at 500 μmol m−2∙s-1 for a 10 h minimum photoperiod and shade was used to avoid overheating in the greenhouse. In the deacclimation experiment, dormant canes were harvested from from field-grown ‘Cabernet Franc’ grapevines in March of 2017, after vines had been exposed to >1200 chilling hours (NC model), and chopped into single node cuttings. Cuttings were incubated with cut ends in cups of water under permissive growing conditions (22 °C and 16/8 h light/dark) in a growth room.

extract_protocol:
Total RNA was extracted using SpectrumTM Plant Total RNA Kit (Sigma Aldrich, St Louis, MO, USA) following the protocol suggested by the manufacturer
Libraries were constructed with Lexogen QuantSeq 3’mRNA-Seq Prep Kit (Lexogen, Greenland, NH, USA) following standard practices as a service provided by Cornell University Institute of Genomic Diversity (Ithaca, NY, USA). Sequencing of the libraries was accomplished using NextSeq500 (Illumina, Inc., San Diego, CA, USA) with 95 samples per lane at Cornell University Institute of Biotechnology (Ithaca, NY, USA). The read length was 85 bp and 75 bp in the acclimation and deacclimation experiment, respectively. For each library, sequencing was conducted in triplicate to justify technical validity.

treatment_protocol: The acclimation experiment involved two treatments (control and ABA) in quadruplicates using randomized complete block design. For control treatment, the solution was composed of deionized water with 0.05% (v/v) Tween-20 (Acros Organic, Hampton, NH, USA) as surfactant. For ABA treatment, the solution was composed of 500 mg· L-1 (1.9 mM) S-ABA diluted from ProTone® SG (Valent BioSciences Corporation, Libertyville, IL, USA) and 0.05 % (v/v) Tween-20 as surfactant. Treatments were applied at noon of 18 Aug 2018 when the leaf age of base node was 95 days. Both treatments were sprayed on all grapevine leaves until runoff to ensure a full coverage. In  the deacclimation experiment, cuttings were randomized and divided into six groups, corresponding to six timepoints for post treatment sample collection. When single bud cuttings developed to ‘woolly buds’ stage, treatments were applied on each group with a hand sprayer to runoff. Control treatment was deionized water, and ABA treatment was 1322 mg· L-1 (5mM) S-ABA diluted from ProTone® SG (Valent BioSciences Corporation, Libertyville, IL, USA).

tag: genotype

value: Cabernet Franc

value: ABA

tag: experiment

value: Acclimation

value: leaf

tag: molecule subtype

value: 3' mRNA


title: iDART_SMART-seq APOBEC1-YTH Cell 116


title: 472329_EQZ_S42

description: SK-UT-1 Compound A 5uM 24h round 3

value: Compound A 5uM


title: EV #1 Replicate 1

value: Adipose derived MSCs


title: EV #2 Replicate 2


title: Sample 72_Acclimation_ABA_24_1

description: 11939_5751_124885_HFGFNBGXG_NSF022_E02_ABA_2018_A_1_4_1_CCTAAG_R1

tag: tissue


title: CIDOP_PWWPMPP8_rep2

value: Mouse embryonic stem cells


title: iDART_SMART-seq APOBEC1-YTH Cell 110

tag: treatment


title: 472328_EQY_S41

description: SK-UT-1 MC-2985 5uM 24h round 3

value: Leiomyosarcoma cells


title: iDART_SMART-seq APOBEC1-YTH Cell 111


title: Sample 71_Acclimation_Control_2_1

description: 11939_5751_124881_HFGFNBGXG_NSF022_A02_ABA_2018_C_1_2_1_TCAGGA_R1

value: Control


title: iDART_SMART-seq APOBEC1-YTH Cell 109


title: 472327_EQX_S40

description: SK-UT-1 MC-2984 5uM 24h round 3

value: round 3


title: CIDOP_PWWPMPP8_rep1


title: ChIP_H3K36me1_Setd2KO_rep2

data_processing:
Quality controls of ChIP-seq Fastq files were performed by FastQC. ChIP-seq Fastq read files are mapped to the mm10 reference genome using Bowtie2 with default parameters. To determine for ChIP-seq peaks with a broad profile, datasets were processed using MACS2 with --broad and --g mm options. H3K36me3, H3K36me2 and H3K36me1 bigWig files were normalized using drosophila spike-ins, which were mapped to dm6 reference genome using Bowtie2 with default parameters. The normalization factor was determined as described in manufactured protocol (Spike-in Normalization from Active Motif). For each sample, normalized BigWig files were generated using Deeptools bamCoverage with --bs 50, --normalizeUsing RPKM and --scaleFactor options, where scaleFactor is the normalization factor specific to each sample.
Genome_build: mm10
Supplementary_files_format_and_content: bw files correpond RPKM-normalized bigwig binary files (50bp bins), which can be visualized using the Integrative Genomics Viewer (IGV) software.

extract_protocol:
Two 15cm-dishes with 2.10^7 cells in 20mL of culture media were used for each ChIP-seq experiment.  ChIP-seq was performed as described in ChIP-IT High sensitivity Kit from Active Motif with a few adaptations. Chromatin is sonicated by Bioruptor: 30sec ON – 30sec OFF, 10 cycles, high power. Sonicate for a total of 40 cycles for histones and of 30 cycles for TFs with 10min break on ice every 10 cycles. For quantitative ChIP reaction drosophila spike-in from Active Motif was used. For histone methylation of lysine 36, 25µg chromatin was used with 50ng Spike-in Chromatin + 4µg antibody + 2ug Spike-in Antibody. Spike-in antibody also required a blocking step. ChIP-DNA was eluted in 36µL with pre-warmed Elution Buffer then ChIP-DNA concentration was quantified with the Qubit dsDNA HS Assay Kit. 2,5ng to 10ng of ChIP-DNA were used for library preparation.
2,5ng to 10ng ChIP-DNA were used for library preparation. ChIP-seq library preparation was performed as described in TruSeq ChIP Sample Preparation kit from Illumina with few adaptations. The Enrich DNA Fragment step is proceeded before Purify Ligation Products step. AMPure XP beads were air-dry 7min. 1µL library was diluted 1:10 in H20 to quantified library concentration by Qubit DNA HS assay quantification. Agilent High Sensitivity DNA Electrophoresis was run to check DNA fragment size. Before sequencing, ChIP-seq libraries were quantified by qPCR. Libraries were sequenced 50bp or 100bp single-reads with 50 million reads of depth sequencing on HiSeq 2000 Illumina or NovaSeq 6000 Illumina machine at the MGX platforms.

tag: chip antibody

value: H3K36me1, Abcam ab9048


title: 472326_EQW_S41

description: SK-UT-1 NKL54 5uM 24h round 3

value: NKL54 5uM


title: iDART_SMART-seq APOBEC1-YTH Cell 108


title: Sample 74_Acclimation_ABA_48_4

description: 11939_5751_124889_HFGFNBGXG_NSF022_A03_ABA_2018_A_4_5_1_TCTTAA_R1


title: EV #1 Replicate 3

value: empty vector


title: iDART_SMART-seq APOBEC1-YTH Cell 107


title: ChIP_H3K36me1_Setd2KO_rep1

value: Drosophila spike-in chromatin


title: ChIP_H3K36me1_Setdb1KO_rep2

value: 5 days with 800 nM 4-hydroxytamoxifen (4-OHT)


title: 472324_EQU_S40

description: SK-UT-1 Compound A 5uM 24h round 2

value: round 2


title: iDART_SMART-seq APOBEC1-YTH Cell 113

value: HEK293T Cells

value: 1microg/mL doxycycline; 24 hours


title: Sample 67_Acclimation_Control_48_3

description: 11769_5751_120113_H22JMBGXG_NSF021_A09_ABA_2018_C_3_5_1_AAGCTC_R1

value: Cabernet Franc

value: Acclimation


title: ChIP_H3K36me1_Setdb1KO_rep1


title: iDART_SMART-seq APOBEC1-YTH Cell 105


title: 472323_EQT_S28

description: SK-UT-1 MC-2985 5uM 24h round 2


title: Sample 66_Acclimation_Control_48_2

description: 11769_5751_120112_H22JMBGXG_NSF021_H08_ABA_2018_C_2_5_1_CAGGAC_R1

value: leaf

value: 3' mRNA


title: iDART_SMART-seq APOBEC1-YTH Cell 104


title: 472321_EQR_S26

description: SK-UT-1 NKL54 5uM 24h round 2


title: Sample 70_Acclimation_ABA_48_2

description: 11769_5751_120116_H22JMBGXG_NSF021_D09_ABA_2018_A_2_5_1_CCAATT_R1

value: ABA


title: ChIP_H3K36me1_WT_rep2

value: Mouse embryonic stem cells


title: iDART_SMART-seq APOBEC1-YTH Cell 106


title: iDART_SMART-seq APOBEC1-YTH Cell 103


title: Sample 64_Acclimation_ABA_24_4

description: 11769_5751_120110_H22JMBGXG_NSF021_F08_ABA_2018_A_4_4_1_CAATGC_R1


title: 472320_EQQ_S25

description: SK-UT-1 SAHA 2.5uM 24h round 2

value: Leiomyosarcoma cells

value: SAHA 2.5uM


title: 472322_EQS_S27

description: SK-UT-1 MC-2984 5uM 24h round 2


title: Sample 69_Acclimation_ABA_48_1

description: 11769_5751_120115_H22JMBGXG_NSF021_C09_ABA_2018_A_1_5_1_TCGTTC_R1


title: ChIP_H3K36me1_WT_rep1


title: iDART_SMART-seq APOBEC1-YTH Cell 102


title: 472319_EQP_S24

description: SK-UT-1 Compound A 5uM 24h round1

value: Compound A 5uM

value: round 1


title: ChIP_H3K36me2_Setd2KO_rep2

value: H3K36me2, Abcam ab9049


title: Sample 65_Acclimation_Control_48_1

description: 11769_5751_120111_H22JMBGXG_NSF021_G08_ABA_2018_C_1_5_1_ACGTCT_R1

value: Control


title: iDART_SMART-seq APOBEC1-YTH Cell 101


title: Sample 63_Acclimation_ABA_24_3

description: 11769_5751_120109_H22JMBGXG_NSF021_E08_ABA_2018_A_3_4_1_GAAGTG_R1


title: Sample 62_Acclimation_ABA_24_2

description: 11769_5751_120108_H22JMBGXG_NSF021_D08_ABA_2018_A_2_4_1_TTCCGC_R1


title: ChIP_H3K36me2_Setd2KO_rep1

value: Drosophila spike-in chromatin


title: Sample 68_Acclimation_Control_48_4

description: 11769_5751_120114_H22JMBGXG_NSF021_B09_ABA_2018_C_4_5_1_GACGAT_R1


title: 472325_EQV_S38

description: SK-UT-1 SAHA 2.5uM 24h round 3

value: round 3


title: ChIP_H3K36me2_Setdb1KO_rep2

value: 5 days with 800 nM 4-hydroxytamoxifen (4-OHT)


