title: 20006861HC mouse hippocampus, wild-type, treated with lamivudine

city: Badalona

first: Alessandra

last: Borgognone

state: Barcelona

address: Carretera de Canyet, s/n

institute: IrsiCaixa

description:
Expression_Profile.mm10.gene_raw_counts.xlsx
LINE1_raw_counts.txt

data_processing:
Sequence reads were trimmed for adaptors/low-quality sequences using Trimmomatic v0.38
Trimmed sequences were mapped to GrCM38/mm10 using HISAT v2.1.0 using recommended parameters
Read count extraction and normalization for genes were performed using StringTie v2.1.3b
Locus-specific quantification and read count extraction LINE-1 elements were performed using Telescope
Assembly: mm10
Supplementary files format and content: tab-delimited excel file includes raw gene counts for each sample
Supplementary files format and content: tab-delimited text file includes raw LINE1 counts for each sample

source_name: Hippocampus

growth_protocol: Trisomic (Ts65Dn, TS) male mice were obtained by breeding B6EiC4Sn.BLiA-Ts(1716)65Dn/DnJ females with C57BL/6 × 6JOlaHsd (B6C3F1/OlaHsd) hybrid males. Mice were genotyped, and ∼25% of the offspring presented with trisomy. Wild-type (WT) littermates were used as controls. After weaning, male mice were group housed with three to four animals per cage on a conventional 12:12 light cycle in controlled environmental conditions of humidity (50%–70%) and temperature (21 ± 1°C). Water and standard rodent chow were available ad lib. Experiments were conducted using 3–4 month-old male mice

extract_protocol:
Brain tissue was disaggregated using TissueLyser, and total RNA was extracted using RNeasy Plus Mini Kit protocol (Qiagen)
Total RNA samples were sent to Macrogen (South Korea) for library preparation and sequencing

treatment_protocol: Lamivudine 3 mg/kg (Epivir, 10 mg/ml, oral solution) in the drinking water

value: Hippocampus

tag: genotype

value: WT

value: Lamivudine


title: HCV_DAA_DMSO1

status: Public on Jul 11 2024

type: SRA

city: Cantoblanco

first: Juan

middle: Carlos

last: Oliveros

state: Madrid

address: Darwin 3

country: Spain

institute: CNB, CSIC

library_source: transcriptomic

data_processing:
Reads in fastq format were aligned against human genome using RNA-STAR (--sjdbOverhang 49)
Human genes in ENSEMBL file Homo_sapiens.GRCh38.87.gtf were quantified using QoRTs.jar QC command (--stranded  --singleEnded)
Assembly: GRCh38
Supplementary files format and content: Text-tabulated file containing raw counts for each sample and gene annotations

molecule: total RNA

organism: Homo sapiens

source_name: Human hepatoma

extract_protocol:
Total RNA was extracted using  guanidiium thyocyanate and acid phenol a phase separation, with a final isopropanol precipitation. Total RNA was treated with DNAseI and re-extracted using the same method. Total RNA was depleted from ribosomal RNA using RiboZero following manufacturer´s instructions.
TruSeq Stranded Total RNA library Prep kit (Illumina)

tag: tissue

value: Human hepatoma

tag: cell line

tag: infection

value: HCV

tag: state

value: quiescent

tag: treatment

value: DAA


title: 293T WT-ZBTB3, ZBTB3, 0.01 Dox, rep1

city: Boston

first: Jared

last: Brown

state: MA

address: Mailtop CLS11007, 450 Brookline Ave

department: Data Science

country: USA

institute: Dana Farber Cancer Institute

library_source: genomic

data_processing:
Alignment/filtering: All ChIP-seq samples were processed identically. Initial reads (.fastq) were screened for short/low quality sequences using fastp (v0.23.2) (options -q 16 -u 35 -e 22 -l 34). Filtered, paired .fastq file were aligned to the UCSC release of the hg38.p13 reference genome using the STAR aligner (v2.7.5b) in paired end mode (options –winAnchorMultimapNmax 100 –twopassMode Basic –outReadsUnmapped None –outSAMstrandField intronMotif –outSAMunmapped None –outMultimapperOrder Random –outSAMmultNmax 1 –alignIntronMax 1 –alignEndsType EndToEnd –alignMatesGapMax 1000). Aligned .bam files were filtered using SAMtools (v1.10) to initially remove mapped fragments fully contained within the ENCODE exclusion list for GRCh38 (dataset: ENCFF356LFX) followed by further filtering to remove optical (sequencing) duplicate alignments as identified by Picard (v1.2) and mapped fragments over 1kb. Duplicate fragments not identified as optical were downsampled to remove duplicate rates in excess of that expected by the local binding rates of duplicate and unique reads as fitted by a monotonic cubic spline on log counts; this is a slight modification of the approach described in Tian S., et al. (2019).
Normalization: Samples were rendered comparable within experiment and identifiable excess variation due to differences in sequending depth was removed/accounted for through the use of normalization scale factors. Factors were calculated through an approach integrating techniques from the TMM and Median-Ratio methods. Specifically, fragment counts across 75BP bins were tabulated and neighboring bins with similar length-normalized counts (less than 33% difference) were merged to increase per-bin information; the percent-change limit implicitly provides robustness to peaks, which tend to not be merged. Following merging, bin-specific pseudo-counts were calculated as the across-sample geometric mean of bin counts. Finally, sample-specific scale factors are estimated as the median of ratios between sample-bin-counts and bin-pseudo-counts. When necessary, normalized signal tracks are calculated by dividing the raw signal track by the sample-specific scale factor.
Peak calling: Per-sample peaks were called using a custom implementation of the MACS2 (v2.2.7.1) tools. ChIP fragments (.bam) were converted to a BedGraph using ‘pileup’ in paired-end mode then scaled by the previously estimated normalization factor with ‘bgdopt’.
Assembly: hg38
Supplementary files format and content: Processed *.bw files contain genome-wide signal tracks of aligned and filtered fragments, normalized by scaling with the sample-specific scale-factor.
Supplementary files format and content: Processed *peaks.bed files contain sample-specific peaks as called by MACS2.
Supplementary files format and content: Processed *MergedPeaks.bed files contain peak regions merged across those discovered in sample-specific testing.
Supplementary files format and content: Processed *MergedPeakCounts.csv files contain fragment counts corresponding to each merged peak across samples.
Supplementary files format and content: Processed *SampleMetaData.csv files contain sample-specific meta-data including sample-specific normalization size-factors.

molecule: genomic DNA

source_name: HEK 293T - ZBTB3 KO

extract_protocol:
Cells were pelleted by centrifugation and resuspended in 8.25 ml of PBS and 8.25 ml of 2% formaldehyde and incubator for 10 minutes at room temperature. Cross-linking was quenched by the addition of 1665 µl of 1 M Tris/HCl pH 8.0 and 832.5 µl of 2.5 M glycine. Cells were pelleted and washed twice with PBS. Cross-linked cells were resuspended in LB1 Buffer (50 mM HEPES/KOH pH 7.5, 140 mM NaCl, 1 mM EDTA, 10% Glycerol, 0.5% NP-40, 0.25% Triton X-100 in distilled water) and rotated for 10 minutes at 4°C. Cells were pelleted and resuspended in LB2 (10 mM Tris/HCl pH 8.0, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA in distilled water) and rotated for 10 minutes at 4°C. Cells were pelleted and resuspended in home-made RIPA Buffer (50mM Tris/HCl pH 8.0, 150 mM NaCl, 5 mM EDTA, 0.5% Na-deoxycholate, 0.1% SDS, 1% Triton X-100, in distilled water) sonicated (Covaris, E220). Samples were transferred into DNA LoBind tubes (Eppendorf) and clarified by centrifugation. Antibody-bead conjugates were made with either Protein-A (ThermoFisher). Beads were washed twice with home-made RIPA Buffer and resuspended with the appropriate amount of beads (according to manufacturer’s instructions), and rotated overnight at 4°C. Antibody-bead complexes were applied to lysates and rotated overnight at 4°C. Beads were removed via magnet and washed twice with home-made RIPA Buffer , twice with Low salt wash Buffer (150 mM NaCl, 20 mM Tris-HCl, pH 8.0, 2 mM EDTA, 1% Triton X-100, and 0.1% SDS in distilled water), twice with High salt wash Buffer (250 mM NaCl, 20 mM Tris/HCl pH 8.0, 2 mM EDTA, 1% Triton X-100, and 0.1% SDS in distilled water) and twice with LiCl Buffer (2.5 g deoxycholic acid, 1 mM EDTA, 250 mM LiCl, 0.5% NP-40, 10 mM Tris/HCl pH 8.0, 0.02% NaN3 in distilled water). Beads were washed briefly with TE buffer and DNA was eluted in ChIP elution buffer (50mM Tris-HCl, pH 8.0, 10mM EDTA, 1% SDS in distilled water) and de-crosslinked overnight at 65°C. DNA was purified by column purification (DNA Clean and Concentration, Zymo Research) and quantified by ScreenTape HS D1000 (Agilent) and Qubit (ThermoFisher).
Library preparation was done using SMARTer® ThruPLEX® DNA-Seq Kit (Takara, #R400675).

value: HEK 293T - ZBTB3 KO

tag: cell type

value: Kidney

tag: chip antibody


title: 20006861C mouse cortex, wild-type, treated with lamivudine

organism: Mus musculus

source_name: Cortex

value: Cortex


title: input_1.mkD.clN.sorted.bam.ratio.CPM.bw

city: New York

first: Nils

last: Weinhold

state: NY

address: 1275 York Avenue

institute: Memorial Sloan Kettering Cancer Center

data_processing:
ChIP sequencing reads were trimmed using Cutadapt and aligned to the human reference genome (hg19) using BWA. We applied read filtering to remove reads that were marked as duplicates (picard) (“Picard Toolkit.” 2019. Broad Institute, GitHub Repository. https://broadinstitute.github.io/picard/; Broad Institute), reads that were not primary alignments, unmapped, mapped to multiple locations, or contained > 4 mismatches (samtools). Deeptools bamCoverage was used to create normalized bigWig files using CPM (counts per million) normalization. We further used deeptools computeMatrix, plotHeatmap and plotProfile for visualization of ChIP-Seq data at TSS and TTS. MACS2 callpeak was used to identify ChIP-Seq peaks relative to input data. To compare peaks from different conditions we retained peaks with P-values > 2 (-log10) from the narrowPeak output files. The ChIPpeakAnno package was used in R to create Venn diagrams of colocalized peaks in different conditions.
Assembly: hg19
Supplementary files format and content: bigWig files

source_name: HeLa

extract_protocol:
Chromatin immunoprecipitation (ChIP) assays were conducted using the Zymo-Spin ChIP kit (Zymo Research Corp., #D5210) following manufacturer’s instructions.
DNA libraries were prepared by Zymo Research Epigenetics Services

value: HeLa


title: 20006860HC mouse hippocampus, wild-type, treated with lamivudine


title: HCV_DMSO2


title: HCV_DMSO3


title: 293T K166A, Input, 0.1 Dox, rep2

description: input for 293T-p402_ChIP_ZBTB3_dox-0-1-24h_REP2_230707_TAGCTT_S10_peaks.bed


title: 293T K166A, Input, 1 Dox, rep1

description: input for 293T-p402_ChIP_ZBTB3_dox-1-24h_REP1_230707_GGCTAC_S11_peaks.bed


title: SAT2

city: Los Angeles

first: Seung Hyuk

middle: T.

last: Lee

state: CA

address: 695 Charles E. Young Drive South

institute: UCLA

description:
matrix.mtx.gz
features.tsv.gz
barcodes.tsv.gz
meta_data.tsv.gz

library_source: transcriptomic single cell

data_processing:
Sequence reads were aligned to the GRCh37 human genome reference using STARSolo in STAR v2.7.5a with the the ‘--soloFeatures GeneFull’ parameter to account for full pre-mRNA transcripts
We used demuxlet, implemented in the popscle software tool, to assign droplets to the one of the 8 donors.
Assembly: hg19
Supplementary files format and content: Matrix market format for gene counts
Supplementary files format and content: Tab-separated text file for meta data, barcodes (column names), and gene names (row names).

molecule: polyA RNA

source_name: subcutaneous adipose tissue

extract_protocol:
To isolate nuclei, the tissue was minced over dry ice and transferred into ice-cold lysis buffer consisting of 0.1% IGEPAL, 10 mM Tris-HCl, 10 mM NaCl, and 3 mM MgCl2. After a 10 minute incubation period, the lysate was gently homogenized with a dounce homogenizer and filtered through a 70-μm MACS smart strainer (Miltenyi Biotec #130-098-462) for debris removal. Nuclei were centrifuged at 500g for 5 min at 4 °C and washed in 1 ml of resuspension buffer (RSB) consisting of 1× PBS, 1.0% BSA, and 0.2 U/μl RNase inhibitor. Nuclei were then further filtered using a 40-μm Flowmi cell strainer (Sigma Aldrich # BAH136800040), centrifuged at 500g for 5 min at 4 °C, and re-suspended in wash buffer.
Libraries were prepared using the 10x Single Cell 3’ Reagent Kit v3.1
Illumina NovaSeq SP

value: subcutaneous adipose tissue


title: si52_gH2Ax_1.mkD.clN.sorted.bam.ratio.CPM.bw


title: 20006860C mouse cortex, wild-type, treated with lamivudine


title: adult forebrain, genome-wide, rep7

city: Baltimore

first: Mollie

last: Meffert

address: 725 N. Wolfe St.

