title: ChIP_seq_BRM_bcl7ab_IP2

data_processing:
The raw reads were mapped to the reference genome (Arabidopsis thaliana genome, TAIR10) with Bowtie for Illumina (Galaxy Version 1.1.2) for DNA sequencing on web https://usegalaxy.org/ with default setting, except that the paired-end was required.
MACS2 (Galaxy Version 2.1.1) was used for peak calling using the following parameters “gsize=119,667,750, bw=300, q=0.05, nomodel, extsize=200”.
The alignments were first converted to Wiggle (WIG) files and the bigwig files were generated using bamCoverage with “-bs 10”, “--normalizeUsing RPKM (reads per kilobase per million)” in DeepTools and then the data were imported into the Integrative Genomics Viewer (IGV) for visualization.
Assembly: TAIR10
Supplementary files format and content: bed files

extract_protocol:
Lysates were clarified from sonicated protein-DNA complexes were isolated with GFP antibody.
About 2 ng of ChIP DNA immuoprecipitated by anti-GFP antibody was used for ChIP-seq library construction. Blunting end, adapter ligation and amplification were carried out using Illumina Genomic DNA Sample Prep Kits according to the manufacturer's protocol. Novaseq was used for high-throughput sequencing of the ChIP-seq library.


title: E11.5 neuraltube, wildtype, enhancer-capture HiC rep1

status: Public on Jan 03 2024

type: SRA

city: Irvine

first: Evgeny

last: Kvon

address: McGaugh Hall

country: USA

institute: University of California, Irvine

description: NT.ibed

library_source: genomic

data_processing:
Ligated reads were trimmed using DpnII restriction recognition sites and mapped to the DpnII-digested reference genome (mm10) using HiCUP (Wingett et al. 2015), followed by quality filtering and deduplication. For each tissue, the ecHi-C experiment produced, on average, 20 million unique on-target paired-end reads, resulting in a total of 200 million valid read pairs
Next, all DpnII fragments overlapping with the same bait region were merged into a single fragment in silico. Subsequently, the rest of the DpnII fragments were merged based on the size distribution of the pooled fragments that overlapped with bait regions. The mean fragment size of pooled fragments is ~3,000 bp. Significant interactions were called by CHiCAGO (score > 5) with default setting (Cairns et al. 2016; Freire-Pritchett et al. 2021) using combined replicates from HiCUP pipeline, by using the design file with the following parameters: --minFragLen=300 --maxFragLen=20000 --binsize=20000 --maxLBrownEst=3000000 --removeAdjacent=FALSE. We removed significant interactions that didn’t have valid ditag reads on neighboring fragments to avoid spurious interaction spikes (Schoenfelder et al. 2015). Regions >2 Mb from the bait regions were excluded from the analysis.
Supplementary files format and content: (capture hic) iBED