title: iDART_SMART-seq APOBEC1-YTH Cell 100

value: HEK293T Cells


title: 472318_EQO_S39

description: SK-UT-1 MC-2985 5uM 24h round1


title: ChIP_H3K36me2_Setdb1KO_rep1


title: 472317_EQN_S22

description: SK-UT-1 MC-2984 5uM 24h round 1


title: iDART_SMART-seq APOBEC1-YTH Cell 99

value: 1microg/mL doxycycline; 24 hours


title: Sample 60_Acclimation_Control_24_3

description: 11769_5751_120106_H22JMBGXG_NSF021_B08_ABA_2018_C_3_4_1_ATAAGA_R1

value: Cabernet Franc


title: Sample 61_Acclimation_Control_24_4

description: 11769_5751_120107_H22JMBGXG_NSF021_C08_ABA_2018_C_4_4_1_GGTGAG_R1

value: Acclimation


title: ChIP_H3K36me2_WT_rep2


title: 472316_EQM_S38

description: SK-UT-1 NKL54 5uM 24h round 1

value: NKL54 5uM


title: iDART_SMART-seq APOBEC1-YTH Cell 98


title: ChIP_H3K36me2_WT_rep1


title: 472315_EQL_S20

description: SK-UT-1 SAHA 2.5uM 24h round 1


title: iDART_SMART-seq APOBEC1-YTH Cell 97


title: iDART_SMART-seq APOBEC1-YTH Cell 96


title: Sample 57_Acclimation_ABA_4_4

description: 11769_5751_120103_H22JMBGXG_NSF021_G07_ABA_2018_A_4_3_1_ACAACG_R1

value: leaf

value: 3' mRNA


title: Sample 58_Acclimation_Control_24_1

description: 11769_5751_120104_H22JMBGXG_NSF021_H07_ABA_2018_C_1_4_1_ATATCC_R1


title: ChIP_H3K36me3_doubleKO_rep1

value: Mouse embryonic stem cells

value: H3K36me3, Abcam ab9050


title: 472314_EQK_S19

description: SK-UT-1 MC-2985 5uM 6h round 3

value: Leiomyosarcoma cells


title: Sample 56_Acclimation_ABA_4_3

description: 11769_5751_120102_H22JMBGXG_NSF021_F07_ABA_2018_A_3_3_1_AATGAA_R1

value: ABA


title: Sample 59_Acclimation_Control_24_2

description: 11769_5751_120105_H22JMBGXG_NSF021_A08_ABA_2018_C_2_4_1_AGTACT_R1


title: iDART_SMART-seq APOBEC1-YTH Cell 95


title: ChIP_H3K36me3_doubleKO_rep2


title: ChIP_H3K36me3_Setd2KO_rep2


title: ChIP_H3K36me3_Setd2KO_rep1


title: 472312_EQI_S17

description: SK-UT-1 NKL54 5uM 6h round 3


title: iDART_SMART-seq APOBEC1-YTH Cell 94


title: iDART_SMART-seq APOBEC1-YTH Cell 93


title: 472313_EQJ_S18

description: SK-UT-1 MC-2984 5uM 6h round 3


title: Sample 55_Acclimation_ABA_4_2

description: 11769_5751_120101_H22JMBGXG_NSF021_E07_ABA_2018_A_2_3_1_CGCCTG_R1


title: 472311_EQH_S16

description: SK-UT-1 SAHA 2.5uM 6h round 3

value: SAHA 2.5uM


title: Sample 54_Acclimation_ABA_4_1

description: 11769_5751_120100_H22JMBGXG_NSF021_D07_ABA_2018_A_1_3_1_GGTATA_R1


title: ChIP_CTCF_Setdb1KO_rep2

data_processing:
Quality controls of ChIP-seq Fastq files were performed by FastQC. ChIP-seq Fastq read files are mapped to the mm10 reference genome using Bowtie2 with default parameters. To determine for ChIP-seq peaks with a narrow profile, datasets were processed using MACS2 with default parameters and --g mm option. For profiles characterized by enrichments in broad regions, datasets were processed using MACS2 with --broad and --g mm options. BigWig files were generated using Deeptools bamCoverage with --bs 50 and --normalizeUsing RPKM options.
Genome_build: mm10
Supplementary_files_format_and_content: bw files correpond RPKM-normalized bigwig binary files (50bp bins), which can be visualized using the Integrative Genomics Viewer (IGV) software.

extract_protocol:
Two 15cm-dishes with 2.10^7 cells in 20mL of culture media were used for each ChIP-seq experiment.  ChIP-seq was performed as described in ChIP-IT High sensitivity Kit from Active Motif with a few adaptations. Chromatin is sonicated by Bioruptor: 30sec ON – 30sec OFF, 10 cycles, high power. Sonicate for a total of 40 cycles for histones and of 30 cycles for TFs with 10min break on ice every 10 cycles. For ChIP reaction, 20µg chromatin was used with 4µg antibody for histone and 30µg chromatin + 4µg antibody for none-histone proteins. ChIP-DNA was eluted in 36µL with pre-warmed Elution Buffer then ChIP-DNA concentration was quantified with the Qubit dsDNA HS Assay Kit. 2,5ng to 10ng of ChIP-DNA were used for library preparation.
2,5ng to 10ng ChIP-DNA were used for library preparation. ChIP-seq library preparation was performed as described in TruSeq ChIP Sample Preparation kit from Illumina with few adaptations. The Enrich DNA Fragment step is proceeded before Purify Ligation Products step. AMPure XP beads were air-dry 7min. 1µL library was diluted 1:10 in H20 to quantified library concentration by Qubit DNA HS assay quantification. Agilent High Sensitivity DNA Electrophoresis was run to check DNA fragment size. Before sequencing, ChIP-seq libraries were quantified by qPCR. Libraries were sequenced 50bp or 100bp single-reads with 50 million reads of depth sequencing on HiSeq 2000 Illumina or NovaSeq 6000 Illumina machine at the MGX platforms.

value: CTCF (D31H2), Cell Signalling 3418S


title: 472310_EQG_S15

description: SK-UT-1 UNTREATED 6h round 3

value: UNTREATED


title: Sample 53_Acclimation_Control_4_4

description: 11769_5751_120099_H22JMBGXG_NSF021_C07_ABA_2018_C_4_3_1_CACTAA_R1

value: Control


title: iDART_SMART-seq APOBEC1-YTH Cell 92


title: iDART_SMART-seq APOBEC1-YTH Cell 91


title: 472309_EQF_S14

description: SK-UT-1 MC-2985 5uM 6h round 2

value: round 2


title: ChIP_CTCF_Setdb1KO_rep1

value: 5 days with 800 nM 4-hydroxytamoxifen (4-OHT)


