title: Week2_Vehicle_IgG_Rep1

value: Mecp2 Flox; CreER

value: Vehicle

value: Week 2

value: 18 weeks

value: Normal Rabbit IgG Millipore #12-370, RRID:AB_145841; 1:125 dilution


title: scATAC_C3-AC-Control

status: Public on Dec 16 2024

type: SRA

city: Chicago

first: Yu

last: Zhao

state: IL

address: 5841 S. Maryland Ave

department: Section of Genetic Medicine, Department of Medicine

country: USA

institute: The University of Chicago

library_source: genomic single cell

data_processing:
scATAC-seq raw sequencing data were processed using the Cell Ranger ATAC 2.0.0, and the 10X human transcriptome GRCh38-2020-A-2.0.0 as the reference. Further filtering was conducted using ArchR(v.1.0.3). Only high quality individual cells are kept for downstream analysis (doublet filter ratio = 2.0, minimum fragments per cell = 5000, minimum TSS enrichment score = 6).
Assembly: hg38
Supplementary files format and content: Fragments files and tabix index of fragments files

molecule: genomic DNA

organism: Homo sapiens

source_name: ascending colon

extract_protocol:
Intact mucosal tissues were rinsed in 1.5 ml ice-cold PBS [Thermo Fisher 10010023] six times. Mucosal tissues from the same regions were combined and minced by iris scissors. Minced tissues were transferred to 2 ml fresh chelator solution (HBSS Ca/Mg-Free [Thermo Fisher 14175095], 10 mM EGTA [Fisher Scientific 50-255-956], 10 mM HEPES [Thermo Fisher 15630080], and 10% FBS [Gemini Bio 100-106]). The tissues were incubated at 37°C for 15 minutes with end-over-end rotation, then cooled on ice for 10 minutes. The epithelium was separated from lamina propria by mechanical agitation (shaking 20 times). Visualizing epithelial sheets in the solution, the supernatant was collected and spun down at 300g for 5 minutes at 4°C. The remnant tissue chunks were rinsed in ice-cold PBS and incubated in 2 ml enzyme solution (HBSS Ca/Mg-Free [Thermo Fisher 14175095], 10 mM HEPES [Thermo Fisher 15630080], 200 μg/ml Liberase TM [Millipore Sigma 5401127001] and DNase I [Gold Bio D-301-100]) at 37°C for 20 minutes. The spun-down epithelium was resuspended and incubated in 2 ml TrypLE express [Thermo Fisher 12605010], at 37°C for 5 minutes. Both incubations were applied with end-over-end rotation. Tissues were gently triturated with a P1000 pipette after incubations and no visible tissue chunks remained after trituration. Cells were filtered through a 40 μM cell strainer [Falcon/VWR 21008–949]. After filtration, epithelial cells and cells from lamina propria were combined and spun down at 300 g for 5 minutes at 4°C. Cell pellet from each region were resuspended in 200 μl cold wash buffer (HBSS Ca/Mg-Free [Thermo Fisher 14175095] and 10% FBS [Gemini Bio 100-106]). Cell suspension was then diluted by 2 ml lysis buffer [Miltenyi Biotec 130-094-183] and sat for 3 minutes at room temperature to eliminate red blood cells. Cells in suspensions were spun at 300g for 5 minutes at 4°C. Cell pellets were resuspended in 200 μl suspension buffer (PBS and 0.04% BSA [Miltenyi Biotec 130-091-376]) and assessed for density and viability with Trypan Blue [Thermo Fisher 15250061]. Only cell suspensions with >85% viability were used for downstream single cell assays.
Single nuclei were isolated from single cell suspensions following the manufacturer’s protocol for the Chromium Single cell ATAC (v 1.1). Briefly, single nuclei were transposed before loading to chip H. Transposed nuclei were partitioned into GEMS in Chromium controller. GEMs were incubated for barcoding, followed by fragment indexing. Approximately 8,000 single nuclei were transposed and loaded to a channel with a target recovery for 5,000 nuclei. Libraries were sequenced on Illumina NovaSeq 6000 platforms.

tag: tissue

value: ascending colon

tag: Sex

value: Male

tag: age

tag: disease

value: Control

tag: inflammation


title: T_2S_C

city: Houston

first: Amrit

last: Koirala

state: TX

address: 1 Baylor Plaza

institute: Baylor College of Medicine

description: Replicate C

library_source: transcriptomic

data_processing:
Sequenced reads were trimmed for adaptor sequence using TrimGalore
Reads were mapped to the UCSC zebrafish reference genome danRer11 using STAR
featureCounts was used to evaluate gene expression level as read counts
Assembly: Danio rerio GRCz11 (Ensembl Release 98)
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

molecule: polyA RNA

organism: Danio rerio

source_name: Zebrafish embryo explants

growth_protocol: Explants were cultured in explant media from their time of isolation from the embryo at approximately 3 hours post until collection

extract_protocol:
Total RNA was isolated using Trizol reagent, then purified by sodium acetate precipitation and eluted in 10 mM Tris pH7.5
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Explants of N and T conditions were isolated from embryos injected at the 1-cell stage with 10 pg ndr2 or 0.5 pg CA-acvr1b* mRNA, respectively

tag: condition

value: constitutively active Nodal receptor CA-acvr1b* (T)

tag: developmental stage

value: 2-somite (2S)

tag: approx time (hours post fertilization)

tag: stage index


title: CreER + TMX Week 4 Replicate 3 [Sample_95]

first: Sameer

middle: Subhash

last: Bajikar

address: 1250 Moursund St

department: Molecular and Human Genetics

data_processing:
Raw reads were trimmed before mapping by Trimmomatic-0.39 using default parameters
STAR v2.7.2d was used to align trimmed reads to the Mus musculus genome (GRCm38.p6, https://www.ncbi.nlm.nih.gov/assembly/GCF_000001635.26) and to obtain read counts with default parameters except -sjdbOverhang149
Differential gene expression analysis using DESeq2 package v1.34.0
Assembly: mm10
Supplementary files format and content: tab delimited table of raw counts per sample
Supplementary files format and content: tab delimited table of normalized expression of detected genes per sample

organism: Mus musculus

source_name: Hippocampus

extract_protocol:
Qiagen miRNeasy with DNase digestion
RNA libraries were prepared by Genewiz using polyA selection and standard Illumina protocols

treatment_protocol: 16-week old mice were treated with tamoxifen (100 mg/kg) or vehicle for 3 injections every other day. Whole hippocampal tissue was dissected at the indicated timepoint after first injection.

value: Hippocampus

tag: genotype

value: CreER

tag: treatment

value: Tamoxifen

tag: timepoint

value: Week 4

value: 20 weeks

value: male

tag: strain


title: T_2S_A

description: Replicate A


title: Mecp2_flox + TMX Week 4 Replicate 3 [Sample_91]

value: Mecp2 Flox


title: PabWT_12h_2_FPKM

city: Tel Aviv

first: Metsada

last: Pasmanik-Chor

address: Ramat Aviv

department: Biology

country: Israel

institute: Tel Aviv University

data_processing:
rRNA reads, low quality reads, adaptors and reads with unknown bases (N>5%) were filtered using SOAPnuke software (version：v1.5.2, parameters: -n 0.001 -l 20 -q 0.4 -A0.25, website: https://github.com/BGI-flexlab/SOAPnuke). After reads filtering, mapping was performed to reference genome using HISAT2 (Version: v2.0.4 Parameters: --phred33 --sensitive --no-discordant --no-mixed -I 1 -X1000 --rna-strandness RF Website: http://www.ccb.jhu.edu/software/hisat) (Kim, Langmead and Salzberg, 2015). On average 85.62% of the reads are mapped. StringTie (Version: v1.0.4, Parameters: -f 0.3 -j 3 -c 5 -g 100 -s 10000 -p 8 –rf, Website: http://ccb.jhu.edu/software/stringtie) (Pertea et al., 2015) was used to reconstruct transcripts, and with genome annotation information we identify novel transcripts by using Cuffcompare (Version: v2.2.1, Parameters: -p 12, Website: http://cole-trapnell-lab.github.io/cufflinks) (Trapnell et al., 2012) and predict the coding ability of those new transcripts using CPC (Version: v0.9-r2, Parameters: Default, Website: http://cpc.cbi.pku.edu.cn) (Kong et al., 2007)
Assembly: GCF_002917755.1_EL10_1.0_NCBI)
Supplementary files format and content: FASTQ
Supplementary files format and content: FPKM expression data, excel file

molecule: total RNA

organism: Beta vulgaris

growth_protocol: Seeds of Beta vulgaris cv. Red Egyptian were germinated for 10 days. The seedlings were then transferred into pots and grown in a growth chamber at 21 °C with a photoperiod of 12 h.

extract_protocol:
Total RNA was isolated with the RNeasy Plant Mini Kit (QIAGEN) from mock, PabhrcC-, and PabWT inoculated leaves at 12 hpi and 48 hpi (three biological replicates for each treatment, in total 18 samples were collected).
Oligo dT beads were used to enrich mRNA with poly A tail. RNA fragmentation and first strand cDNAs were generated using random N6-primed reverse transcription, followed by the second strand cDNA synthesis. The synthesized cDNA was subjected to end-repair and then was 3' adenylated.

treatment_protocol: Mature leaves from 1.5-month old beet plants were infiltrated with mock (ddH2O), suspension of PabhrcC- (108 CFU/mL), and PabWT (108 CFU/mL).

value: wild-type Pab


title: Mecp2_flox + TMX Week 4 Replicate 2 [Sample_90]


title: scATAC_C2-AC-Control

value: Female


title: Pab_hrcC_48h_2_FPKM

source_name: Mature leaves from 1.5-month old beet plants

value: PabhrcC- (inactive mutant)


title: N_SR_C

description: Replicate C

value: Nodal ligand ndr2 (N)

value: sphere (SR)


title: N_SR_B

description: Replicate B


title: Mecp2_flox + TMX Week 4 Replicate 1 [Sample_89]


title: scATAC_C1-AC-Control

value: ascending colon


title: WT + TMX Week 4 Replicate 4 [Sample_88]

value: Wild-type


title: pDNA_12h_scRNA-seq

city: Daejeon

first: In-Hwan

last: Jang

address: 125, Gwahak-ro, Yuseong-gu, Daejeon, Republic of Korea

department: Immunotherapy Research Center

country: South Korea

institute: Korea Research Institute of Bioscience and Biotechnology

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v7.1.0
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files

growth_protocol: The culture method of THP-1 was consistent with the culture method recommended by ATCC

extract_protocol:
Total RNA was isolated by TRIzol Reagent
RNA libraries for RNA-seq were prepared using TruSeq Standarded Total RNA Library Prep Gold Kit following manufacturer's protocols.

treatment_protocol: Sample 1-12: Bulk RNA-seq based on time course analysis (12-24-36 hours) of four conditions experiment: control, STING inhibitor (H151)-treatment, pDNA-transfected, H151-treatment and pDNA-transfected. Sample 13-16: Bulk RNA sequencing of sorted cells with biological replicates of 2. Samples were derived from total RNA extracted from EGFP protein negative and positive THP-1 cells sorted by fluorescence-activated cell sorter (FACS) after 12 hours of pDNA transfection. All pDNA transfection experiments used TransIT-2020 Transfection Reagent. Sample 17: Single-cell RNA sequencing of THP-1 cells 12 hours after transfection with pDNA.

tag: cell line

tag: cell type

value: Monocyte

value: WT

value: Transfected with 2 μg and 4 μg pDNA


title: Pab_hrcC_12h_3_FPKM

value: Mature leaves from 1.5-month old beet plants


title: WT + TMX Week 4 Replicate 3 [Sample_87]

value: Hippocampus


title: N_SR_A

description: Replicate A


title: Pab_hrcC_12h_2_FPKM


title: Pab_hrcC_12h_1_FPKM


title: GFP_pos2 (biol rep2)

description: GFP_pos2 (biol rep2)

data_processing:
HISAT2 software (ver. 2.2.0) was used to index the reference genome and map sequencing reads of samples.
Samtools (ver. 1.15.1) was used to convert BAM files
FeatureCounts (ver. 2.0.1) software was used to calculate the generated BAM files
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

value: Transfected with 3μg pDNA


title: Pab_hrcC_48h_3_FPKM


title: N_SH_C

description: Replicate C

value: shield (SH)


title: Mock_48h_4_FPKM

value: Mock


title: N_SH_B

description: Replicate B


title: WT + TMX Week 4 Replicate 2 [Sample_86]

value: Tamoxifen

value: Week 4

value: 20 weeks

value: male


title: Mock_48h_3_FPKM


title: GFP_neg2 (biol rep2)

description: GFP_neg2 (biol rep2)


title: Mecp2_flox; CreER + Vehicle Week 4 Replicate 6 [Sample_84]

value: Mecp2 Flox; CreER

value: Vehicle


title: Mock_48h_2_FPKM


title: GFP_neg1 (biol rep1)

description: GFP_neg1 (biol rep1)


title: U_30_B

description: Replicate B

value: uninjected (U) controls

value: 30% epiboly (30)


title: WT + TMX Week 4 Replicate 1 [Sample_85]

value: Wild-type


title: N_90_C

description: Replicate C

value: Nodal ligand ndr2 (N)

value: 90% epiboly (90)


title: N_SH_A

description: Replicate A


title: GFP_pos1 (biol rep1)

description: GFP_pos1 (biol rep1)

value: Monocyte

value: WT


title: Mecp2_flox; CreER + Vehicle Week 4 Replicate 5 [Sample_83]

value: Hippocampus


title: pDNA_H151_36h

value: Treated with 1 μM H151 and transfected with 3μg pDNA


title: N_90_B

description: Replicate B


title: Mock_12h_3_FPKM

value: Mature leaves from 1.5-month old beet plants


title: Mecp2_flox; CreER + Vehicle Week 4 Replicate 4 [Sample_82]


title: pDNA_H151_24h


title: N_90_A

description: Replicate A


title: pDNA_H151_12h


title: pDNA _36h

description: pDNA _36h

value: Treated with same amount of DMSO and transfected with 3μg pDNA


title: Mock_12h_1_FPKM

value: Mock


title: N_75_C

description: Replicate C

value: 75% epiboly (75)


title: Mecp2_flox; CreER + Vehicle Week 4 Replicate 2 [Sample_80]

value: Week 4

value: 20 weeks


title: N_75_B

description: Replicate B


title: Mecp2_flox; CreER + Vehicle Week 4 Replicate 1 [Sample_79]