molecule: genomic DNA

organism: Mus musculus

source_name: neuraltube

extract_protocol:
E11.5 embryos were collected for dissection using approved institutional protocols. Tissue from multiple embryos was pooled together in the same collection tube, and at least two separate collection tubes were collected for each tissue for biological replication.
Tissues were incubated with collagenase (Gibco) in a thermomixer at 37 ℃ until the cells were dissociated, about 10 to 20 min. The single-cell solution was fixed by adding formaldehyde (Sigma-Aldrich) to a final concentration of 2% at RT for 10 min as described previously. Ice-cold glycine solution was added to a final concentration of 200 mM to quench crosslinking. Cells were then resuspended in cold lysis buffer (50 mM Tris, pH 7.5, 150 mM NaCl, 5 mM EDTA, 0.5% NP-40, 1.15% Triton X-100 and 1X protease inhibitor cocktail (Thermo Scientific)) and incubated on ice for 15 min. Nuclei pellets were obtained by centrifuge at 750 g for 5 min at 4 ℃, followed by snap-freezing and storage at -80 ℃. Frozen nuclei pellets (2-6 million) were thawed on ice, followed by adding SDS and Triton X-100 to remove non-crosslinked proteins and sequester SDS, and digested using DpnII (NBE) overnight at 37 ℃. The ends of restriction fragments were labeled with biotinylated dCTP and ligated at room temperature for 4 hours. After de-crosslinking and precipitation, ligated products were sheared using a Covaris sonicator (duty cycle: 10%, intensity: 5, cycles per burst: 200, treatment time: 180 s in total) to an average fragment size of 200bp. The ligated sheared 3C libraries (10-12 ug for each replicate) were pulled down using Streptavidin Dynabeads (Thermo Scientific) to get rid of unligated fragments, followed by end repair, adaptor ligation and library amplification according to modified Agilent SureSelectXT protocol. The ecHi-C library was created by performing a target-enrichment protocol using capture RNA probes according to Agilent SureSelect XT protocol with an input amount of 750 ng of Hi-C library per sample.
Following hybridization to the RNA oligo library, each ecHi-C library was amplified using 13 cycles and post amplification libraries were size selected at 200-500bp in length using Agencourt AMPure XP beads from Beckman Coulter. Libraries were sequenced (paired-end 100 or 150 bp) using Illumina NovaSeq 6000 to enrich enhancer-centric interactions yielding a total of 1 billion unique paired-end reads.

tag: tissue

value: neuraltube

tag: age


title: E11.5 hindbrain, wildtype, enhancer-capture HiC rep1

description: HB.ibed

source_name: hindbrain

value: hindbrain


title: EGFP(R96Q)+Arg-tRNA_Gln(CUG)_mRNA_rep2

city: Chicago

first: Tao

last: Pan

state: Illinois

address: 929 E. 57th Street

department: Biochemistry and Molecular Biology

institute: University of Chicago

library_source: transcriptomic

data_processing:
Paired end reads were mapped to human hg38 genome by STAR with the annotation file gencode.v26.annotation.gtf from GENCODE database (https://www.gencodegenes.org) and with options --limitBAMsortRAM 62425435837 --outSAMattributes NH HI AS nM NM MD jM jI XS --outFilterMultimapNmax 50 --outFilterMismatchNmax 15 --outSJfilterDistToOtherSJmin 10 0 5 10 --alignIntronMin 15 --outFilterScoreMinOverLread 0 --outFilterMatchNminOverLread 0 --outFilterMatchNmin 15 --readFilesCommand zcat --outSAMtype BAM SortedByCoordinate --outReadsUnmapped Fastx --quantMode GeneCounts --twopassMode Basic --outSAMstrandField intronMotif.
Uniqule mapped reads were extracted by samtools view with options -bS -q 255 -f 0x2, and then sorted and indexed with samtools.
Uniquely mapped reads were counted by featureCounts with options --verbose -s 1 -B -C -p -t exon -g gene_id --extraAttributes gene_type.
Assembly: hg38
Supplementary files format and content: comma separated value (csv) - indicates expression level of each gene

molecule: polyA RNA

organism: Homo sapiens

growth_protocol: HEK293 cells were authenticated and tested negative for mycoplasma. HEK293 cells were cultured at 37°C with 5% CO2 in Dulbecco’s Modified Eagle’s (DMEM) high-glucose medium (Cytiva Cat. SH30022.01) supplemented with 10% heat-inactivated fetal bovine serum and 100U/ml Penicillin-Streptomycin.

extract_protocol:
RNA-seq experiments were performed on 3 independent replicates from HEK293 cells overexpressing the mistranslation reporters with and without cognate mc-tRNAs. HEK293 cells were sorted on the FACSAria Fusion 5-18 cell sorter for mCherry+, i.e., successfully transfected, cell populations 48 h post-transfection. Total RNAs were extracted from sorted cells with TRIzolTM reagent (Invitrogen Cat. 15596026). 1 µg of total RNA per sample was used as input for RNA-seq library construct. Total RNA samples were polyA-selected to enrich mature mRNA species.
RNA quality and quantity was assessed using the Agilent bio-analyzer. Strand-specific RNA-SEQ libraries were prepared using a TruSEQ based mRNA-SEQ library protocol (Illumina). Library quality and quantity was assessed using the Agilent bio-analyzer and libraries were sequenced using an Illumina NovaSEQ6000 (Illumina provided reagents and protocols).