title: 472308_EQE_S37

description: SK-UT-1 MC-2984 5uM 6h round 2


title: Sample 51_Acclimation_Control_4_2

description: 11769_5751_120097_H22JMBGXG_NSF021_A07_ABA_2018_C_2_3_1_GTGCCA_R1


title: ChIP_CTCF_WT_rep1


title: iDART_SMART-seq APOBEC1-YTH Cell 89

value: HEK293T Cells


title: 472307_EQD_S12

description: SK-UT-1 NKL54 5uM 6h round 2


title: Sample 50_Acclimation_Control_4_1

description: 11769_5751_120096_H22JMBGXG_NSF021_H06_ABA_2018_C_1_3_1_AATAGC_R1


title: 472306_EQC_S11

description: SK-UT-1 SAHA 2.5uM 6h round 2


title: Sample 49_Acclimation_ABA_2_4

description: 11769_5751_120095_H22JMBGXG_NSF021_G06_ABA_2018_A_4_2_1_GCATGG_R1


title: ChIP_SMC1_Setdb1KO_rep2

value: SMC1, Bethyl Laboratories A300-055A


title: iDART_SMART-seq APOBEC1-YTH Cell 86

value: 1microg/mL doxycycline; 24 hours


title: iDART_SMART-seq APOBEC1-YTH Cell 88


title: Sample 47_Acclimation_ABA_2_2

description: 11769_5751_120093_H22JMBGXG_NSF021_E06_ABA_2018_A_2_2_1_TAGGCT_R1

value: Cabernet Franc

value: Acclimation


title: 472305_EQB_S10

description: SK-UT-1 UNTREATED 6h round2


title: iDART_SMART-seq APOBEC1-YTH Cell 87


title: Sample 48_Acclimation_ABA_2_3

description: 11769_5751_120094_H22JMBGXG_NSF021_F06_ABA_2018_A_3_2_1_CTCCAT_R1

value: leaf


title: ChIP_SMC1_Setdb1KO_rep1


title: ChIP_SMC1_WT_rep2


title: 472303_EPZ_S8

description: SK-UT-1 MC-2984 5uM 6h round 1

value: round 1


title: ChIP_SMC1_WT_rep1

value: Mouse embryonic stem cells


title: iDART_SMART-seq APOBEC1-YTH Cell 85


title: Sample 46_Acclimation_ABA_2_1

description: 11769_5751_120092_H22JMBGXG_NSF021_D06_ABA_2018_A_1_2_1_ACAGAT_R1

value: 3' mRNA


title: ChIP_MED12_Setdb1KO_rep2

value: MED12, Bethyl Laboratories A300-774A


title: 472302_EPY_S7

description: SK-UT-1 NKL54 5uM 6h round 1

value: Leiomyosarcoma cells

value: NKL54 5uM


title: 472304_EQA_S9

description: SK-UT-1 MC-2985 5uM 6h round1


title: Sample 52_Acclimation_Control_4_3

description: 11769_5751_120098_H22JMBGXG_NSF021_B07_ABA_2018_C_3_3_1_TCGAGG_R1


title: ChIP_MED12_Setdb1KO_rep1


title: iDART_SMART-seq APOBEC1-YTH Cell 90


title: Sample 45_Acclimation_Control_2_4

description: 11769_5751_120091_H22JMBGXG_NSF021_C06_ABA_2018_C_4_2_1_AAGACA_R1


title: iDART_SMART-seq APOBEC1-YTH Cell 83


title: ChIP_CTCF_WT_rep2

value: CTCF (D31H2), Cell Signalling 3418S


title: 472301_EPX_S6

description: SK-UT-1 SAHA 2.5uM 6h round 1

value: SAHA 2.5uM


title: Sample 44_Acclimation_Control_2_3

description: 11769_5751_120090_H22JMBGXG_NSF021_B06_ABA_2018_C_3_2_1_TGACAC_R1

value: Control


title: 472300_EPW_S5

description: SK-UT-1 UNTREATED 6h round1

value: UNTREATED


title: ChIP_MED12_WT_rep2


title: iDART_SMART-seq APOBEC1-YTH Cell 82


title: ChIP_MED12_WT_rep1


title: Sample 43_Acclimation_Control_2_2

description: 11769_5751_120089_H22JMBGXG_NSF021_A06_ABA_2018_C_2_2_1_CTCTCG_R1


title: Sample 42_Acclimation_Control_0_4

description: 11769_5751_120088_H22JMBGXG_NSF021_H05_ABA_2018_A_4_1_1_GATTGT_R1

value: pre-treatment


title: iDART_SMART-seq APOBEC1-YTH Cell 81

value: HEK293T Cells


title: iDART_SMART-seq APOBEC1-YTH Cell 80


title: Sample 40_Acclimation_Control_0_2

description: 11769_5751_120086_H22JMBGXG_NSF021_F05_ABA_2018_A_2_1_1_ACCGTG_R1


title: ChIP_Ser5P_Setdb1KO_rep1

value: Phospho RNApolII Ser5 (1H4B6), Sigma MABE954

value: 5 days with 800 nM 4-hydroxytamoxifen (4-OHT)


title: ChIP_Ser5P_Setdb1KO_rep2


title: Sample 41_Acclimation_Control_0_3

description: 11769_5751_120087_H22JMBGXG_NSF021_G05_ABA_2018_A_3_1_1_CAACAG_R1

value: Cabernet Franc


title: ChIP_Ser5P_WT_rep2


title: iDART_SMART-seq APOBEC1-YTH Cell 84

value: 1microg/mL doxycycline; 24 hours


title: iDART_SMART-seq APOBEC1-YTH Cell 78


title: SK-UT-1 cells, MEF2D NKL54 ChIP

description: MEF2D bound regions in NKL54 treated cells

data_processing:
Basecalls performed using the ShortRead R/Biocoductor package
ChIP-seq reads were aligned to the hg38 genome assembly using bowtie2 version 2.3.4.3 with default configuration for unpaired reads
Duplicate reads were flagged using samtools but no duplicates were removed
peaks were called using MACS2 version 2.1.1 with the following setting: ChIP threshold (0.2), Enrichment Fold (2.5), Rescue Fold (3).
Genome_build: hg38
Supplementary_files_format_and_content: narrowPeak files were generated by MACS2 as a BED6+4 format file containing the peak locations together with peak summit, pvalue and qvalue; Columns content represent: chr, start, end, peak name, score, strand, fold-change, -log10pvalue, -log10qvalue, relative summit position to peak start

extract_protocol:
Lysates were obtained with a two-step protocol (nuclei were obtained with an hypotonic buffer (20mM TRIS-HCl pH8; 85 mM KCl; 0.5% NP-40), and nuclear membrane was lysed with Lysis buffer (10mM TRIS pH7.5; 1% NP-40, 0.5% Na-deossicholate; 0.1% SDS); then lysates were clarified from sonicated nuclei (30', medium power, Bioruptor Diagenode) and histone-DNA complexes were isolated with protein A/antibodies (2μg of anti-H3K27ac (Abcam ab4729) , 2.5 μg of anti-MEF2D (BD Bioscience), 4μg of anti-HDAC4 (Paroni et al, 2004) and anti-HDAC9 (home-made antibody) antibodies or control IgG. Washes were performed in LOW SALT IMMUNE COMPLEX WASH BUFFER (0.1% SDS, 1% TRITON, 20mM Tris-HCl pH8, 150 mM NaCl), HIGH SALT WASH BUFFER (0.1% SDS, 1% TRITON, 2mM EDTA, 20mM Tris-HCl pH8, 500 mM NaCl), LiCl Immune Complex Wash Buffer (0.25M LiCl, 1% NP40, 0.2% Na-deossicolato, 1mM EDTA, 10Mm Tris-HCl pH8) and TE. RNA was digested with RNAseA (2μg). DNA was de-crosslinked and purified with Zymo DNA columns.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, 5 μg of DNA were used. DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on Illumina HiSeq 2000 following the manufacturer's protocols.
TruSeq ChIP Library

value: below 20

value: MEF2D (BD Biosciences, clone 9 610775)


title: SK-UT-1 cells, HDAC9 NKL54 ChIP

description: HDAC9 bound regions in NKL54 treated cells

value: HDAC9 (Di Giorgio et al, 2019 PMID 31754707)


title: iDART_SMART-seq APOBEC1-YTH Cell 79


title: ChIP_Ser5P_WT_rep1

value: Mouse embryonic stem cells


title: SK-UT-1 cells, HDAC4 NKL54 ChIP

description: HDAC4 bound regions in NKL54 treated cells

value: HDAC4 (Paroni et al, 2004 PMID 15075374 )


title: SK-UT-1 cells, HDAC9 WT ChIP

description: HDAC9 bound regions in wt cells

value: Leiomyosarcoma cells

value: DMSO


title: iDART_SMART-seq APOBEC1-YTH Cell 77


title: Sample 38_Acclimation_Control_0_4

description: 11769_5751_120084_H22JMBGXG_NSF021_D05_ABA_2018_C_4_1_1_CGCAAC_R1

value: Acclimation

value: leaf

value: 3' mRNA


title: SK-UT-1 cells, HDAC4 WT ChIP

description: HDAC4 bound regions in wt cells


title: iDART_SMART-seq APOBEC1-YTH Cell 76


title: ChIP_H3K4me1_Setdb1KO_rep2

value: H3K4me1, Abcam ab8895


title: Sample 37_Acclimation_Control_0_3

description: 11769_5751_120083_H22JMBGXG_NSF021_C05_ABA_2018_C_3_1_1_GTTACC_R1

value: Control

value: pre-treatment


title: SK-UT-1 cells, H3K27ac NKL54 ChIP

description: Open chromatin evaluation in NKL54 treated cells

value: H3K27ac (Abcam, ab4729)


title: Sample 36_Acclimation_Control_0_2

description: 11769_5751_120082_H22JMBGXG_NSF021_B05_ABA_2018_C_2_1_1_TTGGTA_R1


title: iDART_SMART-seq APOBEC1-YTH Cell 75

value: HEK293T Cells


title: ChIP_H3K4me1_Setdb1KO_rep1

value: 5 days with 800 nM 4-hydroxytamoxifen (4-OHT)


title: SK-UT-1 cells, H3K27ac WT ChIP

description: Open chromatin evaluation in wt cells


title: ChIP_H3K4me1_WT_rep2


title: iDART_SMART-seq APOBEC1-YTH Cell 74

value: 1microg/mL doxycycline; 24 hours


title: Sample 35_Acclimation_Control_0_1

description: 11769_5751_120081_H22JMBGXG_NSF021_A05_ABA_2018_C_1_1_1_AGATAG_R1

value: Cabernet Franc


title: Sample 39_Acclimation_Control_0_1

description: 11769_5751_120085_H22JMBGXG_NSF021_E05_ABA_2018_A_1_1_1_TGGCGA_R1


title: iDART_SMART-seq APOBEC1-YTH Cell 73


title: SK-UT-1 cells, Input NKL54

description: Input

value: below 20


title: ChIP_H3K4me1_WT_rep1


title: SK-UT-1 cells, MEF2D WT ChIP

description: MEF2D bound regions in wt cells

value: MEF2D (BD Biosciences, clone 9 610775)


title: ChIP_H3K27ac_Setdb1KO_rep2

value: Mouse embryonic stem cells

value: H3K27ac, Abcam ab4729


title: SK-UT-1 cells, Input WT

description: Input

value: Leiomyosarcoma cells


title: Sample 34_Deacclimation_Control_72_3

value: Deacclimation

value: bud


title: ChIP_H3K27ac_Setdb1KO_rep1


title: iDART_SMART-seq APOBEC1-YTH Cell 72


title: CRISPR-3

city: London

first: Rocio

last: Sancho

state: London

address: Great Maze Pond, Guy's hospital

department: Centre for Stem Cells and Regenerative Medicine

country: United Kingdom

institute: KCL

data_processing:
FastQC
Trimmommatic to trim adaptors
STAR for genome alignment
FeatureCount for genarating count matrix
Genome_build: GRCh38/hg38
Supplementary_files_format_and_content: count files

source_name: pancreatic progenitor_HNF1A-CSISPR

growth_protocol: Human iPSCs were differentiated into pancreatic progenitors for a period of 14 days using the STEMdiff™ Pancreatic Progenitor Kit following manufacturer’s instructions, with some modifications: cell seeding prior to differentiation was 500,000 cells/well for 12-well plates and 42,000 cells/well for 96-well plates and stage 1 was extended to 3 days.