value: Mecp2 Flox; CreER

value: male


title: pDNA _24h

description: pDNA _24h


title: 3tag_mRNAseq WT, R4

city: WIEN

first: Pierre

last: Bourguet

address: Dr. Bohr Gasse 3

country: Austria

institute: GMI

description:
Library name: 3tag_mRNAseq_WT_R4
WT_R4

data_processing:
Reads were demultiplexed, trimmed, collapsed to remove duplicates, mapped, and quantified. The code and documentation are available at https://github.com/pierre-bourguet/3-tag-rna-seq, but we provide the most important details below. Read1, which starts directly in the transcript at the site of Tn5 cutting, was used for mapping. Read2, which contains the sample-specific index, UMI, polyA tail, and eventually the 3’ end of the transcript, was used for demultiplexing and UMI extraction. Specifically, we used the first 7 bases of read2 to identify indices specific to each well in the plate, and the next 8 bases to extract UMIs. For read1, the 3’ end was trimmed for polyA and adapter contamination and reads shorter than 50bp were discarded. UMIs were prepended to read1 and these chimeric reads were used to collapse duplicates into a single read with clumpify (bbmap v38.26) (Bushnell, 2014), with no mismatches allowed in the UMI and two mismatches allowed in the transcript sequence. Mapping was performed with STAR v2.7.11a (Dobin et al., 2013) and mapped reads were counted with Salmon v1.10.1 in alignment mode (Patro et al., 2017) in sense and antisense. We used the TAIR10 genome and AtRTD3 transcriptome reference (Zhang et al., 2022). Because the AtRTD3 GFF and fasta files were sometimes discordant, we regenerated a fasta file from a fixed GFF file using AGAT v1.0.0. We observed that the 3’-end of transcripts were often located outside of transposable element gene annotations, likely because they do not include 3’ UTRs, but within TAIR10 TE annotations. For this reason, and to avoid overlapping annotations, we removed “transposable element gene” annotations from AtRTD3 and added the 31189 transposable element annotations from TAIR10 instead.
Assembly: TAIR10 genome with AtRTD3 annotations
Supplementary files format and content: bigwig files of uniquely mapped reads normalized to library size (bigwig)
Supplementary files format and content: tab-delimited text file including RPM values for each sample

organism: Arabidopsis thaliana

source_name: 28-day-old rosette leaves

growth_protocol: grown in soil in long days at 21°C in a climatic chamber

extract_protocol:
Total RNA was extracted using the RNA isolation kit provided by the VBC core facilities. The kit uses a lysis step based on guanidine thiocyanate (adapted from (Boom et al., 1990) and carboxylate-modified Sera-Mag Speed beads and was applied using the KingFisher instrument (Thermo). For transcriptomes of cdca7 and ddm1 cdca7 mutants (Fig. 2, 3), we pooled three 31-day-old plants (two rosette leaves each), and used two or three biological replicates per genotype. For transcriptomes of complemented cdca7 mutants (Fig. 4, 5), we used one rosette leaf from 28-day-old plants.
Libraries were prepared in 96-well plates using a custom-protocol described previously (Clavel et al., 2024). The oligo d(T) primers used for reverse transcription contain 8-bp unique molecular identifiers (UMIs), 7-bp barcodes for multiplexing, and a Truseq adapter. After reverse transcription, samples are pooled and RNA-cDNA duplexes tagmented with Tn5. Using primers matching the Truseq and Tn5 adapters, the 3’ ends of mRNA transcripts are subsequently amplified by PCR, while P5 and P7 sequences and plate-specific dual indices are added for Illumina sequencing. This protocol improves speed and cost-efficiency compared with conventional library preparation protocols, and UMIs ensure accurate transcript quantification. We started from 80 ng of total RNA in 4 µl, adding 1 µl of 0.2 µM primers for reverse transcription. RNAs were denatured 3 min at 72°C and kept on ice. We mixed 1 µl of the SMARTScribe reverse transcriptase (Takara) in a final volume of 10 µl with 1x SMARTScribe buffer, 1.75 mM dNTPs, 2 mM DTT, 3 mM MnCl2 for 1h at 42°C followed by inactivation for 15 min at 70°C. All samples were pooled together and purified using 1.2x volume of SPRI beads (Molecular Biology Services, IMP, Vienna, Austria). After mixing and 2 min at room temperature, beads were collected on a magnet, washed two times with 70% ethanol, dried, and eluted in 60 µl of 10 mM Tris-HCl pH 8.0. To assemble transposomes, we mixed Tn5 (0.38 mg / ml) with 18 µM of annealed adapters, 50% glycerol and 1x Tn5 loading buffer (6x buffer: 300 mM Hepes KOH pH 7.2, 600 mM NaCl, 0.5 mM EDTA, 6 mM DTT, 0.6% Triton-X-100) and incubated for 1h at 37°C. For tagmentation, 16 µl of pooled RNA-cDNA was mixed with 16 µl of transposome and 32 µl of 2x tagmentation buffer (20 mM Tris (hydroxymethyl)aminomethane, 10mM MgCl2, adjusted to pH 7.6 and 20% (vol/vol) dimethylformamide). After 8 min at 55°C, we added 16 µl of 0.2% SDS and incubated 5 min at room temperature. Nucleic acids were purified with 2x SPRI bead volume as indicated above with a 48 µl elution. For PCR, we pre-incubated at 95°C the KAPA HiFi HotStart 2X ReadyMix for 90 s to activate the polymerase and amplified libraries in 100 µl final volume using 1 µM of primers and 46 µl of purified cDNA-RNA duplexes with the following program: 72°C for 3 min, 95°C for 30 sec, (95°C for 20 sec, 65°C for 30 sec, 72°C for 30 sec) for 12 cycles, 72°C for 5 min. Libraries were purified with 0.8x volume of SPRI beads as indicated above and eluted in 62 µl. After controlling for appropriate fragment size distribution on a 5200 Fragment Analyzer System (Agilent), libraries were sequenced as paired-end 150 bp reads on a NovaSeq S4 (Fig. 2, 3) or a NovaseqX 10B (Fig. 4, 5) flow cell.

value: 28-day-old rosette leaves

tag: batch

value: B


title: N_75_A

description: Replicate A


title: pDNA_12h


title: 3tag_mRNAseq WT, R5

description:
Library name: 3tag_mRNAseq_WT_R5
WT_R5


title: Mecp2_flox; CreER + TMX Week 4 Replicate 6 [Sample_78]

value: Tamoxifen


title: Mecp2_flox; CreER + TMX Week 4 Replicate 5 [Sample_77]


title: H151_36h

value: Treated with 1 μM H151 and transfection reagent


title: N_50_C

description: Replicate C

value: Nodal ligand ndr2 (N)

value: 50% epiboly (50)


title: Mock_12h_2_FPKM


title: 3tag_mRNAseq WT, R3

description:
Library name: 3tag_mRNAseq_WT_R3
WT_R3

value: WT


title: 3tag_mRNAseq WT, R2

description:
Library name: 3tag_mRNAseq_WT_R2
WT_R2


title: N_50_B

description: Replicate B


title: Mecp2_flox; CreER + Vehicle Week 4 Replicate 3 [Sample_81]

value: Hippocampus

value: Vehicle


title: Mecp2_flox; CreER + TMX Week 4 Replicate 4 [Sample_76]


title: 3tag_mRNAseq WT, R1

description:
Library name: 3tag_mRNAseq_WT_R1
WT_R1


title: H151_24h

value: Monocyte


title: Mecp2_flox; CreER + TMX Week 4 Replicate 3 [Sample_75]


title: N_50_A

description: Replicate A


title: 3tag_mRNAseq cdca7_b, R6

description:
Library name: 3tag_mRNAseq_cdca7_b_R6
cdca7_b_R6


title: NC_36h

value: Treated with same amount of DMSO and transfection reagent


title: N_30_C

description: Replicate C

value: 30% epiboly (30)


title: 3tag_mRNAseq cdca7_b, R5

description:
Library name: 3tag_mRNAseq_cdca7_b_R5
cdca7_b_R5


title: Mecp2_flox; CreER + TMX Week 4 Replicate 2 [Sample_74]


title: N_30_B

description: Replicate B


title: NC_24h


title: Mecp2_flox; CreER + TMX Week 4 Replicate 1 [Sample_73]


title: N_30_A

description: Replicate A


title: NC_12h


title: 3tag_mRNAseq cdca7_b, R4

description:
Library name: 3tag_mRNAseq_cdca7_b_R4
cdca7_b_R4


title: N_2S_C

description: Replicate C

value: 2-somite (2S)


title: H151_12h


title: CreER + TMX Week 3 Replicate 3 [Sample_71]

value: CreER

value: Week 3

value: 19 weeks


title: 3tag_mRNAseq cdca7_b, R3

description:
Library name: 3tag_mRNAseq_cdca7_b_R3
cdca7_b_R3


title: 3tag_mRNAseq cdca7_b, R2

description:
Library name: 3tag_mRNAseq_cdca7_b_R2
cdca7_b_R2


title: CreER + TMX Week 3 Replicate 4 [Sample_72]

value: male


title: N_2S_B

description: Replicate B


title: CreER + TMX Week 3 Replicate 2 [Sample_70]


title: N_2S_A

description: Replicate A


title: OR95AC

city: Dallas

first: Bingqing

last: Xie

state: Texas

address: 6001 Forest Park Rd

department: Internal medicine

institute: University of Texas Southwestern medical center

description: 10x RNA

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the CellRanger software (v7.0.1)
Extract high-quality cells with 200-6000 genes and greater than 1000 UMIs per cell and mitochondria percentage less than 50 using Seurat V4.3
Assembly: hg38
Supplementary files format and content: Each process sample contains the following files: barcodes.tsv.gz (cell barcodes),  features.tsv.gz (gene features), and  matrix.mtx.gz (sparse count matrix).

growth_protocol: No growth

extract_protocol:
Tissues were incubated in buffered EGTA at 37 Celsius for 15 minutes to separate epithelium from lamina propria. Epithelium was digested in TrypLE express at 37 Celsius for 5 minutes. Lamina propria was digested in liberase TM at 37 Celsius for 20 minutes.
Amplication product of cDNA was processed with Dnase fragmentation, A tailling, ligation of adaptors and index PCR per 10x Genomics 3'RNA v3.1 library construction protocol.

treatment_protocol: No treatment

tag: patient

value: control

tag: race

value: caucasian

tag: history

tag: treatment (biological)

value: no

tag: sample region


title: 3tag_mRNAseq cdca7_b, R1

description:
Library name: 3tag_mRNAseq_cdca7_b_R1
cdca7_b_R1

tag: tissue

value: 28-day-old rosette leaves

value: B


title: Mecp2_flox; CreER + Vehicle Week 6 Replicate 5 [Sample_107]

value: Mecp2 Flox; CreER

value: Week 6

tag: age

value: 22 weeks

tag: Sex


title: OR06TI_non

description: 10x RNA

tag: condition

value: CD

value: non


title: CreER + TMX Week 3 Replicate 1 [Sample_69]

value: Hippocampus

value: Tamoxifen


title: 3tag_mRNAseq cdca7_ab, R5

description:
Library name: 3tag_mRNAseq_cdca7_ab_R5
cdca7_ab_R5


title: Mecp2_flox + TMX Week 3 Replicate 4 [Sample_68]

value: Mecp2 Flox


title: 3tag_mRNAseq cdca7_ab, R4

description:
Library name: 3tag_mRNAseq_cdca7_ab_R4
cdca7_ab_R4


title: Mecp2_flox + TMX Week 3 Replicate 3 [Sample_67]


title: HA82TI_inf

description: 10x RNA

value: unknown

value: inf


title: OR07TI_non

description: 10x RNA


title: Mecp2_flox + TMX Week 3 Replicate 2 [Sample_66]

value: Week 3

value: 19 weeks


title: HA82TI_ad

description: 10x RNA

value: adjacent


title: 3tag_mRNAseq cdca7_ab_R35A_N42L, R5

description:
Library name: 3tag_mRNAseq_cdca7_ab_R35A_N42L_R5
cdca7_ab_R35A_N42L_R5


title: 3tag_mRNAseq F2_ddm1, R3

description:
Library name: 3tag_mRNAseq_F2_ddm1_R3
F2_ddm1_R3

source_name: 31-day-old rosette leaves

value: 31-day-old rosette leaves

value: A


title: 3tag_mRNAseq F2_ddm1_cdca7a_2, R3

description:
Library name: 3tag_mRNAseq_F2_ddm1_cdca7a_2_R3
F2_ddm1_a_2_R3


title: 3tag_mRNAseq F2_ddm1, R2

description:
Library name: 3tag_mRNAseq_F2_ddm1_R2
F2_ddm1_R2


title: OR95TI

description: 10x RNA

value: control

value: caucasian

value: no


title: Mecp2_flox + TMX Week 3 Replicate 1 [Sample_65]

value: male


title: 3tag_mRNAseq F2_ddm1_cdca7a_2, R2

description:
Library name: 3tag_mRNAseq_F2_ddm1_cdca7a_2_R2
F2_ddm1_a_2_R2


title: HA79TI_inf

description: 10x RNA


title: 3tag_mRNAseq cdca7_ab_R35A_N42L, R4

description:
Library name: 3tag_mRNAseq_cdca7_ab_R35A_N42L_R4
cdca7_ab_R35A_N42L_R4

value: 28-day-old rosette leaves

value: B


title: HA79TI_ad

description: 10x RNA

value: CD


title: WT + TMX Week 3 Replicate 4 [Sample_64]

value: Hippocampus

value: Wild-type


title: 3tag_mRNAseq ddm1_cdca7b_2, R2

description:
Library name: 3tag_mRNAseq_ddm1_cdca7b_2_R2
ddm1_b_2_R2


title: 3tag_mRNAseq cdca7_ab_R35A_N42L, R3

description:
Library name: 3tag_mRNAseq_cdca7_ab_R35A_N42L_R3
cdca7_ab_R35A_N42L_R3


title: 3tag_mRNAseq cdca7_ab_R35A_N42L, R2

description:
Library name: 3tag_mRNAseq_cdca7_ab_R35A_N42L_R2
cdca7_ab_R35A_N42L_R2


title: HA70TI_ad

description: 10x RNA


title: 3tag_mRNAseq cdca7_ab_R35A_N42L, R6

description:
Library name: 3tag_mRNAseq_cdca7_ab_R35A_N42L_R6
cdca7_ab_R35A_N42L_R6


title: WT + TMX Week 3 Replicate 3 [Sample_63]

value: Tamoxifen


title: WT + TMX Week 3 Replicate 2 [Sample_62]


title: 3tag_mRNAseq cdca7_ab_R35A_N42L, R1

description:
Library name: 3tag_mRNAseq_cdca7_ab_R35A_N42L_R1
cdca7_ab_R35A_N42L_R1