institute: Johns Hopkins University School of Medicine

description:
Rep7
Forebrain_CIMERA-seq_sample_5-7_peakcalling.summary.txt
Forebrain_CIMERA-seq_sample_5-7_peaks.bed.txt
Forebrain_CIMERA-seq_sample_5-7_peaks.bed.mouse.annotation.txt

data_processing:
Sequencing data were processed using SCRAP (SCRAP release 2.0) bioinformatic pipeline to identify the significant sncRNA:targetRNA interactions in each sample (Eadara et al. 2023; Mills et al. 2022), for which code is deposited at https://github.com/Meffert-Lab/SCRAP.
Peak calling was performed by setting SCRAP variables to consider only high confidence sncRNA binding sites across the genome supported by at least 3 chimeric sncRNA:target RNA reads in at least 2 sample libraries.  Peak calling was performed as groups: group1: Forebrain CIEMRA-seq sample 1-4 group 2: Forebrain CIMERA-seq sample 5-7 group 3: Excitatory neuron selective CIMERA-seq sample 1-3 group 4: IgG CIMERA-seq sample 1-2
Assembly: mm10
Supplementary files format and content: tab-delimited txt files include counts for each chimeric RNA (sncRNA:target RNA pairs)
Library strategy: CIMERA-seq

source_name: forebrain

extract_protocol:
Mouse brain tissue in Homogenization buffer (1X HBSS supplemented with 5 mM MgCl2, 10 mM HEPES (pH 7.4) and 1X HALT protease/phosphatase inhibitor) is homogenized by 12 passes through a 21G needle. UV irradiate homogenates 3x with (4000 µJ/cm2 x 100) on a perfluoroalkoxy (PFA) petri dish, mixing samples between rounds. Transfer irradiated tissue homogenate to a microfuge tube and centrifuge 900 x g for 5 minutes at 4 °C.  Immunoprecipitation from the cell pellets were done with anti-Ago2 (2D4, Wako, 018-22021)  for total CIMERA-seq, anti-myc (9B11, Cell Signaling, 2276) for cell-selective CIMERA-seq, and anti-IgG1 (Invitrogen, 14-4714-82) for negative control.
Libraries were prepared by intermolecular ligation of small non-coding RNA and target RNA, RNA isolation from Ago protein, ligation of 3’ and 5’ adaptors, reverse transcription, minimal PCR amplification, gel purification and size selection.
custom sequencing libraries with 150 base-pair paired-end sequencing and a read depth of 61 – 138 million reads per sample (Illumina HiSeq X or NovaSeq)

treatment_protocol: The mouse line with conditional tAgo2 expression in excitatory neurons was generated by crossing B6Tg(Camk2a-Cre/ERT2) (Erdmann et al. 2007), and B6.Cg-Gt(ROSA)26Sortm1(CAG-GFP/Eif2c2)Zjh/J (Jackson Laboratory #017626). Tamoxifen (2 mg) was administered to mice intraperitoneally once per day for 5 days. Gene induction was allowed to occur for 14-21 days after the final injection before tissue harvest at 10-12 weeks of age.

value: forebrain

tag: strain


title: 293T K166A, Input, 0.1 Dox, rep1

description: input for 293T-p402_ChIP_ZBTB3_dox-0-1-24h_REP1_230707_GATCAG_S9_peaks.bed


title: si52_S96_1.mkD.clN.sorted.bam.ratio.CPM.bw


title: mock_DAA_DMSO3

value: Mock


title: HCV_DMSO1


title: si52_Rpb1_1.mkD.clN.sorted.bam.ratio.CPM.bw


title: siNT_gH2Ax_1.mkD.clN.sorted.bam.ratio.CPM.bw


title: 20006859HC mouse hippocampus, trisomic Ts65Dn, treated with lamivudine


title: 20006859C mouse cortex, trisomic Ts65Dn, treated with lamivudine


title: siNT_Rad52_1.mkD.clN.sorted.bam.ratio.CPM.bw


title: mock_DAA_DMSO2


title: 293T K166A, Input, 0.01 Dox, rep1

description: input for 293T-p402_ChIP_ZBTB3_dox-0-01-24h_REP1_230707_CAGATC_S7_peaks.bed


title: 200059146HC mouse hippocampus, wild-type, non-treated

value: Non treated


title: mock_DAA_DMSO1


title: 293T K166A, Input, 1 Dox, rep2

description: input for 293T-p402_ChIP_ZBTB3_dox-1-24h_REP2_230707_CTTGTA_S12_peaks.bed


title: 293T WT-ZBTB3, Input, 1 Dox, rep2

description: input for 293T-p401_ChIP_ZBTB3_dox-1-24h_REP2_230707_GCCAAT_S6_peaks.bed


title: mock_DMSO3


title: siNT_Rpb1_1.mkD.clN.sorted.bam.ratio.CPM.bw


title: 293T WT-ZBTB3, Input, 1 Dox, rep1

description: input for 293T-p401_ChIP_ZBTB3_dox-1-24h_REP1_230707_ACAGTG_S5_peaks.bed


title: 200059146C mouse cortex, wild-type, non-treated


title: mock_DMSO2


title: siNT_S96_1.mkD.clN.sorted.bam.ratio.CPM.bw


title: 200058403HC mouse hippocampus, wild-type, non-treated


title: 293T WT-ZBTB3, Input, 0.1 Dox, rep2

description: input for 293T-p401_ChIP_ZBTB3_dox-0-1-24h_REP2_230707_TGACCA_S4_peaks.bed


title: 293T, W128A-Overexpressed, 1 Dox 48h, rep3

description:
P404_DOX_3
ZBTB9_ecMatrix.csv
ZBTB9_ecMetaData.csv

data_processing:
Alignment/gene quantification: Initial reads (.fastq) were screened for short/low quality sequences using fastp (v0.23.2) (options -q 22 -u 20 -e 26 -l 50). Filtered, paired .fastq file were aligned to the UCSC release of the hg38.p13 reference genome using the STAR aligner (v2.7.5b) in paired end mode (options –sjdbScore 2 –sjdbOverhang 100 –outSAMunmapped Within –outFilterType BySJout –outSAMattributes NH HI AS NM MD –outFilterMultimapNmax 20 –outFilterMismatchNmax 999 –outFilterMismatchNoverLmax 0.04 –alignIntronMin 20 –alignIntronMax 1000000 –alignMatesGapMax 1000000 –alignSjoverhangMin 8 –alignSJDBoverhangMin 1 –quantMode TranscriptomeSAM –quantTranscriptomeMan IndelSoftclipSingleend). Optical (sequencing) duplicate alignments as identified by Picard (v1.2) were filtered out and gene-transcript quantification was performed by RSEM (v1.3.3) as the expected number of sequenced transcripts or "expected counts" (ECs).
Normalization: Sample-specific size-factors are computed within cell-type by the method of median-ratio as described in DESeq.
Assembly: hg38
Supplementary files format and content: Processed *ecMatrix.csv files contain the "expected count" transcript quantification output of RSEM.
Supplementary files format and content: Processed *ecMeta.csv files contain metadata relating to the columns of the count matrices.

source_name: HEK 293T - ZBTB9 KO

extract_protocol:
1 ✕ 106 cells were collected by centrifugation for 5 minutes and washed with ice-cold PBS followed by total RNA extraction using RNeasy kit (Qiagen, #74106) per manufacturer’s instructions.
RNA was sent to Novogene for library preparation and sequencing.

value: HEK 293T - ZBTB9 KO

value: DMSO

tag: time


title: mock_DMSO1


title: HCV_DAA_pro4

value: proliferating


title: 293T WT-ZBTB3, Input, 0.1 Dox, rep1

description: input for 293T-p401_ChIP_ZBTB3_dox-0-1-24h_REP1_230707_TTAGGC_S3_peaks.bed


title: 293T WT-ZBTB3, Input, 0.01 Dox, rep2

description: input for 293T-p401_ChIP_ZBTB3_dox-0-01-24h_REP2_230707_CGATGT_S2_peaks.bed


title: 200058403C mouse cortex, wild-type, non-treated

value: WT


title: 293T, W128A-Overexpressed, 1 Dox 48h, rep1

description:
P404_DOX_1
ZBTB9_ecMatrix.csv
ZBTB9_ecMetaData.csv


title: 293T K166A, Input, 0.01 Dox, rep2

description: input for 293T-p402_ChIP_ZBTB3_dox-0-01-24h_REP2_230707_ACTTGA_S8_peaks.bed


title: 293T WT-ZBTB3, Input, 0.01 Dox, rep1

description: input for 293T-p401_ChIP_ZBTB3_dox-0-01-24h_REP1_230707_ATCACG_S1_peaks.bed


title: 200054527C mouse cortex, wild-type, non-treated

description:
Expression_Profile.mm10.gene_raw_counts.xlsx
LINE1_raw_counts.txt


title: 293T, W128A-Overexpressed, 1 Dox 48h, rep2

description:
P404_DOX_2
ZBTB9_ecMatrix.csv
ZBTB9_ecMetaData.csv


title: 293T, W128A-Overexpressed, DMSO 48h, rep3

description:
P404_DMSO_3
ZBTB9_ecMatrix.csv
ZBTB9_ecMetaData.csv


title: HCV_DAA_pro2


title: Human donor 2, expanded, scRNAseq

city: Philadelphia

first: Antonia

last: Rotolo

state: PA

address: 3900 Chestnut Street, Apt 521

institute: University of Pennsylvania

description: 10x Genomics

data_processing:
The demultiplexing, barcode processing, gene counting and aggregation were made using the Cell Ranger software v6.0.2 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: CanFam6 and GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Peripheral Blood

extract_protocol:
iNKT scRNA-seq libraries were prepared from both freshly purified iNKTs and matched iNKT cellular products at the end of the expansion. Each library was generated from 10,000 cells with viability >90% as confirmed by Trypan Blue. Human and canine iNKT cells were immunomagnetically purified from PBMCs using PE-conjugated human CD1d tetramers loaded with the αGC analogue PBS57 (NIH Tetramer Core Facility) and anti-PE microbeads (Miltenyi Biotec). After purification, cells were resuspended in PBS with 0.04% w/v BSA for scRNAseq library preparation. For canine and human iNKT expansion, CD1d+ artificail antgen presenting cells were pulsed overnight with αGC 100ng/ml (KRN7000, Cayman Chemicals) and irradiated on the following day (i-aAPC, 10,000 rad). Purified iNKT cells were seeded in round-bottom 96-wells at 1:1 ratio with i-aAPC and maintained at 38-38.8˚C in IMDM medium containing 25 mM Hepes (Gibco), 10% heat inactivated FBS (Atlanta Biologicals), 1% Pen/Strep (Gibco), 1% glutamax (Gibco), 1% non-essential amino acids (Gibco), 1mM sodium pyruvate (Gibco) and 50µM 2-Mercaptoethanol (Gibco). Cross-reactive human IL-15 (Miltenyi Biotec, 30 ng/ml) was supplemented 24-48h after stimulation. Human IL-15 and human IL-2 (Miltenyi Biotec, 30 ng/ml and 100 IU/ml respectively), human IL-7 and human IL-21 (Peprotech, 10 ng/ml) were added 6 days after stimulation and then every other day. To generate clinical scale iNKT products, iNKTs were restimulated twice, i.e., during the second and third week of expansion.8 days after the last restimulation, 10,000 iNKTs were resuspended in PBS with 0.04% w/v BSA for scRNA-seq library preparation.
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics). Briefly, iNKT cells were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: Peripheral Blood

value: primary human iNKT

value: iNKT cells

value: healthy, female

tag: age

value: 27 year old

value: Expanded


title: HCV_DAA_pro1

value: Human hepatoma

value: HCV

value: DAA


title: 200054526C  mouse cortex, wild-type, non-treated

value: Cortex


title: 293T, W128A-Overexpressed, DMSO 48h, rep1

description:
P404_DMSO_1
ZBTB9_ecMatrix.csv
ZBTB9_ecMetaData.csv

value: Kidney


title: Human donor 1, expanded, scRNAseq

description: 10x Genomics

value: healthy, male

value: 26 year old


title: 200054526HC mouse hippocampus, wild-type, non-treated

value: Hippocampus

value: Non treated


title: 200054525C mouse cortex, trisomic Ts65Dn, non-treated


title: HCV_pro4

value: proliferating


title: Human donor 2, baseline, scRNAseq

description: 10x Genomics

value: Freshly isolated


title: 200054524HC mouse hippocampus, trisomic Ts65Dn, non-treated


title: HCV_pro3


title: 293T, W128A-Overexpressed, 1 Dox 24h, rep3

description:
p404_1_3
ZBTB9_ecMatrix.csv
ZBTB9_ecMetaData.csv

value: HEK 293T - ZBTB9 KO

value: DMSO


title: Human donor 1, baseline, scRNAseq

description: 10x Genomics

value: Peripheral Blood

value: primary human iNKT

value: iNKT cells


title: HCV_pro2


title: 293T, W128A-Overexpressed, 1 Dox 24h, rep2

description:
p404_1_2
ZBTB9_ecMatrix.csv
ZBTB9_ecMetaData.csv


title: HCV_DAA_pro3


title: REF6, miRNA

city: Indianapolis

first: Michael

middle: T

last: Eadon

state: IN

address: 950 W Walnut St

institute: Indiana University

data_processing:
Sequence reads uploaded to Qiagen GeneGlobe Data Analysis Center (https://www.qiagen.com/us/resources/geneglobe)
Reads were mapped to different databases for mature, hairpin, noncoding RNA, mRNA and other RNA using bowtie v1.2
Reads were aligned to the human referece genome Hg38 using STAR with parameters ajusted to short reads and Integrative Genomics Viewer (IGV) alignment.
Read counts and UMI counts for each RNA category (mature, hairpin, piRNA, tRNA, rRNA, mRNA and otherRNA) were calculated for each sample, using miRbase V21 for miRNA, and piRNABank for piRNA.
Processed data are provided as UMI counts. The remaining processing and normalization steps described in the paper were not performed to the data available in this series.
Assembly: Hg38
Supplementary files format and content: csv

source_name: Kidney

extract_protocol:
Kidney tissue was obtained from a clinical biopsy, placed in Michels solution and frozen on OCT within 24 h. 10 um of cross-sectional biopsy tissue was cut on a cryotome and placed in PicoPure RNA extraction buffer. RNA was extracted according to protocol.
Nephrectomies were obtained and frozen on OCT within 24 h. 10 um of cross-sectional biopsy tissue was cut on a cryotome and placed in PicoPure RNA extraction buffer. RNA was extracted according to protocol.
QIASeq miRNA Library Kit
RNA seq, 15-20 million input reads per sample

