title: 125_C.LS.V2

city: New York

first: Ana

last: Pavel

state: NY

address: One Gustave L. Levy Place

department: Dermatology

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

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).

value: Skin biopsy

tag: tissue disease state

value: LS

tag: week


title: 122_A.NL.V2

status: Public on Jan 25 2022

type: RNA

country: USA

description: Gene expression data from skin biopsy

molecule: total RNA

organism: Homo sapiens

tag: tissue

value: NL

tag: treatment

value: Placebo


title: iDART_SMART-seq APOBEC1-YTH Cell 309

type: SRA

city: Durham

first: Matthew

last: Tegowski

state: NC

address: 153 Research Dr.

department: Biochemistry

institute: Duke University

library_source: transcriptomic

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: 124A_B.LS.V10

description: Gene expression data from skin biopsy


title: 124_B.LS.V7

description: Gene expression data from skin biopsy


title: 117_B.LS.V2

description: Gene expression data from skin biopsy


title: 126_A.NL.V2

description: Gene expression data from skin biopsy


title: 118_A.NL.V2

description: Gene expression data from skin biopsy


title: 121_B.LS.V2

description: Gene expression data from skin biopsy


title: 119_B.LS.V2

description: Gene expression data from skin biopsy


title: Terminal Ileum KO 1

city: Stony Brook

first: Pawan

last: Kumar

address: 100 Nicolls Road

institute: Stony Brook University

data_processing:
For total RNA-seq: Sequencing analysis was done using RNA-seq for Eukaryotes Analysis v3 by Banana Slug Genomics Center at University of California Santa Cruz
For total RNA-seq: Raw sequencing reads (paired-end reads) that  were produced by Illumina sequencer were quality checked for potential sequencing issues and contaminants using FastQC. Adapter sequences and primers were trimmed from the sequencing reads using Trimmomatic, then followed by removing the polyA tail, polyN, and read portions with quality score below 28 using PRINSEQ
For total RNA-seq: Trimmed reads were mapped to the reference genome (GRCm38/mm10) using (STAR) with NCBI RefSeq annotated genes as transcriptome index data. Read alignment coverage and summary statistics for visualization were computed using SAMtools, BEDtools, and UCSC Genome Browser utilities
For total RNA-seq: Using Cufflinks work flow, the sequencing reads aligned to RefSeq annotated genes were quanti fied using Cuffquant. Cuffnorm was then used to normalize the gene expression levels across the studied samples with FPKM computed for sample correlation assessment. Differential expression analysis between samples was performed using Cuffidff with the computed results from Cuffquant.
Genome_build: mm10

organism: Mus musculus

source_name: Murine small intestinal tissue

extract_protocol:
Mice were given DSS in drinking water. On day 6 terminal ileum tissues were extracted and stored at -20°C in RNAlater. RNA from the terminal ileum of DSS treated Il17rafl/fl;Atoh1-cre+ and their littermate cre- mice was isolated using TRIZOL extraction methods as per manufacture instructions (Life Technologies).
Libraries prepared using the NEBNext Ultra II Directional RNA Library Prep Kit (NEB) according to manufacturer’s supplied protocol. Library quality was confirmed by size analysis using Bioanalyzer High Sensitivity DNA Analysis (Agilent). All the libraries were sequenced on an Illimuna NextSeq 500 using high-output kit

tag: strain

value: Terminal Ileum

tag: age

value: 6 weeks


title: iDART_SMART-seq APOBEC1-YTH Cell 316


title: 120A_B.LS.V10

description: Gene expression data from skin biopsy


title: iDART_SMART-seq APOBEC1-YTH Cell 313


title: iDART_SMART-seq APOBEC1-YTH Cell 307


title: iDART_SMART-seq APOBEC1-YTH Cell 306


title: Terminal Ileum WT 3


title: iDART_SMART-seq APOBEC1-YTH Cell 308


title: 116A_B.LS.V10

description: Gene expression data from skin biopsy


title: 116_B.LS.V7

description: Gene expression data from skin biopsy


title: 115_A.NL.V2

description: Gene expression data from skin biopsy


title: iDART_SMART-seq APOBEC1-YTH Cell 304


title: iDART_SMART-seq APOBEC1-YTH Cell 305


title: iDART_SMART-seq APOBEC1-YTH Cell 302


title: Terminal Ileum WT 1


title: iDART_SMART-seq APOBEC1-YTH Cell 301


title: Terminal Ileum WT 2


title: 114_B.LS.V2

description: Gene expression data from skin biopsy


title: iDART_SMART-seq APOBEC1-YTH Cell 300


title: 112_C.LS.V2

description: Gene expression data from skin biopsy


title: iDART_SMART-seq APOBEC1-YTH Cell 298


title: iDART_SMART-seq APOBEC1-YTH Cell 297


title: iDART_SMART-seq APOBEC1-YTH Cell 296


title: 113_A.NL.V2

description: Gene expression data from skin biopsy


title: iDART_SMART-seq APOBEC1-YTH Cell 294


title: iDART_SMART-seq APOBEC1-YTH Cell 293


title: mRNA_library

city: Marseille cedex 09

first: Saran

last: Pankaew

address: Parc Scientifique et Technologique de Luminy

country: France

institute: Center of Immunology Marseille Luminy

data_processing:
Reads from mRNA libraries were mapped to mm10  transcripts and cells using CellRanger software (v3.0.1), giving an mRNA_barcodes.tsv.gz, mRNA_features.tsv.gz and mRNA_matrix.mtx.gz files.
Reads from the HTO library were processed with CITE-seq-count (v1.4.3), giving for both sample an HTO_barcodes.tsv.gz, HTO_features.tsv.gz and HTO_matrix.mtx.gz files
We utilized data demultiplexing via MULTIseqDemux and selected the cells identified by the HTO ["Thymus-fit-Ptendel-ACCCACCAGTAAGAC","Spleen-fit-Ptendel-CTTTGTCTTTGTGAG","Thymus-fit-Wt-GGTCGAGAGCATTCA","Spleen-fit-Wt-TATGCTGCCACGGTA"]
Genome_build: mm10
Supplementary_files_format_and_content: tsv and mtx files

source_name: Thymus and spleen

extract_protocol: 10x Genomics Chromium Single-Cell 3’ v3 protocol

value: Thymus and spleen


title: iDART_SMART-seq APOBEC1-YTH Cell 295


title: iDART_SMART-seq APOBEC1-YTH Cell 299


title: 111_A.NL.V2

description: Gene expression data from skin biopsy


title: CUT&RUN IgG control of Chd4

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

description: CUT&RUN with anti IgG antibody

library_source: genomic

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

molecule: genomic DNA

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.

tag: cell type

value: Embryonic stem cells

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

tag: antibody

value: Anti IgG Antibody (CST, 3900)


title: CUT&RUN Te1-KO Chd4

description: CUT&RUN with anti Chd4 antibody

value: Anti Chd4 Antibody (CST, 12011)

tag: genotype

value: Tet1 Knockout


title: 110_B.LS.V2

description: Gene expression data from skin biopsy


title: 109A_C.LS.V10

description: Gene expression data from skin biopsy


title: iDART_SMART-seq APOBEC1-YTH Cell 303


title: iDART_SMART-seq APOBEC1-YTH Cell 292


title: iDART_SMART-seq APOBEC1-YTH Cell 291


title: iDART_SMART-seq APOBEC1-YTH Cell 289


title: iDART_SMART-seq APOBEC1-YTH Cell 290


title: CUT&RUN Te1-Mut Chd4

description: CUT&RUN with anti Chd4 antibody

value: Tet1 Mutant


title: 108_A.NL.V2

description: Gene expression data from skin biopsy


title: CUT&RUN Te1-WT Chd4

description: CUT&RUN with anti Chd4 antibody

value: Tet1 Wild Type


title: iDART_SMART-seq APOBEC1-YTH Cell 288


title: iDART_SMART-seq APOBEC1-YTH Cell 287


title: 107_C.LS.V2

description: Gene expression data from skin biopsy


title: CUT&Tag IgG control of Sin3a

description: CUT&Tag with anti IgG antibody


title: iDART_SMART-seq APOBEC1-YTH Cell 286


title: iDART_SMART-seq APOBEC1-YTH Cell 285


title: 109_C.LS.V7

description: Gene expression data from skin biopsy


title: 106_C.LS.V10

description: Gene expression data from skin biopsy


title: CUT&Tag Te1-KO Sin3a

description: CUT&Tag with anti Sin3a antibody

value: Anti Sin3a Antibody (Abcam, ab3479)


title: iDART_SMART-seq APOBEC1-YTH Cell 284


title: CUT&Tag Te1-Mut Sin3a

description: CUT&Tag with anti Sin3a antibody


title: iDART_SMART-seq APOBEC1-YTH Cell 283


title: iDART_SMART-seq APOBEC1-YTH Cell 282


title: iDART_SMART-seq APOBEC1-YTH Cell 280


title: CUT&Tag IgG control of Ezh2 and H3K27ac

description: CUT&Tag with anti IgG antibody


title: CUT&Tag Te1-WT Sin3a

description: CUT&Tag with anti Sin3a antibody


title: 104_A.NL.V2

description: Gene expression data from skin biopsy

value: Skin biopsy


title: iDART_SMART-seq APOBEC1-YTH Cell 279


title: CUT&Tag Te1-KO H3K27ac

description: CUT&Tag with anti H3K27ac antibody

value: Anti H3K27ac Antibody (Abcam, ab4729)


title: iDART_SMART-seq APOBEC1-YTH Cell 277


title: iDART_SMART-seq APOBEC1-YTH Cell 278


title: iDART_SMART-seq APOBEC1-YTH Cell 276


title: iDART_SMART-seq APOBEC1-YTH Cell 275


title: iDART_SMART-seq APOBEC1-YTH Cell 274


title: iDART_SMART-seq APOBEC1-YTH Cell 341


title: CUT&Tag Te1-WT H3K27ac

description: CUT&Tag with anti H3K27ac antibody


title: iDART_SMART-seq APOBEC1-YTH Cell 273


title: iDART_SMART-seq APOBEC1-YTH Cell 272


title: iDART_SMART-seq APOBEC1-YTH Cell 281


title: CUT&Tag Tet1-KO Ezh2

description: CUT&Tag with anti Ezh2 antibody

value: Anti Ezh2 Antibody (CST, 5246)