title: WT + TMX Week 3 Replicate 1 [Sample_61]


title: 3tag_mRNAseq ddm1_cdca7b_1, R3

description:
Library name: 3tag_mRNAseq_ddm1_cdca7b_1_R3
ddm1_b_1_R3


title: HA68TI_inf

description: 10x RNA


title: HA70TI_inf

description: 10x RNA


title: 3tag_mRNAseq ddm1_cdca7b_2, R3

description:
Library name: 3tag_mRNAseq_ddm1_cdca7b_2_R3
ddm1_b_2_R3


title: Mecp2_flox; CreER + Vehicle Week 3 Replicate 6 [Sample_60]

value: Mecp2 Flox; CreER

value: Vehicle


title: HA68TI_ad

description: 10x RNA


title: 3tag_mRNAseq cdca7_ab, R2

description:
Library name: 3tag_mRNAseq_cdca7_ab_R2
cdca7_ab_R2


title: 3tag_mRNAseq ddm1_cdca7b_2, R1

description:
Library name: 3tag_mRNAseq_ddm1_cdca7b_2_R1
ddm1_b_2_R1


title: 3tag_mRNAseq cdca7_ab_p6966, R5

description:
Library name: 3tag_mRNAseq_cdca7_ab_p6966_R5
cdca7_ab_p6966_R5


title: Mecp2_flox; CreER + Vehicle Week 3 Replicate 5 [Sample_59]

value: Week 3


title: 3tag_mRNAseq ddm1_cdca7ab_2, R3

description:
Library name: 3tag_mRNAseq_ddm1_cdca7ab_2_R3
ddm1_ab_2_R3


title: HA66AC_inf

description: 10x RNA

value: african

value: inf


title: HA66AC_ad

description: 10x RNA

value: adjacent


title: HA65TI

description: 10x RNA

value: indian


title: 3tag_mRNAseq cdca7_ab_p6966, R4

description:
Library name: 3tag_mRNAseq_cdca7_ab_p6966_R4
cdca7_ab_p6966_R4


title: 3tag_mRNAseq ddm1_cdca7ab_2, R2

description:
Library name: 3tag_mRNAseq_ddm1_cdca7ab_2_R2
ddm1_ab_2_R2

value: 31-day-old rosette leaves

value: A


title: Mecp2_flox; CreER + Vehicle Week 3 Replicate 3 [Sample_57]

value: 19 weeks


title: 3tag_mRNAseq ddm1_cdca7b_1, R2

description:
Library name: 3tag_mRNAseq_ddm1_cdca7b_1_R2
ddm1_b_1_R2


title: 3tag_mRNAseq ddm1_cdca7ab_1, R3

description:
Library name: 3tag_mRNAseq_ddm1_cdca7ab_1_R3
ddm1_ab_1_R3


title: HA65AC

description: 10x RNA

value: control

value: no


title: 3tag_mRNAseq cdca7_ab, R3

description:
Library name: 3tag_mRNAseq_cdca7_ab_R3
cdca7_ab_R3

value: 28-day-old rosette leaves

value: B


title: Mecp2_flox; CreER + Vehicle Week 3 Replicate 1 [Sample_55]

value: Hippocampus

value: male


title: 3tag_mRNAseq cdca7_ab_p6966, R3

description:
Library name: 3tag_mRNAseq_cdca7_ab_p6966_R3
cdca7_ab_p6966_R3


title: 3tag_mRNAseq ddm1_cdca7ab_1, R2

description:
Library name: 3tag_mRNAseq_ddm1_cdca7ab_1_R2
ddm1_ab_1_R2


title: HA63AC_inf

description: 10x RNA

value: CD


title: Mecp2_flox; CreER + Vehicle Week 3 Replicate 2 [Sample_56]

value: Mecp2 Flox; CreER


title: Mecp2_flox; CreER + TMX Week 3 Replicate 6 [Sample_54]

value: Tamoxifen


title: 3tag_mRNAseq cdca7_ab_p6966, R2

description:
Library name: 3tag_mRNAseq_cdca7_ab_p6966_R2
cdca7_ab_p6966_R2


title: 3tag_mRNAseq cdca7_ab_p6966_d4nt, R2

description:
Library name: 3tag_mRNAseq_cdca7_ab_p6966_d4nt_R2
cdca7_ab_p6966_d4nt_R2


title: 3tag_mRNAseq cdca7_ab_p6966, R1

description:
Library name: 3tag_mRNAseq_cdca7_ab_p6966_R1
cdca7_ab_p6966_R1


title: 3tag_mRNAseq ddm1_cdca7a_1, R2

description:
Library name: 3tag_mRNAseq_ddm1_cdca7a_1_R2
ddm1_a_1_R2


title: HA63AC_ad

description: 10x RNA


title: HA62TI

description: 10x RNA

value: caucasian


title: HA62AC

description: 10x RNA


title: 3tag_mRNAseq ddm1_cdca7b_1, R1

description:
Library name: 3tag_mRNAseq_ddm1_cdca7b_1_R1
ddm1_b_1_R1


title: Mecp2_flox; CreER + TMX Week 3 Replicate 4 [Sample_52]

value: Week 3


title: 3tag_mRNAseq cdca7_ab_p6966_d4nt, R1

description:
Library name: 3tag_mRNAseq_cdca7_ab_p6966_d4nt_R1
cdca7_ab_p6966_d4nt_R1


title: 3tag_mRNAseq cdca7_ab_p6966_d26nt, R7

description:
Library name: 3tag_mRNAseq_cdca7_ab_p6966_d26nt_R7
cdca7_ab_p6966_d26nt_R7


title: Mecp2_flox; CreER + TMX Week 3 Replicate 5 [Sample_53]


title: 3tag_mRNAseq ddm1_cdca7ab_1, R1

description:
Library name: 3tag_mRNAseq_ddm1_cdca7ab_1_R1
ddm1_ab_1_R1


title: HA61TI_inf

description: 10x RNA

value: inf


title: Mecp2_flox; CreER + TMX Week 3 Replicate 3 [Sample_51]


title: Mecp2_flox; CreER + Vehicle Week 3 Replicate 4 [Sample_58]

value: Vehicle


title: HA61TI_ad

description: 10x RNA

value: adjacent


title: 3tag_mRNAseq cdca7_ab_p6966_d26nt, R6

description:
Library name: 3tag_mRNAseq_cdca7_ab_p6966_d26nt_R6
cdca7_ab_p6966_d26nt_R6


title: 3tag_mRNAseq cdca7_ab_p6966_d26nt, R5

description:
Library name: 3tag_mRNAseq_cdca7_ab_p6966_d26nt_R5
cdca7_ab_p6966_d26nt_R5


title: Mecp2_flox; CreER + TMX Week 3 Replicate 2 [Sample_50]


title: 3tag_mRNAseq cdca7_ab_p6966_d26nt, R4

description:
Library name: 3tag_mRNAseq_cdca7_ab_p6966_d26nt_R4
cdca7_ab_p6966_d26nt_R4


title: HA60TI_ad

description: 10x RNA


title: HA60TI_inf

description: 10x RNA


title: CreER + TMX Week 2 Replicate 4 [Sample_48]

value: CreER

value: Week 2

value: 18 weeks


title: HA59TI_inf

description: 10x RNA


title: CreER + TMX Week 2 Replicate 3 [Sample_47]


title: 3tag_mRNAseq cdca7_ab_p6966_d26nt, R3

description:
Library name: 3tag_mRNAseq_cdca7_ab_p6966_d26nt_R3
cdca7_ab_p6966_d26nt_R3


title: 3tag_mRNAseq cdca7_ab_p6966_d26nt, R2

description:
Library name: 3tag_mRNAseq_cdca7_ab_p6966_d26nt_R2
cdca7_ab_p6966_d26nt_R2


title: Mecp2_flox; CreER + TMX Week 3 Replicate 1 [Sample_49]

value: 19 weeks


title: HA59TI_ad

description: 10x RNA


title: CreER + TMX Week 2 Replicate 2 [Sample_46]


title: 3tag_mRNAseq cdca7_ab_p6966_d26nt, R1

description:
Library name: 3tag_mRNAseq_cdca7_ab_p6966_d26nt_R1
cdca7_ab_p6966_d26nt_R1


title: CreER + TMX Week 2 Replicate 1 [Sample_45]


title: HA57AC_inf

description: 10x RNA

value: african


title: Mecp2_flox + TMX Week 2 Replicate 4 [Sample_44]

value: Mecp2 Flox


title: HA56TI_ad

description: 10x RNA

value: no


title: 3tag_mRNAseq ddm1_2_G5, R3

description:
Library name: 3tag_mRNAseq_ddm1_2_G5_R3
ddm1_2_G5_R3

value: 31-day-old rosette leaves

value: A


title: 3tag_mRNAseq cdca7b_2, R3

description:
Library name: 3tag_mRNAseq_cdca7b_2_R3
b_2_R3


title: 3tag_mRNAseq ddm1_2_G5, R1

description:
Library name: 3tag_mRNAseq_ddm1_2_G5_R1
ddm1_2_G5_R1


title: 3tag_mRNAseq Col_0, R3

description:
Library name: 3tag_mRNAseq_Col_0_R3
Col_0_R3


title: 3tag_mRNAseq cdca7_ab_dNter, R5

description:
Library name: 3tag_mRNAseq_cdca7_ab_dNter_R5
cdca7_ab_dNter_R5

value: 28-day-old rosette leaves

value: B


title: 3tag_mRNAseq ddm1_cdca7a_1, R1

description:
Library name: 3tag_mRNAseq_ddm1_cdca7a_1_R1
ddm1_a_1_R1


title: 3tag_mRNAseq ddm1_2_G5, R2

description:
Library name: 3tag_mRNAseq_ddm1_2_G5_R2
ddm1_2_G5_R2


title: 3tag_mRNAseq ddm1_2_G2, R3

description:
Library name: 3tag_mRNAseq_ddm1_2_G2_R3
ddm1_2_G2_R3


title: 3tag_mRNAseq Col_0, R2

description:
Library name: 3tag_mRNAseq_Col_0_R2
Col_0_R2


title: 3tag_mRNAseq ddm1_2_G2, R1

description:
Library name: 3tag_mRNAseq_ddm1_2_G2_R1
ddm1_2_G2_R1


title: 3tag_mRNAseq cdca7b_2, R2

description:
Library name: 3tag_mRNAseq_cdca7b_2_R2
b_2_R2


title: 3tag_mRNAseq cdca7_ab_dNter, R4

description:
Library name: 3tag_mRNAseq_cdca7_ab_dNter_R4
cdca7_ab_dNter_R4


title: HA55TI

description: 10x RNA

value: control


title: HA55AC

description: 10x RNA

value: caucasian


title: 3tag_mRNAseq cdca7b_1, R3

description:
Library name: 3tag_mRNAseq_cdca7b_1_R3
b_1_R3


title: 3tag_mRNAseq cdca7_ab_dNter, R3

description:
Library name: 3tag_mRNAseq_cdca7_ab_dNter_R3
cdca7_ab_dNter_R3


title: HA57AC_ad

description: 10x RNA

value: CD


title: 3tag_mRNAseq Col_0, R1

description:
Library name: 3tag_mRNAseq_Col_0_R1
Col_0_R1


title: 3tag_mRNAseq cdca7_ab_dNter, R6

description:
Library name: 3tag_mRNAseq_cdca7_ab_dNter_R6
cdca7_ab_dNter_R6


title: Mecp2_flox + TMX Week 2 Replicate 2 [Sample_42]

value: Hippocampus

value: Tamoxifen

value: male


title: 3tag_mRNAseq cdca7b_1, R2

description:
Library name: 3tag_mRNAseq_cdca7b_1_R2
b_1_R2


title: 3tag_mRNAseq cdca7_ab_dNter, R2

description:
Library name: 3tag_mRNAseq_cdca7_ab_dNter_R2
cdca7_ab_dNter_R2


title: WT + TMX Week 2 Replicate 4 [Sample_40]

value: Wild-type


title: 3tag_mRNAseq cdca7b_1, R1

description:
Library name: 3tag_mRNAseq_cdca7b_1_R1
b_1_R1


title: HA54TI

description: 10x RNA

value: multiple


title: HA54AC

description: 10x RNA


title: Mecp2_flox + TMX Week 2 Replicate 3 [Sample_43]

value: Week 2

value: 18 weeks


title: WT + TMX Week 2 Replicate 3 [Sample_39]


title: 3tag_mRNAseq cdca7_ab_dCter, R8

description:
Library name: 3tag_mRNAseq_cdca7_ab_dCter_R8
cdca7_ab_dCter_R8


title: 3tag_mRNAseq cdca7ab_2, R3

description:
Library name: 3tag_mRNAseq_cdca7ab_2_R3
ab_2_R3


title: 3tag_mRNAseq cdca7_ab_dCter, R6

description:
Library name: 3tag_mRNAseq_cdca7_ab_dCter_R6
cdca7_ab_dCter_R6


title: 3tag_mRNAseq cdca7_ab_dCter, R7

description:
Library name: 3tag_mRNAseq_cdca7_ab_dCter_R7
cdca7_ab_dCter_R7


title: HA51AC

description: 10x RNA


title: 3tag_mRNAseq cdca7ab_1, R3

description:
Library name: 3tag_mRNAseq_cdca7ab_1_R3
ab_1_R3


title: Mecp2_flox; CreER + Vehicle Week 2 Replicate 6 [Sample_36]

value: Mecp2 Flox; CreER

value: Vehicle


title: HA52AC

description: 10x RNA

value: african

value: no


title: HA51TI

description: 10x RNA


title: 3tag_mRNAseq cdca7ab_1, R2

description:
Library name: 3tag_mRNAseq_cdca7ab_1_R2
ab_1_R2

value: 31-day-old rosette leaves

value: A


title: 3tag_mRNAseq cdca7ab_2, R1

description:
Library name: 3tag_mRNAseq_cdca7ab_2_R1
ab_2_R1


title: WT + TMX Week 2 Replicate 2 [Sample_38]


title: Mecp2_flox; CreER + Vehicle Week 2 Replicate 4 [Sample_34]


title: 3tag_mRNAseq cdca7_ab_dCter, R3

description:
Library name: 3tag_mRNAseq_cdca7_ab_dCter_R3
cdca7_ab_dCter_R3

value: 28-day-old rosette leaves

value: B


title: HA49TI

description: 10x RNA

value: control

value: caucasian


title: Mecp2_flox; CreER + Vehicle Week 2 Replicate 5 [Sample_35]

value: Hippocampus


title: 3tag_mRNAseq cdca7a_2, R1

description:
Library name: 3tag_mRNAseq_cdca7a_2_R1
a_2_R1


title: Mecp2_flox + TMX Week 2 Replicate 1 [Sample_41]