extract_protocol:
Differentiated cells at different stages were detached using Accutase for 10 min at 37C and neutralized with 5% FBS in Dulbecco's phosphate-buffered saline (DPBS). Cells were centrifuged at 300g for 5 min and kept at -80C until RNA extraction. RNA was extracted using the RNeasy Mni Kit.
NEBNext Ultra II RNA Library Preparation with polyA selection
Dual 8bp indexing, followed by sequencing using the Illumina HiSeq 2000 sequencer

treatment_protocol: poly A selection

value: human iPSC-derived pancreatic progenitor

value: CRISPR

tag: genotype/variation

value: heterozygous p291fsinsC mutation


title: iDART_SMART-seq APOBEC1-YTH Cell 70


title: Sample 32_Deacclimation_Control_72_1

value: Control

value: 3' mRNA


title: iDART_SMART-seq APOBEC1-YTH Cell 71


title: CRISPR-2


title: Sample 31_Deacclimation_Control_6_3


title: ChIP_H3K27ac_WT_rep1

tag: strain


title: iDART_SMART-seq APOBEC1-YTH Cell 69

tag: cell line


title: CRISPR-1


title: ChIP_H3K9me3_doubleKO_rep2

value: H3K9me3, Abcam ab8898


title: Sample 30_Deacclimation_Control_6_2


title: WT-3

source_name: pancreatic progenitor_HNF1A-WT

value: WT


title: iDART_SMART-seq APOBEC1-YTH Cell 68

value: HEK293T Cells

tag: transgene


title: Sample 29_Deacclimation_Control_6_1


title: ChIP_H3K9me3_doubleKO_rep1

value: 5 days with 800 nM 4-hydroxytamoxifen (4-OHT)


title: iDART_SMART-seq APOBEC1-YTH Cell 67

value: 1microg/mL doxycycline; 24 hours


title: WT-2


title: Sample 28_Deacclimation_Control_48_4

value: Cabernet Franc


title: Sample 27_Deacclimation_Control_48_3


title: Sample 26_Deacclimation_Control_48_2


title: iDART_SMART-seq APOBEC1-YTH Cell 65


title: iDART_SMART-seq APOBEC1-YTH Cell 66


title: ChIP_H3K9me3_Setd2KO_rep2


title: Sample 33_Deacclimation_Control_72_2


title: ChIP_H3K27ac_WT_rep2


title: WT-1


title: ChIP_H3K9me3_Setd2KO_rep1


title: sgRNA-enrichment_20k-sgRNAs_Lane5_NextSeq

city: Dallas

first: Yihan

state: Texas

address: 5323 Harry Hines Blvd.

institute: UT Southwestern

data_processing:
custom pipeline
Mapping and library combination were performed by using 10X Cellranger V3.1.0
Genome_build: hg38
Supplementary_files_format_and_content: summary of UMI count of each sgRNA for every cell barcode

source_name: MDA-MB-231 cells

growth_protocol: MDA-MB-231 cells were cultured in alpha modified MEM plus 10% FBS, 1mM sodium pyruvate, 10mM HEPES, 1X Glutamax supplement, 1X MEM non-essential amino acid, 1 mg/mL insulin, 1ng/mL hydrocortisone, 25 ug/mL EGF and pen/strep at 37C and 5% CO2.

extract_protocol:
Cells were collected, washed once with PBS. Then the cells were stained with Cell Hashing antibodies and resuspended in PBS containing 0.05% BSA to the desired concentration and immediately load on the 10X Chromium controller for the single-cell RNA-seq preparation.
For single-cell library preparation, we follow the standard protocol of 10X Chromium 3’ V3 kit. After the cDNA amplification, 50ng of samples were separated for the sgRNA enrichment library preparation.

treatment_protocol: A lentivirus library containing 20139 sgRNAs was constructed and packaged by transfecting HEK293T cells. The virus was collected 48 hours after transfection and concentrated by using Lenti-X lentivirus concentrator. For virus infection, 5X10^4 MDA-MB-231 cells were seeded in 24 well plate per well with 500 µl complete medium plus 1µg/ml polybrene. The following day, the medium was changed to fresh complete medium with antibiotics to screen for infected cells.

value: MDA-MB-231 cells

value: Single-cell Expression, sgRNA enrichment

tag: lane


title: K33-1

city: Beijing

first: Liuhui

last: Fu

address: Zhongguancun North Street

department: Institute for Immunology

institute: Tsinghua university

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to GRCm38.90 whole genome using bowtie2
FPKM were calculated using RSEM tool
Genome_build: GRCm38.90
Supplementary_files_format_and_content: FPKM values for each Sample

growth_protocol: ILC2 were purified from the lungs of Stat3fl/fl and VavicreStat3fl/fl mice after a short-term exposure of papain, and cultured in vitro for about 5 days with 10 ng/ml IL-2 alone.

extract_protocol:
Total RNA was isolated with the RNeasy Micro Kit (QIAGEN)
RNA libraries were prepared for sequencing using standard protocols

treatment_protocol: The expanded ILC2 were treated with 10 ng/ml IL-33 for another 2 days and then analyzed.

value: Lung

tag: cell type


title: sgRNA-enrichment_20k-sgRNAs_Lane4_NextSeq


title: K33-2


title: iDART_SMART-seq APOBEC1-YTH Cell 64


title: sgRNA-enrichment_20k-sgRNAs_Lane6_NextSeq


title: iDART_SMART-seq APOBEC1-YTH Cell 63


title: Sample 25_Deacclimation_Control_48_1


title: Sample 24_Deacclimation_Control_24_3


title: W33-2


title: sgRNA-enrichment_20k-sgRNAs_Lane3_NextSeq


title: iDART_SMART-seq APOBEC1-YTH Cell 62


title: W33-1


title: Sample 23_Deacclimation_Control_24_2


title: iDART_SMART-seq APOBEC1-YTH Cell 61


title: KC-2

value: control


title: sgRNA-enrichment_20k-sgRNAs_Lane1_NextSeq


title: Sample 21_Deacclimation_Control_12_3

value: Deacclimation


title: iDART_SMART-seq APOBEC1-YTH Cell 59


title: HTO_MDA-MB-231-YWsg1P1_Lane5

data_processing:
custom pipeline
Mapping and library combination were performed by using 10X Cellranger V3.1.0
Genome_build: hg38
Supplementary_files_format_and_content: summary of UMI count of each HTO for every cell barcode

value: Single-cell Expression, HTO enrichment


title: WC-2


title: WC-1


title: Sample 20_Deacclimation_Control_12_2

value: bud


title: HTO_MDA-MB-231-YWsg1P1_Lane6


title: Sample 19_Deacclimation_Control_12_1


title: HTO_MDA-MB-231-YWsg1P1_Lane4


title: iDART_SMART-seq APOBEC1-YTH Cell 60


title: iDART_SMART-seq APOBEC1-YTH Cell 58


title: iDART_SMART-seq APOBEC1-YTH Cell 57


title: HTO_MDA-MB-231-YWsg1P1_Lane3


title: MSC_aGVHD_V3

city: Tianjin

first: Quan

last: Gu

address: 288 Nanjing Road

institute: State Key Laboratory of Experimental Hematology, Institute of Hematology & Blood Diseases Hospital

data_processing:
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina Novaseq platform and 150 bp paired-end reads were generated
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality
Prior to differential gene expression analysis, for each sequenced library, the read counts were adjusted by edgeR program package through one scaling normalized factor. Differential expression analysis of two conditions was performed using the edgeR R package (3.18.1). The P values were adjusted using the Benjamini & Hochberg method. Corrected P-value of 0.05 and absolute foldchange of 2 were set as the threshold for significantly differential expression
Gene Ontology (GO) enrichment analysis of differentially expressed genes was implemented by the clusterProfiler R package, in which gene length bias wascorrected. GO terms with corrected Pvalue less than 0.05 were considered significantly enriched by differential expressed genes.
KEGG is a database resource for understanding high-level functions and utilities of the biological system, such as the cell, the organism and the ecosystem, from molecular-level information, especially large-scale molecular datasets generated by genome sequencing and other high-through put experimental technologies (http://www.genome.jp/kegg/). We used clusterProfiler R package to test the statistical enrichment of differential expression genes in KEGG pathways.
Genome_build: GRCm38 (mm10)
Supplementary_files_format_and_content: tab-delimited tex files include FPKM values for each samples

source_name: MSCs

growth_protocol: Cells were isolated from mice and cultured in medium containing DMEM (high-glucose), FBS and P/S.

extract_protocol:
We isolated MSCs by digesting unfractionated BM.
RNA libraries were prepared for sequencing using standard illumina protocols

treatment_protocol: Cells in aGVHD_V group were treated with vehicle(DMSO) and cells in aGVHD_R group were treated with R (0.5 um).

value: MSCs

value: MSCs isolated from aGVHD mice and treated with vehicle in vitro


title: KC-1


title: iDART_SMART-seq APOBEC1-YTH Cell 56


title: Sample 18_Deacclimation_Control_0_3

value: Control

value: pre-treatment


title: MSC_aGVHD_V2


title: Sample 17_Deacclimation_Control_0_2

value: 3' mRNA


title: Sample 16_Deacclimation_Control_0_1


title: HTO_MDA-MB-231-YWsg1P1_Lane2


title: MSC_aGVHD_V1


title: iDART_SMART-seq APOBEC1-YTH Cell 55


title: sgRNA-enrichment_20k-sgRNAs_Lane2_NextSeq


title: iDART_SMART-seq APOBEC1-YTH Cell 54


title: HTO_MDA-MB-231-YWsg1P1_Lane1


title: Sample 15_Deacclimation_ABA_72_3

value: ABA


title: MSC_aGVHD_R3

value: MSCs isolated from aGVHD mice and treated with R in vitro


title: MDA-MB-231-YWsg1P1_Lane6_NextSeq

data_processing:
Basecalls performed 10X Cellranger V3.1.0
Mapping and library combination were performed by using 10X Cellranger V3.1.0
Genome_build: hg38
Supplementary_files_format_and_content: sample matrix in hdf5 format

value: Single-cell Expression, transcriptome


title: iDART_SMART-seq APOBEC1-YTH Cell 53

data_processing:
Alignment to hg38 and UMI deduplication using Cell Ranger 3.1.0 (10x Genomics scRNA-seq samples only)
SMART-seq2 and bulk RNAseq samples: Trimming of adaptor sequences (Flexbar 3.0.3)
SMART-seq2 and bulk RNAseq samples:  Alignment using STAR 2.7.5c, and deduplication using SAMtools (1.11) fixmate and markdup
All samples: Identification of m6A sites using Bullseye
All samples: Expression normalization and integrated clustering of cells using Seurat (3.2.1)
Genome_build: hg38
Supplementary_files_format_and_content: Bed files for bulk RNAare a list of m6A sites identified within each replicate using Bullseye. High confidence m6A sites in paper were a result of keeping only these sites that occur in at least 2 of 3 APOBEC1-YTH replicates
Supplementary_files_format_and_content: a bed file consisting of APOBEC1-mediated C-to-U editing sites identified by downstream analysis