tag: disease

value: Reference

tag: tissue source

value: Nephrectomy

tag: segment

value: Bulk

tag: storage

value: OCT at -80C


title: 200054527HC mouse hippocampus, wild-type, non-treated

value: WT


title: 293T, W128A-Overexpressed, 1 Dox 24h, rep1

description:
p404_1_1
ZBTB9_ecMatrix.csv
ZBTB9_ecMetaData.csv

value: Kidney


title: 293T, W128A-Overexpressed, 0.1 Dox 24h, rep3

description:
p404_01_3
ZBTB9_ecMatrix.csv
ZBTB9_ecMetaData.csv


title: 200054524C mouse cortex, trisomic Ts65Dn, non-treated

value: Cortex


title: 200048166HC mouse hippocampus, trisomic Ts65Dn, treated with lamivudine

value: Lamivudine


title: REF5, miRNA


title: 293T, W128A-Overexpressed, DMSO 48h, rep2

description:
P404_DMSO_2
ZBTB9_ecMatrix.csv
ZBTB9_ecMetaData.csv


title: 200048166C  mouse cortex, trisomic Ts65Dn, treated with lamivudine


title: 293T, W128A-Overexpressed, 0.1 Dox 24h, rep2

description:
p404_01_2
ZBTB9_ecMatrix.csv
ZBTB9_ecMetaData.csv


title: REF4, miRNA


title: mock_DAA_pro3

value: Human hepatoma

value: Mock

value: DAA


title: mock_DAA_pro2

value: proliferating


title: 200048165HC mouse hippocampus, trisomic Ts65Dn, treated with lamivudine

value: Hippocampus


title: 200048165C  mouse cortex, trisomic Ts65Dn, treated with lamivudine


title: REF3, miRNA


title: REF20, miRNA


title: mock_DAA_pro1


title: 293T, W128A-Overexpressed, 0.01 Dox 24h, rep3

description:
p404_001_3
ZBTB9_ecMatrix.csv
ZBTB9_ecMetaData.csv

value: HEK 293T - ZBTB9 KO

value: DMSO


title: REF19, miRNA


title: 200047368HC mouse hippocampus, trisomic Ts65Dn, treated with lamivudine


title: 200047368C  mouse cortex, trisomic Ts65Dn, treated with lamivudine


title: REF18, miRNA


title: HCV_pro1

value: HCV


title: REF17, miRNA


title: mock_DAA_pro4


title: 293T, W128A-Overexpressed, 0.01 Dox 24h, rep1

description:
p404_001_1
ZBTB9_ecMatrix.csv
ZBTB9_ecMetaData.csv


title: 200047153HC mouse hippocampus, trisomic Ts65Dn, treated with lamivudine


title: mock_pro4


title: mock_pro2


title: mock_pro3


title: 293T, W128A-Overexpressed, 0.01 Dox 24h, rep2

description:
p404_001_2
ZBTB9_ecMatrix.csv
ZBTB9_ecMetaData.csv


title: REF16, miRNA


title: 293T, W128A-Overexpressed, DMSO 24h, rep1

description:
p404_DMSO_1
ZBTB9_ecMatrix.csv
ZBTB9_ecMetaData.csv


title: mock_pro1


title: 200047151HC mouse hippocampus, trisomic Ts65Dn, treated with lamivudine


title: REF15, miRNA


title: 200047151C  mouse cortex, trisomic Ts65Dn, treated with lamivudine


title: REF14, miRNA


title: 293T, W128A-Overexpressed, DMSO 24h, rep2

description:
p404_DMSO_2
ZBTB9_ecMatrix.csv
ZBTB9_ecMetaData.csv


title: 200047153C  mouse cortex, trisomic Ts65Dn, treated with lamivudine


title: mESC_IVT_Label_Rep1

city: Hangzhou

first: Xiaoyu

last: Li

state: Zhejiang

address: 866 Yuhangtang Road

department: SCHOOL OF BASIC MEDICAL SCIENCES

country: China

institute: Zhejiang University

description: in vitro transcribed (IVT) RNA, polyA_RNA template

data_processing:
For batch paired-end reads of m5C-seq libraries, a sample-barcoded-sequence (Pos 1-6) and random-4-base (pos7-10) in Read1 and a 10nt unique molecular identifier (UMI) was included in the adaptor that ligates to the 3’end of cDNA so it locates in Read2 (Pos1-10). Firstly, m5C-seq batch libraries were demultiplexed into individual samples, using fastq-multx（with -m 1 parameters）that distributes reads into a sample FASTQ file(Read1.fq file and Read2.fq file) according to the sample-barcoded-sequence in Read1 (Pos 1-6). For every individual sample, only Read2 data with UMI was used for subsequent analyses. Illumina sequencing reads were first treated with trim_galore(version 0.6.4) for adapter removal and quality trimming. Work commands are as follows: trim_galore --fastqc --phred33 --length 30. We then used Seqkit (version 0.10.0) to deduplicate based on 10 bp UMI at the 5′ end of reads R2, key process parameters are as follows: seqkit rmdup -s. Finally, Fastp (version 0.23.2) was used to remove the 10 bp UMI in the deduplication read. 10 bases at the 3′ end of inserted sequences were also removed, using the key parameters: fastp -f 10 -t 10 -l 20.
Processed reads were mapped to reference genome (human GRCh19 reference / mouse mm10 reference) using HISAT2-3N (version 2.2.1-3n-0.0.3). The key parameters are as follows: hisat3n --base-change C,T --directional-mapping --repeat -p 20 -k 1. Considering a creditable m5C signal, the alignments are further filtering using python house-scripts, the alignments hosts >=3 C-to-T mismatches or >= 3 other type mismatches or the length of alignments < 20nt are filtered. Next, we parse BAM file using pysamstats (version 1.1.2), with commands as follow: pysamstats -D 100000 -S "nofilter" -t variation.
To call m5C signal, C-to-T rate of each C nucleotide in the reference sequences was calculated for both treat (TET2 +) and control (TET2 –) samples. Two parameters were deﬁned to evaluate the dynamic change of C-to-T rate in the treat and control samples: difference of C-to-T rate (Diff) and fold change of C-to-T rate (FC). Diff was calculated by subtracting the mismatch rate in the treat sample from that in the corresponding control sample, while FC was calculated by dividing the C-to-T rate in the control sample that in the treat sample. C position was identiﬁed as an m5C site when the following criteria were met: (1) label sample coverage >= 20; (2) ctrl sample coverage >= 5; (3) C2T reads number >= 5 in both treat sample replications and C2T_reads_num >= 10 at least in one treat sample; (4) diff (treat sample -ctrl sample) >= 5% in both replications; (5) FC (treat sample/ctrl sample) >= 3 in both replications; (6) both control sample mismatch ratio <= 5%; (7) region around C position（+-50nt）mismatches number <= 6 in treat sample. To give our final m5C signal list, we overlapped two lists from two samples, only counted overlapped signals into our final m5C list.
To call m5C signal in KO samples, we took our final m5C list as a reference to find the C-to-T rate in KO samples. Then, we calculated the C-to-T rate fold change and difference between KO samples and WT samples. For enzyme-dependent sites, the C-to-T rate of KO sample is decrease to less than 60% of the WT-sample, the C-to-T rate difference (treat sample – control sample) is required to be >1.5%. To give our final KO-dependent sites list, we overlapped two lists from two KO repeats, and only counted overlapped signals into our final KO-dependent list.
Assembly: hg19(UCSC)/mm10(UCSC)/tRNA-reference(tRNAdb)
Supplementary files format and content: tab-delimited text file includes every C base coverage and C-to-T signal
Supplementary files format and content: excel file,in xls file format
Library strategy: m5C-seq

source_name: mESC

growth_protocol: The mESC cell line was cultured in a complete ESC culture medium, comprising Dulbecco's modified Eagle's medium (DMEM) supplemented with 15% heat-inactivated fetal bovine serum (FBS), 0.1 mM 2-mercaptoethanol, 2 mM L-glutamine, 0.1 mM non-essential amino acids, 1000 U/mL recombinant leukemia inhibitory factor (LIF), and 100 U/mL penicillin/streptomycin. For differentiation assays, mESC cells were cultured without LIF for six days. HeLa and HEK 293T cell lines were cultured in DMEM supplemented with 10% FBS and 100 U/mL penicillin/streptomycin.

extract_protocol:
Total RNA extraction from the cell lines was accomplished using the RNA isolater total RNA extraction reagent (Vazyme, R401-01). Prior to size selection, RNA underwent DNase I treatment at 37 ℃ for 15 min and subsequently was purified using RNA isolater extraction and ethanol precipitation (Vazyme, EN401-01). The small RNA fraction, characterized by a size of less than 200nt, was enriched from the total RNA utilizing the RNA Clean & Concentrator-25 Kit (Zymo, R1018). For mRNA purification, two successive rounds of poly(A)+ selection were performed employing oligo(dT)25 dynabeads (Life Technologies, 61005). Additionally, chromatin-associated RNA was isolated following subcellular fractionation assay, DNase I treatment, and rRNA depletion (Vazyme, N406-01). Modification-free control RNAs were prepared from HeLa or mESC mRNA, adhering to a previously published protocol (PMID: 34594034, 36593412).
The RNA samples were initially dephosphorylated using T4 polynucleotide kinase (Vazyme, N102-01) at 37℃ for 1 hour, followed by ethanol precipitation. Subsequently, they were ligated to the 3' RNA linker using T4 RNA ligase 2, truncated at 25°C for 2 hours, followed by an overnight incubation at 16°C (Beyotime, R0635L). To remove excess adaptors, the samples underwent treatment with 5´ Deadenylase (NEB, M0331S), RecJf (NEB, M0264S), and Proteinase K (NEB, P8102). RNA samples intended for group comparisons were pooled and then purified through Tris-phenol extraction followed by ethanol precipitation. The barcoded and pooled samples were labeled by 5-(2-azidoethyl)-1,3-indandione (AI) and subsequently subjected to a click reaction. The m5C-modified RNA was subjected to RNA pull-down to be enriched, followed by reverse transcription using the HiScript III RT SuperMix (Vazyme, R323-01). The excess reverse transcription primer was digested with exonuclease I (NEB, M0293S). The cDNA was purified by silane beads and then performed to 5′ adapter ligation on beads with T4 RNA ligase 1, high concentration (NEB, M0437M). cDNA was purified using silane beads (Invitrogen, 37002D), and subsequently, the purified cDNA was amplified using the KAPA HiFi HotStart ReadyMix (Roche, KK2602). Finally, PCR products were purified using 1.8X VAHTS DNA Clean Beads (Vazyme, N411-02) and 7% TBE gel.