value: Mecp2 Flox

value: Tamoxifen


title: Mecp2_flox; CreER + Vehicle Week 2 Replicate 3 [Sample_33]

value: male


title: 3tag_mRNAseq cdca7_ab_dCter, R1

description:
Library name: 3tag_mRNAseq_cdca7_ab_dCter_R1
cdca7_ab_dCter_R1


title: 3tag_mRNAseq cdca7_ab_dNter, R1

description:
Library name: 3tag_mRNAseq_cdca7_ab_dNter_R1
cdca7_ab_dNter_R1


title: 3tag_mRNAseq cdca7a_2, R2

description:
Library name: 3tag_mRNAseq_cdca7a_2_R2
a_2_R2


title: HA50AC

description: 10x RNA


title: HA49AC

description: 10x RNA


title: WT + TMX Week 2 Replicate 1 [Sample_37]

value: Wild-type


title: Mecp2_flox; CreER + Vehicle Week 2 Replicate 2 [Sample_32]

value: Week 2


title: 3tag_mRNAseq cdca7_ab_dCter, R5

description:
Library name: 3tag_mRNAseq_cdca7_ab_dCter_R5
cdca7_ab_dCter_R5


title: HA50TI

description: 10x RNA


title: 3tag_mRNAseq cdca7a_1, R3

description:
Library name: 3tag_mRNAseq_cdca7a_1_R3
a_1_R3


title: HA43TI_inf

description: 10x RNA

value: CD

value: inf


title: 3tag_mRNAseq cdca7_ab_dCter, R2

description:
Library name: 3tag_mRNAseq_cdca7_ab_dCter_R2
cdca7_ab_dCter_R2


title: 3tag_mRNAseq cdca7a_1, R2

description:
Library name: 3tag_mRNAseq_cdca7a_1_R2
a_1_R2


title: Mecp2_flox; CreER + Vehicle Week 2 Replicate 1 [Sample_31]

value: Mecp2 Flox; CreER

value: Vehicle

value: 18 weeks


title: 3tag_mRNAseq cdca7a_1, R1

description:
Library name: 3tag_mRNAseq_cdca7a_1_R1
a_1_R1

value: 31-day-old rosette leaves


title: Mecp2_flox; CreER + TMX Week 2 Replicate 6 [Sample_30]


title: 3tag_mRNAseq cdca7_ab_CDCA7, R4

description:
Library name: 3tag_mRNAseq_cdca7_ab_CDCA7_R4
cdca7_ab_CDCA7_R4


title: HA43TI_ad

description: 10x RNA

value: adjacent


title: 3tag_mRNAseq cdca7_ab_CDCA7, R5

description:
Library name: 3tag_mRNAseq_cdca7_ab_CDCA7_R5
cdca7_ab_CDCA7_R5

value: 28-day-old rosette leaves


title: Mecp2_flox; CreER + TMX Week 2 Replicate 5 [Sample_29]


title: 3tag_mRNAseq cdca7_ab_CDCA7, R2

description:
Library name: 3tag_mRNAseq_cdca7_ab_CDCA7_R2
cdca7_ab_CDCA7_R2

value: B


title: TWGBS cdca7ab_ddm1_1, rep2

description: Library name: TWGBS_cdca7ab_ddm1_1_rep2

library_source: genomic

data_processing:
Libraries for cdca7α/β and ddm1 mutants (Fig. 2, 3) were randomly subsampled to 30 million reads to improve depth homogeneity, since there were up to 2-fold more reads in some samples. The data were analyzed with the nfcore methylseq pipeline v2.3.0 (https://nf-co.re/methylseq) (Ewels et al., 2020) with Nextflow (v22.10.7). Cytosine positions covered by fewer than 3 reads (--meth_cutoff 3) were excluded. Tagmentation creates gaps in the double-stranded DNA which are later filled by unmethylated cytosines during gap repair. These nucleotides were excluded from the analysis by trimming reads with the "clip" and "ignore" options, using M-bias plots to ensure the removal of unmethylated fragment ends. The parameters were as follow: --meth_cutoff 4 --comprehensive --cytosine_report --clip_r1 14 --three_prime_clip_r1 4 --three_prime_clip_r2 2 --ignore_3prime_r2 17. Note that the unmethylated cytosines are incorporated at the 5' end of read 2, while the options mentioned above suggest we ignored the 3' end of read 2 instead, but methylseq v2.3.0 had an issue which made it clip the wrong end of read 2 (see https://github.com/nf-core/methylseq/issues/299). Using M-bias plots, we noticed a 5' bias on read 1 that resembled the Tn5 sequence bias (Wolpe et al. 2023), and removed it by clipping 14 nucleotides at the 5' end of read 1. We also excluded additional small methylation biases at the 3' end of read 1 and read 2.
Assembly: TAIR10
Supplementary files format and content: methylation ratios provided for CG, CHG and CHH as bigwig files

extract_protocol:
Genomic DNA was extracted from rosette leaves with the DNeasy Plant Pro kit (Qiagen, reference 69206), following the manufacturer’s instructions.
Illumina libraries of sodium bisulfite-converted DNA were prepared with a tagmentation-based approach (Wang et al. 2013) with modifications (Montgomery and Berger, 2023, bioRxiv). Briefly, we tagmented 50 ng of DNA with Tn5 (Molecular Biology Services, IMP, Vienna, Austria). Tagmented DNA was purified with the Zymo DNA Clean and Concentrator kit (Zymo Research) instead of SPRI beads. After oligonucleotide replacement, gap repair, and purification, we used the entirety of the eluted DNA for bisulfite conversion, which was performed with the EZ DNA Methylation-Gold Kit from Zymo (reference D5006). The rest of the protocol was performed as indicated by Wang et al (2013). Directional libraries were amplified with Nextera-compatible unique dual indices and sequenced on a NovaSeq 6000 instrument using an S4 flow cell to generate paired-end 150 bp reads with around 25 million reads per sample.

value: A


title: TWGBS cdca7ab_ddm1_2, rep2

description: Library name: TWGBS_cdca7ab_ddm1_2_rep2


title: TWGBS cdca7ab_2, rep2

description: Library name: TWGBS_cdca7ab_2_rep2


title: HA38TI_ad

description: 10x RNA

value: caucasian

value: no


title: Mecp2_flox; CreER + TMX Week 2 Replicate 3 [Sample_27]

value: Hippocampus


title: HA37TI_non

description: 10x RNA

value: non


title: TWGBS cdca7ab_1, rep2

description: Library name: TWGBS_cdca7ab_1_rep2


title: 3tag_mRNAseq cdca7_ab_CDCA7_no_YFP, R2

description:
Library name: 3tag_mRNAseq_cdca7_ab_CDCA7_no_YFP_R2
cdca7_ab_CDCA7_no_YFP_R2


title: Mecp2_flox; CreER + TMX Week 2 Replicate 1 [Sample_25]

value: Tamoxifen

value: male


title: Mecp2_flox; CreER + TMX Week 2 Replicate 2 [Sample_26]

value: Week 2


title: HA36TI_non

description: 10x RNA

value: CD


title: TWGBS cdca7b_2, rep2

description: Library name: TWGBS_cdca7b_2_rep2


title: 3tag_mRNAseq cdca7_ab_CDCA7, R3

description:
Library name: 3tag_mRNAseq_cdca7_ab_CDCA7_R3
cdca7_ab_CDCA7_R3


title: HA37AC_non

description: 10x RNA


title: TWGBS cdca7b_1, rep2

description: Library name: TWGBS_cdca7b_1_rep2


title: HA36AC_non

description: 10x RNA


title: CreER + TMX Week 1 Replicate 4 [Sample_24]

value: CreER

value: Week 1

value: 17 weeks


title: Mecp2_flox; CreER + TMX Week 2 Replicate 4 [Sample_28]

value: Mecp2 Flox; CreER

value: 18 weeks


title: 3tag_mRNAseq cdca7_ab_C183S_C209S, R7

description:
Library name: 3tag_mRNAseq_cdca7_ab_C183S_C209S_R7
cdca7_ab_C183S_C209S_R7


title: HA38TI_inf

description: 10x RNA

value: inf


title: 3tag_mRNAseq cdca7_ab_C183S_C209S, R6

description:
Library name: 3tag_mRNAseq_cdca7_ab_C183S_C209S_R6
cdca7_ab_C183S_C209S_R6

value: 28-day-old rosette leaves


title: 3tag_mRNAseq cdca7_ab_C183S_C209S, R5

description:
Library name: 3tag_mRNAseq_cdca7_ab_C183S_C209S_R5
cdca7_ab_C183S_C209S_R5

value: B


title: TWGBS cdca7a_2, rep2

description: Library name: TWGBS_cdca7a_2_rep2

value: 31-day-old rosette leaves

value: A


title: HA35TI_non

description: 10x RNA

value: african


title: HA31AC_non

description: 10x RNA

value: caucasian

value: no


title: HA31TI_non

description: 10x RNA

value: non


title: CreER + TMX Week 1 Replicate 1 [Sample_21]

value: Hippocampus

value: Tamoxifen

value: male


title: 3tag_mRNAseq cdca7_ab_C183S_C209S, R4

description:
Library name: 3tag_mRNAseq_cdca7_ab_C183S_C209S_R4
cdca7_ab_C183S_C209S_R4


title: TWGBS cdca7a_1, rep2

description: Library name: TWGBS_cdca7a_1_rep2


title: Mecp2_flox + TMX Week 1 Replicate 4 [Sample_20]

value: Mecp2 Flox


title: TWGBS ddm1_2_G5, rep2

description: Library name: TWGBS_ddm1_2_G5_rep2


title: TWGBS ddm1_2_G2, rep2

description: Library name: TWGBS_ddm1_2_G2_rep2


title: 3tag_mRNAseq cdca7_ab_C183S_C209S, R3

description:
Library name: 3tag_mRNAseq_cdca7_ab_C183S_C209S_R3
cdca7_ab_C183S_C209S_R3


title: CreER + TMX Week 1 Replicate 3 [Sample_23]

value: CreER

value: Week 1


title: Mecp2_flox + TMX Week 1 Replicate 3 [Sample_19]

value: 17 weeks


title: 3tag_mRNAseq cdca7_ab_C183S_C209S, R1

description:
Library name: 3tag_mRNAseq_cdca7_ab_C183S_C209S_R1
cdca7_ab_C183S_C209S_R1


title: TWGBS Col_0, rep2

description: Library name: TWGBS_Col_0_rep2


title: 3tag_mRNAseq cdca7_ab_C183S_C209S, R2

description:
Library name: 3tag_mRNAseq_cdca7_ab_C183S_C209S_R2
cdca7_ab_C183S_C209S_R2


title: TWGBS cdca7ab_ddm1_2, rep1

description: Library name: TWGBS_cdca7ab_ddm1_2_rep1


title: Mecp2_flox + TMX Week 1 Replicate 2 [Sample_18]


title: HA27TI_ad

description: 10x RNA

value: CD

value: adjacent


title: 3tag_mRNAseq cdca7_a, R3

description:
Library name: 3tag_mRNAseq_cdca7_a_R3
cdca7_a_R3

value: 28-day-old rosette leaves


title: Mecp2_flox + TMX Week 1 Replicate 1 [Sample_17]


title: HA26AC_non

description: 10x RNA


title: HA27AC_non

description: 10x RNA


title: CreER + TMX Week 1 Replicate 2 [Sample_22]


title: HA26TI_non

description: 10x RNA


title: WT + TMX Week 1 Replicate 4 [Sample_16]

value: Wild-type


title: HA22AC_non

description: 10x RNA


title: TWGBS cdca7b_2, rep1

description: Library name: TWGBS_cdca7b_2_rep1

value: 31-day-old rosette leaves


title: 3tag_mRNAseq cdca7_a, R1

description:
Library name: 3tag_mRNAseq_cdca7_a_R1
cdca7_a_R1

value: B


title: TWGBS cdca7b_1, rep1

description: Library name: TWGBS_cdca7b_1_rep1

value: A


title: 3tag_mRNAseq cdca7_ab_CDCA7, R1

description:
Library name: 3tag_mRNAseq_cdca7_ab_CDCA7_R1
cdca7_ab_CDCA7_R1


title: 3tag_mRNAseq cdca7_a_p6966, R4

description:
Library name: 3tag_mRNAseq_cdca7_a_p6966_R4
cdca7_a_p6966_R4


title: WT + TMX Week 1 Replicate 3 [Sample_15]


title: 3tag_mRNAseq cdca7_a_p6966, R5

description:
Library name: 3tag_mRNAseq_cdca7_a_p6966_R5
cdca7_a_p6966_R5


title: HA27TI_inf

description: 10x RNA

value: caucasian

value: inf


title: WT + TMX Week 1 Replicate 2 [Sample_14]


title: HA17AC_non

description: 10x RNA

value: african

value: no

value: non


title: HA19TI_non

description: 10x RNA


title: HA19TI_ad

description: 10x RNA


title: 3tag_mRNAseq cdca7_a_p6966, R3

description:
Library name: 3tag_mRNAseq_cdca7_a_p6966_R3
cdca7_a_p6966_R3


title: TWGBS cdca7a_1, rep1

description: Library name: TWGBS_cdca7a_1_rep1


title: WT + TMX Week 1 Replicate 1 [Sample_13]

value: Hippocampus

value: Tamoxifen

value: male


title: TWGBS cdca7a_2, rep1

description: Library name: TWGBS_cdca7a_2_rep1


title: Mecp2_flox; CreER + Vehicle Week 1 Replicate 6 [Sample_12]

value: Mecp2 Flox; CreER

value: Vehicle

value: Week 1


title: 3tag_mRNAseq cdca7_a_p6966, R2

description:
Library name: 3tag_mRNAseq_cdca7_a_p6966_R2
cdca7_a_p6966_R2


title: HA16AC_non

description: 10x RNA

value: CD


title: 3tag_mRNAseq cdca7_a_p6966, R1

description:
Library name: 3tag_mRNAseq_cdca7_a_p6966_R1
cdca7_a_p6966_R1

value: 28-day-old rosette leaves


title: TWGBS cdca7ab_2, rep1

description: Library name: TWGBS_cdca7ab_2_rep1


title: TWGBS ddm1_2_G5, rep1

description: Library name: TWGBS_ddm1_2_G5_rep1


title: HA14TI

description: 10x RNA

value: control

value: multiple


title: Mecp2_flox; CreER + Vehicle Week 1 Replicate 5 [Sample_11]

value: 17 weeks


title: Mecp2_flox; CreER + Vehicle Week 1 Replicate 4 [Sample_10]


title: HA14AC

description: 10x RNA


title: Mecp2_flox; CreER + Vehicle Week 1 Replicate 3 [Sample_9]


title: 3tag_mRNAseq cdca7_a_p6966_d4nt, R3

description:
Library name: 3tag_mRNAseq_cdca7_a_p6966_d4nt_R3
cdca7_a_p6966_d4nt_R3

value: B


title: 3tag_mRNAseq cdca7_a_p6966_d4nt, R4

description:
Library name: 3tag_mRNAseq_cdca7_a_p6966_d4nt_R4
cdca7_a_p6966_d4nt_R4


title: ddm1, input, rep2

description:
Library name: ChIP_ddm1_input_rep2
score file normalized to depth

library_source: other

data_processing:
The data were analyzed using the nfcore/chipseq pipeline v2.0.0 (https://nf-co.re/chipseq/2.0.0/) (Ewels et al., 2020) with Nextflow (v22.10.7). We used custom arguments for read length (150 bp), fragment size (275), and blacklisted mitochondrial and chloroplast genomes. To get the average value for each annotation, we used the bigWigAverageOverBed script from UCSC tools (https://github.com/ucscGenomeBrowser/kent-core/tree/master). We further analyzed the data with deepTools v3.3.1 (Ramírez et al., 2016). To normalize by H3 or by the WT, we used bigwigCompare with a bin size of 10 bp, ignoring non-covered regions with skipNonCoveredRegions. To produce average profile plots (metaplots), annotations were scaled to an arbitrary size of 1000 bp and the enrichment value was calculated by 50 bp bins, using computeMatrix scale-regions.
Assembly: TAIR10
Supplementary files format and content: Enrichment score provided as BigWig files. Input and H3 are normalized to depth and use variable steps. H2A.W, H2A.Z, H3K9me2 and H3K27me1 are normalized to depth, log2 normalized to H3, and use a fixed 10bp step.