value: HEK293T Cells

value: 1microg/mL doxycycline; 24 hours


title: Sample 22_Deacclimation_Control_24_1

value: Cabernet Franc


title: Sample 14_Deacclimation_ABA_72_2


title: iDART_SMART-seq APOBEC1-YTH Cell 52


title: MSC_aGVHD_R2


title: MDA-MB-231-YWsg1P1_Lane5_NextSeq

value: MDA-MB-231 cells


title: MSC_aGVHD_R1


title: Sample 13_Deacclimation_ABA_72_1


title: iDART_SMART-seq APOBEC1-YTH Cell 51


title: iDART_SMART-seq APOBEC1-YTH Cell 49


title: MDA-MB-231-YWsg1P1_Lane3_NextSeq


title: Sample 10_Deacclimation_ABA_6_1


title: Dnmt3Cmutant_WGBS_E18-5

city: paris

first: teissandier

last: aurelie

address: 26 rue d'Ulm

institute: institut curie

description: bisulfite-treated DNA

data_processing:
Adapters were trimmed using Atropos v1.1.16. Trimmed reads were cleaned by removal of 5bp in 5' end of read1 and 12bp in 5' end of read2 using Cutadapt v1.12. Reads shorter than 15bp were discarded. Cleaned reads were aligned onto the mouse reference genome assembly (GRCm38/mm10) using Bismark v0.18.2 with Bowtie2-2.2.9 allowing one mismatch in a seed alignment. Only reads mapping uniquely to the genome were kept, and methylation calls were extracted after duplicate removal by considering only CpG dinucleotides covered by a minimum of five reads.
Genome_build: mm10
Supplementary_files_format_and_content: bigWig file with DNA methylation level (percentage)

source_name: Prospermatogonia E18.5

extract_protocol: Germ cells (prospermatogonia) were isolated from single-cell dissociated E18.5 fetal testis by FACS  (BD FACSAria II; DAPI negative/Oct4-GFP positive), DNA was extracted using QIAmp DNA Micro Kit, quantified on Qubit, and spiked in with unmethylated Lambda DNA to a 0,1% of the total DNA mass of the sample, followed by bisulfite treatment using the Imprint DNA Modification Kit (SIGMA).

tag: Sex

value: male

value: Prospermatogonia (Oct4-GFP positive cells sorted by FACS)


title: Dnmt3Amutant_WGBS_E18-5

description: bisulfite-treated DNA


title: Dnmt3Lmutant_WGBS_E18-5

description: bisulfite-treated DNA


title: iDART_SMART-seq APOBEC1-YTH Cell 50


title: iDART_SMART-seq APOBEC1-YTH Cell 48


title: d2PGCLC_Ovol2b-Tg_rep2

city: Fukuoka city

first: Yuki

last: Naitou

state: Japan

address: 3-1-1, Maidashi, Higashi-ku, Fukuoka city

country: Japan

institute: Kyushu university

data_processing:
Obtained reads were mapped to the mouse mm10 genome using Hisat2. Mapped reads were counted by featureCounts. Principal component analysis (PCA) was performed using R software with FactoMineR. For differentially expressed gene (DEG) analysis, the false discovery rate (FDR) and log2 fold-change were calculated using edgeR. The DAVID database was used for Gene ontology (GO) analysis.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with TPM values for every gene and every sample

source_name: primordial germ cell like cells at day 2 of Ovol2b OE

extract_protocol:
Total RNAs were extracted and purified using an RNeasy Micro Kit, and mRNAs were isolated with the NEBNext poly(A) mRNA magnetic isolation module (NEB).
Purified RNAs were subjected to library construction using a NEBNext Ultra Directional RNA Library Prep Kit for Illumina (NEB). cDNAs were enriched by 12-cycle PCR.

value: primordial germ cell like cells

value: Ovol2b OE


title: Sample 8_Deacclimation_ABA_48_2

value: Deacclimation

value: bud


title: MDA-MB-231-YWsg1P1_Lane1_NextSeq


title: Sample 9_Deacclimation_ABA_48_3


title: iDART_SMART-seq APOBEC1-YTH Cell 47

extract_protocol:
SMART-seq2 cells: Single cells were sorted using a FACS Aria II (BD) directly into lysis buffer provided with the SMART-seq HT Kit (Takara, Cat. 634438). The SMART-seq HT Kit was then used for reverse transcription and cDNA amplification. Sequencing libraries were constructed from cDNA using the Nextera XT kit (Illumina, FC-131-1096) and dual Nextera-compatible CDI indexes from IDT. Samples were pooled and sequenced targeting 5,000,000 reads/library (150bp paried-end) on a Novaseq6000 using the S4 flowcell.   10X Genomics cells: A single cell suspension was prepared according to manufacturer's instruction for Chromium v3 3' end sequencing (10x Genomics, Manual Part #CG00053). Samples were sequenced targeting 80,000 reads per cell on a Novaseq6000 using the S1 flowcell.  Bulk RNA-seq: Trizol was used to extract total RNA from iDART cells. The UltraII Directional RNA Library Prep Kit (NEB, E7760) with NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB, 7490) was used to generate sequencing libraries using 900ng of input RNA. The samples were sequenced targeting ~30 million reads (50bp paired-end sequencing) per sample on a Novaseq6000 using the S1 flowcell.
SMART-seq2 scRNA-seq: cDNA libraries were generated using the SMART-seq HT Kit (Takara, Cat. 634438). Final libraries were prepared using Nextera XT DNA Library Prep Kit (Illumina, FC-131-1096).   10x scRNA-seq: Libraries were generated from a single cell suspension using the 10x Genomics NextGEM Single Cell 3' Kit, v3.1 chemistry (10x Genomics)  Bulk-RNA seq: The UltraII Directional RNA Library Prep Kit (NEB, E7760) with NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB, 7490) was used to generate sequencing libraries using 900ng of input RNA.


title: Dnmt3L WT/WT_scRNAseq_GermCells_10dpp

data_processing:
Raw count matrices were generated using Cell Ranger v3.0.2 and were imported to Seurat v3.1.1.
Genome_build: mm10
Supplementary_files_format_and_content: A single gene x. cell-barcode matrix file (MTX). Each matrix is stored in Market Exchange Format (MEX). It also contains TSV files with genes and barcode sequences corresponding to row and column indices, respectively.

source_name: scRNAseq from germ cells enriched by FACS at 10dpp

extract_protocol:
RNA was extrated form 6000 cells according to manufacturer’s instructions of 10X genomics Single Cells 3' V2 or V3
Library were preformed according to manufacturer’s instructions of 10X genomics Single Cells 3' V2 or V3

value: Dnmt3A WT/WT

value: Germ cell enriched by FACS

tag: 10x genomics

value: Single cell 3' V2


title: d2PGCLC_Ovol2b-Tg_rep1


title: iDART_SMART-seq APOBEC1-YTH Cell 46


title: Dnmt3A WT/WT_scRNAseq_GermCells_10dpp

value: Single cell 3' V3


title: Sample 7_Deacclimation_ABA_48_1

value: ABA

value: 3' mRNA


title: Sample 6_Deacclimation_ABA_24_3


title: iDART_SMART-seq APOBEC1-YTH Cell 44


title: iDART_SMART-seq APOBEC1-YTH Cell 45


title: d2PGCLC_Ovol2a-Tg_rep1

source_name: primordial germ cell like cells at day 2 of Ovol2a OE

value: epiblast like cells

value: Ovol2a OE


title: Sample 12_Deacclimation_ABA_6_3


title: MDA-MB-231-YWsg1P1_Lane4_NextSeq

value: Single-cell Expression, transcriptome


title: Dnmt3A WT/WT_scRNAseq_WholeTestis_10dpp

source_name: scRNAseq from single cell suspension of the whole testis at 10dpp


title: Sample 5_Deacclimation_ABA_24_2

value: Cabernet Franc


title: MDA-MB-231-YWsg1P1_Lane2_NextSeq

value: MDA-MB-231 cells


title: Sample 11_Deacclimation_ABA_6_2


title: Sample 4_Deacclimation_ABA_24_1


title: iDART_SMART-seq APOBEC1-YTH Cell 43

value: HEK293T Cells

value: 1microg/mL doxycycline; 24 hours


title: EpiLC_Ovol2b-Tg_rep1

source_name: epiblast like cells of Ovol2b OE


title: iDART_SMART-seq APOBEC1-YTH Cell 42


title: Wildtype_WGBS_E18-5

description: bisulfite-treated DNA

value: male

value: Wildtype

value: Prospermatogonia (Oct4-GFP positive cells sorted by FACS)


title: Dnmt3A KO/KO_scRNAseq_GermCells_10dpp

value: Dnmt3A KO/KO


title: Sample 3_Deacclimation_ABA_12_3

value: Deacclimation

value: bud


title: EpiLC_Ovol2a-Tg_rep2

source_name: epiblast like cells of Ovol2a OE


title: iDART_SMART-seq APOBEC1-YTH Cell 41


title: Dnmt3L KO/KO_scRNAseq_GermCells_10dpp

value: Dnmt3L KO/KO

value: Germ cell enriched by FACS

value: Single cell 3' V2


title: Sample 2_Deacclimation_ABA_12_2

value: ABA

value: 3' mRNA


title: Sample 1_Deacclimation_ABA_12_1


title: ESC_Ovol2b-Tg_rep2

source_name: embryonic stem cells of Ovol2b OE

value: embryonic stem cells

value: Ovol2b OE


title: Prdm1-Dnmt3AcKO/KO_scRNAseq_GermCells_10dpp

value: Single cell 3' V3


title: d2PGCLC_Ovol2a-Tg_rep2

value: epiblast like cells

value: Ovol2a OE


title: iDART_SMART-seq APOBEC1-YTH Cell 39

value: HEK293T Cells

value: 1microg/mL doxycycline; 24 hours


title: WGBS Te1 KO (Replicate #2)