value: mESC

value: Mouse embryonic stem cells

value: TET2 oxidation and AI Labeling

tag: fraction

value: in vitro transcribed (IVT) RNA


title: 200046065HC mouse hippocampus, trisomic Ts65Dn, non-treated

value: Non treated


title: 293T, ZBTB9-Overexpressed, 1 Dox 48h, rep2

description:
P403_DOX_2
ZBTB9_ecMatrix.csv
ZBTB9_ecMetaData.csv

value: ZBTB9 WT


title: 293T, ZBTB9-Overexpressed, 1 Dox 48h, rep1

description:
P403_DOX_1
ZBTB9_ecMatrix.csv
ZBTB9_ecMetaData.csv

value: Kidney


title: 293T, W128A-Overexpressed, DMSO 24h, rep3

description:
p404_DMSO_3
ZBTB9_ecMatrix.csv
ZBTB9_ecMetaData.csv


title: 200046065C mouse cortex, trisomic Ts65Dn, non-treated

description:
Expression_Profile.mm10.gene_raw_counts.xlsx
LINE1_raw_counts.txt

value: Cortex


title: REF12, miRNA

value: Reference

value: Nephrectomy

value: Bulk

value: OCT at -80C


title: 200046064C mouse cortex, wild-type, non-treated

value: WT


title: mESC_IVT_Label_Rep2


title: 293T, ZBTB9-Overexpressed, DMSO 48h, rep2

description:
P403_DMSO_2
ZBTB9_ecMatrix.csv
ZBTB9_ecMetaData.csv


title: mRNA_mESC_Nsun6_KO_Label_Rep1

value: Nsun6 knockout

value: polyA RNA


title: REF10, miRNA


title: mRNA_mESC_Nsun6_KO_Label_Rep2


title: 200044043HC mouse hippocampus, trisomic Ts65Dn, non-treated

value: Hippocampus


title: 200044043C mouse cortex, trisomic Ts65Dn, non-treated


title: mRNA_mESC_Nsun6_KO_Ctrl_Rep2

value: control


title: M9, miRNA

value: Thin basement membrane disease

value: Biopsy

tag: gender

value: Female


title: 293T, ZBTB9-Overexpressed, DMSO 48h, rep1

description:
P403_DMSO_1
ZBTB9_ecMatrix.csv
ZBTB9_ecMetaData.csv

value: HEK 293T - ZBTB9 KO

tag: genotype

value: DMSO


title: 293T, ZBTB9-Overexpressed, 1 Dox 48h, rep3

description:
P403_DOX_3
ZBTB9_ecMatrix.csv
ZBTB9_ecMetaData.csv

value: ZBTB9 WT


title: 293T, ZBTB9-Overexpressed, 1 Dox 24h, rep3

description:
p403_1_3
ZBTB9_ecMatrix.csv
ZBTB9_ecMetaData.csv

value: Kidney


title: mRNA_mESC_Nsun6_KO_Ctrl_Rep1

value: mESC

value: Mouse embryonic stem cells


title: M8, miRNA

tag: tissue

value: Minimal change disease

value: Male


title: 293T, ZBTB9-Overexpressed, 1 Dox 24h, rep2

description:
p403_1_2
ZBTB9_ecMatrix.csv
ZBTB9_ecMetaData.csv

tag: cell line


title: 200044042HC mouse hippocampus, trisomic Ts65Dn, non-treated

value: Non treated


title: REF13, miRNA

value: Reference

value: Nephrectomy

value: Bulk

value: OCT at -80C


title: mESC_IVT_Ctrl_Rep2

value: WT

value: control

value: in vitro transcribed (IVT) RNA


title: mRNA_mESC_Nsun5_KO_Label_Rep2

value: Nsun5 knockout

value: TET2 oxidation and AI Labeling

value: polyA RNA


title: 200046064HC mouse hippocampus, wild-type, non-treated

value: Hippocampus


title: 200044042C mouse cortex, trisomic Ts65Dn, non-treated

value: Cortex


title: 293T, ZBTB9-Overexpressed, DMSO 48h, rep3

description:
P403_DMSO_3
ZBTB9_ecMatrix.csv
ZBTB9_ecMetaData.csv

value: HEK 293T - ZBTB9 KO

value: Kidney

value: ZBTB9 WT

value: DMSO


title: M7, miRNA

value: Minimal change disease

value: Biopsy

value: Male


title: mRNA_mESC_Nsun5_KO_Label_Rep1

value: mESC

value: Mouse embryonic stem cells


title: 293T, ZBTB9-Overexpressed, 1 Dox 24h, rep1

description:
p403_1_1
ZBTB9_ecMatrix.csv
ZBTB9_ecMetaData.csv


title: mRNA_mESC_Nsun5_KO_Ctrl_Rep2


title: REF1, miRNA

value: Reference

value: Nephrectomy

value: Bulk

value: OCT at -80C


title: M6, miRNA


title: 200044041HC mouse hippocampus, wild-type, non-treated

value: WT

value: Non treated


title: mESC_IVT_Ctrl_Rep1

value: control

value: polyA RNA


title: 293T, ZBTB9-Overexpressed, 0.1 Dox 24h, rep3

description:
p403_01_3
ZBTB9_ecMatrix.csv
ZBTB9_ecMetaData.csv

value: HEK 293T - ZBTB9 KO


title: REF11, miRNA

value: Kidney


title: M5, miRNA

value: Female


title: 200044041C mouse cortex, wild-type, non-treated

value: Cortex


title: 293T, ZBTB9-Overexpressed, 0.1 Dox 24h, rep2

description:
p403_01_2
ZBTB9_ecMatrix.csv
ZBTB9_ecMetaData.csv

value: ZBTB9 WT

value: DMSO


title: mRNA_mESC_Nsun5_KO_Ctrl_Rep1

value: Nsun5 knockout


title: M4, miRNA

value: Minimal change disease

value: Biopsy

value: Male


title: 293T, ZBTB9-Overexpressed, 0.1 Dox 24h, rep1

description:
p403_01_1
ZBTB9_ecMatrix.csv
ZBTB9_ecMetaData.csv


title: 200044040HC mouse hippocampus, wild-type, non-treated

value: Hippocampus


title: mRNA_mESC_Nsun3_KO_Label_Rep2

value: mESC

value: Mouse embryonic stem cells

value: Nsun3 knockout

value: TET2 oxidation and AI Labeling


title: 293T, W128A-Overexpressed, 0.1 Dox 24h, rep1

description:
p404_01_1
ZBTB9_ecMatrix.csv
ZBTB9_ecMetaData.csv


title: 200044040C mouse cortex, wild-type, non-treated

value: WT

value: Non treated


title: M3, miRNA

value: Bulk

value: OCT at -80C


title: mRNA_mESC_Nsun3_KO_Label_Rep1

value: polyA RNA


title: 293T, ZBTB9-Overexpressed, 0.01 Dox 24h, rep2

description:
p403_001_2
ZBTB9_ecMatrix.csv
ZBTB9_ecMetaData.csv

value: HEK 293T - ZBTB9 KO

value: Kidney


title: 200044039C mouse cortex, wild-type, non-treated

value: Cortex


title: M2, miRNA


title: 200040008HC mouse hippocampus, trisomic Ts65Dn, non-treated


title: M12, miRNA


title: M11, miRNA


title: mRNA_mESC_Nsun3_KO_Ctrl_Rep1

value: control


title: 293T, ZBTB9-Overexpressed, 0.01 Dox 24h, rep1

description:
p403_001_1
ZBTB9_ecMatrix.csv
ZBTB9_ecMetaData.csv

value: ZBTB9 WT

value: DMSO


title: M10, miRNA

value: Minimal change disease

value: Biopsy

value: Female


title: 293T, ZBTB9-Overexpressed, DMSO, rep2

description:
p403_DMSO_2
ZBTB9_ecMatrix.csv
ZBTB9_ecMetaData.csv


title: 200040007HC mouse hippocampus, trisomic Ts65Dn, non-treated

value: Hippocampus


title: mRNA_mESC_Nsun2_KO_Label_Rep2

value: mESC

value: Mouse embryonic stem cells

value: Nsun2 knockout


title: M1, miRNA


title: mRNA_mESC_Nsun2_KO_Label_Rep1

value: TET2 oxidation and AI Labeling


title: 293T, ZBTB9-Overexpressed, 0.01 Dox 24h, rep3

description:
p403_001_3
ZBTB9_ecMatrix.csv
ZBTB9_ecMetaData.csv


title: AKI9, miRNA

value: AKI

value: Bulk

value: Male


title: mRNA_mESC_Nsun2_KO_Ctrl_Rep2

value: polyA RNA


title: 293T, ZBTB9-Overexpressed, DMSO, rep1

description:
p403_DMSO_1
ZBTB9_ecMatrix.csv
ZBTB9_ecMetaData.csv

value: HEK 293T - ZBTB9 KO

value: Kidney


title: 200039067HC mouse hippocampus, trisomic Ts65Dn, non-treated

description:
Expression_Profile.mm10.gene_raw_counts.xlsx
LINE1_raw_counts.txt

value: Non treated


title: mRNA_mESC_Nsun2_KO_Ctrl_Rep1

value: control


title: 293T, ZBTB9-KO, 1 Dox 48h, rep3

description:
Z9KO_DOX_3
ZBTB9_ecMatrix.csv
ZBTB9_ecMetaData.csv

value: ZBTB9 WT

value: 1 Dox


title: 200036216HC mouse hippocampus, wild-type, non-treated

value: WT


title: AKI6, miRNA

value: Biopsy

value: OCT at -80C


title: 200039067C  mouse cortex, trisomic Ts65Dn, non-treated

value: Cortex


title: mRNA_mESC_Nsun3_KO_Ctrl_Rep2

value: mESC

value: Mouse embryonic stem cells

value: Nsun3 knockout


title: 200040007C  mouse cortex, trisomic Ts65Dn, non-treated


title: mRNA_mESC_Dnmt2_KO_Label_Rep1

value: Dnmt2 knockout

value: TET2 oxidation and AI Labeling


title: 293T, ZBTB9-KO, 1 Dox 48h, rep2

description:
Z9KO_DOX_2
ZBTB9_ecMatrix.csv
ZBTB9_ecMetaData.csv


title: AKI47, miRNA

value: AKI

value: Bulk


title: mRNA_mESC_Dnmt2_KO_Label_Rep2

value: polyA RNA


title: 200040008C  mouse cortex, trisomic Ts65Dn, non-treated


title: 293T, ZBTB9-KO, 1 Dox 48h, rep1

description:
Z9KO_DOX_1
ZBTB9_ecMatrix.csv
ZBTB9_ecMetaData.csv

value: HEK 293T - ZBTB9 KO

value: Kidney


title: 293T, ZBTB9-Overexpressed, DMSO, rep3

description:
p403_DMSO_3
ZBTB9_ecMatrix.csv
ZBTB9_ecMetaData.csv

value: DMSO


title: 200036216C mouse cortex, wild-type, non-treated

value: Non treated


title: mRNA_mESC_Dnmt2_KO_Ctrl_Rep2

value: control


title: 293T, ZBTB9-KO, DMSO 48h, rep2

description:
Z9KO_DMSO_2
ZBTB9_ecMatrix.csv
ZBTB9_ecMetaData.csv

value: ZBTB9 WT


title: mRNA_mESC_Dnmt2_KO_Ctrl_Rep1


title: 293T, ZBTB9-KO, DMSO 48h, rep1

description:
Z9KO_DMSO_1
ZBTB9_ecMatrix.csv
ZBTB9_ecMetaData.csv


title: AKI44, miRNA

value: Biopsy


title: 200032616HC mouse hippocampus, trisomic Ts65Dn, non-treated

value: Hippocampus


title: AKI45, miRNA

value: OCT at -80C


title: AKI43, miRNA


title: 200014639HC mouse hippocampus, wild-type, treated with lamivudine

value: WT

value: Lamivudine


title: caRNA_mESC_Label_Rep2

molecule: nuclear RNA

value: mESC

value: Mouse embryonic stem cells

value: nuclear RNA


title: 293T, ZBTB9-KO, 0.1 Dox 24h, rep3

description:
ZBTB9KO_01_3
ZBTB9_ecMatrix.csv
ZBTB9_ecMetaData.csv

value: 0.1 Dox


title: caRNA_mESC_Label_Rep1

value: TET2 oxidation and AI Labeling


title: AKI42, miRNA

value: AKI

value: Bulk


title: 293T, ZBTB9-KO, 0.1 Dox 24h, rep2

description:
ZBTB9KO_01_2
ZBTB9_ecMatrix.csv
ZBTB9_ecMetaData.csv

value: HEK 293T - ZBTB9 KO

value: Kidney


title: AKI41, miRNA


title: 200014638HC mouse hippocampus, trisomic Ts65Dn, treated with lamivudine


title: caRNA_mESC_Ctrl_Rep2

description: ct.FR.mpmat.txt


title: AKI4, miRNA

value: Female


title: 293T, ZBTB9-KO, DMSO 48h, rep3

description:
Z9KO_DMSO_3
ZBTB9_ecMatrix.csv
ZBTB9_ecMetaData.csv

value: DMSO


title: 293T, ZBTB9-KO, 0.1 Dox 24h, rep1

description:
ZBTB9KO_01_1
ZBTB9_ecMatrix.csv
ZBTB9_ecMetaData.csv

value: ZBTB9 WT


title: 293T, ZBTB9-KO, DMSO 24h, rep3

description:
ZBTB9KO_WT_3
ZBTB9_ecMatrix.csv
ZBTB9_ecMetaData.csv


title: caRNA_mESC_Ctrl_Rep1

description: ct.FR.mpmat.txt

value: control


title: mRNA_mESC_WT_Control_Label_Rep2

value: polyA RNA


title: 200014638C  mouse cortex, trisomic Ts65Dn, treated with lamivudine

value: Cortex


title: AKI46, miRNA

value: Biopsy

value: OCT at -80C


title: 200014637HC mouse hippocampus, trisomic Ts65Dn, treated with lamivudine

value: Hippocampus

value: Lamivudine


title: 200032616C mouse cortex, trisomic Ts65Dn, non-treated

value: Non treated


title: 293T, ZBTB9-KO, DMSO 24h, rep2

description:
ZBTB9KO_WT_2
ZBTB9_ecMatrix.csv
ZBTB9_ecMetaData.csv


title: mRNA_mESC_WT_Control_Label_Rep1

value: mESC

value: Mouse embryonic stem cells

value: WT


title: 200014637C  mouse cortex, trisomic Ts65Dn, treated with lamivudine


title: AKI34, miRNA

value: AKI

value: Bulk


title: 200014639C  mouse cortex, wild-type, treated with lamivudine


title: 190022706HC mouse hippocampus, trisomic Ts65Dn, treated with lamivudine


title: 293T, ZBTB9-KO, DMSO 24h, rep1

description:
ZBTB9KO_WT_1
ZBTB9_ecMatrix.csv
ZBTB9_ecMetaData.csv

value: HEK 293T - ZBTB9 KO

value: Kidney


title: mRNA_mESC_WT_Control_Ctrl_Rep2


title: 293T, K116A-Overexpressed, 1 Dox 48h, rep3

description:
P402_DOX_3
ZBTB3_ecMatrix.csv
ZBTB3_ecMetaData.csv

value: HEK 293T - ZBTB3 KO

value: 1 Dox


title: 190022706C  mouse cortex, trisomic Ts65Dn, treated with lamivudine


title: mRNA_mESC_WT_Control_Ctrl_Rep1

value: control


title: AKI30, miRNA


title: AKI3, miRNA

value: Male


title: AKI29, miRNA


title: 190022697C mouse cortex, wild-type, treated with lamivudine

value: Cortex


title: mRNA_mESC_D6_Label_Rep2

value: TET2 oxidation and AI Labeling

value: polyA RNA


title: 293T, K116A-Overexpressed, DMSO 48h, rep2

description:
P402_DMSO_2
ZBTB3_ecMatrix.csv
ZBTB3_ecMetaData.csv

value: DMSO


title: 190022697HC  mouse hippocampus, wild-type, treated with lamivudine

value: Hippocampus

value: Lamivudine


title: mRNA_mESC_D6_Label_Rep1

value: mESC


title: mRNA_mESC_D6_Ctrl_Rep2

value: Mouse embryonic stem cells


title: 190021821HC  mouse hippocampus, wild-type, treated with lamivudine

value: WT


title: 293T, K116A-Overexpressed, DMSO 48h, rep3

description:
P402_DMSO_3
ZBTB3_ecMatrix.csv
ZBTB3_ecMetaData.csv


title: mRNA_mESC_D6_Ctrl_Rep1


title: 293T, K116A-Overexpressed, DMSO 48h, rep1

description:
P402_DMSO_1
ZBTB3_ecMatrix.csv
ZBTB3_ecMetaData.csv


title: AKI23, miRNA

value: AKI

value: Biopsy

value: OCT at -80C


title: 190021820HC  mouse hippocampus, wild-type, treated with lamivudine

description:
Expression_Profile.mm10.gene_raw_counts.xlsx
LINE1_raw_counts.txt


title: 293T, K116A-Overexpressed, 1 Dox 48h, rep1

description:
P402_DOX_1
ZBTB3_ecMatrix.csv
ZBTB3_ecMetaData.csv

value: Kidney


title: mRNA_mESC_WT/D0_Label_Rep2


title: AKI32, miRNA

value: Bulk


title: 190021820C mouse cortex, wild-type, treated with lamivudine


title: AKI25, miRNA


title: 293T, K116A-Overexpressed, 1 Dox 48h, rep2

description:
P402_DOX_2
ZBTB3_ecMatrix.csv
ZBTB3_ecMetaData.csv

value: HEK 293T - ZBTB3 KO

value: 1 Dox


title: 293T, K116A-Overexpressed, 1 Dox 24h, rep3

description:
p402_1_3
ZBTB3_ecMatrix.csv
ZBTB3_ecMetaData.csv


title: mRNA_mESC_WT/D0_Label_Rep1


title: 293T, K116A-Overexpressed, 1 Dox 24h, rep2

description:
p402_1_2
ZBTB3_ecMatrix.csv
ZBTB3_ecMetaData.csv


title: mRNA_mESC_WT/D0_Ctrl_Rep2

value: control


title: 190017769HC mouse hippocampus, trisomic Ts65Dn, treated with lamivudine


title: 190021821C mouse cortex, wild-type, treated with lamivudine

value: Cortex


title: AKI14, miRNA

value: Male


title: 293T, K116A-Overexpressed, 1 Dox 24h, rep1

description:
p402_1_1
ZBTB3_ecMatrix.csv
ZBTB3_ecMetaData.csv


title: 190017769C mouse cortex, trisomic Ts65Dn, treated with lamivudine


title: 293T, K116A-Overexpressed, 0.1 Dox 24h, rep3

description:
p402_01_3
ZBTB3_ecMatrix.csv
ZBTB3_ecMetaData.csv

value: 0.1 Dox


title: AKI13, miRNA

value: Female


title: AKI24, miRNA


title: Kyp ATACseq Rep2

city: Paris

first: Jing

last: An

address: 630 Rue Noetzlin

country: France

institute: Universite Paris Saclay

description: Bio rep 2

data_processing:
Adapters trimming: Sequencing reads were trimmed with trimmomatic with the following command "java -jar trimmomatic-0.38.jar SE -threads $NB_CORE $input $output ILLUMINACLIP:TruSeq3-SE.fa:2:30:10 LEADING:5 TRAILING:5 MINLEN:30"
Read mapping: Trimmed reads were mapped using bowtie2 v 2.3.5 with the following setting "bowtie2 --very-sensitive" against the genome of SollycM82_v1.0.
Quality filtering: mapped reads were filtered with samtools v.1.9 with the command "samtools view -h -b -q 30 " to remove reads of quality under 30
Duplicate filtering: duplicated reads were removed with samtools v.1.9 with the commands "samtools fixmate -m"  and "samtools markdup -r "
Bigwig generation: read density was scored with s3norm with the default parameters
Assembly: SollycM82_v1.0
Supplementary files format and content: s3norm normalized bigwigs

organism: Solanum lycopersicum

source_name: Leaf

growth_protocol: Plants were grown in pots in growth chambers at 24 °C under long-day (16 h of light) conditions.