molecule: other

extract_protocol:
Tissues were frozen in liquid nitrogen and ground in a 5-ml grinding jar on a Retsch Mixer Mill MM 200 at 30 Hz for 45 s. Tubes were kept at room temperature until the powder showed signs of thawing. We added 35 ml of nuclei isolation buffer (NIB, 10 mM MES-KOH pH 5.3, 250 mM sucrose, 10 mM NaCl, 10 mM KCl, 2.5 mM EDTA, 0.1 mM spermine, 0.1 mM spermidine, 2.5 mM ß-mercaptoethanol, 0.3% Triton X-100 and protease inhibitors) (Lorkovic 2004 MBC), followed by vortexing until homogeneous. The extract was filtered through two layers of Miracloth, which were washed with 10 ml of NIB and spun at 3,400 rpm at 4°C for 5 min. Pellets were resuspended in 25 ml of NIB, vortexed and incubated for 10 min on ice to fully dissolve chlorophyll content. Tubes were spun as above and pellets were carefully washed with 5 ml of shearing buffer (10 mM Tris-HCl pH 8.0, 1 mM EDTA, 0.1% SDS, and protease inhibitors) without resuspending and spun again. This washing step was repeated and pellets were resuspended in 0.9 ml of shearing buffer. One ml of the extracted chromatin was transferred to Covaris glass tubes and sonication was conducted at 4°C for 900 seconds per sample (peak power 140.0; duty factor: 5.0; Cycles/Burst: 200). Sheared chromatin was spun for 5 min at 4°C at 15,000 rpm. The supernatant was collected and spun again, and the supernatant was transferred to a 5 ml tube. Fifteen µl of chromatin were kept to control for sonication efficiency. Chromatin was diluted to 3.5 ml to reduce SDS concentration with a ChIP dilution buffer (16.7 mM Tris-HCl pH 8.0, 167 mM NaCl, 1.2 mM EDTA, 1.1% Triton X-100, 0.01% SDS and protease inhibitors). For preclearing, 200 µl of Dynabeads protein A (Thermofisher, reference 1001D) were added to the chromatin and rotated 1 h at 4°C. Beads were discarded by collecting supernatants after two centrifugations at maximum speed for 30 s. A hundred µl of pre-cleared chromatin was kept at -20°C for input control, and the remaining chromatin was aliquoted with 500 µl per immunoprecipitation (IP) and incubated with 5 µg of anti-H3 (Abcam, ab1791), anti-H2A.W.6/7, anti-H2A.Z.9/11, anti-H3K27me1 (Millipore, 17-643) or anti-H3K9me2 (Abcam, ab1220) antibodies at 4 °C overnight with rotation. After incubation, samples were mixed with 30 µl of protein A magnetic beads, rotated at 4°C for 3 h, and washed two times with a low-salt buffer (20 mM Tris-HCl pH 8.0, 150 mM NaCl, 2 mM EDTA, 1% Triton X-100 and 0.1% SDS), once with a high-salt buffer (20 mM Tris-HCl pH 8.0, 500 mM NaCl, 2 mM EDTA, 1% Triton X-100 and 0.1% SDS), once with a LiCl buffer (10 mM Tris-HCl pH 8.0, 1 mM EDTA, 0.25 M LiCl, 1% IGEPAL CA-630 and 0.1% deoxycholic acid) and twice with TE buffer (10 mM Tris-HCl pH 8.0 and 1 mM EDTA). Elution was done with 200 µl of 0.1 M NaHCO3 and 1% SDS, incubated at 65°C for 15 min. We added 20.4 µl of reverse cross-link buffer (0.4 M Tris-HCl pH 8.0, 2 M NaCl, 10 mM EDTA, 0.6 mg ml−1 proteinase K (Thermo Fisher Scientific)) and incubated at 45°C for 3 h and 65°C for 16 h. RNA was subsequently degraded for 30 min at room temperature with 10 µg of RNase A (Thermo Fisher Scientific), and DNA was purified with the ChIP DNA Clean & Concentrator kit (Zymo, reference D5205).
Libraries were prepared with the NEBNext Ultra II DNA library prep kit for Illumina (New England Biolabs), following the manufacturer's instructions. Fragment size distribution was analyzed on a 5200 Fragment Analyzer System (Agilent), and size selection with SPRI beads (Molecular Biology Services, IMP, Vienna, Austria) was applied to remove large fragments and self-ligated adapters, when necessary. To maximize comparability, if only one sample had undesired fragments, we size-selected all samples for a given antibody. For size selection, briefly, DNA was diluted to 100 µl, we mixed in 60 µl of magnetic SPRI beads, collected the supernatant, and added 40 µl of magnetic SPRI beads, washed two times with 80% ethanol, and eluted DNA. Sequencing was carried out on a NovaSeq 6000 instrument using an S4 flow cell to generate paired-end 150 bp reads with around 25 million reads per sample.

treatment_protocol: 1.5 g of rosette leaves from 31-d-old plants were fixed in 37 ml 1% formaldehyde in PBS by vacuum-infiltration for 10 min. The cross-linking reaction was quenched by adding glycine to a final concentration of 125 mM.

value: 31-day-old rosette leaves

tag: chip antibody

value: input

value: C


title: HA11TI

description: 10x RNA

value: african

value: no


title: Col_0, input, rep2

description:
Library name: ChIP_Col_0_input_rep2
score file normalized to depth

tag: genotype


title: HA11AC

description: 10x RNA


title: cdca7ab_1, input, rep2

description:
Library name: ChIP_cdca7ab_1_input_rep2
score file normalized to depth


title: Mecp2_flox; CreER + Vehicle Week 1 Replicate 2 [Sample_8]

value: Hippocampus

tag: treatment


title: HA08TI

description: 10x RNA


title: Mecp2_flox; CreER + Vehicle Week 1 Replicate 1 [Sample_7]

tag: timepoint


title: 3tag_mRNAseq cdca7_a_p6966_d4nt, R2

description:
Library name: 3tag_mRNAseq_cdca7_a_p6966_d4nt_R2
cdca7_a_p6966_d4nt_R2


title: Mecp2_flox; CreER + TMX Week 1 Replicate 6 [Sample_6]

value: Tamoxifen

tag: strain


title: TWGBS Col_0, rep1

description: Library name: TWGBS_Col_0_rep1

value: A


title: HA08AC

description: 10x RNA


title: 3tag_mRNAseq cdca7_a_p6966_d26nt, R5

description:
Library name: 3tag_mRNAseq_cdca7_a_p6966_d26nt_R5
cdca7_a_p6966_d26nt_R5


title: Mecp2_flox; CreER + TMX Week 1 Replicate 5 [Sample_5]

value: Mecp2 Flox; CreER

value: male


title: ddm1, input, rep1

description:
Library name: ChIP_ddm1_input_rep1
score file normalized to depth


title: Col_0, input, rep1

description:
Library name: ChIP_Col_0_input_rep1
score file normalized to depth


title: HA07TI

description: 10x RNA

value: caucasian


title: 3tag_mRNAseq cdca7_a_p6966_d26nt, R4

description:
Library name: 3tag_mRNAseq_cdca7_a_p6966_d26nt_R4
cdca7_a_p6966_d26nt_R4


title: Mecp2_flox; CreER + TMX Week 1 Replicate 3 [Sample_3]

value: Week 1


title: Mecp2_flox; CreER + TMX Week 1 Replicate 4 [Sample_4]


title: cdca7ab_1, input, rep1

description:
Library name: ChIP_cdca7ab_1_input_rep1
score file normalized to depth


title: 3tag_mRNAseq cdca7_a_p6966_d26nt, R3

description:
Library name: 3tag_mRNAseq_cdca7_a_p6966_d26nt_R3
cdca7_a_p6966_d26nt_R3

value: 28-day-old rosette leaves


title: HA04TI

description: 10x RNA

value: control

value: unknown


title: cdca7ab_2, input, rep2

description:
Library name: ChIP_cdca7ab_2_input_rep2
score file normalized to depth


title: cdca7ab_2, input, rep1

description:
Library name: ChIP_cdca7ab_2_input_rep1
score file normalized to depth


title: 3tag_mRNAseq cdca7_a_p6966_d26nt, R2

description:
Library name: 3tag_mRNAseq_cdca7_a_p6966_d26nt_R2
cdca7_a_p6966_d26nt_R2


title: HA07AC

description: 10x RNA


title: 3tag_mRNAseq cdca7_a_p6966_d26nt, R1

description:
Library name: 3tag_mRNAseq_cdca7_a_p6966_d26nt_R1
cdca7_a_p6966_d26nt_R1


title: Col_0, H3K9me2, rep2

description:
Library name: ChIP_Col_0_H3K9me2_rep2
score file normalized to depth and log2 normalized to H3


title: 3tag_mRNAseq cdca7_a_p6966_d4nt, R1

description:
Library name: 3tag_mRNAseq_cdca7_a_p6966_d4nt_R1
cdca7_a_p6966_d4nt_R1


title: HA02TI

description: 10x RNA


title: 500 nM simvastatin Donor 4 [066F]

city: Oakland

first: Marisa

last: Medina

state: CA

address: 5700 Martin Luther King Jr. Way

department: Pediatrics

institute: UCSF

data_processing:
Aligned using 2-pass alignment with STAR
Duplicate sequence fragments removed using Picard MarkDuplicates
Quantification of annotated genes using FeatureCounts
Library size adjustment, variance stabilization, and differential expression analysis in DESeq2
Genome_build: hg19
Supplementary_files_format_and_content: Raw gene counts; Library size adjusted and variance stabilized gene expression levels

source_name: primary human hepatocytes

extract_protocol:
RNA was extracted using the Qiagen RNAeasy mini-kit with QIAshredders
Illumina polyA-selected, strand-specific (dUTP second strand marking protocol), paired-end library preparation

treatment_protocol: Plated cells were treated for 24 hours with 0, 500, or 2000 nM activated simvastatin

value: Female

tag: bmi

tag: smoking

value: No

tag: alcohol use

value: primary human hepatocytes

value: 500 nM simvastatin


title: 3tag_mRNAseq cdca7_a_CDCA7, R2

description:
Library name: 3tag_mRNAseq_cdca7_a_CDCA7_R2
cdca7_a_CDCA7_R2

tag: batch

value: B


title: ddm1, H3K9me2, rep2

description:
Library name: ChIP_ddm1_H3K9me2_rep2
score file normalized to depth and log2 normalized to H3

value: 31-day-old rosette leaves

value: C


title: Mecp2_flox; CreER + TMX Week 1 Replicate 2 [Sample_2]

value: Hippocampus

value: 17 weeks


title: HA04AC

description: 10x RNA

tag: patient

tag: race

value: no


title: 3tag_mRNAseq cdca7_a_CDCA7, R3

description:
Library name: 3tag_mRNAseq_cdca7_a_CDCA7_R3
cdca7_a_CDCA7_R3


title: Control Donor 4 [066E]

tag: cell type

value: 0 nM simvastatin


title: cdca7ab_1, H3K9me2, rep2

description:
Library name: ChIP_cdca7ab_1_H3K9me2_rep2
score file normalized to depth and log2 normalized to H3


title: 3tag_mRNAseq cdca7_a_CDCA7, R1

description:
Library name: 3tag_mRNAseq_cdca7_a_CDCA7_R1
cdca7_a_CDCA7_R1


title: HA02AC

description: 10x RNA

value: african

tag: history

tag: treatment (biological)

tag: sample region


title: ddm1, H3K9me2, rep1

description:
Library name: ChIP_ddm1_H3K9me2_rep1
score file normalized to depth and log2 normalized to H3

tag: tissue


title: 2000 nM simvastatin Donor 3 [066D]

tag: age

tag: Sex

value: 1-2 beers currently once a week

value: 2000 nM simvastatin


title: Col_0, H3K9me2, rep1

description:
Library name: ChIP_Col_0_H3K9me2_rep1
score file normalized to depth and log2 normalized to H3

tag: chip antibody

tag: genotype


title: 500 nM simvastatin Donor 3 [066C]

tag: treatment


title: 3tag_mRNAseq cdca7_ab_CDCA7_no_YFP, R1

description:
Library name: 3tag_mRNAseq_cdca7_ab_CDCA7_no_YFP_R1
cdca7_ab_CDCA7_no_YFP_R1

value: 28-day-old rosette leaves


title: cdca7ab_2, H3K9me2, rep1

description:
Library name: ChIP_cdca7ab_2_H3K9me2_rep1
score file normalized to depth and log2 normalized to H3


title: uro_stm2457_rip2

city: Heidelberg

first: Jinyun

last: Xu

address: Im Neuenheimer Feld 280

country: Germany

institute: German Cancer Research Center

data_processing:
Raw reads were  trimmed using TrimGalore (version 0.6.10).
Trimmed reads were then mapped to rRNA (sourced from the National Center for Biotechnology Information Nucleotide database) using Bowtie2 (version 2.5.2). Unmapped reads were then aligned to the human genome and transcriptome using HISAT2 (version 2.2.1).
Duplicate reads and those with low mapping quality were filtered out using filterdup function from MACS2 (version 2.2.9.1)
Peak calling was performed using MACS2 (version 2.2.9.1) with --nomodel and --extsize 200 parameters, and peaks with a q-value < 0.01 were considered significant.
Significant peaks identified in both biological replicates were then merged using BEDtools (version 2.31.1).
Differentially bound sites were identified using Diffbind (version 3.6.1) with default parameters.
Assembly: hg38
Supplementary files format and content: bigwig
Supplementary files format and content: The differentially bound sites were in csv file.