title: iDART_SMART-seq APOBEC1-YTH Cell 271


title: iDART_SMART-seq APOBEC1-YTH Cell 270


title: 100_A.NL.V2

description: Gene expression data from skin biopsy

value: NL

value: Placebo


title: CUT&Tag Te1-Mut Ezh2

description: CUT&Tag with anti Ezh2 antibody


title: iDART_SMART-seq APOBEC1-YTH Cell 269

value: HEK293T Cells

value: 1microg/mL doxycycline; 24 hours


title: iDART_SMART-seq APOBEC1-YTH Cell 268


title: 102_A.LS.V10

description: Gene expression data from skin biopsy

value: LS


title: CUT&Tag Te1-WT Ezh2

description: CUT&Tag with anti Ezh2 antibody


title: iDART_SMART-seq APOBEC1-YTH Cell 267


title: 97_A.LS.V7

description: Gene expression data from skin biopsy


title: CUT&Tag IgG control of H3K4me3 and H3K27me3

description: CUT&Tag with anti IgG antibody


title: iDART_SMART-seq APOBEC1-YTH Cell 265


title: CUT&Tag Te1-Mut H3K27ac

description: CUT&Tag with anti H3K27ac antibody


title: iDART_SMART-seq APOBEC1-YTH Cell 266


title: 98_A.LS.V10

description: Gene expression data from skin biopsy


title: 95_A.LS.V2

description: Gene expression data from skin biopsy


title: 105_C.LS.V7

description: Gene expression data from skin biopsy


title: 101_A.LS.V7

description: Gene expression data from skin biopsy


title: 94_A.LS.V7

description: Gene expression data from skin biopsy


title: 94A_A.LS.V10

description: Gene expression data from skin biopsy


title: iDART_SMART-seq APOBEC1-YTH Cell 264


title: CUT&Tag Te1-KO H3K27me3

description: CUT&Tag with anti H3K27me3 antibody

value: Anti H3K27me3 Antibody (CST, 9733)


title: iDART_SMART-seq APOBEC1-YTH Cell 263


title: iDART_SMART-seq APOBEC1-YTH Cell 262


title: CUT&Tag Te1-Mut H3K27me3

description: CUT&Tag with anti H3K27me3 antibody

value: Embryonic stem cells


title: iDART_SMART-seq APOBEC1-YTH Cell 261


title: 92_A.NL.V2

description: Gene expression data from skin biopsy


title: iDART_SMART-seq APOBEC1-YTH Cell 260


title: iDART_SMART-seq APOBEC1-YTH Cell 259


title: CUT&Tag Te1-WT H3K27me3

description: CUT&Tag with anti H3K27me3 antibody

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


title: iDART_SMART-seq APOBEC1-YTH Cell 257


title: iDART_SMART-seq APOBEC1-YTH Cell 258


title: 91_A.LS.V2

description: Gene expression data from skin biopsy


title: CUT&Tag Te1-KO H3K4me3

description: CUT&Tag with anti H3K4me3 antibody

value: Anti H3K4me3 Antibody (Active Motif, 39060)


title: 90_B.LS.V7

description: Gene expression data from skin biopsy


title: iDART_SMART-seq APOBEC1-YTH Cell 255


title: iDART_SMART-seq APOBEC1-YTH Cell 254


title: CUT&Tag Te1-Mut H3K4me3

description: CUT&Tag with anti H3K4me3 antibody


title: CUT&Tag Te1-WT H3K4me3

description: CUT&Tag with anti H3K4me3 antibody


title: iDART_SMART-seq APOBEC1-YTH Cell 253


title: iDART_SMART-seq APOBEC1-YTH Cell 252


title: iDART_SMART-seq APOBEC1-YTH Cell 251


title: HTO_library

description: Anti-CD45 and CMH-I antibody tagged with hashtag oligonucleotide

value: Thymus and spleen


title: CUT&Tag IgG control of Tet1-M2

description: CUT&Tag with anti IgG antibody

value: Anti IgG Antibody (CST, 3900)


title: iDART_SMART-seq APOBEC1-YTH Cell 250


title: iDART_SMART-seq APOBEC1-YTH Cell 249


title: CUT&Tag Tet1-WT Untag M2 control

description: CUT&Tag with anti Flag-M2 antibody

value: Anti Flag-M2 Antibody (CST, 2368)

value: Tet1 Knockout


title: 88_B.LS.V2

description: Gene expression data from skin biopsy


title: iDART_SMART-seq APOBEC1-YTH Cell 248


title: CUT&Tag Tet1-Mut Flag-M2

description: CUT&Tag with anti Flag-M2 antibody

value: Tet1 Mutant


title: iDART_SMART-seq APOBEC1-YTH Cell 247


title: 90A_B.LS.V10

description: Gene expression data from skin biopsy

value: Skin biopsy


title: 82_A.NL.V2

description: Gene expression data from skin biopsy


title: 85_B.LS.V10

description: Gene expression data from skin biopsy


title: 84_B.LS.V7

description: Gene expression data from skin biopsy


title: 86_A.LS.V2

description: Gene expression data from skin biopsy


title: iDART_SMART-seq APOBEC1-YTH Cell 245


title: iDART_SMART-seq APOBEC1-YTH Cell 256


title: CUT&Tag Tet1-WT Flag-M2

description: CUT&Tag with anti Flag-M2 antibody

value: Tet1 Wild Type


title: 81_B.LS.V2

description: Gene expression data from skin biopsy


title: iDART_SMART-seq APOBEC1-YTH Cell 244


title: iDART_SMART-seq APOBEC1-YTH Cell 243


title: ATAC-seq Tet1 KO (Replicate #3)


title: 80_A.NL.V2

description: Gene expression data from skin biopsy


title: iDART_SMART-seq APOBEC1-YTH Cell 241


title: ATAC-seq Tet1 KO  (Replicate #2)


title: iDART_SMART-seq APOBEC1-YTH Cell 242


title: iDART_SMART-seq APOBEC1-YTH Cell 240


title: iDART_SMART-seq APOBEC1-YTH Cell 239


title: ATAC-seq Tet1 KO (Replicate #1)


title: iDART_SMART-seq APOBEC1-YTH Cell 238


title: iDART_SMART-seq APOBEC1-YTH Cell 236


title: iDART_SMART-seq APOBEC1-YTH Cell 237


title: ATAC-seq Tet1 Mut  (Replicate #2)


title: iDART_SMART-seq APOBEC1-YTH Cell 235


title: iDART_SMART-seq APOBEC1-YTH Cell 246


title: ATAC-seq Tet1 Mut (Replicate #1)


title: iDART_SMART-seq APOBEC1-YTH Cell 232


title: iDART_SMART-seq APOBEC1-YTH Cell 234


title: ATAC-seq Tet1 WT (Replicate #3)


title: iDART_SMART-seq APOBEC1-YTH Cell 231


title: 76_B.LS.V7

description: Gene expression data from skin biopsy


title: iDART_SMART-seq APOBEC1-YTH Cell 233


title: 76A_B.LS.V10

description: Gene expression data from skin biopsy


title: iDART_SMART-seq APOBEC1-YTH Cell 230


title: 75_B.LS.V2

description: Gene expression data from skin biopsy


title: ATAC-seq Tet1 WT (Replicate #2)


title: 79_A.LS.V2

description: Gene expression data from skin biopsy


title: iDART_SMART-seq APOBEC1-YTH Cell 229


title: 73_C.LS.V2

description: Gene expression data from skin biopsy


title: iDART_SMART-seq APOBEC1-YTH Cell 227


title: ATAC-seq Tet1 Mut (Replicate #3)


title: 74_C.LS.V7

description: Gene expression data from skin biopsy


title: RNA-seq Tet1 KO  (Replicate #3)


title: 78A_B.LS.V10

description: Gene expression data from skin biopsy


title: 71_A.LS.V2

description: Gene expression data from skin biopsy


title: iDART_SMART-seq APOBEC1-YTH Cell 225


title: iDART_SMART-seq APOBEC1-YTH Cell 224


title: RNA-seq Tet1 KO  (Replicate #2)


title: iDART_SMART-seq APOBEC1-YTH Cell 223


title: 72A_A.LS.V10

description: Gene expression data from skin biopsy


title: RNA-seq Tet1 KO (Replicate #1)


title: 72_A.LS.V7

description: Gene expression data from skin biopsy


title: iDART_SMART-seq APOBEC1-YTH Cell 222


title: 74_A_C.LS.V10

description: Gene expression data from skin biopsy


title: RNA-seq Tet1 Mut  (Replicate #3)


title: iDART_SMART-seq APOBEC1-YTH Cell 219


title: ATAC-seq Tet1 WT (Replicate #1)


title: iDART_SMART-seq APOBEC1-YTH Cell 217


title: iDART_SMART-seq APOBEC1-YTH Cell 216


title: 70_B.LS.V7

description: Gene expression data from skin biopsy


title: iDART_SMART-seq APOBEC1-YTH Cell 226


title: iDART_SMART-seq APOBEC1-YTH Cell 215


title: RNA-seq Tet1 Mut (Replicate #1)


title: 67_C.LS.V7

description: Gene expression data from skin biopsy


title: iDART_SMART-seq APOBEC1-YTH Cell 214


title: iDART_SMART-seq APOBEC1-YTH Cell 218


title: 69_B.LS.V2

description: Gene expression data from skin biopsy


title: iDART_SMART-seq APOBEC1-YTH Cell 212


title: iDART_SMART-seq APOBEC1-YTH Cell 211


title: RNA-seq Tet1 WT(Replicate #2)