extract_protocol:
Approximately 100 mg of 4-weeks-old tomato fourth leaves were ground, passed through a 100 µm filter and the nuclei were isolated using nuclei isolation buffer (0.25M sucrose, 10mM Tris-HCl pH8, 10mM MgCl2, 1% Triton X-100, 5mM 2-mercapto-ethanol, 0.1 mM  protease inhibitors). The nuclei were re-suspended in 2× TD buffer (20 mM Tris-HCl pH 7.6, 10 mM MgCl2, Dimethyl Formamide 20%) and 2.5 µl of Tn5 transposase (Illumina FC-121-1030) were added. Transposition reaction was performed at 37 °C for 30 min, and DNA was purified using a Qiagen MinElute Kit (QIAGEN, Cat.No.28004).
DNA libraries were amplified for a total of 10 cycles as described by Buenrostro et al. (Nat Methods.2013) and Jegu et al. (Genome Biol. 2017). DNA libraries were checked for quality and quantified using a 2100 Bioanalyzer (Agilent) and subjected to 2 × 75 bp high-throughput sequencing by NextSeq 500 (Illumina).

value: Kyp

value: Leaf

value: Non

tag: cultivar


title: Kyp ATACseqRep1

description: Bio rep 1


title: 190017768HC mouse hippocampus, trisomic Ts65Dn, treated with lamivudine

value: Hippocampus

value: Lamivudine


title: mRNA_mESC_WT/D0_Ctrl_Rep1

value: mESC

value: Mouse embryonic stem cells

value: WT

value: polyA RNA


title: 293T, K116A-Overexpressed, 0.1 Dox 24h, rep1

description:
p402_01_1
ZBTB3_ecMatrix.csv
ZBTB3_ecMetaData.csv

value: Kidney


title: M82 ATACseq Rep2

description: Bio rep 2


title: 190017764HC  mouse hippocampus, wild-type, treated with lamivudine


title: GMP_atac.3

city: St Louis

first: Jeffery

last: Magee

state: Missouri

address: 660 South Euclid Ave

institute: Washington University In St Louis

description: ATAC-Seq

data_processing:
Sequencing reads were demultiplexed and aligned to mouse genome (mm10) by bowtie2 (versoin 2.2.6)
Signal strength relative to the control samples were generated using MACS2.
Optimal set of peaks were generated using the Kundaje lab ATAC-seq and DNase-seq processing pipeline (https://github.com/kundajelab/atac_dnase_pipelines, version 0.33)
genome build/assembly: GRCm38/mm10
processed data files format and content: bigwig, narrowPeak

source_name: bone marrow

extract_protocol:
per Corces et al., Nature Methods 14:959
tagmentation with Tn5 transposase

value: bone marrow

value: GMP

value: wildtype


title: 293T, K116A-Overexpressed, 0.01 Dox 24h, rep3

description:
p402_001_3
ZBTB3_ecMatrix.csv
ZBTB3_ecMetaData.csv

value: HEK 293T - ZBTB3 KO


title: 190017764C mouse cortex, wild-type, treated with lamivudine

value: Cortex


title: M82 ATACseq Rep1

description: Bio rep 1


title: GMP_atac.2

description: ATAC-Seq


title: AKI2, miRNA

value: AKI

value: Biopsy

value: Bulk

value: OCT at -80C


title: 190017740HC  mouse hippocampus, wild-type, treated with lamivudine


title: GMP_atac.1

description: ATAC-Seq


title: 190017768C mouse cortex, trisomic Ts65Dn, treated with lamivudine


title: 293T, K116A-Overexpressed, 0.1 Dox 24h, rep2

description:
p402_01_2
ZBTB3_ecMatrix.csv
ZBTB3_ecMetaData.csv

value: 0.1 Dox


title: HiC_Kyp_rep2

data_processing:
Adapters trimming: Sequencing reads were trimmed with trimmomatic with the following command "java -jar trimmomatic-0.38.jar PE $input1 $input2 $output1Paired $output1Unpaired $output2Paired $output2Unpaired ILLUMINACLIP:TruSeq3-PE.fa:2:30:10 LEADING:5 TRAILING:5 MINLEN:30"
Read mapping: Trimmed reads were mapped using HiC-Pro v 2.11.4 with the following setting "BOWTIE2_GLOBAL_OPTIONS = --very-sensitive -L 30 --score-min L,-0.6,-0.6 --end-to-end --reorder BOWTIE2_LOCAL_OPTIONS =  --very-sensitive -L 20 --score-min L,-0.6,-0.6 --end-to-end --reorder GENOME_FRAGMENT = SollycM82_v1.0_dpnii.bed" against the genome of SollycM82_v1.0.
Assembly: SollycM82_v1.0
Supplementary files format and content: allValidPairs.txt files for generating contact matrices

extract_protocol:
In situ Hi-C experiments were performed according to Concia et al (2020) using DpnII and DdeI enzyme (New England Biolabs).
DNA libraries were prepared using NEBNext Ultra II DNA library preparation kit (NEB) according to the manufacturer’s instructions (10 cycles for the PCR amplification step). DNA libraries were checked for quality and quantified using a 2100 Bioanalyzer (Agilent) and the libraries were subjected to 2 × 75 bp high-throughput sequencing by NextSeq 500 (Illumina).

value: Kyp mutant

value: Leaf

value: Normal condition

tag: bio rep

value: Bio rep 2


title: HiC_Kyp_rep1

tag: treatment

value: Bio rep 1


title: AKI12, miRNA

value: Female


title: 190017740C mouse cortex, wild-type, treated with lamivudine

value: WT

value: Lamivudine


title: 293T, K116A-Overexpressed, DMSO, rep3

description:
p402_DMSO_3
ZBTB3_ecMatrix.csv
ZBTB3_ecMetaData.csv

tag: cell type

value: Kidney

value: DMSO


title: 190017738HC  mouse hippocampus, wild-type, treated with lamivudine

value: Hippocampus


title: Canine donor 4, expanded, scRNAseq

description: 10x Genomics

organism: Canis lupus familiaris

value: Peripheral Blood

value: primary canine iNKT

value: iNKT cells

value: mixed canine breed, healthy, female

value: 6 year old

value: Expanded


title: Canine donor 3, expanded, scRNAseq

description: 10x Genomics

value: 4 year old


title: HiC_M82_rep2

value: Leaf


title: 190017738C mouse cortex, wild-type, treated with lamivudine

value: Cortex


title: 293T, K116A-Overexpressed, DMSO, rep1

description:
p402_DMSO_1
ZBTB3_ecMatrix.csv
ZBTB3_ecMetaData.csv

value: HEK 293T - ZBTB3 KO


title: Canine donor 2, expanded, scRNAseq

description: 10x Genomics

value: 8 year old


title: 190017735HC  mouse hippocampus, wild-type, treated with lamivudine


title: HiC_M82_rep1

value: Normal condition

value: Bio rep 1


title: 293T, K116A-Overexpressed, 0.01 Dox 24h, rep2

description:
p402_001_2
ZBTB3_ecMatrix.csv
ZBTB3_ecMetaData.csv


title: 293T, ZBTB3-Overexpressed, 1 Dox 48h, rep3

description:
P401_DOX_3
ZBTB3_ecMatrix.csv
ZBTB3_ecMetaData.csv

value: ZBTB3 WT

value: 1 Dox


title: Canine donor 1, expanded, scRNAseq

description: 10x Genomics

value: mixed canine breed, healthy, male

value: 1 year old


title: M82 ChIP-seq_Input Rep1

data_processing:
Adapters trimming: Sequencing reads were trimmed with trimmomatic with the following command "java -jar trimmomatic-0.38.jar SE $input $output ILLUMINACLIP:TruSeq3-SE.fa:2:30:10 LEADING:5 TRAILING:5 MINLEN:30"
Read mapping: Trimmed reads data were mapped using bowtie2 v 2.3.5 with the following setting "bowtie2 --very-sensitive" against the genome of SollycM82_v1.0.
Filtering step: Mapped reads were filtered with samtools v.1.9 with the command "samtools view -h -b -q 30  "mapping_quality >= 30"
Duplicate filtering: duplicated reads were removed with samtools v.1.9 with the command "samtools fixmate -m  and samtools markdup -r "
Peak calling: peaks of read density were called with macs2 2.2.7.1 with the command "macs2 callpeak  -t sample.bam  -c Input.bam -g 829069930 -p 0.05 --extsize 150 --bw 500 -B -n --outdir (with respectively narrow or broad mode)
Bigwig generation: read density was scored with deeptools the default bamCoverage paramaters
Assembly: SollycM82_v1.0
Supplementary files format and content: Bamcoverage bigwig for plots generated with ComputeMatrix plotprofile of Deeptools

extract_protocol:
ChIP-seq assays were performed on 4-week-old tomato fourth branch of leaves according to Bio-protocol of Ramirez-Prado, J.S. et al (2021) by using aAnti-RNAPII (Abcam, ab26721), Anti-H3K4ac (Active Motif, 39382), Anti-H3K4me3 H3K4me3 (Millipore 07-473), Anti-H3K4me2 (active motif, 39142), Anti-H3K4me1 (active motif, 39300), Anti-H3K9ac (Millipore, 07-352), Anti-H3K9me2 (Abcam, ab1220), Anti-H3K14ac (Millipore, 07-353), Anti-H3K14me1 (Active Motif, 61510), Anti-H3K18ac (Millipore, 07-354), Anti-H3K23me3 (Active Motif, 61500), Anti-H3K23me1 (Active Motif, 39388), Anti-H3K27ac (Abcam, ab4729), Anti-H3K27me3 (Millipore 07-449), Anti-H3K27me2 (Abcam, 24684), Anti-H3K27me1 (Millipore, 07-488), Anti-H3K36ac (Active Motif, 39380), Anti-H3K36me3 (Abcam, ab9050), Anti-H3K56ac (Active Motif, 39282), Anti-H3K56me2 (Active Motif, 39278), Anti-H3K56me1 (Active Motif, 39274), Anti-H3K79ac (Active Motif, 39566), Anti-H4K5ac (Active Motif, 39700), Anti-H4K8ac (Active Motif, 61104), Anti-H4K12ac (Active Motif, 61531), Anti-H4K16ac (Active Motif, 39930), Anti-H4K20ac (Active Motif, 61531) antibodies.
ChIP-seq libraries were prepared from 10ng of DNA using NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB) according to manufacturer’s instructions. DNA libraries were checked for quality and quantified using an Agilent 2100 Bioanalyzer (Agilent) and subjected to 1 × 75 bp high-throughput sequencing by NextSeq 500 (Illumina).

value: WT

value: Non

tag: chip antibody


title: 190017735C mouse cortex, wild-type, treated with lamivudine

value: Lamivudine


title: 293T, K116A-Overexpressed, 0.01 Dox 24h, rep1

description:
p402_001_1
ZBTB3_ecMatrix.csv
ZBTB3_ecMetaData.csv

value: Kidney


title: 190017325HC  mouse hippocampus, wild-type, treated with lamivudine

value: Hippocampus


title: 293T, ZBTB3-Overexpressed, 1 Dox 48h, rep2

description:
P401_DOX_2
ZBTB3_ecMatrix.csv
ZBTB3_ecMetaData.csv


title: 293T, ZBTB3-Overexpressed, 1 Dox 48h, rep1

description:
P401_DOX_1
ZBTB3_ecMatrix.csv
ZBTB3_ecMetaData.csv


title: Canine donor 3, baseline, scRNAseq

description: 10x Genomics

value: Peripheral Blood

value: primary canine iNKT

value: iNKT cells

tag: strain

value: mixed canine breed, healthy, female

value: Freshly isolated


title: M82 ChIP-seq_H3K56me1 Rep1

value: Leaf


title: Canine donor 4, baseline, scRNAseq

description: 10x Genomics

value: 6 year old


title: HiC_M82_rep3

value: Normal condition

value: Bio rep 3


title: 190017325C mouse cortex, wild-type, treated with lamivudine

description:
Expression_Profile.mm10.gene_raw_counts.xlsx
LINE1_raw_counts.txt

value: Cortex


title: Canine donor 2, baseline, scRNAseq

description: 10x Genomics

value: 8 year old


title: 293T, K116A-Overexpressed, DMSO, rep2

description:
p402_DMSO_2
ZBTB3_ecMatrix.csv
ZBTB3_ecMetaData.csv

value: HEK 293T - ZBTB3 KO

value: DMSO

tag: time


title: 293T, ZBTB3-Overexpressed, DMSO 48h, rep3

description:
P401_DMSO_3
ZBTB3_ecMatrix.csv
ZBTB3_ecMetaData.csv

value: ZBTB3 WT


title: 190017324HC mouse hippocampus, trisomic Ts65Dn, treated with lamivudine

value: Lamivudine


title: Canine donor 1, baseline scRNAseq

description: 10x Genomics

value: mixed canine breed, healthy, male

tag: age

value: 1 year old


title: M82 ChIP-seq_H3K27me1 Rep1

value: WT

value: Non

value: Bio rep 1


title: 293T, ZBTB3-Overexpressed, DMSO 48h, rep2

description:
P401_DMSO_2
ZBTB3_ecMatrix.csv
ZBTB3_ecMetaData.csv

value: Kidney


title: 190017324C mouse cortex, trisomic Ts65Dn, treated with lamivudine


title: M82 ChIP-seq_H3K23me1 Rep1


title: 293T, ZBTB3-Overexpressed, DMSO 48h, rep1

description:
P401_DMSO_1
ZBTB3_ecMatrix.csv
ZBTB3_ecMetaData.csv


title: 293T, ZBTB3-Overexpressed, 1 Dox 24h, rep3

description:
p401_1_3
ZBTB3_ecMatrix.csv
ZBTB3_ecMetaData.csv

value: 1 Dox


title: M13-3

city: Montreal

first: Sylvain

last: Meloche

state: Quebec

address: 2950, Chemin de Polytechnique

country: Canada

institute: Institute of Research in Immunology and Cancer

data_processing:
Basecalls performed using Illumina RTA 2.4.11.
Samples demultiplexed using bcl2fastq 2.20 allowing 1 mismatch in the index.
Sequenced reads were trimmed for sequencing adapters and low quality extremities and mapped to the reference genome using STAR version 2.5.1b
Readcounts were computed by STAR during sequence alignment based on gene annotations from Gencode version M23 (based on Ensembl 98)
Expression values were also computed using RSEM version 1.2.28 based on Gencode version M23
Assembly: GRCm38
Supplementary files format and content: Readcounts: Tab-delimited file where columns are Ensembl gene identifier, counts for unstranded RNA, counts for 1st strand aligned, counts for 2nd strand aligned
Supplementary files format and content: RSEM: Tab-delimited file where columns correspond to a standard RSEM output for gene values (first line identifies the column)

source_name: Cells isolated from liver tumor expressing Yes Y537F

growth_protocol: Primary hepatocytes were isolated from C57BL/6J mice according to standard protocols. HepYF-M13 cells were established from micro-dissected liver tumors 5-7 months after hydrodynamic injection of constitutively activated Yes Y537F mutant. Cell lines were established after passaging the cells 4 to 5 times over a period of 4 to 6 weeks.