source_name: UROtsa

growth_protocol: UROtsa cells were cultured in RPMI medium supplemented with 5% FBS and 1% penicillin/streptomycin (P/S), and were maintained as adherent monolayers at 37°C in a humidified incubator with a 5% CO2 atmosphere.

extract_protocol:
RNA immunoprecipitation was performed using the Magna RIP RNA-binding Protein Immunoprecipitation kit (Millipore), following the manufacturer's guidelines. Preparation of whole cell lysates was first performed by a freeze-thaw cycle. Lysates were then clarified by centrifugation and subsequently incubated overnight with anti-YTHDC1 primary antibody (Proteintech) at a 1:1000 dilution. Coprecipitated RNA was isolated using phenol:chloroform:isoamyl alcohol (125:24:1).
RNA libraries for RIP-seq were prepared using SmarTer Ultra Low Input RNA v4 and NEBNext ChIP-Seq kit following manufacturer's protocols.

treatment_protocol: UROtsa wildtype cells were treated with DMSO or 50μM STM2457, and were harvested after 24 hours.

tag: rip antibody

tag: cell line

value: UROtsa

value: urothelial cell

value: Wildtype


title: TWGBS cdca7_b, rep2

description: Library name: TWGBS_cdca7_b_rep2


title: Mecp2_flox; CreER + TMX Week 1 Replicate 1 [Sample_1]

value: Mecp2 Flox; CreER

value: Tamoxifen

tag: timepoint

value: Week 1

value: male

tag: strain


title: Control Donor 3 [066B]

value: Female

tag: bmi

tag: smoking

value: No

tag: alcohol use

value: primary human hepatocytes


title: TWGBS cdca7_ab_p6909_CDCA7a, rep3

description: Library name: TWGBS_cdca7_ab_p6909_CDCA7a_rep3

tag: batch

value: B


title: uro_dmso_rip2

tag: cell type

value: DMSO


title: cdca7ab_1, H3K9me2, rep1

description:
Library name: ChIP_cdca7ab_1_H3K9me2_rep1
score file normalized to depth and log2 normalized to H3

value: 31-day-old rosette leaves

value: C


title: ddm1, H3K27me1, rep2

description:
Library name: ChIP_ddm1_H3K27me1_rep2
score file normalized to depth and log2 normalized to H3

value: H3K27me1 Millipore 17-643


title: 2000 nM simvastatin Donor 2 [065F]

value: Male

value: 1/2 to 1 pack per day currently for 30 years

value: 2000 nM simvastatin


title: TWGBS cdca7_ab_p6966_CDCA7a, rep1

description: Library name: TWGBS_cdca7_ab_p6966_CDCA7a_rep1

value: 28-day-old rosette leaves


title: HA01TI

description: 10x RNA

tag: patient

tag: condition

value: control

tag: race

value: unknown

tag: history

tag: treatment (biological)

value: no


title: uro_dmso_input2

value: UROtsa

value: urothelial cell

value: Wildtype


title: TWGBS WT, rep1

description: Library name: TWGBS_WT_rep1

tag: tissue

value: WT


title: uro_stm2457_input2

tag: genotype


title: Col_0, H3K27me1, rep2

description:
Library name: ChIP_Col_0_H3K27me1_rep2
score file normalized to depth and log2 normalized to H3

tag: chip antibody


title: Control Donor 2 [065D]

tag: age

tag: Sex

value: No

value: primary human hepatocytes

tag: treatment

value: 0 nM simvastatin


title: 500 nM simvastatin Donor 2 [065E]

value: 500 nM simvastatin


title: cdca7ab_2, H3K27me1, rep2

description:
Library name: ChIP_cdca7ab_2_H3K27me1_rep2
score file normalized to depth and log2 normalized to H3

value: 31-day-old rosette leaves

value: C


title: uro_stm2457_rip1

tag: rip antibody

tag: cell line


title: HA01AC

description: 10x RNA

tag: sample region


title: TWGBS cdca7_ab, rep1

description: Library name: TWGBS_cdca7_ab_rep1

value: B


title: TWGBS cdca7_a, rep2

description: Library name: TWGBS_cdca7_a_rep2


title: cdca7ab_1, H3K27me1, rep2

description:
Library name: ChIP_cdca7ab_1_H3K27me1_rep2
score file normalized to depth and log2 normalized to H3

value: H3K27me1 Millipore 17-643


title: 2000 nM simvastatin Donor 1 [065C]

value: Female

tag: bmi

tag: smoking

tag: alcohol use

value: 2000 nM simvastatin


title: 500 nM simvastatin Donor 1 [065B]

tag: cell type


title: uro_dmso_rip1

value: DMSO


title: TWGBS cdca7_a_p6909_CDCA7a, rep2

description: Library name: TWGBS_cdca7_a_p6909_CDCA7a_rep2

value: 28-day-old rosette leaves

tag: batch


title: Control Donor 1 [065A]


title: uro_stm2457_input1


title: Col_0, H3K27me1, rep1

description:
Library name: ChIP_Col_0_H3K27me1_rep1
score file normalized to depth and log2 normalized to H3


title: ddm1, H3K27me1, rep1

description:
Library name: ChIP_ddm1_H3K27me1_rep1
score file normalized to depth and log2 normalized to H3


title: TWGBS cdca7_a_p6966_d4nt_CDCA7a, rep2

description: Library name: TWGBS_cdca7_a_p6966_d4nt_CDCA7a_rep2


title: TWGBS cdca7_a_p6966_d4nt_CDCA7a, rep3

description: Library name: TWGBS_cdca7_a_p6966_d4nt_CDCA7a_rep3


title: Conv MF_RXRα Ctrl_GFP_4

city: Boston

first: CBDM

last: Lab

state: MA

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

institute: Harvard Medical School

data_processing:
Reads were mapped to the mouse reference genome (mm10) with STAR 2.7.3a
Non-uniquely mapped reads were discarded.
The uniquely mapped reads were assigned to genes using featureCounts with GENCODE annotation (vM25)
Assembly: mm10
Supplementary files format and content: tab-delimited text files include raw read counts for each Sample

source_name: peritoneal exudate

extract_protocol:
The cells were double-sorted directly into 5 μl TCL (Qiagen) buffer containing 1% 2-mercaptoenthonol (Sigma). Cells were sorted by their corresponding gRNA-conjugated fluorescence reporter, as DAPI-CD19-LYVE1+CD206+ from BMC mice at Day25 after immune reconstitution.  Total RNA was purified using RNAClean XP beads (Beckman Coulter). Polyadenylated mRNA was selected using an anchored oligo(dT) primer (5′–AAGCAGTGGTATCAACGCAGAGTACT30VN-3) and then reverse transcribed to cDNA. First-strand cDNA was subjected to limited PCR amplification followed by Tn5 transposon-based fragmentation using the Nextera XT DNA Library Preparation Kit (Illumina).
Libraries were constructed following the Smart-seq2 RNA-seq library preparation protocol.

treatment_protocol: Peritoneal exudate were isolated by peritoneal lavage, fluorescent antibodies staining, and flow sorting.

value: peritoneal exudate

value: Day25 post BM reconstitution

value: Male

tag: strain


title: TWGBS cdca7_a_p6966_CDCA7a, rep1

description: Library name: TWGBS_cdca7_a_p6966_CDCA7a_rep1


title: cdca7ab_2, H3K27me1, rep1

description:
Library name: ChIP_cdca7ab_2_H3K27me1_rep1
score file normalized to depth and log2 normalized to H3


title: URO_DC1_KO3

data_processing:
Raw RNA-seq data quality was first evaluated using FastQC (version 0.11.9).
Adaptor sequences were trimmed using Trimmomatic (version 0.33).
Reads were then aligned using HISAT2 (version 2.2.1).
The mapped reads quantified using featureCounts(version 2.0.6).
Data were finally normalized geometrically using DEseq2 (version 1.42.0).
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes normalized counts for each sample.

extract_protocol:
Total RNA was extracted from cells using TRIzol reagent (Thermo Fisher Scientific) and following the manufacturer's protocol. Samples were then digested with DNAse I to remove potential genomic DNA contamination and cleaned with the RNA Clean & Concentrator kit (Zymo Research).
RNA libraries for RNA-seq were prepared using Illumina TruSeq Stranded RNA kit following manufacturer's protocols.

value: UROtsa

value: urothelial cell

value: YTHDC1 knockout


title: TWGBS cdca7_a_p6909_CDCA7a, rep1

description: Library name: TWGBS_cdca7_a_p6909_CDCA7a_rep1


title: ddm1, H3, rep2

description:
Library name: ChIP_ddm1_H3_rep2
score file normalized to depth


title: Col_0, H3, rep2

description:
Library name: ChIP_Col_0_H3_rep2
score file normalized to depth


title: Conv MF_RXRα Ctrl_GFP_3

value: WT


title: Conv MF_RXRα Ctrl_GFP_2


title: URO_DC1_KO2


title: cdca7ab_2, H3, rep2

description:
Library name: ChIP_cdca7ab_2_H3_rep2
score file normalized to depth


title: TWGBS cdca7_ab, rep2

description: Library name: TWGBS_cdca7_ab_rep2


title: TWGBS cdca7_a_p6966_d26nt_CDCA7a, rep2

description: Library name: TWGBS_cdca7_a_p6966_d26nt_CDCA7a_rep2


title: URO_DC1_KO1


title: TWGBS cdca7_ab_p6909_CDCA7a, rep4

description: Library name: TWGBS_cdca7_ab_p6909_CDCA7a_rep4


title: 3tag_mRNAseq cdca7_a, R2

description:
Library name: 3tag_mRNAseq_cdca7_a_R2
cdca7_a_R2


title: URO_Ctrl3

value: Control


title: Conv MF_RXRα Ctrl_GFP_1


title: cdca7ab_1, H3, rep2

description:
Library name: ChIP_cdca7ab_1_H3_rep2
score file normalized to depth


title: Conv MF_RXRα Mutant_RFP_4

value: RXR{alpha} mutant


title: ddm1, H3, rep1

description:
Library name: ChIP_ddm1_H3_rep1
score file normalized to depth

value: 31-day-old rosette leaves


title: TWGBS cdca7_ab_p6966_d4nt_CDCA7a, rep2

description: Library name: TWGBS_cdca7_ab_p6966_d4nt_CDCA7a_rep2


title: Conv MF_RXRα Mutant_RFP_2


title: Col_0, H3, rep1

description:
Library name: ChIP_Col_0_H3_rep1
score file normalized to depth

value: C


title: TWGBS cdca7_ab_p6966_CDCA7a, rep2

description: Library name: TWGBS_cdca7_ab_p6966_CDCA7a_rep2

value: B


title: uro_dmso_input1

value: Wildtype


title: IAH8R-BS-RNA-seq-rep1

city: Monrovia

first: Jianjun

last: Chen

department: Systems Biology

institute: Beckman Research Institute of City of Hope

data_processing:
Bisulfite treated reads were preprocessed by TRIMGALORE and then aligned to hg38 by Bismark
Aligned reads were deduplicated and methylation ratio was caluculated by Bisnmark
Assembly: hg38
Supplementary files format and content: Methylated gene list

source_name: Blood lymphoblasts

growth_protocol: Culture the cells with full medium

extract_protocol:
Zymo Direct-Zol RNA Microprep Kit and Promega mRNA isolation Kit for RNA-seq
For RNA-seq, about 300 ng mRNA of each sample was used for library preparation according to the manufacture’s protocol of KAPA mRNA HyperPrep Kit (Illumina Platforms). 10cycles of PCR amplification were performed. KAPA Pure Beads (Kapa Biosystems) were used for library purification. The quality of each library was verified using a Qubit fluorometer (Thermo Fisher Scientific) and further evaluated by the 2100 Bioanalyzer (Agilent Technologies).

treatment_protocol: Transfection were conducted at 1200 rpm/min for 2 hours at 32 °C. Drugs were added to the medium directly 24 hours before collection.

value: Blood lymphoblasts

value: B-ALL PDX

value: malignant B cells

value: bisulfite treated RNAs


title: URO_Ctrl1


title: cdca7ab_2, H3, rep1

description:
Library name: ChIP_cdca7ab_2_H3_rep1
score file normalized to depth


title: Conv MF_RARγ Ctrl_GFP_2

value: peritoneal exudate


title: Conv MF_RARγ Ctrl_GFP_1

value: Day25 post BM reconstitution


title: URO_Ctrl2


title: Conv MF_RXRα Mutant_RFP_3

value: Male


title: TWGBS WT, rep2

description: Library name: TWGBS_WT_rep2

value: 28-day-old rosette leaves


title: cdca7ab_1, H3, rep1

description:
Library name: ChIP_cdca7ab_1_H3_rep1
score file normalized to depth


title: TWGBS cdca7_ab_p6966_CDCA7a, rep3

description: Library name: TWGBS_cdca7_ab_p6966_CDCA7a_rep3


title: SU-DHL-4-shYTHDF2-2-rep2

data_processing:
RNA-seq reads aligned to the GRCh38 genome assembly using STAR_2.6.0a, and the frequency of genes was counted using Htseq 0.11.2. Raw counts were normalized by edgeR bioconductor package and outputed as rpkm.txt file
Assembly: hg38
Supplementary files format and content: tab-delimited text file contains raw counts for each sample

growth_protocol: Culture the cells with full medium and check the gene knock out or overexpression by western blots

extract_protocol:
Zymo Direct-Zol RNA Microprep Kit for RNA-seq, Zymo Oligo Clean & Concentrator Kit for RIP-seq, Zymo RNA & Concentrator for MeRIP-seq.
For RNA-seq, about 300 ng total RNA of each sample was used for library preparation according to the manufacture’s protocol of KAPA mRNA HyperPrep Kit (Illumina Platforms). 10cycles of PCR amplification were performed. KAPA Pure Beads (Kapa Biosystems) were used for library purification. The quality of each library was verified using a Qubit fluorometer (Thermo Fisher Scientific) and further evaluated by the 2100 Bioanalyzer (Agilent Technologies). For RIP-seq, the libraries were conducted using the KAPA Stranded mRNA-Seq Kit (Kapa Biosystems) after depletion of ribosome RNA (rRNA). For MeRIP-seq, the libraries were conducted usign the KAPA Stranded mRNA-Seq Kit (Kapa Biosystems).