title: iDART_SMART-seq APOBEC1-YTH Cell 221


title: 70A_B.LS.V10

description: Gene expression data from skin biopsy


title: iDART_SMART-seq APOBEC1-YTH Cell 210


title: iDART_SMART-seq APOBEC1-YTH Cell 209


title: iDART_SMART-seq APOBEC1-YTH Cell 220


title: RNA-seq Tet1 Mut (Replicate #2)


title: iDART_SMART-seq APOBEC1-YTH Cell 207


title: 66_C.LS.V2

description: Gene expression data from skin biopsy


title: Drd2/3 KO LSK Rep3

city: Muenster

first: Hyun-Woo

last: Jeong

state: NRW

department: Dept. Tissue Morphogenesis

country: Germany

institute: Max-Planck-Institute for Molecular Biomedicine

data_processing:
illumina bcl2fastq (v2.19.1.403) used for basecalling and demultiplexing
Tophat (v2.1.1) used for alignment
HTSeq-count (v0.6.1) used for transcriptome abundance measurement
DESeq2(v1.18.1) used for differential gene expression analyses
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample

source_name: Femur/Tibia

growth_protocol: Mice are grow up in animal facility of Institute

extract_protocol:
Adult mouse bone samples were crashed with pestle, treated with collagenase IV, and digested to single cells. These single cell suspension were stained for FACS sorting. FACS sorted cell population were directly lysis into RLT buffer and RNA were extracted using RNeasy plus Micro Kit (Qiagen)
Double strand cDNA was synthesized using SMART-Seq v4 Ultra Low Input RNA kit for Sequencing (Takara) and sequencing library was constructed with Nextera XT DNA Library preparation kit (illumina).

treatment_protocol: No treatment

tag: genotype/variation

value: Drd2 Drd3 double knockout

value: 8-12 weeks

tag: sorting antibody

value: Lin- Sca1+ cKit+

value: whole bone marrow Lin-Sca1+cKit+ cells


title: 65A_C.LS.V10

description: Gene expression data from skin biopsy


title: iDART_SMART-seq APOBEC1-YTH Cell 205

value: HEK293T Cells

value: 1microg/mL doxycycline; 24 hours


title: 64_C.LS.V2

description: Gene expression data from skin biopsy

value: LS


title: RNA-seq Tet1 WT (Replicate #3)

value: Embryonic stem cells


title: 68_C.LS.V10

description: Gene expression data from skin biopsy


title: iDART_SMART-seq APOBEC1-YTH Cell 213


title: iDART_SMART-seq APOBEC1-YTH Cell 204


title: iDART_SMART-seq APOBEC1-YTH Cell 202


title: 65_C.LS.V7

description: Gene expression data from skin biopsy


title: WT LSK Rep3

value: wild type


title: iDART_SMART-seq APOBEC1-YTH Cell 201


title: RNA-seq Tet1 WT (Replicate #1)

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


title: iDART_SMART-seq APOBEC1-YTH Cell 199


title: iDART_SMART-seq APOBEC1-YTH Cell 200


title: 63_C.LS.V7

description: Gene expression data from skin biopsy


title: 62_C.LS.V2

description: Gene expression data from skin biopsy


title: iDART_SMART-seq APOBEC1-YTH Cell 208


title: iDART_SMART-seq APOBEC1-YTH Cell 198


title: WT LSK Rep1


title: Drd2/3 KO LSK Rep2


title: iDART_SMART-seq APOBEC1-YTH Cell 206


title: iDART_SMART-seq APOBEC1-YTH Cell 197


title: 61_C.LS.V10

description: Gene expression data from skin biopsy


title: Drd2/3 KO LSK Rep1


title: iDART_SMART-seq APOBEC1-YTH Cell 203


title: iDART_SMART-seq APOBEC1-YTH Cell 195


title: 60_C.LS.V7

description: Gene expression data from skin biopsy


title: iDART_SMART-seq APOBEC1-YTH Cell 193


title: LSK-Halo Rep2

description:
whole bone Lin-Sca1+cKit+ cells
Halo_LSK-2

value: Haloperidol

value: LSK cells


title: LSK-Halo Rep3

description:
whole bone Lin-Sca1+cKit+ cells
Halo_LSK-3


title: iDART_SMART-seq APOBEC1-YTH Cell 194


title: WT LSK Rep2


title: LSK-Halo Rep1

description:
whole bone Lin-Sca1+cKit+ cells
Halo_LSK-1


title: iDART_SMART-seq APOBEC1-YTH Cell 191


title: iDART_SMART-seq APOBEC1-YTH Cell 192


title: 59_A.NL.V2

description: Gene expression data from skin biopsy

value: NL

value: Placebo


title: LSK-DMSO Rep3

description:
whole bone Lin-Sca1+cKit+ cells
LSK_DMSO-3

value: DMSO


title: iDART_SMART-seq APOBEC1-YTH Cell 190


title: LSK-DMSO Rep2

description:
whole bone Lin-Sca1+cKit+ cells
LSK_DMSO-2


title: iDART_SMART-seq APOBEC1-YTH Cell 188


title: iDART_SMART-seq APOBEC1-YTH Cell 189


title: 57A_C.LS.V10

description: Gene expression data from skin biopsy

value: Skin biopsy


title: iDART_SMART-seq APOBEC1-YTH Cell 187


title: 58_C.LS.V2

description: Gene expression data from skin biopsy


title: LSK-DMSO Rep1

description:
whole bone Lin-Sca1+cKit+ cells
LSK_DMSO-1


title: iDART_SMART-seq APOBEC1-YTH Cell 185


title: iDART_SMART-seq APOBEC1-YTH Cell 184


title: iDART_SMART-seq APOBEC1-YTH Cell 186


title: iDART_SMART-seq APOBEC1-YTH Cell 196


title: 55A_B.LS.V10

description: Gene expression data from skin biopsy


title: 57_C.LS.V7

description: Gene expression data from skin biopsy


title: GBM cell line U373-GPR56 Knockdown

city: Bangalore

first: Nameeta

last: Shah

address: Bommasandra

country: India

institute: Mazumdar Shaw Center for Translational Research

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using STAR v2.7.9a with default parameters
Count values were calculated using bedtools  v2.30.0 coverage function
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited GTF files include count values for each Sample

source_name: GBM cell line U373

growth_protocol: GPR56 control and knockdown cells were cultured in in DMEM with10% FBS containing 200µg/ml hygromycin (Selection medium).

extract_protocol:
Total RNA was isolated from the cells using Macherey Nagel Total RNA and Protein Isolation Kit (Cat#: 740933.50, Macherey-Nagel, Germany).
RNA library's construction was performed according to the manufacturer's protocol using the NEB Ultra RNA-seq Library Prep kit protocol (NEB, USA).

tag: disease state

value: GBM

value: GPR56 Knockdown


title: C40 Gw-F13 rep 3

city: Colmar

first: Isabelle

middle: Rachel

last: Martin

state: Grand-Est

address: UMR_A 1131 INRAE - Université de Strasbourg Santé de la vigne et qualité du vin 28 rue de Herrlisheim

department: SVQV

institute: INRAE

description:
GFLV F13 strain was transferred to the certified rootstock Kober by in vitro heterologous grafting.
Data for this sample is not included in the normalized_counts_matrix.txt file, as the sample was removed from the analysis as part of QC.

data_processing:
Alignment TopHat2 (v.2.0.11; 47).
Quantification HTSeq-count (v.6.0.0; 49).
DEG study R (v.3.3.2) and the DESeq2 package.
P-values adjustment with the Benjamini-Hochberg procedure.
Gene categorization TopGo R package (v2.32.0; 51).
Genome_build: Vitis vinifera PN40024 (12X.v2) reference genome.
Supplementary_files_format_and_content: *_quantification.txt: One raw quantification file per sample.
Supplementary_files_format_and_content: normalized_counts_matrix.txt: Matrix of the raw and normalized counts.

organism: Vitis vinifera

source_name: Leaf

growth_protocol: GFLV strains were transferred to the certified rootstock Kober 5BB clone 259 by in vitro heterologous grafting. After removal of the C. quinoa stems, grapevine rootstocks were further grown and micro-propagated in tissue culture. Infected rootstocks were grafted with V. vinifera cv. Gewurztraminer or Chardonnay using green-grafting in an environmental growth chamber.

extract_protocol:
RNeasy Plant Mini Kit (Qiagen) according to the manufacturer's instructions with the addition of DNase.
TruSeq Stranded mRNA sample prep kit (Illumina). Using poly(A) selection, mRNAs were isolated, fragmented and reverse-transcribed. Experiments were performed on an Illumina HiSeq 3000 using a paired-end read length of 2 x 150 base-pairs with Illumina Hiseq3000/4000 SBS sequencing kits.

treatment_protocol: Virus inoculation occurred via the grafting method. No other treatment was performed.

tag: cultivar

value: Gewurztraminer

tag: phenological stage

value: visible clusters, 4 to 6 expanded leaves

value: Leaf Level N2 and N3

tag: viral strain

value: F13 GFLV


title: iDART_SMART-seq APOBEC1-YTH Cell 182

value: HEK293T Cells

value: 1microg/mL doxycycline; 24 hours


title: 56_C.LS.V2

description: Gene expression data from skin biopsy

tag: tissue disease state

value: LS


title: iDART_SMART-seq APOBEC1-YTH Cell 183


title: C39 Gw-F13 rep 2

description: GFLV F13 strain was transferred to the certified rootstock Kober by in vitro heterologous grafting.


title: GBM cell line U373-GPR56 control

value: control


title: iDART_SMART-seq APOBEC1-YTH Cell 228


title: C38 Gw-B844 rep 3

description: GFLV B844 strain was transferred to the certified rootstock Kober by in vitro heterologous grafting.