extract_protocol:
Total RNA was isolated using TRIzol (Invitrogen) + RNeasy mini kit (Qiagen, #74106)
ssRNA-seq; cDNA libraries were prepared from total RNA using a PolyA selection and the KAPA RNA Hyperprep Kit and were further amplified for sequencing.

treatment_protocol: Cells were maintained in DMEM supplemented with 10% fetal bovine serum and antibiotics.

value: Liver tumor


title: M82 ChIP-seq_H3K56me2 Rep1

value: Leaf


title: 180061596HC  mouse hippocampus, wild-type, treated with lamivudine

value: Hippocampus


title: 180061596C mouse cortex, wild-type, treated with lamivudine


title: M82 ChIP-seq_H3K14me1 Rep1


title: M82 ChIP-seq_H3K9me2 Rep1


title: M13-2


title: M13-1


title: AKI10, miRNA

tag: disease

value: AKI

value: Biopsy

value: Bulk

value: OCT at -80C

value: Female


title: 293T, ZBTB3-Overexpressed, 1 Dox 24h, rep2

description:
p401_1_2
ZBTB3_ecMatrix.csv
ZBTB3_ecMetaData.csv

value: HEK 293T - ZBTB3 KO

value: ZBTB3 WT


title: M82 ChIP-seq_H3K27me3 Rep1


title: Hep-3

source_name: Primary murine hepatocytes

value: Liver

value: hepatocytes C57BL/6J mice

tag: strain background


title: 180060242C mouse cortex, wild-type, treated with lamivudine

value: Cortex

value: WT

value: Lamivudine


title: 293T, ZBTB3-Overexpressed, 1 Dox 24h, rep1

description:
p401_1_1
ZBTB3_ecMatrix.csv
ZBTB3_ecMetaData.csv

value: Kidney


title: M82 ChIP-seq_H3K27me2 Rep1

value: Non

value: Bio rep 1


title: Hep-2


title: M82 ChIP-seq_H4K20ac Rep1

value: Leaf


title: 180060241HC  mouse hippocampus, wild-type, treated with lamivudine

value: Hippocampus


title: 293T, ZBTB3-Overexpressed, 0.1 Dox 24h, rep2

description:
p401_01_2
ZBTB3_ecMatrix.csv
ZBTB3_ecMetaData.csv

value: 0.1 Dox


title: 293T, ZBTB3-Overexpressed, 0.1 Dox 24h, rep3

description:
p401_01_3
ZBTB3_ecMatrix.csv
ZBTB3_ecMetaData.csv


title: M82 ChIP-seq_H4K16ac Rep1


title: 180060241C mouse cortex, wild-type, treated with lamivudine


title: 180060240HC  mouse hippocampus, wild-type, treated with lamivudine


title: 293T, ZBTB3-Overexpressed, 0.1 Dox 24h, rep1

description:
p401_01_1
ZBTB3_ecMatrix.csv
ZBTB3_ecMetaData.csv


title: M82 ChIP-seq_H4K12ac Rep1


title: TERT-del-US-h_RNAseq_rep4

city: Stanford

first: Kazuteru

last: Hasegawa

address: Lorry Lokey Stem Cell Research Building (SIM1), G2165 265 Campus Drive

institute: Stanford University

description:
TERT-CreER/flox-4
processed data file: RNAseq_CountTable.xlsx
processed data file: FLOXvsWT_results.csv

data_processing:
Paired-end 75bp RNA-seq reads were quality trimmed using Trim_Galore.
Trimmed paired reads were aligned to the mm10 mouse genome build using command line versions of TopHat v2.0.4 and Bowtie2 v2.0.0-6.
Subsequent data processing and analysis from the transcriptomes was performed in the R software. For analysis in DESeq2, .bam files output from Bowtie were used to generate a matrix of genomic features and read counts using the GenomicRanges and GenomicFeatures packages available from Bioconductor. A transcript annotation file was generated from the UCSC database and counts for each gene were summed from reads aligning to gene exons.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: RNAseq_CountTable.xlsx
Supplementary_files_format_and_content: FLOXvsWT_results.csv

source_name: Undifferentiated spermatogonia

extract_protocol:
Total RNA was treated with DNase and purified using columns.
Libraries were constructed using SMARTer® Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian (Takara Bio).

treatment_protocol: Eight- to twelve-week-old mice were injected with tamoxifen. At day 7, MCAM-high:KIT-: Tdtomato+ cells were sorted into Trizol reagent.

value: 8-12 weeks

value: Spermatogonial stem cells

tag: time point

value: 7 days after tamoxifen injection

tag: marker expression


title: TERT-del-US-h_RNAseq_rep3

description:
TERT-CreER/flox-3
processed data file: RNAseq_CountTable.xlsx
processed data file: FLOXvsWT_results.csv


title: 293T, ZBTB3-Overexpressed, 0.01 Dox 24h, rep3

description:
p401_001_3
ZBTB3_ecMatrix.csv
ZBTB3_ecMetaData.csv


title: M82 ChIP-seq_H4K8ac Rep1


title: TERT-del-US-h_RNAseq_rep2

description:
TERT-CreER/flox-2
processed data file: RNAseq_CountTable.xlsx
processed data file: FLOXvsWT_results.csv


title: 180060240C mouse cortex, wild-type, treated with lamivudine


title: 180060242HC  mouse hippocampus, wild-type, treated with lamivudine


title: 180058460HC  mouse hippocampus, wild-type, treated with lamivudine


title: M82 ChIP-seq_H4K5ac Rep1


title: 293T, ZBTB3-Overexpressed, 0.01 Dox 24h, rep1

description:
p401_001_1
ZBTB3_ecMatrix.csv
ZBTB3_ecMetaData.csv


title: M82 ChIP-seq_H3K79ac Rep1


title: Hep-1


title: 180058460C mouse cortex, wild-type, treated with lamivudine


title: TERT-hetero-US-h_RNAseq_rep3

description:
TERT-CreER/+-3
processed data file: RNAseq_CountTable.xlsx
processed data file: FLOXvsWT_results.csv


title: 180058459HC mouse hippocampus, trisomic Ts65Dn, treated with lamivudine

description:
Expression_Profile.mm10.gene_raw_counts.xlsx
LINE1_raw_counts.txt


title: 293T, ZBTB3-Overexpressed, DMSO, rep2

description:
p401_DMSO_2
ZBTB3_ecMatrix.csv
ZBTB3_ecMetaData.csv

value: DMSO


title: 293T, ZBTB3-Overexpressed, DMSO, rep3

description:
p401_DMSO_3
ZBTB3_ecMatrix.csv
ZBTB3_ecMetaData.csv

value: HEK 293T - ZBTB3 KO


title: M82 ChIP-seq_H3K36me3 Rep1


title: M82 ChIP-seq_H3K56ac Rep1


title: TERT-hetero-US-h_RNAseq_rep2

description:
TERT-CreER/+-2
processed data file: RNAseq_CountTable.xlsx
processed data file: FLOXvsWT_results.csv


title: 293T, ZBTB3-Overexpressed, DMSO, rep1

description:
p401_DMSO_1
ZBTB3_ecMatrix.csv
ZBTB3_ecMetaData.csv

value: ZBTB3 WT


title: M82 ChIP-seq_H3K36ac Rep1


title: 293T, ZBTB3-Overexpressed, 0.01 Dox 24h, rep2

description:
p401_001_2
ZBTB3_ecMatrix.csv
ZBTB3_ecMetaData.csv


title: 293T, ZBTB3-KO, 1 Dox 48h, rep3

description:
Z3KO_DOX_3
ZBTB3_ecMatrix.csv
ZBTB3_ecMetaData.csv

value: 1 Dox


title: AKI36, miRNA

value: AKI

tag: tissue source

value: Biopsy

tag: segment

value: Bulk

tag: storage

value: OCT at -80C


title: M82 ChIP-seq_H3K27ac Rep1

tag: genotype

value: WT

tag: tissue


title: 180055640C  mouse cortex, wild-type, treated with lamivudine

value: Cortex

value: Lamivudine


title: 180055640HC mouse hippocampus, wild-type, treated with lamivudine


title: 22-25 mm Adult Calvaria, ecadYFPdepleted, DAPI neg

first: Claire

last: Arata

email: carata@usc.edu, clairearata@gmail.com

address: 1425 San Pablo St

department: Stem Cell

institute: University of Southern California

description: 10x Genomics

data_processing:
Data analysis was performed with Seurat version 4.1.1, and datasets were filtered by nFeature_RNA > 200, nFeature_RNA < 2500, and percent.mt < 25. Filtered cells were normalized with SCTransform and datasets were integrated based on the tutorial “Integration and Label Transfer” from Seurat (https://satijalab.org/seurat/archive/v3.0/integration.html). The data were processed using the FindNeighbors() and FindClusters() functions and data were visualized with UMAP (30 principal components). The osteogenic subset of the integrated Seurat object was converted into a Monocle cell dataset and Monocle was performed following the Monocle3 recommended parameters (https://cole-trapnell-lab.github.io/monocle3/docs/trajectories/#learn-graph).
Assembly: GRCz11
Supplementary files format and content: Tab-separated values files, matrix files and rds files

organism: Danio rerio

source_name: calvaria

growth_protocol: The Institutional Animal Care and Use Committee of the University of Southern California approved all animal experiments (Protocol 20771). Zebrafish embryos (Danio rerio) were raised in embryo media at 28.5°C. For adults, in the institute vivarium according to Protocol 20771.

extract_protocol:
We dissected the calvaria from 20 juvenile (9-11mm) from ecad:YFP (one dataset) or sp7:GFP (one dataset), and separately 10 adult (22-25 mm) ecad:YFP (one dataset) or Tubingen (one dataset), fish away from brain tissue in Ringer’s solution. 9-11 mm stages Calvaria were mechanically minced with a razor and all tissue was transferred to a 1.5 mL tube for enzymatic dissociation (0.25% trypsin (Life Technologies, 15090-046), 1 mM EDTA, and 400 mg/mL Collagenase D (Sigma, 11088882001) in PBS). Tissue was incubated on a nutator at 28.5 °C for ~45 min and the enzymatic reaction was stopped by adding 6X stop solution (6 mM CaCl2 and 30% fetal bovine serum (FBS) in PBS).  Cells were pelleted by centrifugation (300 g) at 4 °C, rinsed in suspension media (1% FBS, 0.8 mM CaCl2 (Sigma-Aldrich, St. Louis, MO) in phenol red-free Leibovitz’s L15 medium (Life Technologies)), and resuspended in a final volume of 500 uL. DAPI was added to the resuspended cells, and cells were fluorescence-activated cell sorted (FACS) to isolate live cells that were DAPI negative and when applicative, ecad:YFP/sp7:GFP negative to deplete epithelial cells.
scRNAseq libraries were prepared using 10X Genomics Chromium Single Cell 3′ Library and Gel Bead Kit v.2 according to the manufacturer’s instructions and sequenced using Illumina NextSeq or HiSeq machines at a depth of at least 50,000 reads per cell for each library. Juvenile and adult stages were performed in replicates, and sequenced data was aligned using Cellranger v3.0.0 from 10X Genomics against the GRCz11 genome. All parameters were set to their default values.

value: various

value: calvaria

value: adult (22-25 mm)

value: tubingen


title: M82 ChIP-seq_H3K23me3 Rep1

tag: cultivar

value: Leaf

value: Non

value: Bio rep 1


title: 293T, ZBTB3-KO, 1 Dox 48h, rep2

description:
Z3KO_DOX_2
ZBTB3_ecMatrix.csv
ZBTB3_ecMetaData.csv

tag: cell line

value: HEK 293T - ZBTB3 KO

value: Kidney


title: TERT-del-US-h_RNAseq_rep1

description:
TERT-CreER/flox-1
processed data file: RNAseq_CountTable.xlsx
processed data file: FLOXvsWT_results.csv

value: 8-12 weeks

value: Spermatogonial stem cells

value: 7 days after tamoxifen injection


title: 9-11 mm Juvenile Calvaria, ecadYFPdepleted, DAPI neg

description: 10x Genomics

value: juvenile (9-11 mm)


title: AAV_VGF_6

city: Hamburg

first: Marcel

middle: Seungsu

last: Woo

state: Hamburg

address: Falkenried 94

department: Neurology

country: Germany

institute: UKE

data_processing:
STAR v.2.4 alignment to genome
featurCounts v.1.5.1 for gene loci counting
DESeq2 for differential expression analysis
Assembly: GRCm38 - mm10
Supplementary files format and content: tab-delimited text file including raw gene counts of every sample

source_name: Neuronal culture

growth_protocol: Neuronal cultures were grown in PNGM (LONZA) medium.

extract_protocol: RNA was harvested using Rneasy mini plus kit (Qiagen)

treatment_protocol: Neurons were transduced at DIV7 with AAVs harboring EGFP or VGF.