value: YTHDF2 KD

value: Transfection of shRNAs


title: Conv MF_RARγ Mutant_RFP_3

value: RAR{gamma} mutant


title: SU-DHL-4-shYTHDF2-2-rep1


title: ddm1, H2A.Z.9_11, rep2

description:
Library name: ChIP_ddm1_H2A.Z.9_11_rep2
score file normalized to depth and log2 normalized to H3


title: Conv MF_RARγ Mutant_RFP_2


title: TWGBS cdca7_ab_p6966_CDCA7a, rep4

description: Library name: TWGBS_cdca7_ab_p6966_CDCA7a_rep4


title: TWGBS cdca7ab_ddm1_1, rep1

description: Library name: TWGBS_cdca7ab_ddm1_1_rep1

value: A


title: Col_0, H2A.Z.9_11, rep2

description:
Library name: ChIP_Col_0_H2A.Z.9_11_rep2
score file normalized to depth and log2 normalized to H3


title: TWGBS cdca7_ab, rep3

description: Library name: TWGBS_cdca7_ab_rep3


title: SU-DHL-4-shYTHDF2-1-rep2


title: IAH8R-BS-RNA-seq-rep2

value: WT


title: cdca7ab_1, H2A.Z.9_11, rep2

description:
Library name: ChIP_cdca7ab_1_H2A.Z.9_11_rep2
score file normalized to depth and log2 normalized to H3

value: 31-day-old rosette leaves


title: Conv MF_RARγ Mutant_RFP_1


title: SU-DHL-4-shNS-rep2

value: shNS


title: TWGBS cdca7_ab_p6909_CDCA7a, rep5

description: Library name: TWGBS_cdca7_ab_p6909_CDCA7a_rep5

value: B


title: Input_Chipmentation_rep2

data_processing:
Low-quality reads were removed using Sickle and adapter sequences were trimmed using cutadapt (v1.14).
Reads were aligned to the corresponding genome by bowtie2 (v2.3.4.3) with the following parameters: -X 1000 --fr --no-mixed --no-discordant.
Non-uniquely mapped and mitochondrial DNA reads were removed using a combination of SAMtools functions.
PCR duplicates were removed using Picard (‘MarkDuplicates’, v2.8.0).
Bigwig files were generated using deepTools (‘bamCoverage’, v3.0.2).
Assembly: mm10
Supplementary files format and content: *.bw: bigwig files
Library strategy: ChIPmentation

extract_protocol:
Peritoneal exudate were isolated by peritoneal lavage, fluorescent antibodies staining, and flow sorting by CD11b hi F4/80 hi cells. Cells were fixed with 1% fresh formaldehyde (Thermo Fisher Scientific) for 10 minutes at room temperature with rotation, followed by quenching using 0.125 M glycine for 5 minutes. After washing with ice-cold PBS supplemented with cOmplete protease inhibitor (Roche), cells were resuspended in lysis buffer (10 mM Tris-HCl pH 8.0, 2 mM EDTA, 0.25% SDS, 1x protease inhibitor), and sonicated on the Covaris M220 ultra-sonicator to obtain 200-300 bp DNA fragments using the following settings: peak incident power 50, duty factor 10%, cycles per burst 200, time 8 minutes. Keep 2 µL of supernatant from two replicates as the input DNA at -20 °C. The remaining supernatant was incubated overnight at 4°C on a rotator with 3 µg of anti-RXRα (D6H10) Rabbit mAb (#3085, Cell Signaling), or Rabbit IgG (#2729, Cell Signaling) antibodies pre-coupled to Protein A Dynabeads (Invitrogen). The beads were washed twice sequentially on a pre-cold magnet (Invitrogen) using RIPA-LS wash buffer (10mM Tris-HCl pH 8.0, 140 mM NaCl, 1 mM EDTA, 0.1% SDS, 0.1% sodium deoxycholate, 1% Triton X-100), RIPA-HS wash buffer (10mM Tris-HCl pH 8.0, 500 mM NaCl, 1 mM EDTA, 0.1% SDS, 0.1% sodium deoxycholate, 1% Triton X-100), and RIPA-LiCl wash buffer (10 mM Tris-HCl pH 8.0, 250 mM LiCl, 1mM EDTA, 0.5% NP-40, 0.5% sodium deoxycholate) and followed by a wash with 10 mM Tris-HCl pH 8.0. After washing, the beads were then resuspended in 25 µL tagmentation reaction mix containing 1 µL Tn5 transposase (Illumina), and incubated at 37°C for 5 minutes. After removing the tagmentation reaction mix, beads were washed twice with RIPA-LS wash buffer and once with TE buffer (10 mM Tris-HCl pH 8.0, 500 mM EDTA), followed by elution with 48 µL elution buffer (10 mM Tris-HCl pH 8.0, 300 mM NaCl, 5 mM EDTA, 0.4% SDS) containing 2 µL Proteinase K (NEB) at 55°C for 1 hour and 65°C for 8 hours for de-crosslinking. The input DNA was also incubated with tagmentation reaction mix, and de-crosslinked with Proteinase K. DNA was purified using MinElute Reaction Cleanup Kit (QIAGEN).
Libraries were indexed and amplified using the NEBNext High-Fidelity 2x PCR Master Mix (M0541S, NEB) and ATAC-seq primers, followed by purification using AMPure XP beads.

tag: chipmentation antibody

value: 6~8 weeks old


title: SU-DHL-4-shYTHDF2-1-rep1

value: Blood lymphoblasts


title: Input_Chipmentation_rep1


title: RXRα_Chipmentation_rep2

value: anti-RXRα ( #3085, Cell signaling technology)


title: TWGBS cdca7_ab_p6966_d26nt_CDCA7a, rep4

description: Library name: TWGBS_cdca7_ab_p6966_d26nt_CDCA7a_rep4


title: SU-DHL-4-shNS-rep1

value: malignant B cells


title: Col_0, H2A.Z.9_11, rep1

description:
Library name: ChIP_Col_0_H2A.Z.9_11_rep1
score file normalized to depth and log2 normalized to H3

value: C


title: RXRα_Chipmentation_rep1

value: peritoneal exudate


title: TWGBS cdca7_ab_p6966_CDCA7a, rep5

description: Library name: TWGBS_cdca7_ab_p6966_CDCA7a_rep5


title: TWGBS cdca7_b, rep3

description: Library name: TWGBS_cdca7_b_rep3


title: HOS

first: Yi

address: 6770 Bertner Avenue

institute: The Texas Heart Institute at Baylor College of Medicine

description: LV tissue from a Holt-Oram syndrome (HOS) Patient P198, profiled by 10X Genomics 3'v3 snRNA-seq

data_processing:
Raw sequencing reads were aligned to the genome (build GRCh38) using the 10X Genomics toolkit CellRanger version 7.1.0 (cellranger count) with default parameters.
Assembly: GRCh38
Supplementary files format and content: TSV files: Tab-separated tables. MTX files: long-format matrix files. CSV files: comma-seperated tables.

molecule: nuclear RNA

source_name: Heart left ventricle

extract_protocol:
Cardiac tissue was collected from the LV free wall in the operating room during cardiac transplant surgery. The sample was kept in cold saline on ice during transfer to the laboratory for preservation. It was carefully dissected into multiple aliquots, which were flash-frozen and stored at –80 °C. Nuclear isolation was performed. Briefly, frozen cardiac tissue was dissociated by using a Dounce homogenizer. Single nuclei were isolated via fluorescence-activated cell sorting.
SnRNA-seq was performed by using the 10X Genomics platform. Isolated nuclei were loaded into the 10X Genomics Chromium Controller to obtain the gel beads in emulsion. The sequencing libraries were then prepared according to the manufacturer’s protocols for the Single-cell 3’ Reagents Kits v3. Sequencing was performed by using the NovaSeq 6000 system.

value: Heart left ventricle

value: Cardiac cells

value: Female

tag: patient id

tag: patient diagnosis

value: Holt-Oram syndrome (HOS)


title: ddm1, H2A.Z.9_11, rep1

description:
Library name: ChIP_ddm1_H2A.Z.9_11_rep1
score file normalized to depth and log2 normalized to H3

tag: tissue

tag: genotype


title: cdca7ab_2, H2A.Z.9_11, rep2

description:
Library name: ChIP_cdca7ab_2_H2A.Z.9_11_rep2
score file normalized to depth and log2 normalized to H3

tag: chip antibody


title: LPM_RFP_Thrb_Mut_2

extract_protocol:
The cells were double-sorted directly into 5 μl TCL (Qiagen) buffer containing 1% 2-mercaptoenthonol (Sigma). NR mutant LPMs were sorted by their corresponding gRNA-conjugated fluorescence reporter, as DAPI-CD19-CD3-Ly6C-CD11bhiF4/80hi from BMC mice at 4 weeks after immune reconstitution.   Total RNA was purified using RNAClean XP beads (Beckman Coulter). Polyadenylated mRNA was selected using an anchored oligo(dT) primer (5′–AAGCAGTGGTATCAACGCAGAGTACT30VN-3) and then reverse transcribed to cDNA. First-strand cDNA was subjected to limited PCR amplification followed by Tn5 transposon-based fragmentation using the Nextera XT DNA Library Preparation Kit (Illumina).
Libraries were constructed following the Smart-seq2 RNA-seq library preparation protocol.

tag: age

value: 4 weeks post reconstitution

tag: Sex

value: Male


title: TWGBS cdca7_ab_p6966_d26nt_CDCA7a, rep5

description: Library name: TWGBS_cdca7_ab_p6966_d26nt_CDCA7a_rep5

value: 28-day-old rosette leaves


title: TWGBS WT, rep3

description: Library name: TWGBS_WT_rep3

value: WT


title: cdca7ab_1, H2A.Z.9_11, rep1

description:
Library name: ChIP_cdca7ab_1_H2A.Z.9_11_rep1
score file normalized to depth and log2 normalized to H3

value: 31-day-old rosette leaves


title: cdca7ab_2, H2A.Z.9_11, rep1

description:
Library name: ChIP_cdca7ab_2_H2A.Z.9_11_rep1
score file normalized to depth and log2 normalized to H3


title: LPM_RFP_Thrb_Mut_1

tag: treatment


title: iPSC1 CL3 Producvie ATACseq

city: Suwon

first: Seunghee

last: Jeong

address: 2066 Seobu-ro, Janna-gu, Suwon, Gyeonggi-do, South Korea

institute: Sunkyunkwan University

data_processing:
FASTQ files were aligned with the human genome (GRCh37.p13), and peak calling was executed using the PEPATAC pipeline. Adapter sequences were removed using Skewer, reads were mapped to the GRCh37 build of the human genome using bowtie2, and reads were sorted and isolated using Samtools, while removing duplicates with samblaster. MACS2 was applied for peak calling, extending the peak summits by 250 bp in both directions and filtering based on the ENCODE blacklist.
Assembly: GRCh37 from GENCODE, release 13 was used for analysis
Supplementary files format and content: narrowPeak

growth_protocol: All individual hiPSC clones were maintained using the Stem Cell TeSR-E8 kit in matrigel-coated plates. Upon reaching 70~90% confluency, we conducted passaging and differentiation.

extract_protocol:
Extraction was carried out when individual hiPSC clones achieved 70~90% confluency, indicating suitability for passaging or cardiomyocytes differentiation. Cell collection was facilitated using 0.5 mM EDTA. Initially, cell counts were prepared for ATAC-seq, with the remaining cells utilized for RNA-seq.
ATAC libraries for ATAC-seq were prepared using Omni-ATAC-seq protocol (J. D. Buenrostro et al., Current Protocols in Molecular Biology, 2015). Breifly, nuclear isolation was performed using lysis buffer, and DNA was transposed using Illumina Tn5 transposase, followed by index PCR for tagmentation-based NGS library preparation.

tag: cell line

value: human induced pluripotent stem cells


title: iPSC1 CL2 Nonproductive ATACseq


title: TWGBS cdca7_a, rep3

description: Library name: TWGBS_cdca7_a_rep3

value: B


title: iPSC1 CL1 Producvie ATACseq


title: LPM_GFP_Thra_Mut_1


title: iPSC1 CL2 Nonproductive RNAseq

data_processing:
Sequenced reads were quality-tested using FASTQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc). Paired-end reads were aligned to the Gencode GRCh37.p13 reference genome (https://www.gencodegenes.org) using STAR (v.2.7.3a) with the default settings. Gene counts were quantified using featureCounts based on the hg19 GenCode annotation reference.
Assembly: GRCh37 from GENCODE, release 13 was used for analysis
Supplementary files format and content: tab-deliminated text file includes raw counts for each samples

extract_protocol:
Extraction was carried out when individual hiPSC clones achieved 70~90% confluency, indicating suitability for passaging or cardiomyocytes differentiation. Cell collection was facilitated using 0.5 mM EDTA. Initially, cell counts were prepared for ATAC-seq, with the remaining cells utilized for RNA-seq.
RNA libraries for RNA-seq were prepared using TruSeq Stranded mRNA Sample Prep Kit following manufacturer's protocols.