value: B844 GFLV


title: iDART_SMART-seq APOBEC1-YTH Cell 180


title: 53_B.LS.V2

description: Gene expression data from skin biopsy

tag: week


title: B47 Gw-F13 rep 1

tag: tissue


title: B53 Gw-B844 rep 2


title: iDART_SMART-seq APOBEC1-YTH Cell 179

tag: treatment


title: iDART_SMART-seq APOBEC1-YTH Cell 178

tag: cell line


title: iDART_SMART-seq APOBEC1-YTH Cell 177

tag: transgene


title: B52 Gw-B844 rep 1


title: 52_B.LS.V10

description: Gene expression data from skin biopsy


title: C51 Gw-control rep 3

description: Gw plants corresponding to scions grafted onto uninoculated 5BB rootstocks were used as controls.


title: iDART_SMART-seq APOBEC1-YTH Cell 176


title: B34 Gw-control rep 2


title: iDART_SMART-seq APOBEC1-YTH Cell 181


title: Mtb H37Rv RNA_control_1

city: Chandigarh

first: Indu

last: Verma

state: Chandigarh

address: Research Block A,

institute: Postgraduate Institute of Medical education and Research Chandigarh

description: BTB _2_3

hyb_protocol: 1.0 µg of labelled cRNA (specific activity >15.0 pmol Cy3/ug cRNA) from each sample and control were used for hybridization to microarray slides. Firstly, cRNA was fragmented at 60°C for 30 minutes in presence of gene expression blocking agent and fragmentation Buffer followed by cooling and addition of Hybridization buffer (Agilent). The reaction mixture was mixed and gently loaded onto the array slides for hybridization to Agilent Whole M. tuberculosis Genome Oligo Microarrays for 17 hours at 65°C in a rotating (10rpm) hybridization oven. After incubation, array slide was washed  using GE wash buffers (Agilent) and then dried immediately.

scan_protocol: The array slide was scanned and processed using Agilent Sure Scan Microarray Scanner using one-color scan setting for 8X 15K array slides.

data_processing: The scanned image (.tiff) was analyzed with Agilent Feature Extraction (FE) Software (version 12.0.3.1). Further, to find out the  differentially expressed genes, feature extracted text files of control and test samples were analysed using Agilent Technologies GeneSpring® GX software (version 14.9). Significantly modulated genes were selected based on Benjamini-Hochberg procedure with a fold change > 2 and p < 0.05.

organism: Mycobacterium tuberculosis H37Rv

source_name: Mtb

label_protocol: Amplification and Cyanine 3-CTP (Cy3) labelling was accomplished using  One-Color Microarray-Based Low Input Quick Amp WT Labeling kit (Agilent Technologies) as per manufacturer’s protocol using 300ng of input RNA.  Further, labelled and amplified cRNA samples were purified using RNeasy Mini kit and quantified through NanoDrop ND-1000 UV-VIS Spectrophotometer. cRNA conc. (ng/μL), 260/280 ratio and Cy3 concentration (pmol/μL) were measured to estimate the yield and specific activity of each sample.

growth_protocol: M.tuberculosis H37Rv used as reference, was grown in Sauton's medium prior to RNA extraction to mid log phase,

extract_protocol: For M.tuberculosis RNA isolation, firstly RNA later was removed and clinical specimen were treated with GTC solution (4M guanidine thiocyanate, 0.5% sodium-N-lauryl sarcosine, 25mM tri-sodium citrate, 0.1M β-2-mercaptoethanol and 0.5% Trition-80)  for not more than 5mins for effective removal of eukaryotic RNA. Further, samples were centrifuged at 5000g for 20min at 4°C to collect the bacterial pellet ans supernatant was discarded.  TRIzol was added to the pellet and mycobacterial RNA was extracted using bead beating protocol (0.1mm zirconia beads) and further purified using RNeasy mini kit. Reference M. tuberculosis RNA was processed directly using TRIzol.

treatment_protocol: Clinical specimen (abscess/necrotic tissue) after collection were immediately transferred in RNA later and stored at -800C till RNA extraction.

tag: sample type

value: Mtb H37Rv RNA_control


title: Mtb RNA from clininal specimen of BTB  patient_5

description: BTB _2_1

organism: Mycobacterium tuberculosis

source_name: Spinal TB

tag: source patient gender

value: M

tag: tissue source

value: Spinal TB


title: Mtb RNA from clininal specimen of BTB  patient_6

description: BTB _2_2


title: Mtb H37Rv RNA_control_2

description: BTB _2_4


title: Mtb RNA from clininal specimen of BTB  patient_3

description: BTB _1_3


title: 51_B.LS.V7

description: Gene expression data from skin biopsy


title: 49A_B.LS.V10

description: Gene expression data from skin biopsy


title: iDART_SMART-seq APOBEC1-YTH Cell 174


title: 50_B.LS.V2

description: Gene expression data from skin biopsy


title: 47_B.LS.V10

description: Gene expression data from skin biopsy


title: 49_B.LS.V7

description: Gene expression data from skin biopsy


title: 46_B.LS.V7

description: Gene expression data from skin biopsy


title: iDART_SMART-seq APOBEC1-YTH Cell 173


title: Mtb RNA from clininal specimen of BTB  patient_4

description:
The pathology of joint TB is different from bone and vertebral TB. Thus, sample is excluded from data analysis.
BTB _1_4

source_name: TB of elbow-joint

value: F

value: TB of elbow-joint


title: 15C_csp1_3

city: Parlier

first: Lindsey

last: Burbank

state: California

address: 9611 S Riverbend Ave

institute: USDA-ARS

data_processing:
Guppy, A neural network basecaller that converts Nanopore electronic raw signal from sequencer into bases.
Deepbinner, A signal-level demultiplexer for Oxford Nanopore reads.
Porechop, An adapter trimmer for Oxford Nanopore reads.
Minimap2, A pairwise reads aligner for genomic and spliced nucleotide sequences
Salmon, A transcript quantification tool for RNA-Seq data
Tximport, Imports transcript-level estimates and summarizes abundances, counts, and transcript lengths to the gene-level
DESeq2, Provides methods to test for differential gene expression based on the negative binomial distribution
Supplementary_files_format_and_content: Summary of gene-level abundances, including gene ID and transcipts per million (TMP) values for each sample.

organism: Xylella fastidiosa subsp. fastidiosa

source_name: In vitro bacteria culture

extract_protocol:
Bacteria cells were scraped off PD3 agar plates and flash frozen on dry ice. RNA was purified using Trizol reagent. Oxford Nanopore direct cDNA sequencing kit was was used with  250ng of rRNA depleted RNA for the construction of sequencing libraries.
Nanopre direct cDNA sequencing library

tag: strain

value: Stag's Leap

tag: growth temperature

tag: age

value: 7 days post inoculation


title: Mtb RNA from clininal specimen of BTB  patient_2

description: BTB _1_2


title: 15C_csp1_2

tag: genotype


title: iDART_SMART-seq APOBEC1-YTH Cell 172


title: SAS

city: Nanjing

first: Xia

last: Gao

state: Jiangsu

address: 321 Zhongshan Road

department: Otolaryngology Haed and Neck Surgery

country: China

institute: Nanjing University Medical School Affiliated Nanjing Drum Tower Hospital

description: Control human tongue squamous cell carcinoma cell , untreated, harvested 24h after cell adhesion.

hyb_protocol: 2.5 μg of Cy3 and Cy5 labeled cRNAs were mixed. The cRNA mixture was fragmented by adding 5 μL 10´ Blocking Agent and 1 μL of 25´ Fragmentation Buffer, heated at 60°C for 30 min, and combined with 25 μL 2´ Hybridization buffer. 50 μL hybridization solution was dispensed into the gasket slide and assembled to the m6A-mRNA&lncRNA Epitranscriptomic Microarray slide. The slides were incubated at 65°C for 17 hours in an Agilent Hybridization Oven. The hybridized arrays were washed, fixed and scanned using an Agilent Scanner G2505C

scan_protocol: Scanned on an Agilent Scanner G2505C

data_processing:
Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Raw intensities of IP (immunoprecipitated, Cy5-labelled) and Sup (supernatant, Cy3-labelled) were normalized with average of log2-scaled Spike-in RNA intensities. After Spike-in normalization, the probe signals having Present (P) or Marginal (M) QC flags in at least 1 out of 2 samples were retained as “All Targets Value” in the Excel sheet for further “m6A methylation level” and “m6A quantity” and “expression level” analyses. “m6A methylation level” was calculated for the percentage of modification based on the IP (Cy5-labelled) and Sup (Cy3-labelled) normalized intensities. “m6A quantity” was calculated for the m6A methylation amount based on the IP (Cy5-labelled) normalized intensities. “expression level” was calculated based on the total of IP (Cy5-labelled) and Sup (Cy3-labelled) normalized intensities. Differentially m6A-methylated RNAs or expressed between two comparison groups were identified by filtering with the fold change and statistical significance (p-value) thresholds. Hierarchical Clustering was performed using the R software. GO analysis was performed using topGO package in R environment for statistical computing and graphics, and Pathway analysis was calculated by fisher's exact test.
Raw intensities of IP (immunoprecipitated, Cy5-labelled) and Sup (supernatant, Cy3-labelled) were normalized with average of log2-scaled Spike-in RNA intensities

source_name: Human tongue squamous cell carcinoma cell line

label_protocol: The “IP” RNA and “Sup” RNAs were added with equal amount of calibration spike-in control RNA, separately amplified and labeled with Cy3 (for “Sup”) and Cy5 (for “IP”) using Arraystar Super RNA Labling Kit. The synthesized cRNAs were purified by RNeasy Mini Kit. The concentration and specific actitity (pmol dye/μg cRNA) were measured with NanoDrop ND-1000

growth_protocol: Cultured in RPMI-1640 medium with 10% fetal bovine serum and 1% penicillin/streptomycin

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions

value: SAS


title: 48_B.LS.V2

description: Gene expression data from skin biopsy

value: Skin biopsy


title: Mtb RNA from clininal specimen of BTB  patient_1

description: BTB _1_1


title: iDART_SMART-seq APOBEC1-YTH Cell 175


title: 15C_csp1_1


title: iDART_SMART-seq APOBEC1-YTH Cell 171


title: 15C_WT_3

value: wild type


title: B31 Gw-control rep 1

value: Gewurztraminer

value: visible clusters, 4 to 6 expanded leaves

value: Leaf Level N2 and N3


title: 44_B.LS.V2

description: Gene expression data from skin biopsy


title: iDART_SMART-seq APOBEC1-YTH Cell 170

value: HEK293T Cells

value: 1microg/mL doxycycline; 24 hours


title: SAS-KD

description: Stable METTL3 knockdown  human tongue squamous cell carcinoma cell , harvested 24h after cell adhesion.