first: Meelad

middle: M

last: Dawlaty

state: New York

address: 1301 Morris Park Ave, Price 419, Bronx

department: Genetics

institute: Albert Einstein College of Medicine

data_processing:
Trim Galore (Version 0.3.7) was used to trim the low-quality bases and the adapters.
For RNA-seq, clean reads were mapped to the mouse genome mm10 using TopHat2 (Version 2.0.13) (Kim et al., 2013). HTseq (Version 0.11.0) (Anders et al., 2015) with option ”--stranded=no” was used to calculated read counts mapped to genes. Genes with mean FPKM > 1.0 in any group were retained for differential expression analysis using R package DESeq2 (Love et al., 2014).
For CUT&Tag cleaned reads were mapped to the mouse genome (mm10) using Bowtie2 (Version 2.2.3) (Langmead and Salzberg, 2012) with options: --local --very-sensitive-local --no-unal --no-mixed --no-discordant -I 10 -X 700. Peak calling was performed using MACS2 (Version 2.1.0) (Zhang et al., 2008) with options -f BAMPE --keep-dup all.
For CUT&RUN analysis, we followed the pipelines from CUT&RUNTools (Zhu et al., 2019) for alignment, peak filtering and peak calling. In detail, Bowtie2 was used for genomic mapping with option “--dovetail”. After alignment, reads with fragments≤ 120-bp were filtered out and used for peak calling. MACS2 was applied with the default setting.
For ATAC-seq, clean reads were mapped against the mm10 mouse genome using Bowtie2 with the option “-X 2000 --no-mixed --no-discordant –local”. Unmapped reads, mitochondrial reads and deduplicated reads were removed from each mapped result by SAMtools (Version 1.9) (Li et al., 2009) and Picard(Version 2.3.0, https://broadinstitute.github.io/picard/). Correlation between biological replicates was assessed to ensure high reproducibility before pooling each set of replicates. MACS2 was run with the options “-f BAMPE -g mm --nomodel --nolambda --slocal 10000 --keep-dup all” to call peaks. Peaks from individual samples in each group of Tet1+/+, Tet1m/m and Tet1-/- were merged with bedtools2 (Version 2.26.0) (Quinlan and Hall, 2010) using parameter ‘-d 10’, and mm10 blacklist regions were filtered. Read coverage of ATAC-seq peaks was calculated by HTseq with parameter “–nonunique all”. The differentially accessible regions were identified using DESeq2 with threshold padj < 0.05.
Samtools was used to convert SAM to BAM, sort and index corresponding BAM files. Bigwig files were generated using bamCoverage from deepTools, and bigwig files were analyzed using plotProfile and plotHeatmap.Peaks annotation were implemented by R package "ChIPseeker".
For WGBS, Lamda DNA spike-in was added to confirm the bisulfite conversion efficiency. Through mapping to Lamda DNA, 99.4% C was successfully bisulfite converted. The libraries with DNA fragment length of 100-300 bp were subjected to 100 bp pair-end sequencing on BGI DNBseq platform . the raw reads were filtered by SOAPnuke (Version 1.5.5) (https://github.com/BGI-flexlab/SOAPnuke) with the parameters -n 0.001 -l 20 -q 0.4 -A 0.25 -Q 2 -G to remove adaptor sequences, contamination and low-quality reads. Then the clean data were mapped to mouse genome mm10 by Bismark (Version 0.18.1) (Krueger and Andrews, 2011) with default options. Duplicated sequences were removed by deduplicate_bismark. Methylpy (Version 1.4.0) (Schultz et al., 2015) was used to call methylation state for all Cs over the genome and convert the methylation level to bigwig files. DMRs were identified by R package “bsseq” (Version 1.16.1) from BSmooth (Hansen et al., 2012) pipeline.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig

source_name: Mouse ESCs

growth_protocol: ESCs were cultured on gelatin in serum/LIF and then harvested for subsequent high-throughput sequencing.

extract_protocol:
For RNA-seq, RNA extraction was performed using Omega E.Z.N.A Total RNA kit. For WGBS, DNA extraction was performed using Zymo Quick-DNA Miniprep Kit.
RNA-seq libraries were prepared using illumina library prep kit following manufacterer's protocols at Einstein Epigenomcis core. CUT&Tag libraries were prepared by NEBNext HiFi 2x PCR Master mix. CUT&RUN libraries were prepared using NEB library kit. ATAC-seq libraries were prepared by Nextera DNA CD Indices and NEBNext High-Fidelity 2x PCR Master Mix. WGBS-seq libraries were prepared by BGI company (https://en.genomics.cn/).

treatment_protocol: For CUT&Tag, ESCs were crosslinked, bound to Con-A beads, incubated with primary antibody and treated with pre-loaded pA-Tn5 adapter complex. For CUT&RUN, ESCs were bound to Con-A beads, incubated with primary antibody and treated with MNase.

value: Embryonic stem cells

value: V6.5 Male mixed 129/C57BL/6

value: Tet1 Knockout


title: ESC_Ovol2a-Tg_rep2

source_name: embryonic stem cells of Ovol2a OE


title: iDART_SMART-seq APOBEC1-YTH Cell 38

source_name: Kidney


title: WGBS Te1 KO (Replicate #1)


title: Dnmt3A WT/WT_Cut&Run_Id4GFP_10dpp_H3K27ac_Replicate 4

data_processing:
Library strategy: Cut&Run-seq
Paired-end reads were trimmed using Trim Galore v0.4.4. The alignment was performed onto a concatenated genome using the Mouse reference genome (mm10) and the Escherichia coli genome (str. K-12 substr. MG1655, Genbank: NC_000913) with STAR v2.7.0e reporting randomly one position, allowing 4% of mismatches (--outFilterMultimapNmax 5000 --outSAMmultNmax 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.04 --alignIntronMax 1 --alignMatesGapMax 2000). PCR duplicates were removed using Picard v2.6.0 (http://broadinstitute.github.io/picard/).
Genome_build: mm10
Supplementary_files_format_and_content: bigWig file with normalized coverage (RPKM)

source_name: Cut&Run from Id4-GFP bright + med germ cells (~SSC) at 10dpp

extract_protocol:
DNA was isolated with antibody and PA-Mnase incubation.
Library preparation was performed according to manufacturer’s instructions (Accel-NGS 2S DNA library kit, Swift biosciences 21024, 21096 and adapters 28596) with a modified library amplification program: 98°C for 45sec, (98°C for 10sec, 60°C for 15sec, 68°C for 1min)x15 cycles, hold at 4°C.

value: Dnmt3A WT/WT

tag: antibody

value: H3K27ac Active Motif 39133

value: Id4-GFP bright + med germ cells


title: Dnmt3A WT/WT_Cut&Run_Id4GFP_10dpp_IgG_Replicate 2

value: IgG Sigma 15006


title: iDART_SMART-seq APOBEC1-YTH Cell 37


title: WGBS Te1 Mut (Replicate #2)

value: Tet1 Mutant


title: Dnmt3A WT/WT_Cut&Run_Id4GFP_10dpp_H3K27me3_Replicate 4

value: H3K27me3 Cell signaling 9733S


title: Dnmt3A 2lox/KO_scRNAseq_GermCells_10dpp

description: Mouse (Dnmt3A2lox/KO; Prdm1-Cre-/-)

value: Dnmt3A 2lox/KO

value: Germ cell enriched by FACS


title: WGBS Te1 Mut (Replicate #1)


title: Dnmt3A WT/WT_Cut&Run_Id4GFP_10dpp_H3K27ac_Replicate 3


title: iDART_SMART-seq APOBEC1-YTH Cell 36


title: EpiLC_Ovol2b-Tg_rep2

value: Ovol2b OE


title: d2PGCLC_TKO_rep2

source_name: primordial germ cell like cells at day 2 of TKO mutant

value: primordial germ cell like cells

value: TKO


title: Dnmt3A WT/WT_Cut&Run_Id4GFP_10dpp_H3K27me3_Replicate 3


title: d2PGCLC_TKO_rep1


title: iDART_SMART-seq APOBEC1-YTH Cell 35


title: iDART_SMART-seq APOBEC1-YTH Cell 40


title: iDART_SMART-seq APOBEC1-YTH Cell 34


title: EpiLC_Ovol2a-Tg_rep1

value: epiblast like cells

value: Ovol2a OE


title: Dnmt3A KO/KO_scRNAseq_WholeTestis_10dpp

value: Dnmt3A KO/KO

value: single cell suspension of the whole testis

value: Single cell 3' V3


title: WGBS Te1 WT (Replicate #1)

value: Embryonic stem cells

value: V6.5 Male mixed 129/C57BL/6

value: Tet1 Wild Type


title: d2PGCLC_Ovol3KO_rep2

source_name: primordial germ cell like cells at day 2 of Ovol3 mutant

value: Ovol3 mutant


title: iDART_SMART-seq APOBEC1-YTH Cell 33

value: HEK293T Cells

value: 1microg/mL doxycycline; 24 hours


title: Dnmt3A WT/WT_Cut&Run_Id4GFP_10dpp_H3K27me3_Replicate 2

value: Dnmt3A WT/WT

value: H3K27me3 Cell signaling 9733S

value: Id4-GFP bright + med germ cells


title: ESC_Ovol2b-Tg_rep1

value: embryonic stem cells

value: Ovol2b OE


title: d2PGCLC_Ovol3KO_rep1

value: primordial germ cell like cells


title: iDART_SMART-seq APOBEC1-YTH Cell 32


title: Bb8

city: Nijmegen

first: Jodie

middle: Anne

last: Schildkraut

address: Geert Grooteplein Zuid 10

country: Netherlands

institute: Radboudumc

data_processing:
Illumina demultiplexing bcl2fastq
Mapping using STAR (v2.7.0)
Create count table with GenomicAlignments
Genome_build: NC_010397.1
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Mycobacteroides abscessus

source_name: Frozen reference strain

growth_protocol: Bacteria were grown to early log-phase prior to start of experiment

extract_protocol:
RNA isolation was performed using the Nucleospin RNA kit (Machery Nagel, Düren, Germany), with slight modifications. Following isolation, RNA integrity was determined, ribosomal RNA was depleted and the mRNA library was constructed and sequenced on a NextSeq 500 (Illumina, San Diego, CA).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Bacteria were treated with antibiotica for 4 or 24 hours or left untreated

value: Growth Control

tag: time

value: 4 hours


title: Cb8


title: d2PGCLC_Ovol2KO_rep2

source_name: primordial germ cell like cells at day 2 of Ovol2 mutant

value: Ovol2 mutant


title: Dnmt3A WT/WT_Cut&Run_Id4GFP_10dpp_IgG_Replicate 1

value: IgG Sigma 15006


title: iDART_SMART-seq APOBEC1-YTH Cell 31


title: d2PGCLC_Ovol2KO_rep1


title: Dnmt3A WT/WT_Cut&Run_Id4GFP_10dpp_H3K27ac_Replicate 1

value: H3K27ac Active Motif 39133


title: ESC_Ovol2a-Tg_rep1

value: Ovol2a OE


title: Ab8


title: Dnmt3A WT/WT_Cut&Run_Id4GFP_10dpp_H3K27me3_Replicate 1


title: d2PGCLC_Ovol1KO_rep2

source_name: primordial germ cell like cells at day 2 of Ovol1 mutant

value: Ovol1 mutant


title: Dnmt3A KO/KO_Cut&Run_Id4GFP_10dpp_IgG_Replicate 2

value: Dnmt3A KO/KO


title: WGBS Te1 WT (Replicate #2)