value: Neuronal culture

value: VGF overexpression


title: 293T, ZBTB3-KO, 1 Dox 48h, rep1

description:
Z3KO_DOX_1
ZBTB3_ecMatrix.csv
ZBTB3_ecMetaData.csv

value: ZBTB3 WT

tag: treatment

value: 1 Dox


title: AAV_VGF_5

tag: cell type


title: M82 ChIP-seq_H3K18ac Rep1

value: WT

tag: chip antibody

tag: bio rep


title: TERT-hetero-US-h_RNAseq_rep4

description:
TERT-CreER/+-4
processed data file: RNAseq_CountTable.xlsx
processed data file: FLOXvsWT_results.csv

tag: strain


title: UCEC.P20190911_T

city: Beijing

first: Yu

last: Yang

state: Beijing

address: Haidian District, Beijing Summer Palace Road No. 5

department: Academy for Advanced Interdisciplinary Studies

institute: Peking University

description:
10X
counts.mtx.gz
features.tsv
barcodes.tsv
meta.tsv.gz

data_processing:
For 10X data, Cell Ranger 3.0.0 was used to quantify gene expression level.
Assembly: GRCh38 for RNA expression
Supplementary files format and content: text files for expression matrices, cell metadata

source_name: Tumor

extract_protocol:
Tumors and adjacent normal tissues were cut into approximately 1-2 mm3 pieces in the RPMI-1640 medium (Gibco) with 10% fetal bovine serum (FBS, Gibco), and enzymatically digested with gentleMACS (Miltenyi) for 60 min on a rotor at 37°C, according to manufacturer’s instruction. The dissociated cells were subsequently passed through a 100 µm SmartStrainer and centrifuged at 400 g for 5 min. After the supernatant was removed, the pelleted cells were suspended in red blood cell lysis buffer (TIANDZ) and incubated on ice for 1-2 min to lyse red blood cells. After washing twice with 1× PBS (Gibco), the cell pellets were re-suspended in sorting buffer (PBS supplemented with 1% FBS).
10x Chromium Single cell 5’ Library
Single cell suspensions were stained with antibodies against CD45 and 7AAD for FACS sorting, performed on a BD Aria SORP instrument. Based on FACS analysis, single cells were sorted into 1.5 ml tubes (Eppendorf) and counted manually under the microscope. The concentration of single cell suspensions was adjusted to 500-1200 cells/ul. Cells were loaded between 7,000 and 15,000 cells/chip position using the 10x Chromium Single cell 5’ Library, Gel Bead & Multiplex Kit and Chip Kit (10x Genomics, V3 barcoding chemistry) according to the manufacturer’s instructions. All the subsequent steps were performed following the standard manufacturer’s protocols. Purified libraries were analyzed by an Illumina Hiseq X Ten sequencer with 150-bp paired-end reads.

value: Tumor

tag: patientid

tag: cancer type

value: UCEC


title: 293T, ZBTB3-KO, DMSO 48h, rep3

description:
Z3KO_DMSO_3
ZBTB3_ecMatrix.csv
ZBTB3_ecMetaData.csv

source_name: HEK 293T - ZBTB3 KO

value: DMSO

tag: time


title: 180058459C mouse cortex, trisomic Ts65Dn, treated with lamivudine

data_processing:
Sequence reads were trimmed for adaptors/low-quality sequences using Trimmomatic v0.38
Trimmed sequences were mapped to GrCM38/mm10 using HISAT v2.1.0 using recommended parameters
Read count extraction and normalization for genes were performed using StringTie v2.1.3b
Locus-specific quantification and read count extraction LINE-1 elements were performed using Telescope
Assembly: mm10
Supplementary files format and content: tab-delimited excel file includes raw gene counts for each sample
Supplementary files format and content: tab-delimited text file includes raw LINE1 counts for each sample

source_name: Cortex

extract_protocol:
Brain tissue was disaggregated using TissueLyser, and total RNA was extracted using RNeasy Plus Mini Kit protocol (Qiagen)
Total RNA samples were sent to Macrogen (South Korea) for library preparation and sequencing

value: Cortex

value: Lamivudine


title: 293T, ZBTB3-KO, DMSO 48h, rep2

description:
Z3KO_DMSO_2
ZBTB3_ecMatrix.csv
ZBTB3_ecMetaData.csv


title: M82 ChIP-seq_H3K14ac Rep1

value: Leaf

value: Non

value: Bio rep 1


title: UCEC.P20190911_N

source_name: Adjacent normal tissue

value: Adjacent normal tissue


title: AAV_VGF_4


title: TERT-hetero-US-h_RNAseq_rep1

description:
TERT-CreER/+-1
processed data file: RNAseq_CountTable.xlsx
processed data file: FLOXvsWT_results.csv

tag: age

value: 8-12 weeks

value: Spermatogonial stem cells

tag: time point


title: AAV_VGF_3


title: 293T, ZBTB3-KO, DMSO 48h, rep1

description:
Z3KO_DMSO_1
ZBTB3_ecMatrix.csv
ZBTB3_ecMetaData.csv

value: HEK 293T - ZBTB3 KO

value: Kidney


title: M82 ChIP-seq_H3K9ac Rep1


title: UCEC.P20190910_N


title: AAV_VGF_2

value: Neuronal culture

value: VGF overexpression


title: M82 ChIP-seq_H3K4me3 Rep1


title: UCEC.P20190717_N


title: UCEC.P20190910_T


title: 293T, ZBTB3-KO, 0.1 Dox 24h, rep3

description:
ZBTB3KO_01_3
ZBTB3_ecMatrix.csv
ZBTB3_ecMetaData.csv

value: ZBTB3 WT

value: 0.1 Dox


title: M82 ChIP-seq_H3K4me2 Rep1

value: WT


title: AAV_EGFP_6

value: EGFP overexpression


title: 293T, ZBTB3-KO, 0.1 Dox 24h, rep1

description:
ZBTB3KO_01_1
ZBTB3_ecMatrix.csv
ZBTB3_ecMetaData.csv


title: AAV_VGF_1


title: UCEC.P20190625_T

value: Tumor

value: UCEC


title: UCEC.P20190722_T


title: M82 ChIP-seq_H3K4ac Rep1


title: 293T, ZBTB3-KO, 0.1 Dox 24h, rep2

description:
ZBTB3KO_01_2
ZBTB3_ecMatrix.csv
ZBTB3_ecMetaData.csv


title: 293T, ZBTB3-KO, DMSO 24h, rep3

description:
ZBTB3KO_WT_3
ZBTB3_ecMatrix.csv
ZBTB3_ecMetaData.csv

value: DMSO


title: UCEC.P20190625_N


title: 293T, ZBTB3-KO, DMSO 24h, rep2

description:
ZBTB3KO_WT_2
ZBTB3_ecMatrix.csv
ZBTB3_ecMetaData.csv


title: AAV_EGFP_4


title: SR004262_Input

description: input chromatin

data_processing:
Sequencing reads were demultiplexed and aligned to mouse genome (mm10) by BWA with the ENCODE DCC TF/Histone ChIP-Seq pipeline (https://github.com/ENCODE-DCC/chip-seq-pipeline2, v1.1.6)
Signal strength relative to the control samples were generated using MACS2.
Broad peaks were called using MACS2, and overlapping peaks across pseudo-replicates were genereated using the same approach as that used by the ENCODE pipeline for overlap optimal peaks.
genome build/assembly: GRCm38/mm10
processed data files format and content: bigwig, broadPeak

extract_protocol:
HSCs and HPCs were soted and then fixed for chromatin isolation per Schmidl et l., Nature Methods 10:963.
Chipmentation - Chromatin isolation with the indicated antibody followed by tagmentation with Tn5 as per Schmidl et l., Nature Methods 10:963.

treatment_protocol: PBS or G-CSF 5 mcg daily x2 days

value: bone marrow

value: GMP

value: wildtype


title: AAV_EGFP_3


title: 293T, ZBTB3-KO, DMSO 24h, rep1

description:
ZBTB3KO_WT_1
ZBTB3_ecMatrix.csv
ZBTB3_ecMetaData.csv


title: UCEC.P20190312_T


title: SR004262_H3K27ac_wt_PBS.4

description: H3K27ac Chipmentation in mouse GMP

value: PBS vehicle control


title: AAV_EGFP_2


title: UCEC.P20190312_N

value: Adjacent normal tissue


title: 293T, WT, rep3

description:
HEK293T_WT_3
ZBTB3_ecMatrix.csv
ZBTB3_ecMetaData.csv

source_name: HEK 293T

value: HEK 293T


title: 293T, WT, rep2

description:
HEK293T_WT_2
ZBTB3_ecMatrix.csv
ZBTB3_ecMetaData.csv


title: M82 ChIP-seq_H3K4me1 Rep1

value: Leaf

value: Non

value: Bio rep 1


title: SR004262_H3K27ac_wt_PBS.2

description: H3K27ac Chipmentation in mouse GMP


title: AAV_EGFP_1

value: Neuronal culture


title: SR004262_H3K27ac_wt_PBS.3

description: H3K27ac Chipmentation in mouse GMP


title: AAV_EGFP_5


title: wt_PBS

data_processing:
Generation of fastq files via https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest
Alignment to mm10 genome build via cellranger v6.1.1 https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest
Assembly: mm10
Supplementary files format and content: barcodes.tsv, genes.tsv, matrix.mtx

source_name: Lineage negative, Kit positive bone marrow

extract_protocol: 10x Genomics Chromium single cell preparation 3' ver3.1

value: 8-10 week

value: control


title: SR004262_H3K27ac_wt_PBS.1

description: H3K27ac Chipmentation in mouse GMP


title: UCEC.P20190213_N


title: M82 ChIP-seq_Pol2 Rep1

value: WT


title: 293T, WT, rep1

description:
HEK293T_WT_1
ZBTB3_ecMatrix.csv
ZBTB3_ecMetaData.csv

value: Kidney


title: wt_GCSF

value: G-CSF


title: SR004262_H3K27ac_wt_GCSF.3

description: H3K27ac Chipmentation in mouse GMP

value: G-CSF x2 days


title: GS045

first: Richard

middle: A

last: Friedman

address: 1130 St. Nicholas Av

department: Medicine

institute: Columbia University Irving  Medical Center

data_processing:
RTA (Illumina) was used for base calling. bcl2fastq2 (version 2.19) to convert
from BCL to fastq format, coupled with adaptor trimming.
Peudoalignment was performed with Kallisto (Version 0.44.0 with ENSEMBL 96 annotation
Assembly: GRCh38.p12
Supplementary files format and content: txt file with number of reads for each gene

source_name: Human cardiomyocyte/fibroblast tissue model

extract_protocol:
Tissues were snap frozen in liquid nitrogen and stored at -80*C until use.
To isolate RNA, snap-frozen tissues were added to 300 mL of RNA lysis buffer
(Qiagen) with a stainless-steel bead (BioSpec, 11079123) and homogenized with
a Mini-Beadbeater (Biospec, C321001) for 5-10 seconds or until tissue samples
were not visible. RNA was then isolated using a Qiagen RNeasy Micro Kit
(Qiagen, 74004), according to manufacturer’s instructions.
RNA for each sample was then analyzed for quality/quantity using an
Agilent bioanalyzer, Qubit 2.0 at Columbia’s Molecular Pathology core.
cDNA amplification for Sequencing was performed the SMART-Seq® v4 Ultra® Low
Input RNA Kit (TaKaRa) for according to manufacturer's instructions. A library
was  prepared using the Nextera XT DNA Library Preparation kit (Illumina) with
100-150pg starting material, ccording to manufacturer's instructions. Libraries
were sequenced to a targeted depth of ~40M 100bp paired-end reads on a NovaSeq
6000

treatment_protocol:
The IgG antibody fraction was isolated from patient sera using the NAb Protein
A/G Spin Kit, (Thermo Fisher Scientific, cat. no. 89950), according to the
manufacturer’s protocol. Autoantibody purification from the patients’ sera
was performed.  0.5 mg/mL of the purified IgG was added to the culture medium on
day 14, with tissues stimulated at 2 Hz and maintained for an additional 14 days.
During this time, the frequency of electrical stimulation was stepwise increased
to 6 Hz by day 21 and decreased to 2 Hz thereafter and maintained until day 28.