source_name: Human tongue squamous cell carcinoma cell


title: LG15 2 hours post-NKTT320

city: New Orleans

first: Nell

middle: G

last: Bond

email: nellgbond@gmail.com, nbond@tulane.edu

state: LA

address: Microbiology & Immunology, 1430 Tulane Avenue

institute: Tulane University School of Medicine

data_processing:
RNA-seq for Eukaryotes Analysis v3 was used for sequencing analysis and built by the Banana Slug Genomics Center at the University of California Santa Cruz. First, an Illumina sequencer at the Tulane School of Medicine Genomics Core was used to construct raw sequencing reads which were checked for quality and contaminants using FastQC. Next, Trimmomatic was used to trim adapter sequences and primers from the sequencing reads (Bolger et al., 2014). Removal of polyA tail, polyN, and read segments with a quality score below 28 was accomplished by using PRINSEQ (Schmieder and Edwards, 2011). Following trimming, any reads of length less than 20bp were removed. Quality check was repeated, and high-quality reads were then mapped to the GRCh37/hg19 reference genome using STAR (Kim et al., 2013, Dobin et al., 2013) with NCBI RefSeq (O'Leary et al., 2016) annotated genes transcriptome index data. Raw read counts were normalized across all samples and then used for differential expression analysis using DESeq (Anders and Huber, 2010) and edgeR (Robinson et al., 2010) separately. Genes related to the immune system and with p-values of <0.05 from the edgeR pipeline were identified and categorized by major cell type, which were then plotted on individual heatmaps. Heatmaps were constructed using log2 fold change data and using the ‘pheatmap’ package in R (Kolde, 2019).
GSEA was performed with the R package ‘ClusterProfiler’ at default parameters. Enrichment scores were calculated against the following 4 pathway databases containing a priori-defined gene sets: Gene Ontology (GO) database, Hallmark (H) and Curated (C2) gene sets of the Molecular Signature database (MsigDB), and WikiPathways. Gene sets significantly enriched in the datasets (p < 0.05) were subsequently curated for those relevant to NKT cell biological function. Enrichment plot was generated with the R software package ‘ggplot2’ and heatmaps with the ‘pheatmap’ package.
Genome_build: GRCh37/hg19 reference genome
Supplementary_files_format_and_content: tab delimited text files correspond to transcript read counts calculated by Htseq-count and fpkm-count

organism: Macaca fascicularis

source_name: PBMC

growth_protocol: collection protocol: Whole blood was collected by venipuncture in EDTA vacutainers. Peripheral blood mononuclear cells (PBMCs) were isolated from MCM by density gradient centrifugation. In brief, peripheral blood was diluted 1:1 in PBS and layered over 90% ficoll at a 1:2 ratio. The gradient was then spun at 2,200 rpm for 45 minutes with the brake off. Cells were then isolated, washed and counted according to standard methods. Aliquots of 1M PBMC were pelleted, snap frozen and stored at -80C until RNA extraction.

extract_protocol:
RNA was extracted from snap frozen, unfractionated PBMCs using the Qiagen RNeasy Plus Mini Kit (Qiagen 74134). Briefly, cells were first thawed and pelleted, then lysed following the kit protocol.  gDNA was removed using a gDNA Eliminator spin column, and remaining flow through was added to a RNeasy spin column to bind RNA.  The spin column/RNA was washed, RNA was eluted and stored at -80oC.  Later, samples were concentrated using Zymo Clean & Concentrate-5 Kit (R1013).  Briefly, RNA was thawed, bound, and added to the Zymo-Spin IC Column.  Then RNA bound to the column was washed, eluted, aliquoted and stored at -80oC.
Samples were then submitted for RNA-Seq analysis using a high output, and single read 75 cycle run. Prior to Illumina total RNA library construction, DNase treated RNA was quantitated using the Qubit RNA BR assay kit (ThermoFisher Scientific, #Q10210). RNA quality (RIN) was determined on an Agilent 2100 Bioanalyzer using an Agilent RNA 6000 Nano kit (Agilent, #5067-1511). Cytoplasmic and mitochondrial rRNA was removed from each sample following the Ribo-Zero Gold rRNA Removal Kit Reference Guide from Illumina. After RNA clean up, samples were resuspended in 11ul Elution buffer followed by prime and fragmentation. Illumina compatible total RNA cDNA libraries were generated following the TruSeq Stranded Total RNA Sample Preparation Guide (Illumina #20020596).

value: NKTT320 treated

tag: time pointment

value: 2 hours post-NKTT320

value: Blood


title: LG15 1 day post-NKTT320

value: 1 day post-NKTT320


title: LG15 30 minutes post-NKTT320

value: 30 minutes post-NKTT320


title: 15C_WT_1


title: 43_A.LS.V10

description: Gene expression data from skin biopsy

value: LS

value: Placebo


title: iDART_SMART-seq APOBEC1-YTH Cell 168


title: iDART_SMART-seq APOBEC1-YTH Cell 169


title: LG12 1 day post-NKTT320


title: iDART_SMART-seq APOBEC1-YTH Cell 167


title: 15C_WT_2

value: Stag's Leap


title: LG15 pre-treatment

value: pre-treatment


title: 42_A.LS.V7

description: Gene expression data from skin biopsy


title: 41_A.LS.V2

description: Gene expression data from skin biopsy


title: iDART_SMART-seq APOBEC1-YTH Cell 166


title: 45_A.NL.V2

description: Gene expression data from skin biopsy

value: NL


title: WT replicate 2

city: montreal

first: Stephane

last: Richard

address: 3999 chemin de la cote sainte catherine

country: Canada

institute: McGill University

data_processing: none provided by the submitter

source_name: Skeletal muscle

extract_protocol:
Primary muscle stem cells were purified with FACS and bulk RNA was isolated with the Arcturus PicoPure RNA isolation kit
Paired end, polyA selection

value: WT


title: WT replicate 3


title: WT replicate 1


title: 40A_C.LS.V10

description: Gene expression data from skin biopsy

value: Skin biopsy


title: iDART_SMART-seq APOBEC1-YTH Cell 165


title: LG12 2 hours post-NKTT320


title: 39_C.LS.V2

description: Gene expression data from skin biopsy


title: LG12 30 minutes post-NKTT320


title: 40_C.LS.V7

description: Gene expression data from skin biopsy


title: 38_B.LS.V10

description: Gene expression data from skin biopsy


title: KO replicate 2

value: KO


title: LG11 1 day post-NKTT320


title: iDART_SMART-seq APOBEC1-YTH Cell 163


title: iDART_SMART-seq APOBEC1-YTH Cell 164


title: 36_B.LS.V2

description: Gene expression data from skin biopsy


title: KO replicate 1


title: LG12 pre-treatment


title: 35_C.LS.V10

description: Gene expression data from skin biopsy


title: LG11 30 minutes post-NKTT320


title: iDART_SMART-seq APOBEC1-YTH Cell 162


title: iDART_SMART-seq APOBEC1-YTH Cell 160


title: LG04 1 day post-NKTT320


title: iDART_SMART-seq APOBEC1-YTH Cell 159


title: LG11 2 hours post-NKTT320


title: iDART_SMART-seq APOBEC1-YTH Cell 158


title: LG04 2 hours post-NKTT320


title: KO replicate 3


title: ChIP_H3K36me2_doubleKO_rep1

city: Montpellier

first: Amandine

last: BARRAL

state: Hérault

address: 141 rue de la cardonille

institute: IGH - CNRS

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.
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.

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.

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.
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 â 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, 25Âµg chromatin was used with 50ng Spike-in Chromatin + 4Âµg antibody + 2ug Spike-in Antibody. Spike-in antibody also required a blocking step. ChIP-DNA was eluted in 36ÂµL 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. 1ÂµL 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: H3K36me2, Abcam ab9049

tag: spike-in

value: Drosophila spike-in chromatin


title: ChIP_H3K36me2_doubleKO_rep2

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


title: ChIP_H3K36me1_doubleKO_rep2

value: H3K36me1, Abcam ab9048


title: LG04 30 minutes post-NKTT320

value: NKTT320 treated


title: iDART_SMART-seq APOBEC1-YTH Cell 157

value: HEK293T Cells

value: 1microg/mL doxycycline; 24 hours


title: 31_A.LS.V2

description: Gene expression data from skin biopsy

source_name: Skin biopsy


title: ChIP_H3K36me1_doubleKO_rep1


title: 33_A.LS.V10

description: Gene expression data from skin biopsy


title: iDART_SMART-seq APOBEC1-YTH Cell 156

source_name: Kidney


title: iDART_SMART-seq APOBEC1-YTH Cell 161


title: Hippocampus, Ctr

city: Shanghai

first: Ni

last: Yan

address: 197, Ruijin Er Street

institute: Shanghaijiaotong University

data_processing:
Demultiplexed by bcl2fastq.
Trimmed by fastq (v0.19.4) with default parameters.
Mapped onto the reference genome (mm9) using the bisulfite sequence aligner Bismark (v0.19.0), which internally calls bowtie2.
PCR duplicates were removed by deduplicate_bismark.
Genome_build: mm9
Supplementary_files_format_and_content: The txt files include the frequency of C or T at each CpG site.

source_name: Hippocampus

extract_protocol:
Hippocampus was removed, flash frozen on dry ice. Then genomic DNA was extracted using the Wizard Genomic DNA Purification Kit (A1125, Promega, WA, USA), treated with RNase A and quantified (NanoDrop 1000 Spectrophotometer, Thermo Fisher).
About 3 μg DNA of each sample was fragmented by sonication. Subsequently, library preparation was performed using the SureSelectXT Mouse Methyl-Seq Reagent Kit (Agilent Technologies, CA, USA). DNA was bisulfite-treated using the EZ DNA Methylation-Gold kit. Sequencing libraries were assessed and quantified by Qubit® 3.0 Fluorometer and Agilent 2100. The libraries were then sequenced on a NovaSeq 6000 (Illumina) platform.