title: iPSC1 CL3 Producvie RNAseq


title: TWGBS cdca7_a_p6966_d4nt_CDCA7a, rep4

description: Library name: TWGBS_cdca7_a_p6966_d4nt_CDCA7a_rep4


title: LPM_GFP_Thra_Mut_2


title: ddm1, H2A.W.6_7, rep2

description:
Library name: ChIP_ddm1_H2A.W.6_7_rep2
score file normalized to depth and log2 normalized to H3


title: TWGBS cdca7_a_p6909_CDCA7a, rep3

description: Library name: TWGBS_cdca7_a_p6909_CDCA7a_rep3


title: Col_0, H2A.W.6_7, rep2

description:
Library name: ChIP_Col_0_H2A.W.6_7_rep2
score file normalized to depth and log2 normalized to H3


title: cdca7ab_2, H2A.W.6_7, rep2

description:
Library name: ChIP_cdca7ab_2_H2A.W.6_7_rep2
score file normalized to depth and log2 normalized to H3


title: LPM_BFP_Rxrb_Mut_2


title: cdca7ab_1, H2A.W.6_7, rep2

description:
Library name: ChIP_cdca7ab_1_H2A.W.6_7_rep2
score file normalized to depth and log2 normalized to H3


title: TWGBS cdca7_a_p6966_d26nt_CDCA7a, rep3

description: Library name: TWGBS_cdca7_a_p6966_d26nt_CDCA7a_rep3


title: LPM_BFP_Rxrb_Mut_1


title: ddm1, H2A.W.6_7, rep1

description:
Library name: ChIP_ddm1_H2A.W.6_7_rep1
score file normalized to depth and log2 normalized to H3


title: TWGBS cdca7_ab_p6966_d26nt_CDCA7a, rep3

description: Library name: TWGBS_cdca7_ab_p6966_d26nt_CDCA7a_rep3


title: NC3-IP

city: Guangzhou

first: chen

middle: wei

last: fen

address: 4F, Building 1, Standard Property Unit 3, International Biotech Island

country: China

institute: Forevergen

data_processing:
Illumina CASAVA 1.8 software used for basecalling.
Bioinformatics analysis was applied to investigate differences in m6A-modified circRNA between the GDM and NC groups in placental tissue. Cutadapt (v2.5) was used to trim adapters and filter for sequences. Differential m6A peak were identified using exomePeak R package (v2.13.2). m6A-RNA-related genomic features were visualized using Guitar R package (v1.16.0). Identified m6A peaks which P <0.05 were chosen for the de novo motif analysis using Homer (v4.10.4).
Box-plot was generated to show the number of m6A peaks enriched in circRNA in placental tissue in the GDM and NC groups, and a volcano plot was generated to display the differential m6A-modified circRNA in the GDM and NC groups in placental tissue. The screening criteria were P <0.05 and |Log2(FC)| >1.
Gene ontology (GO) annotations were conducted on maternal genes for differential m6A-modified circRNA at the Biological Process (BP), Molecular Function (MF), and Cellular Component (CC) levels, based on GO database (http://geneontology.org/). Pathway annotations were performed based on Kyoto Encyclopedia of Genes and Genomes (KEGG) database (https://www.kegg.jp/). GO and KEGG analysis were performed using clusterProfiler R package (v3.6.0).
Assembly: hg19
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
Library strategy: MeRIP-Seq

source_name: Placental tissue

extract_protocol:
Total RNA was isolated using TRIzol™ Reagent (15596018, Invitrogen). The concentration of total RNA was measured by Qubit RNA HS assay kit (Q32852, Invitrogen). 100 μg total RNA was fragmented into 100-200 nt RNA fragments using 10X RNA Fragmentation Buffer (100 mM Tris-HCl, 100 mM ZnCl2 in nuclease-free H2O). The reaction was stopped by adding 10X EDTA (0.5M EDTA). Methylated RNA immunoprecipitation was performed using EpiTM m6A immunoprecipitation kit (R1804, Epibiotek). Briefly, fragmented RNA was incubated with anti-m6A monoclonal antibody (ab208577, Abcam) at 4℃ for 3 h and then with protein A/G magnetic beads (8880210002D/10004D, Invitrogen) at 4℃ for an additional 2 h to obtain immunoprecipitated RNA fragments. m6A-enriched RNA was purified using TRIzol™ Reagent.
The library was prepared by smart-seq method. Both the input samples without IP and the m6A IP samples were subjected to 150 bp, paired-end sequencing on an Illumina NovaSeq 6000 sequencer.

value: Placental tissue

tag: disease state

value: normal control


title: LPM_RFP_Rxra_Mut_2


title: Col_0, H2A.W.6_7, rep1

description:
Library name: ChIP_Col_0_H2A.W.6_7_rep1
score file normalized to depth and log2 normalized to H3


title: NC3-Input


title: cdca7ab_1, H2A.W.6_7, rep1

description:
Library name: ChIP_cdca7ab_1_H2A.W.6_7_rep1
score file normalized to depth and log2 normalized to H3


title: NC2-Input


title: NC1-IP


title: LPM_GFP_Rora_Mut_2


title: TWGBS cdca7_ab_p6966_d4nt_CDCA7a, rep1

description: Library name: TWGBS_cdca7_ab_p6966_d4nt_CDCA7a_rep1


title: TWGBS cdca7_b, rep1

description: Library name: TWGBS_cdca7_b_rep1


title: LPM_RFP_Rxra_Mut_1


title: NC1-Input


title: LPM_GFP_Rarg_Mut_1


title: TWGBS cdca7_ab_p6966_d26nt_CDCA7a, rep2

description: Library name: TWGBS_cdca7_ab_p6966_d26nt_CDCA7a_rep2


title: TWGBS cdca7_ab_p6909_CDCA7a, rep2

description: Library name: TWGBS_cdca7_ab_p6909_CDCA7a_rep2


title: LPM_GFP_Rora_Mut_1


title: iPSC1 CL1 Producvie RNAseq


title: LPM_GFP_Rarg_Mut_2


title: TWGBS cdca7_ab_p6909_CDCA7a, rep1

description: Library name: TWGBS_cdca7_ab_p6909_CDCA7a_rep1


title: LPM_BFP_Rarb_Mut_2


title: TWGBS cdca7_a_p6966_d26nt_CDCA7a, rep1

description: Library name: TWGBS_cdca7_a_p6966_d26nt_CDCA7a_rep1


title: NC2-IP


title: TWGBS cdca7_ab_p6966_d26nt_CDCA7a, rep1

description: Library name: TWGBS_cdca7_ab_p6966_d26nt_CDCA7a_rep1


title: GDM3-Input

value: gestational diabetes mellitus patient


title: LPM_BFP_Rarb_Mut_1


title: GDM2-IP


title: TWGBS cdca7_a_p6966_CDCA7a, rep2

description: Library name: TWGBS_cdca7_a_p6966_CDCA7a_rep2


title: TWGBS cdca7_a_p6966_d4nt_CDCA7a, rep1

description: Library name: TWGBS_cdca7_a_p6966_d4nt_CDCA7a_rep1


title: GDM2-Input


title: LPM_RFP_Rara_Mut_1


title: P_EBV_b [257236337193_2]

type: RNA

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

country: France

institute: IPMC/CNRS

description: Gene expression in periodontitis-affected EBV-positive gingival tissue sample

hyb_protocol: The labelled cRNAs were hybridized on SurePrint G3 Human Gene Expression v3 8x60K microarrays per manufacturer’s protocol (Agilent Technologies).

scan_protocol: Arrays were scanned using the Agilent SureScan High Resolution Scanner.

data_processing: Feature extraction data processing. Quantile normalization and paired differential analysis in R / Bioconductor.

label_protocol: To produce cyanine 3-labeled cRNA, the input of 100 ng total RNA samples were amplified and labeled using the single-color Low Input Quick Amp Labeling kit according to manufacturer’s recommendations (Agilent Technologies).

extract_protocol: The total DNA was extracted using the QIAamp DNA Mini kit (Qiagen) according to manufacturer’s instructions. To isolate the total RNA, the hard gingival tissue was thoroughly homogenized using a gentleMACS dissociator with M tube (Miltenyi) and chemical lysis followed by the extraction using RNeasy Mini kit (Qiagen) per manufacturer’s instructions. The concentration and purity of the extracted total RNA and total DNA were determined using a SimpliNano spectrophotometer. The integrity of RNA was assessed using an Agilent Bioanalyzer 2100 and RNA 6000 Nano LabChip kit (Agilent Technologies).

treatment_protocol: Healthy gingival tissues were taken as surgical waste produced after surgical processing of maxillary tuberosity harvested for gingival graft and connective tissue graft techniques in periodontally healthy donors. Periodontitis-affected tissue samples were collected as a surgical waste produced during surgical periodontal therapy. The tissue specimens were directly embedded in a transport media consisting of PBS supplemented with antibiotics/antifungals and kept at 4°C before use. The tissue from the same site in each subject was extensively rinsed with transport media and aseptically split into 2 parts of similar size for subsequent DNA and RNA extractions. Extracted DNA was used for testing the presence and quantity of EBV load, while RNA was used for microarray transcriptomic analysis.

value: Periodontitis-affected gingiva

tag: ebv status

value: EBV-positive

tag: gender


title: GDM1-IP


title: LPM_BFP_Nr4a1_Mut_2

value: peritoneal exudate


title: LPM_BFP_Nr4a1_Mut_1


title: P_EBV_c [257236337194_3]


title: ATAC_UTX_CD8+ Progenitor_3

city: Los Angeles

first: Ho Chung

address: 609 Charles E Young Dr E

department: MIMG

institute: University of California, Los Angeles

description: Library name: Sample 6

data_processing:
The sequencing quality of the libraries was assessed by FastQC, followed by the trimming process using CutAdapt.
Bowtie2 was used to align the sequencing reads to the mm10 mouse genome, and only uniquely mapped reads (MAPQ30) were retained for downstream.
SAMtools was used to convert SAM files into BAM files and sort BAM files.
Picard MarkDuplicates was used to remove duplicate reads in the BAM files.
MACS2 was used for ATAC-seq peak calling (paired-end mode, FDR<0.01).
Assembly: mm10
Supplementary files format and content: The processed data are the differential peak between WT and UTX-deficient progenitor generated by Diffbind package

source_name: pancreatic lymph node

extract_protocol:
Sorted cells were performed Omni-ATAC-seq protocol
the sorted cells were treated with lysis buffer for 3 min on ice, and the extracted nuclei were resuspended in the transposition mix containing 2.5 ul transposase (Illumina) and incubated at 37oC for 30 min with 1,000 rpm shaker. The products were purified with DNA Clean and Concentrator-5 Kit (Zymo Research) and then amplified with PCR for 11 cycles using barcoding primers provided by previous literature. PCR products were performed size selection using AMPure XP Bead (Beckman coulter) to purify DNA fragments from 150-1,000 bp. The concentration and quality control were measured by Qubit and Tapestation.

value: pancreatic lymph node

value: CD8+ T cells


title: GDM1-Input


title: GDM3-IP


title: LPM_BFP_Nr3c2_Mut_2


title: LPM_BFP_Nr3c2_Mut_1


title: ATAC_UTX_CD8+ Progenitor_2

description: Library name: Sample 5


title: P_NEG_d [257236337194_5]

description: Gene expression in periodontitis-affected EBV-negative gingival tissue sample

value: EBV-negative


title: P_EBV_d [257236337194_8]


title: P_EBV_a [257236337192_8]

value: Female


title: ATAC_UTX_CD8+ Progenitor_1

description: Library name: Sample 4


title: P_NEG_c [257236337193_4]


title: LPM_RFP_Rara_Mut_2

value: 4 weeks post reconstitution


title: IAH8R-flag-PABPC1-IP-rep2

data_processing:
Reads were mapped to GRCh38 reference genome by vSTAR_2.6.1d. Raw counts for RNA-seq were calculated using Htseq v0.11.2. Peaks calling for RIP-seq and MeRIP-seq was conducted using exomePeak2 with default settings.
Assembly: hg38
Supplementary files format and content: tab-delimited text file contains raw counts for each sample
Supplementary files format and content: Peak files in tab-delimited text format

value: Blood lymphoblasts

value: PDX cells (IAH8R)

value: malignant B cells

value: Transfection of  falg PABPC1


title: IAH8R-flag-PABPC1-IP-rep1


title: P_NEG_a [257236337192_3]

value: Male


title: LPM_RFP_Nr3c1_Mut_2


title: H_EBV_d [257236337194_1]

description: Gene expression in periodontally healthy EBV-positive gingival tissue sample

value: Healthy gingiva


title: P_NEG_b [257236337192_5]


title: ATAC_WT_CD8+ Progenitor_3

description: Library name: Sample 3

value: WT


title: Dura mater, sham surgery

city: Paris

first: Ruchith

last: Singhabahu

address: 47 bd de l'Hôpital

institute: Institut du Cerveau

description:
Library name: SH
10x Genomics

data_processing:
Using 100 cycles cartridge from ILLUMINA, calculations are based on 80000 reads/cell minimum per sample.
Assembly: Mouse mm39
Supplementary files format and content: Tab-separated value files and matrix files

source_name: Dura mater

extract_protocol:
Mice were euthanized and perfused with 20 mL of PBS. Skullcaps were dissected using small surgical scissors and immediately placed in ice-cold PBS. Dural meninges were carefully peeled off the skullcaps using fine forceps and transferred to tubes for enzymatic digestion in RPMI medium (Gibco, 21875-034) supplemented with 2.5 mg/mL collagenase D (Roche, 11088866001) and 0.1 mg/mL DNase I (Roche, 11284932001) for 20 minutes at 37°C. The tissue was then dissociated by repeated pipetting (25 strokes) and passed through a 35-μm cell strainer. Following centrifugation (5 minutes at 400g, 4°C), cells were resuspended in 150 μL PBS and pooled from two meninges per well in 96-well V-bottom plates. To minimize nonspecific antibody binding, cell preparations were first incubated for 10 minutes at 4°C with anti-CD16/32 (Fc block; BD Biosciences, 5 µg/mL). Subsequently, a fluorescently conjugated antibody cocktail, including Live-or-Dye 405/452 (Biotium, 32003, 0.05 µL/test), was added. Cells were incubated with the antibodies for 30 minutes at 4°C, followed by centrifugation (5 minutes at 500g, 4°C) and a single PBS wash. Finally, cells were resuspended in 600 µL of PBS and sorted using the MoFlo Astrios cell sorter (Beckman Coulter). Dural cells were identified as viable singlets and collected in PBS containing 20% BSA.
singleCell library prep were realized with chromium from 10X Genomics. Chromium Next GEM Single Cell 3' GEM kit and Chip G were used, following manufacturer’s recommendations. 20000 cells were loaded on the chromium and sequenced on ILLUMINA NovaseqXplus.

value: Dura mater

value: female

value: sham


title: Dura mater, JVL-14

description:
Library name: J14
10x Genomics


title: IAH8R-flag-PABPC1-Input-rep2


title: LPM_RFP_Nr3c1_Mut_1


title: ATAC_WT_CD8+ Progenitors_2

description: Library name: Sample 2


title: IAH8R-flag-PABPC1-IP-rep3


title: H_EBV_b [257236337193_1]

value: EBV-positive


title: IAH8R-flag-PABPC1-Input-rep1


title: ATAC_WT_CD8+ Progenitors_1

description: Library name: Sample 1


title: H_EBV_c [257236337193_6]


title: LPM_RFP_Nr2f6_Mut_2

value: peritoneal exudate


title: IAH8R-Cas9-flag-YTHDF2-RNA-MUT-IP-rep-1

value: RNA-MUT-IP

value: Transfection of sgRNAs and flag YTHDF2 proteins


title: LPM_RFP_Nr2f6_Mut_1


title: H_NEG_d [257236337194_6]

description: Gene expression in periodontally healthy EBV-negative gingival tissue sample

value: EBV-negative


title: H_EBV_a [257236337192_1]

value: Female