value: Embryonic stem cells

value: V6.5 Male mixed 129/C57BL/6

value: Tet1 Wild Type


title: d2PGCLC_Ovol1KO_rep1


title: iDART_SMART-seq APOBEC1-YTH Cell 29

value: HEK293T Cells

value: 1microg/mL doxycycline; 24 hours


title: iDART_SMART-seq APOBEC1-YTH Cell 28


title: d2PGCLC_wild type_rep2

source_name: primordial germ cell like cells at day 2 of wild type

value: wild type


title: A9

value: 24 hours


title: C9


title: Dnmt3A KO/KO_Cut&Run_Id4GFP_10dpp_H3K27ac_Replicate 3

value: Id4-GFP bright + med germ cells


title: Dnmt3A WT/WT_Cut&Run_Id4GFP_10dpp_H3K27ac_Replicate 2

value: Dnmt3A WT/WT


title: Cb7

value: Tigecycline


title: iDART_SMART-seq APOBEC1-YTH Cell 26


title: Dnmt3A KO/KO_Cut&Run_Id4GFP_10dpp_H3K27me3_Replicate 2

value: H3K27me3 Cell signaling 9733S


title: iDART_SMART-seq APOBEC1-YTH Cell 30


title: C8


title: Dnmt3A KO/KO_Cut&Run_Id4GFP_10dpp_IgG_Replicate 1


title: B8


title: iDART_SMART-seq APOBEC1-YTH Cell 27


title: Dnmt3A KO/KO_Cut&Run_Id4GFP_10dpp_H3K27me3_Replicate 3


title: EpiLC_Ovol3KO_rep2

source_name: epiblast like cells of Ovol3 mutant

value: epiblast like cells

value: Ovol3 mutant


title: Dnmt3A KO/KO_Cut&Run_Id4GFP_10dpp_H3K27me3_Replicate 1


title: EpiLC_Ovol3KO_rep1


title: Bb7

value: 4 hours


title: Cb6

value: Growth Control 7H9


title: d2PGCLC_wild type_rep1

value: primordial germ cell like cells


title: iDART_SMART-seq APOBEC1-YTH Cell 25


title: EpiLC_TKO_rep2

source_name: epiblast like cells of TKO mutant

value: TKO


title: EpiLC_TKO_rep1


title: iDART_SMART-seq APOBEC1-YTH Cell 21


title: Dnmt3A KO/KO_Cut&Run_Id4GFP_10dpp_H3K27ac_Replicate 2

value: Dnmt3A KO/KO

value: H3K27ac Active Motif 39133


title: B9

value: Growth Control


title: Ab7


title: iDART_SMART-seq APOBEC1-YTH Cell 24

value: HEK293T Cells


title: Dnmt3A KO/KO_Cut&Run_Id4GFP_10dpp_H3K27ac_Replicate 1


title: EpiLC_Ovol2KO_rep2

source_name: epiblast like cells of Ovol2 mutant

value: Ovol2 mutant


title: Ab6


title: EpiLC_Ovol2KO_rep1


title: Dnmt3A KO/KO_RNAseq_Id4GFP_10dpp_Replicate 3

data_processing:
Adapters were trimmed using Atropos v1.1.16. Paired-end read alignment was performed onto the Mouse reference genome (mm10) with STAR v2.7.0a reporting randomly one position, allowing 6% of mismatches (--outFilterMultimapNmax 5000 --outSAMmultNmax 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.06). Repeat annotation was downloaded from RepeatMasker (http://www.repeatmasker.org/). In order to reconstruct full-length LTR copies, we used the perl tool “One code to find them all”. Reconstructed transposons annotation and basic genes annotation from GENCODE v18 were merged and used as input for quantification with FeatureCounts v1.5.1.
Genome_build: mm10
Supplementary_files_format_and_content: Text file with gene expression (count)

source_name: RNA seq from Id4-GFP bright + med germ cells (~SSC) at 10dpp

extract_protocol:
Id4-GFP bright+ med germ cell RNA was extracted using Arcturus PicoPure RNA isolation extraction kit, Dnase-treated using QIAGEN Rnase-Free Dnase Set, and quality-controlled for integrity using Agilent RNA Pico Assay on a Bioanalyzer.
SMARTer Stranded Total RNA-Seq Kit

value: male


title: Bb6


title: iDART_SMART-seq APOBEC1-YTH Cell 22

value: 1microg/mL doxycycline; 24 hours


title: Dnmt3A KO/KO_RNAseq_Id4GFP_10dpp_Replicate 2

value: Id4-GFP bright + med germ cells


title: iDART_SMART-seq APOBEC1-YTH Cell 23


title: EpiLC_Ovol1KO_rep2

source_name: epiblast like cells of Ovol1 mutant

value: Ovol1 mutant


title: iDART_SMART-seq APOBEC1-YTH Cell 19


title: Dnmt3A KO/KO_RNAseq_Id4GFP_10dpp_Replicate 1


title: EpiLC_Ovol1KO_rep1


title: C5

value: 24 hours


title: iDART_SMART-seq APOBEC1-YTH Cell 18


title: B5


title: Dnmt3A WT/WT_RNAseq_Id4GFP_10dpp_Replicate 3

value: Dnmt3A WT/WT


title: A5


title: EpiLC_wild type_rep2

source_name: epiblast like cells of wild type

value: epiblast like cells

value: wild type


title: EpiLC_wild type_rep1


title: iDART_SMART-seq APOBEC1-YTH Cell 17


title: iDART_SMART-seq APOBEC1-YTH Cell 16


title: iDART_SMART-seq APOBEC1-YTH Cell 15


title: Dnmt3A WT/WT_RNAseq_Id4GFP_10dpp_Replicate 2


title: ESC_TKO_rep2

source_name: embryonic stem cells of TKO mutant

value: embryonic stem cells


title: Dnmt3A KO/KO_RNAseq_WholeTestis_25dpp_Replicate 2

source_name: RNA seq from whole testis at 25dpp

extract_protocol:
Whole testis RNA was extracted using Trizol, Dnase-treated using QIAGEN Rnase-Free Dnase Set, and quality-controlled for integrity using Agilent RNA Assay on a TapeStation 4200.
TruSeq Stranded mRNA Kit

value: Whole testis


title: Dnmt3A WT/WT_RNAseq_Id4GFP_10dpp_Replicate 1


title: Bb5

value: Clofazimine

value: 4 hours


title: Cb5


title: ESC_TKO_rep1

value: TKO


title: iDART_SMART-seq APOBEC1-YTH Cell 20


title: Dnmt3A KO/KO_RNAseq_WholeTestis_25dpp_Replicate 1

value: Dnmt3A KO/KO


title: iDART_SMART-seq APOBEC1-YTH Cell 14


title: Ab5


title: ESC_Ovol3KO_rep2

source_name: embryonic stem cells of Ovol3 mutant

value: Ovol3 mutant


title: iDART_SMART-seq APOBEC1-YTH Cell 13

source_name: Kidney

value: HEK293T Cells


title: Dnmt3A WT/WT_RNAseq_WholeTestis_25dpp_Replicate 2


title: ESC_Ovol3KO_rep1


title: iDART_SMART-seq APOBEC1-YTH Cell 12


title: ESC_Ovol2KO_rep2

source_name: embryonic stem cells of Ovol2 mutant

value: Ovol2 mutant


title: iDART_SMART-seq APOBEC1-YTH Cell 11


title: C4


title: Dnmt3A WT/WT_RNAseq_WholeTestis_25dpp_Replicate 1

value: male


title: A4


title: Dnmt3A KO/KO_RNAseq_WholeTestis_19dpp_Replicate 2

source_name: RNA seq from whole testis at 19dpp


title: ESC_Ovol2KO_rep1


title: iDART_SMART-seq APOBEC1-YTH Cell 10

value: 1microg/mL doxycycline; 24 hours


title: Cb3

value: Cefoxitin


title: ESC_Ovol1KO_rep2

source_name: embryonic stem cells of Ovol1 mutant

value: Ovol1 mutant


title: Dnmt3A KO/KO_RNAseq_WholeTestis_19dpp_Replicate 1


title: Dnmt3A WT/WT_RNAseq_WholeTestis_19dpp_Replicate 2


title: Bb3

source_name: Frozen reference strain


title: iDART_SMART-seq APOBEC1-YTH Cell 9


title: ESC_Ovol1KO_rep1


title: Dnmt3A WT/WT_RNAseq_WholeTestis_19dpp_Replicate 1


title: iDART_SMART-seq APOBEC1-YTH Cell 8


title: iDART_SMART-seq APOBEC1-YTH Cell 7


title: Primary Mammary Epithelial Cells (Non Infected)

city: Gandarbal

first: Basharat

middle: Ahmad

last: Bhat

state: Kashmir

address: Shuhama

department: Animal Biotechnology

country: India

institute: Sher-e-Kashmir University of Agricultural Sciences and Technology

description: Control

data_processing:
The raw reads acquired from RNA seq were filtered by removing the adapter sequences and low quality reads. All the filtered reads were submitted to FastQC for quality control analysis. Each library was investigated for distribution of base quality score, sequence quality score, Average base content per read, GC distribution in the reads and for over-represented sequences.
On the basis FastQC report, we trimmed the reads wherever necessary and retained only high quality reads for down stream analysis. For filtering low quality reads Trimgalore was used. To identify lncRNAs, first we built the reference genome index through Bowtie and used TopHat to map all sequenced reads to the Capra hircus reference genome (ARS1).
To identify novel lncRNAs from PMECs with high confidence,  an inflexible pipeline was used to filter transcripts with any coding capacity. First, the transcripts <200nts long or with single exon were filtered out. Next, four independent algorithms, CNCI, PLEK, CPAT and Pfam were applied to extract potential noncoding transcripts.
For DE analysis, reads were mapped to the lncRNA reference using CuffDiff. DE genes were screened based on p-value < 0.05 and absolute log2FC ≥ 1. The expression value of lncRNAs was calculated in terms of RPKM (reads per kilo base per million) and EDGE tests were used for identification of DE genes between different groups.
To regulate false discovery because of multiple testing, p-values were Bonferroni-corrected. Expression was considered significant only at a fold-change of ± 2 and a corrected p-value < 0.05.
Supplementary_files_format_and_content: RPKM,fold-change data