treatment_protocol: C57BL/6 mice were exposed to drinking water contaminated with 5000 ppb arsenic trioxide from pre-mating period to lactation period, and the offspring mice continued receiving the ATO treatments in drinking water after weaning until the end of experiment.

value: Hippocampus

value: No treatment


title: Hippocampus, ATO

value: Developmental exposure of 5000 ppb ATO


title: LG04 pre-treatment

value: Blood


title: LG11 pre-treatment


title: 32_A.LS.V7

description: Gene expression data from skin biopsy

value: LS

value: Placebo


title: 30_A.LS.V10

description: Gene expression data from skin biopsy


title: 34_C.LS.V2

description: Gene expression data from skin biopsy


title: iDART_SMART-seq APOBEC1-YTH Cell 155


title: 28_A.LS.V2

description: Gene expression data from skin biopsy


title: Dnmt3A WT/WT_Cut&Run_Id4GFP_10dpp_H3K9me3_Replicate 3

city: paris

first: teissandier

last: aurelie

address: 26 rue d'Ulm

institute: institut curie

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 (GRCm38)
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: H3K9me3 Abcam 176916

tag: cell type

value: Id4-GFP bright + med germ cells


title: MEF2D 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: 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). 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: MEF2D (BD Biosciences, clone 9 610775)


title: Dnmt3A WT/WT_Cut&Run_Id4GFP_10dpp_H3K9me3_Replicate 2


title: iDART_SMART-seq APOBEC1-YTH Cell 154


title: Dnmt3A WT/WT_Cut&Run_Id4GFP_10dpp_H3K9me3_Replicate 1


title: 25_B.LS.V2

first: Ana

last: Pavel

institute: Icahn School of Medicine at Mount Sinai

description: Gene expression data from skin biopsy

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).

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

tag: week


title: 27_B.LS.V10

description: Gene expression data from skin biopsy

tag: treatment


title: 26_B.LS.V7

description: Gene expression data from skin biopsy


title: iDART_SMART-seq APOBEC1-YTH Cell 153

first: Matthew

last: Tegowski

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

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.

tag: cell line

tag: transgene


title: HDAC4 NKL54 ChIP rep2

description: HDAC4 bound regions in NKL54 treated cells

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


title: Dnmt3A KO/KO_Cut&Run_Id4GFP_10dpp_H3K9me3_Replicate 2

value: Dnmt3A KO/KO


title: iDART_SMART-seq APOBEC1-YTH Cell 152

value: HEK293T Cells


title: Dnmt3A KO/KO_Cut&Run_Id4GFP_10dpp_H3K9me3_Replicate 1.2 (Animal #1 split in two, to create technical replicate)


title: HDAC9 WT ChIP rep2

description: HDAC9 bound regions in wt cells

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


title: iDART_SMART-seq APOBEC1-YTH Cell 151

value: 1microg/mL doxycycline; 24 hours


title: Dnmt3A KO/KO_Cut&Run_Id4GFP_10dpp_H3K9me3_Replicate 1.1 (Animal #1 split in two, to create technical replicate)


title: MEF2D WT ChIP rep2

description: MEF2D bound regions in wt cells


title: iDART_SMART-seq APOBEC1-YTH Cell 150


title: HDAC4 WT ChIP rep2

description: HDAC4 bound regions in wt cells


title: 23_A.LS.V2

description: Gene expression data from skin biopsy


title: H3K27ac NKL54 ChIP rep2

description: Open chromatin evaluation in NKL54 treated cells

value: H3K27ac (Abcam, ab4729)


title: iDART_SMART-seq APOBEC1-YTH Cell 149


title: WT_1Y_AUD_rep1

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: auditory cortex

extract_protocol:
Auditory cortex in the brain (adult male mice aged 1 month or 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: brain region

value: auditory cortex

value: WT

tag: Sex

value: male


title: WT_1Y_AUD_rep2

tag: strain


title: H3K27ac WT ChIP rep2

description: Open chromatin evaluation in wt cells


title: iDART_SMART-seq APOBEC1-YTH Cell 148


title: Ash1l_het_1Y_AUD_rep2

tag: age


title: Input NKL54 rep2

description: Input


title: 21_A.LS.V2

address: One Gustave L. Levy Place

description: Gene expression data from skin biopsy

value: LS

value: Placebo


title: Ash1l_het_1Y_AUD_rep1

tag: genotype


title: Input WT rep2

description: Input


title: 22_A.LS.V7

description: Gene expression data from skin biopsy


title: 19_C.LS.V2

description: Gene expression data from skin biopsy


title: 20A_C.LS.V10

description: Gene expression data from skin biopsy


title: 24_A.NL.V2

description: Gene expression data from skin biopsy

value: NL


title: iDART_SMART-seq APOBEC1-YTH Cell 147

address: 153 Research Dr.


title: WT_1M_AUD_rep3


title: iDART_SMART-seq APOBEC1-YTH Cell 145


title: pSS 7

city: Beijing

first: Yu

last: Peng

address: No. 1, Shuaifu yuan

institute: Peking Union Medical College Hospital

data_processing:
Raw data of fastq format were firstly processed through in-house per scripts and clean data were obtained by removing reads containing adapter, reads containing poly-N and low-quality reads.
HTseq v0.6.0 was used to count the reads numbers mapped to each gene.
Differential expression analysis was performed using DESeq2 R package (1.10.1).
Genome_build: mm9
Supplementary_files_format_and_content: FPKM values for each Sample

extract_protocol:
Total RNA of neutrophils was extracted using TRIzol reagent (Invitrogen, USA) and stored at -80℃ for subsequent RNA sequencing (Novogene, China).
A total amount of 3 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.
First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase(RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 150~200 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 µl USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37°C for 15 min followed by 5 min at 95 °C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

value: Neutrophils

tag: subject status

value: primary Sjögren’s syndrome (pSS) patient


title: WT_1M_AUD_rep2


title: pSS 6


title: 20_C.LS.V7

city: New York

description: Gene expression data from skin biopsy


title: 16_A.NL.V2

description: Gene expression data from skin biopsy


title: 17_A.LS.V7

description: Gene expression data from skin biopsy


title: WT_1M_AUD_rep1


title: 18_A.LS.V10

description: Gene expression data from skin biopsy


title: iDART_SMART-seq APOBEC1-YTH Cell 144

city: Durham


title: iDART_SMART-seq APOBEC1-YTH Cell 143


title: Ash1l_het_1M_AUD_rep3


title: pSS 4


title: 15_A.LS.V2

description: Gene expression data from skin biopsy


title: Ash1l_het_1M_AUD_rep2


title: iDART_SMART-seq APOBEC1-YTH Cell 141


title: iDART_SMART-seq APOBEC1-YTH Cell 146


title: iDART_SMART-seq APOBEC1-YTH Cell 142


title: pSS 3


title: pSS 2


title: iDART_SMART-seq APOBEC1-YTH Cell 140


title: 13_C.LS.V7

description: Gene expression data from skin biopsy


title: Ash1l_het_1M_AUD_rep1


title: single cell suspension positively enriched for macrophages using F4/80 magnetic beads from a spleen of a SCD mouse

city: Zürich

first: Raphael

middle: Matthias

last: Buzzi

address: Rämistrasse 100

department: Division of Internal Medicine

country: Switzerland

institute: Universitätsspital and University of Zurich

data_processing:
The Cell Ranger Single-Cell Software Suite (version 4.0.0) was used for cDNA oligopeptide alignment, barcode assignment and UMI counting from fastq data from the Illumina sequencing. For each sample, the cell-containing droplets were filtered from the empty droplets, and this step was followed by the generation of an expression matrix using Cell Ranger Count (version 4.0.0).
Demultiplexing of the cells within each sample was performed with the filtered matrix produced by Cell Ranger in R (version 4.4) using Seurat (version 3.2.3) and the HTODemux function (positive quantile set at 0.99).
The resulting gene expression matrices were further analyzed with Python (version 3.8.8) using the Scanpy (version 1.6.0) library. Cells with a total number of expressed genes > 5,000 or < 500, a proportion of mitochondrial genes < 15%, or a proportion of ribosomal genes < 30% and genes expressed in < 20 cells were excluded from downstream analyses. After filtering, normalization was performed using the scran normalization algorithm implemented in the scran R package (version 1.18.3), which was followed by log normalization. For dimensional reduction, principal component analysis (PCA) of each sample was performed using the tl.pca function with the default settings from the Scanpy library. For cell culture and in vivo samples, a shared nearest neighbor graph was built using the pp.neighbors function based on the first 15 PCAs or first 30 PCAs, respectively. Using the Leiden algorithm, cells were clustered and visualized in 2D using UMAP. For expression intensity projections, the cells were colored according to their log-normalized gene expression. Differentially expressed genes (p-value < 0.05 and a log2-fold change > 0.5) were determined using the tl.rank_genes_groups function from the Scanpy library with a pairwise Wilcoxon rank-sum test.
Genome_build: Ensembl GRCm38.p6 Release M23