tag: patient

value: antibody


title: ko_PBS

value: KO


title: GS044


title: UCEC.P20181122_T

value: Tumor

value: UCEC


title: ko_GCSF


title: SR004262_H3K27ac_wt_GCSF.2

description: H3K27ac Chipmentation in mouse GMP

value: bone marrow

value: GMP

value: wildtype


title: THCA.P20190816_T

value: THCA


title: GS043


title: SR004262_H3K27ac_wt_GCSF.1

description: H3K27ac Chipmentation in mouse GMP


title: UCEC.P20190305_N

value: Adjacent normal tissue


title: THCA.P20190816_N


title: SR004262_H3K27ac_ko_PBS.3

description: H3K27ac Chipmentation in mouse GMP

value: Kmt2c deleted

value: PBS vehicle control


title: GS042


title: THCA.P20190730_T


title: small_RNA_DM_mESC_Nsun6_KO_Label_Rep1

value: mESC

value: Mouse embryonic stem cells

value: Nsun6 knockout

value: TET2 oxidation and AI Labeling

tag: fraction

value: RNA fraction below 200 nt


title: GS041


title: SR004262_H3K27ac_ko_PBS.2

description: H3K27ac Chipmentation in mouse GMP


title: UCEC.P20190213_T


title: small_RNA_DM_mESC_Nsun6_KO_Ctrl_Rep2

value: control


title: THCA.P20190730_N


title: THCA.P20190703_T


title: GS040

value: antibody


title: SR004262_H3K27ac_ko_PBS.1

description: H3K27ac Chipmentation in mouse GMP


title: SR004262_H3K27ac_ko_GCSF.4

description: H3K27ac Chipmentation in mouse GMP

value: G-CSF x2 days


title: THCA.P20190621_T

value: Tumor


title: small_RNA_DM_mESC_Nsun6_KO_Ctrl_Rep1


title: small_RNA_DM_mESC_Nsun6_KO_Label_Rep2


title: small_RNA_DM_mESC_Nsun5_KO_Label_Rep2

value: Nsun5 knockout


title: SR004262_H3K27ac_ko_GCSF.3

description: H3K27ac Chipmentation in mouse GMP

value: bone marrow


title: GS039


title: THCA.P20190612_T


title: GS038


title: small_RNA_DM_mESC_Nsun5_KO_Label_Rep1


title: GS037


title: small_RNA_DM_mESC_Nsun5_KO_Ctrl_Rep2


title: GS036


title: SR004262_H3K27ac_ko_GCSF.2

description: H3K27ac Chipmentation in mouse GMP

value: GMP


title: SR004262_H3K27ac_ko_GCSF.1

description: H3K27ac Chipmentation in mouse GMP


title: THCA.P20190125_N


title: small_RNA_DM_mESC_Nsun3_KO_Label_Rep2

value: Nsun3 knockout


title: small_RNA_DM_mESC_Nsun3_KO_Label_Rep1


title: SR004262_H3K4me1_wt_PBS.3

description: H3K4me1 Chipmentation in mouse GMP

value: wildtype


title: SR004262_H3K4me1_wt_PBS.4

description: H3K4me1 Chipmentation in mouse GMP


title: small_RNA_DM_mESC_Nsun5_KO_Ctrl_Rep1


title: GS035


title: THCA.P20190122_T

value: THCA


title: THCA.P20190122_N

value: Adjacent normal tissue


title: GS033


title: small_RNA_DM_mESC_Nsun3_KO_Ctrl_Rep2


title: GS032


title: THCA.P20190118_N


title: GS031


title: SR004262_H3K4me1_wt_GCSF.4

description: H3K4me1 Chipmentation in mouse GMP


title: THCA.P20190612_N


title: small_RNA_DM_mESC_Nsun3_KO_Ctrl_Rep1


title: THCA.P20190125_T


title: SR004262_H3K4me1_wt_PBS.1

description: H3K4me1 Chipmentation in mouse GMP

value: PBS vehicle control


title: small_RNA_DM_mESC_Nsun2_KO_Label_Rep2

value: mESC

value: Nsun2 knockout


title: THCA.P20190108_N


title: GS029


title: GS030


title: SR004262_H3K4me1_wt_GCSF.3

description: H3K4me1 Chipmentation in mouse GMP


title: small_RNA_DM_mESC_Nsun2_KO_Label_Rep1

value: Mouse embryonic stem cells


title: SR004262_H3K4me1_wt_GCSF.2

description: H3K4me1 Chipmentation in mouse GMP


title: small_RNA_DM_mESC_Nsun2_KO_Ctrl_Rep2


title: GS034


title: THCA.P20181226_T


title: GS028


title: SR004262_H3K4me1_wt_GCSF.1

description: H3K4me1 Chipmentation in mouse GMP


title: RC.P20191223_T

value: RC


title: SR004262_H3K4me1_wt_PBS.2

description: H3K4me1 Chipmentation in mouse GMP


title: GS027


title: SR004262_H3K4me1_ko_PBS.4

description: H3K4me1 Chipmentation in mouse GMP

value: Kmt2c deleted


title: small_RNA_DM_mESC_Nsun2_KO_Ctrl_Rep1

value: control

value: RNA fraction below 200 nt


title: small_RNA_DM_mESC_Dnmt2_KO_Label_Rep2

value: Dnmt2 knockout

value: TET2 oxidation and AI Labeling


title: RC.P20191223_N


title: GS026

value: antibody


title: RC.P20191211_T

value: Tumor


title: THCA.P20190108_T


title: small_RNA_DM_mESC_Dnmt2_KO_Label_Rep1


title: SR004262_H3K4me1_ko_PBS.3

description: H3K4me1 Chipmentation in mouse GMP

value: bone marrow

value: GMP


title: GS025


title: small_RNA_DM_mESC_Dnmt2_KO_Ctrl_Rep2


title: GS024


title: SR004262_H3K4me1_ko_PBS.2

description: H3K4me1 Chipmentation in mouse GMP


title: SR004262_H3K4me1_ko_PBS.1

description: H3K4me1 Chipmentation in mouse GMP


title: small_RNA_DM_mESC_Dnmt2_KO_Ctrl_Rep1


title: GS023


title: SR004262_H3K4me1_ko_GCSF.4

description: H3K4me1 Chipmentation in mouse GMP

value: G-CSF x2 days


title: RC.P20191202_T


title: RC.P20191211_N


title: small_RNA_DM_mESC_Label_Rep2

value: WT


title: GS022


title: small_RNA_DM_mESC_Label_Rep1


title: GS021


title: RC.P20191023_T


title: SR004262_H3K4me1_ko_GCSF.3

description: H3K4me1 Chipmentation in mouse GMP


title: SR004262_H3K4me1_ko_GCSF.2

description: H3K4me1 Chipmentation in mouse GMP


title: RC.P20191023_N

value: Adjacent normal tissue


title: SR004262_H3K4me1_ko_GCSF.1

description: H3K4me1 Chipmentation in mouse GMP


title: small_RNA_DM_mESC_Ctrl_Rep1


title: small_RNA_DM_mESC_Ctrl_Rep2


title: RC.P20191021_T


title: GS020


title: SR004261_Input

description: input chromatin

value: HSC/MPP

value: wildtype


title: Wild-type zebrafish atrial cardiomyocytes, 72 hours post fertilization, rep 3

city: bad nauheim

first: Stefan

last: Günther

address: ludwigtr. 43

institute: MPI for heart and lung research

data_processing:
Trimmomatic version 0.39 was employed to trim reads after a quality drop below a mean of Q15 in a window of 5 nucleotides and keeping only filtered reads longer than 15 nucleotides (Bolger et al., Trimmomatic: a flexible trimmer for Illumina sequence data).
Reads were aligned versus Ensembl zebrafish genome version danRer11 (Ensembl release 104) with STAR 2.7.10a (Dobin et al., STAR: ultrafast universal RNA-seq aligner).
Alignments were filtered to remove: duplicates with Picard 3.0.0 (Picard: A set of tools (in Java) for working with next generation sequencing data in the BAM format), multi-mapping, ribosomal, or mitochondrial reads.
Gene counts were established with featureCounts 2.0.4 by aggregating reads overlapping exons excluding those overlapping multiple genes (Liao et al., featureCounts: an efficient general purpose program for assigning sequence reads to genomic features).
Assembly: danRer11
Supplementary files format and content: count matrix

source_name: embryonic heart

extract_protocol:
miRNeasy micro Kit (Qiagen), using low input DNase protocol
Approximately 1ng of total RNA was used as starting material for SMART®-Seq HT Kit (Takara Bio).

value: embryonic heart

value: cardiomyocyte

value: wild-type

value: 72 hours post fertilization


title: RC.P20191021_N

value: RC


title: GS018


title: GS019


title: SR004261_H3K27ac_wt_PBS.4

description: H3K27ac Chipmentation in mouse HSC/MPP

value: PBS vehicle control


title: RC.P20191202_N


title: RC.P20190925_T


title: Wild-type zebrafish atrial cardiomyocytes, 72 hours post fertilization, rep 2


title: SR004261_H3K27ac_wt_PBS.3

description: H3K27ac Chipmentation in mouse HSC/MPP


title: RC.P20190925_N


title: GS017


title: Wild-type zebrafish atrial cardiomyocytes, 72 hours post fertilization, rep 1


title: SR004261_H3K27ac_wt_PBS.1

description: H3K27ac Chipmentation in mouse HSC/MPP


title: Wild-type zebrafish atrial cardiomyocytes, 48 hours post fertilization, rep 1

value: 48 hours post fertilization


title: RC.P20190919_T


title: GS015


title: SR004261_H3K27ac_wt_GCSF.4

description: H3K27ac Chipmentation in mouse HSC/MPP


title: GS016


title: GS013


title: Wild-type zebrafish atrial cardiomyocytes, 48 hours post fertilization, rep 2


title: Wild-type zebrafish atrial cardiomyocytes, 48 hours post fertilization, rep 3


title: SR004261_H3K27ac_wt_GCSF.3

description: H3K27ac Chipmentation in mouse HSC/MPP


title: Human SyMSC, mix

city: Bunkyo-ku

first: Kentaro

last: Endo

state: Tokyo

address: 1-5-45 Yushima

country: Japan

institute: Institute of Science Tokyo

data_processing:
SOAPnuke v1.5.2
Remove the reads containing the adaptor, the reads whose N content is greater than 5%, and low-quality reads using SOAPnuke (parameter: -l 15 -q 0.2 -n 0.05).
Trimmed sequence reads were mapped to Rnor_6.0 using HISAT2 v2.0.4 (parameter: --sensitive --no-discordant --no-mixed -I 1 -X 1000 -p 8 --rna-strandness RF).
Read count extraction and normalization were performed using HISAT2.
Assembly: GCF_000001405.38_GRCh38.p12
Supplementary files format and content: Tab-delimited text files include TPM values for each sample

source_name: SyMSCs

extract_protocol:
Total RNA was extracted using RNeasy Mini Kit (QIAGEN, Hilden, German).
mRNA was isolated using oligo dT beads and fragmented. Single-strand cDNA was generated using random N6-primed reverse transcription, followed by a secondstrand cDNA with dUTP. After PCR amplification and DNA nanoball synthesis, the products were sequenced by BGISEQ-500.

value: SyMSCs

value: No treatment


title: GS012

value: antibody


title: RC.P20190919_N


title: RC.P20190918_T

value: Tumor


title: SR004261_H3K27ac_wt_GCSF.2

description: H3K27ac Chipmentation in mouse HSC/MPP

value: bone marrow


title: GS011


title: Human SyMSC, inj

value: Injected into rat OA knees


title: SR004261_H3K27ac_wt_GCSF.1

description: H3K27ac Chipmentation in mouse HSC/MPP

value: G-CSF x2 days


title: RC.P20190923_T


title: SR004261_H3K27ac_wt_PBS.2

description: H3K27ac Chipmentation in mouse HSC/MPP


title: RC.P20190923_N

value: Adjacent normal tissue


title: GS010


title: GS009


title: SR004261_H3K27ac_ko_PBS.4

description: H3K27ac Chipmentation in mouse HSC/MPP

value: HSC/MPP

value: Kmt2c deleted


title: Human AdMSC, inj

source_name: AdMSCs

value: AdMSCs


title: PACA.P20191204_T

value: PACA


title: SR004261_H3K27ac_ko_PBS.3

description: H3K27ac Chipmentation in mouse HSC/MPP


title: RC.P20181217_N


title: GS008


title: SR004261_H3K27ac_ko_PBS.2

description: H3K27ac Chipmentation in mouse HSC/MPP


title: mRNA_HEK293T_NSUN6_knockdown_Label_rep2

data_processing:
For batch paired-end reads of m5C-seq libraries, a sample-barcoded-sequence (Pos 1-6) and random-4-base (pos7-10) in Read1 and a 10nt unique molecular identifier (UMI) was included in the adaptor that ligates to the 3’end of cDNA so it locates in Read2 (Pos1-10). Firstly, m5C-seq batch libraries were demultiplexed into individual samples, using fastq-multx（with -m 1 parameters）that distributes reads into a sample FASTQ file(Read1.fq file and Read2.fq file) according to the sample-barcoded-sequence in Read1 (Pos 1-6). For every individual sample, only Read2 data with UMI was used for subsequent analyses. Illumina sequencing reads were first treated with trim_galore(version 0.6.4) for adapter removal and quality trimming. Work commands are as follows: trim_galore --fastqc --phred33 --length 30. We then used Seqkit (version 0.10.0) to deduplicate based on 10 bp UMI at the 5′ end of reads R2, key process parameters are as follows: seqkit rmdup -s. Finally, Fastp (version 0.23.2) was used to remove the 10 bp UMI in the deduplication read. 10 bases at the 3′ end of inserted sequences were also removed, using the key parameters: fastp -f 10 -t 10 -l 20.
Processed reads were mapped to reference genome (human GRCh19 reference / mouse mm10 reference) using HISAT2-3N (version 2.2.1-3n-0.0.3). The key parameters are as follows: hisat3n --base-change C,T --directional-mapping --repeat -p 20 -k 1. Considering a creditable m5C signal, the alignments are further filtering using python house-scripts, the alignments hosts >=3 C-to-T mismatches or >= 3 other type mismatches or the length of alignments < 20nt are filtered. Next, we parse BAM file using pysamstats (version 1.1.2), with commands as follow: pysamstats -D 100000 -S "nofilter" -t variation.
To identify the methyltransferase-dependent m5C sites, we calculated the C-to-T ratios for the m5C-TACseq-identified m5C sites in WT and all knockout/knockdown samples. Then, the fold change and difference of C-to-T ratio between KO/KD samples and WT/Control samples were calculated. For the identification of enzyme-dependent sites by comparing the KO and WT samples, the fold change in C-to-T ratio (KO sample/WT sample) was required to be less than 60% in two replicates, and the difference in C-to-T ratio (WT sample - KO sample) was required to be > 1.5%. Considering the presence of residual enzymes upon knockdown, to identify enzyme-dependent sites by comparing the KD and Control samples, the fold change in C-to-T ratio (KD sample/Control sample) was required to be less than 60% in at least one replicate.
The analysis of CLIP-seq data was performed using CLIP Tool Kit (CTK, v1.1.3). The processed reads were mapped to the mouse genome (Ensembl annotation of mm10) using hisat2 v2.2.1 with default settings.
Assembly: hg19(UCSC)/mm10(UCSC)/tRNA-referenece(tRNAdb)
Supplementary files format and content: tab-delimited text file includes every C base coverage and C-to-T signal
Supplementary files format and content: excel file,in xls file format
Library strategy: m5C-seq

source_name: cell line

value: cell line

value: human embryonic kidney cells

value: NSUN6 knockdown

value: TET2 oxidation and AI Labeling


title: GS007


title: SR004261_H3K27ac_ko_PBS.1

description: H3K27ac Chipmentation in mouse HSC/MPP

source_name: bone marrow

value: PBS vehicle control


title: mRNA_HEK293T_NSUN2_knockdown_Label_rep2

value: NSUN2 knockdown


title: GS006


title: PACA.P20191125_T


title: SR004261_H3K27ac_ko_GCSF.4

description: H3K27ac Chipmentation in mouse HSC/MPP


title: Human AdMSC, mix

value: No treatment


title: mRNA_HEK293T_NSUN2_knockdown_Label_rep1


title: PACA.P20190306_T


title: SR004261_H3K27ac_ko_GCSF.3

description: H3K27ac Chipmentation in mouse HSC/MPP


title: GS005

value: antibody


title: mRNA_HEK293T_shControl_Label_rep2

value: Control


title: RC.P20181224_N

value: RC


title: GS004


title: PACA.P20190225_T

value: Tumor


title: SR004261_H3K27ac_ko_GCSF.2

description: H3K27ac Chipmentation in mouse HSC/MPP

value: bone marrow

value: G-CSF x2 days


title: mRNA_HEK293T_shControl_Label_rep1


title: PACA.P20181128_T


title: SR004261_H3K27ac_ko_GCSF.1

description: H3K27ac Chipmentation in mouse HSC/MPP

value: HSC/MPP