organism: Capra hircus

source_name: Milk

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

value: (Mammary Gland)

value: Primary cells

tag: age

value: Passage 3


title: ESC_wild type_rep2

source_name: embryonic stem cells of wild type

tag: genotype

value: wild type


title: C3

value: 24 hours


title: iDART_SMART-seq APOBEC1-YTH Cell 6


title: ESC_wild type_rep1

value: embryonic stem cells


title: A3


title: B4

value: Clofazimine


title: Primary Mammary Epithelial Cells Infected with S. aureus 3

tag: agent

value: S. aureus


title: iDART_SMART-seq APOBEC1-YTH Cell 5


title: ChIP_H3K4me3_Setdb1KO_rep2

data_processing:
Quality controls of ChIP-seq Fastq files were performed by FastQC. ChIP-seq Fastq read files are mapped to the mm10 reference genome using Bowtie2 with default parameters. To determine for ChIP-seq peaks with a narrow profile, datasets were processed using MACS2 with default parameters and --g mm option. For profiles characterized by enrichments in broad regions, datasets were processed using MACS2 with --broad and --g mm options. BigWig files were generated using Deeptools bamCoverage with --bs 50 and --normalizeUsing RPKM options.
Genome_build: mm10
Supplementary_files_format_and_content: bw files correpond RPKM-normalized bigwig binary files (50bp bins), which can be visualized using the Integrative Genomics Viewer (IGV) software.

source_name: Mouse embryonic stem cells

value: Mouse embryonic stem cells

value: H3K4me3, Abcam ab8580

value: 5 days with 800 nM 4-hydroxytamoxifen (4-OHT)


title: Primary Mammary Epithelial Cells Infected with S. aureus 1


title: Primary Mammary Epithelial Cells Infected with S. aureus 2


title: Cb2

value: Amikacin

value: 4 hours


title: B3


title: ATACseq_Setdb1KO_rep2

data_processing:
Quality controls of ATAC-seq Fastq files were performed by FastQC. ATAC-seq adaptors and ATAC-seq reads were removed or trimmed using Cutadapt. Paire-end reads of ATAC-seq Fastq files were mapped to the mm10 reference genome using Bowtie2 with default parameters. Quality controls of ATAC-seq alignments were performed with ATACseqQC. To determine peaks for ATAC-seq, datasets were processed using MACS2 with default parameters and --g mm and –B options. BigWig files were generated using Deeptools bamCoverage with --bs 50 and --normalizeUsing RPKM options.
Genome_build: mm10
Supplementary_files_format_and_content: bw files correpond RPKM-normalized bigwig binary files (50bp bins), which can be visualized using the Integrative Genomics Viewer (IGV) software.

extract_protocol:
1.10^6 cells were used for each Omni-ATAC-seq experiment.  If there is 5 to 15% of death cells, cells are incubated with DNAse I at 37°C for 30min then cells are collected at 1200g for 3min at 4°C and washed 3 times with 1mL ice-cold PBS. Cells were resuspended into 1mL ice-cold PBS, 50,000 cells (50µL) were transfered into fresh 1,5mL Eppendorf tube. Omni-ATAC-seq was performed as described in Corces et al 2017, Nature Methods. Transposase enzyme was from Netera XT DNA library Preparation Kit.
Omni-ATAC-seq library preparation was performed as described in Buesnrostro et al 2013 Nature Methods with few adaptations. Illumina sequencing primers was from Buenrostro et al 2013 Nature Methods. To determine the number of additional cycles required, Ct corresponding to plateau is identified and ¼ of Ct + 1 defined the number of additional cycles. Then Omni-ATAC-seq libraries were cleaned up with AMPure XP beads to remove DNA fragment smaller than 100bp and longer than 1,5Kb. 30µL H2O was added to libraries obtain a final volume of 50µL then 25µL AMPure XP beads were added and incubate at RT for 15min. AMPure XP beads are placed on magnetic stand for 5min at RT. Supernatants were transfered into fresh tube and 65µL AMPure XP beads were added to samples then incubate at RT for 15min and place on magnetic stand for 5min at RT. Supernatant was removed. AMPure XP beads were whased with 200µL fresh 80%-EtOH twice. AMPure XP beads were air-dry for 7min at RT. 22µL Buffer EB was added to resuspend AMPure XP beads then they are incubated at RT for 2min and placed on magnetic stand for 5min at RT. 20µL ATAC-library samples were transferred into fresh 1,5mL Eppendorf tube. 1µL of library was diluted 1:100 to do qPCR quality control and to run Agilent High Sensitivity DNA Electrophoresis to check DNA fragment size. Before sequencing, ATAC-seq libraries are quantified by qPCR. Libraries were sequenced 75bp paired-end with 50 million reads of depth sequencing on HiSeq 2000 Illumina machine at the MGX platforms.


title: Primary Mammary Epithelial Cells Infected with E. Coli 3

value: E. Coli


title: Bb2


title: iDART_SMART-seq APOBEC1-YTH Cell 2

value: HEK293T Cells

value: 1microg/mL doxycycline; 24 hours


title: iDART_SMART-seq APOBEC1-YTH Cell 3


title: ChIP_H3K4me3_WT_rep2

extract_protocol:
Two 15cm-dishes with 2.10^7 cells in 20mL of culture media were used for each ChIP-seq experiment.  ChIP-seq was performed as described in ChIP-IT High sensitivity Kit from Active Motif with a few adaptations. Chromatin is sonicated by Bioruptor: 30sec ON – 30sec OFF, 10 cycles, high power. Sonicate for a total of 40 cycles for histones and of 30 cycles for TFs with 10min break on ice every 10 cycles. For ChIP reaction, 20µg chromatin was used with 4µg antibody for histone and 30µg chromatin + 4µg antibody for none-histone proteins. ChIP-DNA was eluted in 36µL with pre-warmed Elution Buffer then ChIP-DNA concentration was quantified with the Qubit dsDNA HS Assay Kit. 2,5ng to 10ng of ChIP-DNA were used for library preparation.
2,5ng to 10ng ChIP-DNA were used for library preparation. ChIP-seq library preparation was performed as described in TruSeq ChIP Sample Preparation kit from Illumina with few adaptations. The Enrich DNA Fragment step is proceeded before Purify Ligation Products step. AMPure XP beads were air-dry 7min. 1µL library was diluted 1:10 in H20 to quantified library concentration by Qubit DNA HS assay quantification. Agilent High Sensitivity DNA Electrophoresis was run to check DNA fragment size. Before sequencing, ChIP-seq libraries were quantified by qPCR. Libraries were sequenced 50bp or 100bp single-reads with 50 million reads of depth sequencing on HiSeq 2000 Illumina or NovaSeq 6000 Illumina machine at the MGX platforms.


title: Ab2


title: ATACseq_WT_rep2


title: Primary Mammary Epithelial Cells Infected with E. Coli 2


title: Primary Mammary Epithelial Cells Infected with E. Coli 1


title: Ab3

value: Cefoxitin


title: ATACseq_WT_rep1


title: iDART_SMART-seq APOBEC1-YTH Cell 1


title: ChIP_H3K36me3_Setdb1KO_rep2

data_processing:
Quality controls of ChIP-seq Fastq files were performed by FastQC. ChIP-seq Fastq read files are mapped to the mm10 reference genome using Bowtie2 with default parameters. To determine for ChIP-seq peaks with a broad profile, datasets were processed using MACS2 with --broad and --g mm options. H3K36me3, H3K36me2 and H3K36me1 bigWig files were normalized using drosophila spike-ins, which were mapped to dm6 reference genome using Bowtie2 with default parameters. The normalization factor was determined as described in manufactured protocol (Spike-in Normalization from Active Motif). For each sample, normalized BigWig files were generated using Deeptools bamCoverage with --bs 50, --normalizeUsing RPKM and --scaleFactor options, where scaleFactor is the normalization factor specific to each sample.
Genome_build: mm10
Supplementary_files_format_and_content: bw files correpond RPKM-normalized bigwig binary files (50bp bins), which can be visualized using the Integrative Genomics Viewer (IGV) software.

extract_protocol:
Two 15cm-dishes with 2.10^7 cells in 20mL of culture media were used for each ChIP-seq experiment.  ChIP-seq was performed as described in ChIP-IT High sensitivity Kit from Active Motif with a few adaptations. Chromatin is sonicated by Bioruptor: 30sec ON – 30sec OFF, 10 cycles, high power. Sonicate for a total of 40 cycles for histones and of 30 cycles for TFs with 10min break on ice every 10 cycles. For quantitative ChIP reaction drosophila spike-in from Active Motif was used. For histone methylation of lysine 36, 25µg chromatin was used with 50ng Spike-in Chromatin + 4µg antibody + 2ug Spike-in Antibody. Spike-in antibody also required a blocking step. ChIP-DNA was eluted in 36µL with pre-warmed Elution Buffer then ChIP-DNA concentration was quantified with the Qubit dsDNA HS Assay Kit. 2,5ng to 10ng of ChIP-DNA were used for library preparation.
2,5ng to 10ng ChIP-DNA were used for library preparation. ChIP-seq library preparation was performed as described in TruSeq ChIP Sample Preparation kit from Illumina with few adaptations. The Enrich DNA Fragment step is proceeded before Purify Ligation Products step. AMPure XP beads were air-dry 7min. 1µL library was diluted 1:10 in H20 to quantified library concentration by Qubit DNA HS assay quantification. Agilent High Sensitivity DNA Electrophoresis was run to check DNA fragment size. Before sequencing, ChIP-seq libraries were quantified by qPCR. Libraries were sequenced 50bp or 100bp single-reads with 50 million reads of depth sequencing on HiSeq 2000 Illumina or NovaSeq 6000 Illumina machine at the MGX platforms.

value: H3K36me3, Abcam ab9050

tag: spike-in

value: Drosophila spike-in chromatin


title: iDART_10xGenomics_scDART-seq_APOBEC1-YTHmut Replicate 3

description:
10x files consist of 3 fastqs (R1,R2,I1),
10xGenomics_m6Asites.bed