source_name: spleen

growth_protocol: mice aged 12-16 weeks

extract_protocol:
Spleens were harvested and mechanically disrupted in PBS and passed through a 70-μm cell strainer. The cell suspensions were then centrifuged (300 xg, 5 min, 4°C), incubated in RBC lysis buffer (BioLegend) for 2 min at 37°C and centrifuged once more to obtain spleen cell populations devoid of mature erythrocytes. Macrophages were positively enriched from single-cell suspensions of spleen  using anti-F4/80 antibody (rat, Bioscience)-coated Dynabeads (anti-rat IgG, Invitrogen) . The enriched Macrophages populations from the spleen of SCD mice and control littermates were then processed according to the 10x Genomics Chromium Single Cell 3’ v3.1 Reagent Kits. For all experiments, the sample volume was adjusted to a target capture of 10,000 cells and loaded on the 10x Genomics chromium next-GEM chip G to generate gel-beads-in-emulsion (GEMs). The GEM solution was placed in a thermal cycler for reverse transcription as described by the 10x Genomics instruction guide (53:00 min at 53°C followed by 5:00 min at 85°C).
The resulting barcoded cDNA was then cleaned using Dynabeads MyOne Silane and amplified for 11 cycles (as recommended by the 10x Genomics user guide for a target cell recovery of >6,000 cells). After amplification, for multiplexed experiments, cDNA generated from polyadenylated mRNA for the 3’ gene expression library was separated from DNA from the Cell Surface Protein Feature Barcode for the Cell Surface Protein library with Dynabeads MyOne Silane and SPRIselect reagents based on size. The quality and concentration of both cDNA and DNA were assessed using High-Sensitivity D5000 ScreenTape (Agilent). All samples presented product sizes with a narrow distribution centered around 2000 pb. cDNA and DNA were  then subjected to enzymatic fragmentation, end repair and A-tailing. Adaptors were ligated to the fragmented cDNA and DNA, and the sample index was added during sample index PCR (set for 12 cycles, as recommended by the 10X Genomics user guide to correlate with a cDNA/DNA input of 12-150 ng). Library quality and concentration were assessed using High-Sensitivity D5000 ScreenTape (Agilent). All libraries showed an average fragment size of around 400 pb. For multiplexed runs, 3ʹ Gene Expression and Cell Surface Protein libraries were pooled at a ratio of 4:1 and sequenced using the Illumina NovaSeq 6000 system with a sequencing depth of 50,000 and 12,500 reads per cell, respectively, following the recommendations of 10X Genomics (paired-end reads, single indexing, read 1 = 28 cycles, i7 = 8 cycles, i5 = 0 cycles and read 2 = 91 cycles). For non multiplexed runs, 3ʹ Gene Expression libraries for each sample were pooled at an equimolar amount and sequenced using the Illumina NovaSeq 6000 system with a sequencing depth of 50,000 reads per cell, following the same recommendations of 10x Genomics.

treatment_protocol: no treatment

value: homozygous for Hbatm1Paz, homozygous for Hbbtm1Tow, homozygous for Tg(HBA-HBBs)41Paz (-/-, -/-, Tg/Tg, sickling)= SCD mice

value: spleen

tag: enrichment

value: single-cell suspensions from spleen positively enriched for macrophages  using anti-F4/80 antibody (rat, Bioscience)-coated Dynabeads (anti-rat IgG, Invitrogen)


title: iDART_SMART-seq APOBEC1-YTH Cell 139


title: pSS 1


title: 11_B.LS.V7

description: Gene expression data from skin biopsy

value: Skin biopsy


title: Healthy control 6

source_name: healthy control_Neutrophils

value: healthy control


title: iDART_SMART-seq APOBEC1-YTH Cell 138

value: HEK293T Cells


title: 14_C.LS.V10

description: Gene expression data from skin biopsy


title: single cell suspension positively enriched for macrophages using F4/80 magnetic beads from a spleen of a wild-type mouse

value: homozygous for Hbatm1Paz, heterozygous for Hbbtm1Tow, hemizygous for Tg(HBA-HBBs)41Paz (-/-, +/-, Tg/0, non-sickling)= control hetero


title: pSS 5


title: 12_C.LS.V2

description: Gene expression data from skin biopsy


title: single cell suspension negatively enriched for DCs from a spleen of a SCD mouse

extract_protocol:
Spleens were harvested and mechanically disrupted in PBS and passed through a 70-μm cell strainer. The cell suspensions were then centrifuged (300 xg, 5 min, 4°C), incubated in RBC lysis buffer (BioLegend) for 2 min at 37°C and centrifuged once more to obtain spleen cell populations devoid of mature erythrocytes. DCs were negatively enriched from spleen single-cell suspensions using a Dynabeads DC enrichment kit (Invitrogen) according to the manufacturer’s instructions. The enriched DC populations from the spleen of SCD mice and control littermates were then processed according to the 10x Genomics Chromium Single Cell 3’ v3.1 Reagent Kits. For all experiments, the sample volume was adjusted to a target capture of 10,000 cells and loaded on the 10x Genomics chromium next-GEM chip G to generate gel-beads-in-emulsion (GEMs). The GEM solution was placed in a thermal cycler for reverse transcription as described by the 10x Genomics instruction guide (53:00 min at 53°C followed by 5:00 min at 85°C).
The resulting barcoded cDNA was then cleaned using Dynabeads MyOne Silane and amplified for 11 cycles (as recommended by the 10x Genomics user guide for a target cell recovery of >6,000 cells). After amplification, for multiplexed experiments, cDNA generated from polyadenylated mRNA for the 3’ gene expression library was separated from DNA from the Cell Surface Protein Feature Barcode for the Cell Surface Protein library with Dynabeads MyOne Silane and SPRIselect reagents based on size. The quality and concentration of both cDNA and DNA were assessed using High-Sensitivity D5000 ScreenTape (Agilent). All samples presented product sizes with a narrow distribution centered around 2000 pb. cDNA and DNA were  then subjected to enzymatic fragmentation, end repair and A-tailing. Adaptors were ligated to the fragmented cDNA and DNA, and the sample index was added during sample index PCR (set for 12 cycles, as recommended by the 10X Genomics user guide to correlate with a cDNA/DNA input of 12-150 ng). Library quality and concentration were assessed using High-Sensitivity D5000 ScreenTape (Agilent). All libraries showed an average fragment size of around 400 pb. For multiplexed runs, 3ʹ Gene Expression and Cell Surface Protein libraries were pooled at a ratio of 4:1 and sequenced using the Illumina NovaSeq 6000 system with a sequencing depth of 50,000 and 12,500 reads per cell, respectively, following the recommendations of 10X Genomics (paired-end reads, single indexing, read 1 = 28 cycles, i7 = 8 cycles, i5 = 0 cycles and read 2 = 91 cycles). For non multiplexed runs, 3ʹ Gene Expression libraries for each sample were pooled at an equimolar amount and sequenced using the Illumina NovaSeq 6000 system with a sequencing depth of 50,000 reads per cell, following the same recommendations of 10x Genomics.

value: negative enrichment using a Dynabeads DC enrichment kit (Invitrogen)


title: 10_B.LS.V2

description: Gene expression data from skin biopsy


title: single cell suspension negatively enriched for DCs from a spleen of a wild-type mouse


title: Healthy control 4


title: iDART_SMART-seq APOBEC1-YTH Cell 136

value: 1microg/mL doxycycline; 24 hours


title: iDART_SMART-seq APOBEC1-YTH Cell 135


title: 9_B.LS.V10

description: Gene expression data from skin biopsy


title: Healthy control 3


title: Multiplexed BM-derived cell culture experiment

description: multiplexed experiment with the following ADT_classification allocation to treatment:  - Ctrl-B0301-TotalSeq = M-CSF + vehicle (albumin)  - LPS-B0302-TotalSeq = M-CSF + LPS + vehicle (albumin)  - Heme-B0303-TotalSeq = M-CSF + heme-albumin  - HemeLPS-B0304-TotalSeq = M-CSF + LPS + heme-albumin  - Ctrl-B0305-TotalSeq =GM-CSF + vehicle (albumin)  - LPS-B0306-TotalSeq = GM-CSF + LPS + vehicle (albumin)  - Heme-B0307-TotalSeq = GM-CSF + heme-albumin  - HemeLPS-B0308-TotalSeq = GM-CSF + LPS + heme-albumin

source_name: Bone marrow derived cell cultures

growth_protocol: BM cells were isolated by flushing the femurs and tibias of 8- to 10-week-old mice, followed by straining the BM through a 70-μm filter. Lin— progenitor cells were isolated using a Lin+ cell depletion kit (Lin: CD5, CD11b, CD45R (B220), Gr-1 (Ly-6G/C), 7-4, and Ter-119; Miltenyi Biotec) and 4 x 10^5 cells pro well were plated in tissue culture-treated six-well plates (Nunc Multidishes with UpCell Surface, Thermo Fisher) in 4 ml of complete RPMI-1640 medium (10% fetal calf serum (FCS), 1% L-glutamine) supplemented with 1% penicillin/streptomycin (P/S) and 20 ng/ml recombinant mouse GM-CSF or 100 ng/ml recombinant mouse M-CSF (PeproTech). For the M-CSF-supplemented cultures, half of the medium was removed and new medium supplemented with M-CSF (100 ng/ml) was added. For the GM-CSF-supplemented cultures, fresh medium containing GM-CSF (2x, 40 ng/ml) was added on day 2. On day 3, half of the medium was removed and new medium supplemented with GM-CSF (20 ng/ml) was added.

extract_protocol:
Cells cultured in Multidishes with UpCell™ Surface (Thermo Fisher) were detached by 15 min of incubation at 4°C to obtain single-cell suspensions. Approximately 2 million cells per experimental condition were then stained with 1 μg of TotalSeq™ B0301-B0308 anti-mouse Hashtag antibodies (BioLegend) according to the manufacturer’s instructions and pooled together at equal cell numbers. The pooled multiplexed sample was then processed according to the 10x Genomics Chromium Single Cell 3’ v3.1 Reagent Kits with Feature Barcoding Technology for Cell Surface Protein instruction guide. For all experiments, the sample volume was adjusted to a target capture of 10,000 cells and loaded on the 10x Genomics chromium next-GEM chip G to generate gel-beads-in-emulsion (GEMs). The GEM solution was placed in a thermal cycler for reverse transcription as described by the 10x Genomics instruction guide (53:00 min at 53°C followed by 5:00 min at 85°C).
The resulting barcoded cDNA was then cleaned using Dynabeads MyOne Silane and amplified for 11 cycles (as recommended by the 10x Genomics user guide for a target cell recovery of >6,000 cells). After amplification, for multiplexed experiments, cDNA generated from polyadenylated mRNA for the 3’ gene expression library was separated from DNA from the Cell Surface Protein Feature Barcode for the Cell Surface Protein library with Dynabeads MyOne Silane and SPRIselect reagents based on size. The quality and concentration of both cDNA and DNA were assessed using High-Sensitivity D5000 ScreenTape (Agilent). All samples presented product sizes with a narrow distribution centered around 2000 pb. cDNA and DNA were  then subjected to enzymatic fragmentation, end repair and A-tailing. Adaptors were ligated to the fragmented cDNA and DNA, and the sample index was added during sample index PCR (set for 12 cycles, as recommended by the 10X Genomics user guide to correlate with a cDNA/DNA input of 12-150 ng). Library quality and concentration were assessed using High-Sensitivity D5000 ScreenTape (Agilent). All libraries showed an average fragment size of around 400 pb. For multiplexed runs, 3ʹ Gene Expression and Cell Surface Protein libraries were pooled at a ratio of 4:1 and sequenced using the Illumina NovaSeq 6000 system with a sequencing depth of 50,000 and 12,500 reads per cell, respectively, following the recommendations of 10X Genomics (paired-end reads, single indexing, read 1 = 28 cycles, i7 = 8 cycles, i5 = 0 cycles and read 2 = 91 cycles). For non multiplexed runs, 3ʹ Gene Expression libraries for each sample were pooled at an equimolar amount and sequenced using the Illumina NovaSeq 6000 system with a sequencing depth of 50,000 reads per cell, following the same recommendations of 10x Genomics.

treatment_protocol: On day 3 300 μM heme-albumin (Sigma)  or albumin (CSL, Behring) as a vehicle control was added to the culture medium and the cells were cultured at 37°C. BM cells were harvested for analysis on day 7.

value: vehicle (albumin) or heme-albumin or LPS or LPS+heme-albumin

tag: culture supplement

value: GM-CSF or M-CSF


title: Healthy control 2


title: GM-CSF BM cultures treated with heme

description: multiplexed experiment

treatment_protocol: On day 3, 300 μM heme-albumin (Sigma) or albumin (CSL, Behring) as a control was added to the culture medium and the cells were cultured at 37°C. BM cells were harvested for analysis on day 4, 5, or 7.

value: h;eme

value: GM-CSF


title: iDART_SMART-seq APOBEC1-YTH Cell 134


title: iDART_SMART-seq APOBEC1-YTH Cell 133


title: GM-CSF BM cultures treated with vehicle control (albumin)

description: multiplexed experiment

value: vehicle (albumin)


title: Healthy control 1


title: WT rep3

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


title: iDART_SMART-seq APOBEC1-YTH Cell 131


title: iDART_SMART-seq APOBEC1-YTH Cell 137


title: Healthy control 5

value: Neutrophils


title: iDART_SMART-seq APOBEC1-YTH Cell 132


title: 572_03

city: SHANGHAI

first: XIANGYU

last: ZHOU

state: SHANGHAI

address: Shanghai First Maternity and Infant Hospital

institute: Tongji University

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  K572R overexpression


title: WT rep2


title: iDART_SMART-seq APOBEC1-YTH Cell 130


title: 7_A.NL.V2

description: Gene expression data from skin biopsy

value: NL

value: Placebo


title: 572_02


title: WT rep1


title: 344_03

value: Ehhadh  K344R overexpression


title: iDART_SMART-seq APOBEC1-YTH Cell 129


title: 5_C.LS.V7

description: Gene expression data from skin biopsy

value: Skin biopsy

value: LS


title: 344_02


title: Ash1l_het rep3


title: iDART_SMART-seq APOBEC1-YTH Cell 128

value: HEK293T Cells


title: LR_GG_CoIP_LrhCas9-3xF_native_leader_array_R2

city: Würzburg

first: Tom

last: Gräfenhan

address: Josef-Schneider-Str. 2, Bau D15

department: Core Unit SysMed

institute: University of Wuerzburg

description:
RNA bound to LrhCas9-3xFLAG
eluted after co-immunoprecipitation with anti-FLAG antibody

data_processing:
Base calling with Illumina NextSeq RTA v2.11.3
FASTQ conversion with bcl2fastq v2.20.0.422
FASTQ quality and adapter trimming using Cutadapt (Martin, 2011) version 2.5 (cutadapt parameters: --nextseq-trim=20 -m 1 -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC)
Alignment of reads longer than 11 nt to reference genome using segemehl version 0.2.0 with minimum accuracy 95% (parameters for reademption align: -l 12 -a 95 ) (READemption 0.4.5, Förstner et al., 2014)
Coverage calculation via reademption coverage based on all aligned reads (full-length); Normalization: coverage-tnoar_mil_normalized (counts divided by total number of aligned reads and multiplied by 1,000,000) (READemption 0.4.5, Förstner et al., 2014)
Genome_build: E. coli K-12 BW25113: RefSeq assembly GCF_000750555.1 together with NL-Tagged-SpCas9-Plasmid (native leader, https://benchling.com/s/seq-JlrK1TcQnY4F3exlry0o) or ML-Tagged-SpCas9-Plasmid (mutated leader, https://benchling.com/s/seq-YJpL5iHCvtffFQaxEwFE); L. rhamnosus GG: RefSeq assembly GCF_000026505.1 and Tagged-LrCas9-Plasmid (https://benchling.com/s/seq-n65S4AdjwUw640uzpcNU)
Supplementary_files_format_and_content: wiggle files containing positional read coverage values

organism: Lacticaseibacillus rhamnosus

source_name: L. rhamnosus GG cells

growth_protocol: E. coli cells were grown at 37°C in Luria Bertani (LB) broth (5  g/L NaCl, 5 g/L yeast extract, 10 g/L tryptone) with shaking at 250 rpm. The antibiotic kanamycin was added at 50 µg/mL to maintain plasmids. L. rhamnosus cells were grown at 37°C in De Man, Rogosa and Sharpe (MRS) broth (Becton Dickinson) without agitation. The antibiotic chloramphenicol was added at 10 µg/mL to maintain plasmids.

extract_protocol:
Briefly, the cells harboring corresponding plasmids were lysed, tagged proteins were enriched through immunoprecipitation, and RNA bound to the tagged proteins were extracted using phenol-chloroform-isoamyl alcohol method for RIP-seq. The cells harboring the plasmids encoding untagged proteins were subjected to the same extraction procedures to use as controls.
The extracted RNA was treated with DNase I (Thermo Scientific, EN0525) following the manufacturer’s instructions. cDNA libraries for Illumina sequencing were constructed by Vertis Biotechnologie AG, Germany (http://www.vertis-biotech.com). Briefly, the resulting RNA was subjected to oligonucleotide adapter ligation on the 3′ end, first-strand cDNA synthesis using M-MLV reverse transcriptase (Agilent), and Illumina TruSeq sequencing adapter ligation on the 3′ end. The resulting cDNA was PCR-amplified using Herculase II Fusion DNA Polymerase (Agilent) with 13 amplification cycles following the manufacturer’s instructions, purified using Agencourt AMPure XP kit (Beckman Coulter Genomics) following the manufacturer’s instructions, and analyzed by capillary Electrophoresis.

treatment_protocol: No treatment applied during growth. Bacterial lysates from biological replicates were used for coIP.

value: GG

tag: crispr array leader

value: native leader

tag: antibody for coip

value: ANTI-FLAG M2 (Sigma, cat. #F 1804)

tag: replicate


title: LR_GG_CoIP_WT_native_leader_array_R2

description:
RNA bound non-specifically
eluted after co-immunoprecipitation with anti-FLAG antibody


title: 4_C.LS.V2

description: Gene expression data from skin biopsy

tag: tissue

tag: tissue disease state

tag: week


title: 344_01


title: 8_B.LS.V7

description: Gene expression data from skin biopsy

tag: treatment


title: iDART_SMART-seq APOBEC1-YTH Cell 127

tag: cell line

tag: transgene

value: 1microg/mL doxycycline; 24 hours


title: Ash1l_het rep1

tag: strain


title: 335_03

value: Ehhadh  K335R overexpression


title: iDART_SMART-seq APOBEC1-YTH Cell 126


title: LR_GG_CoIP_LrhCas9-3xF_native_leader_array_R1


title: LR_GG_CoIP_WT_native_leader_array_R1


title: 572_01


title: GM-CSF BM-cultures from Nrf2-/- or wild-type littermates stimulated with heme or the selective Nrf2 activator ML-334

description: multiplexed experiment

growth_protocol: BM cells were isolated by flushing the femurs and tibias of 8- to 10-week-old mice, followed by straining the BM through a 70-μm filter. 4 x 10^5 cells pro well were plated in tissue culture-treated six-well plates (Nunc Multidishes with UpCell Surface, Thermo Fisher) in 4 ml of complete RPMI-1640 medium (10% fetal calf serum (FCS), 1% L-glutamine) supplemented with 1% penicillin/streptomycin (P/S) and 20 ng/ml recombinant mouse GM-CSF or 100 ng/ml recombinant mouse M-CSF (PeproTech). For the M-CSF-supplemented cultures, half of the medium was removed and new medium supplemented with M-CSF (100 ng/ml) was added. For the GM-CSF-supplemented cultures, fresh medium containing GM-CSF (2x, 40 ng/ml) was added on day 2. On day 3, half of the medium was removed and new medium supplemented with GM-CSF (20 ng/ml) was added.

treatment_protocol: On day 3, 150 or 300 μM heme-albumin (Sigma), 10 μM ML-314 (Tocris), 15 μM RA-839 (Tocris), or albumin (CSL, Behring) as a control was added to the culture medium and the cells were cultured at 37°C. BM cells were harvested for analysis on day 7.

value: vehicle (albumin) or heme-albumin or ML-334


title: iDART_SMART-seq APOBEC1-YTH Cell 125


title: 1_C.LS.V2

description: Gene expression data from skin biopsy


title: 2_C.LS.V7

description: Gene expression data from skin biopsy