treatment_protocol: Cells were seeded on 6-well plates one day before transfection and reached 50-70% confluent on the day of transfection. Plasmids used for transfection were prepared with PureYieldTM plasmid Miniprep/Midiprep systems (Promega Cat. A1222/A2492) and ethanol precipitated. Transfections were performed using LipofectamineTM 3000 (InvitrogenTM Cat. L3000015) and following the manufacture’s protocol.

tag: cell line

tag: genotype

value: wt

tag: treatment

value: Transfected with EGFP(R96Q)-mCherry mistranslation reporter together with mc-tRNA Arg-tRNA_Gln(CUG) on a single plasmid


title: ChIP_seq_BRM_bcl7ab_IP1

city: Guangzhou

first: yaoguang

last: yu

address: No. 135, Xingang Xi Road

country: China

institute: SUN YAT-SEN UNIVERSITY

organism: Arabidopsis thaliana

source_name: Young seedlings

growth_protocol: Plants were grown in 1/2MS media with 22 degree in 14h light/10h dark

value: Seedling

tag: developmental stage

value: 14-day-old,short day

tag: antibody

value: GFP (ab290, abcam)


title: Fbxo2GAP_C28

city: Houston

first: Chenghang

last: Zong

state: TX

address: 1 Baylor Plaza

institute: Baylor College of Medicine

library_source: transcriptomic single cell

data_processing:
The fastq files of read 1 were mapped to the reference transcriptome by using STAR.
The reads were assigned to genes by using htseq-count.
The UMI sequences were extracted from read 2 (the first five bases).
The reads with the same UMI were collapsed. The number of UMIs of each gene were counted.
Assembly: mm10
Supplementary files format and content: Tab-separated UMI count matrix; Files: Exon_UMI_matrix.txt

molecule: total RNA

source_name: cochlea

extract_protocol:
After tissue dissociation, single cells are sorted into 96-well plate by FACS.
Libraries were constructed by following SMART-MATQ protocol.

treatment_protocol: Animal were treated with tamoxifen at 3 weeks and cells were harvested at 5 weeks.

value: cochlea

value: tamoxifen at 3 weeks, dissociation with Papain at 5 weeks.


title: E11.5 neuraltube, wildtype, enhancer-capture HiC rep2

description: NT.ibed


title: E11.5 forelimb, wildtype, enhancer-capture HiC rep1

description: FL.ibed

source_name: forelimb

value: forelimb


title: ChIP_seq_BRM_IP2

description: BRM


title: EGFP(R96Q)+Arg-tRNA_Gln(CUG)_mRNA_rep1


title: Fbxo2GAP_C26


title: EGFP(R96Q)_mRNA_rep3

value: Transfected with EGFP(R96Q)-mCherry mistranslation reporter


title: E11.5 forelimb, wildtype, enhancer-capture HiC rep2

description: FL.ibed


title: EGFP(R96C)_mRNA_rep2

value: Transfected with EGFP(R96C)-mCherry mistranslation reporter


title: ChIP_seq_BCL7B_brm-1_IP2


title: Fbxo2GAP_C25


title: E11.5 hindlimb, wildtype, enhancer-capture HiC rep1

description: HL.ibed

source_name: hindlimb

value: hindlimb


title: EGFP(R96C)_mRNA_rep1


title: E11.5 hindbrain, wildtype, enhancer-capture HiC rep2

description: HB.ibed


title: ChIP_seq_BCL7B_brm-1_IP1


title: EGFP(R96Q)_mRNA_rep2


title: ChIP-seq_BRM-GFP brm-1_Drosophila

data_processing:
The raw reads were mapped to the reference genome (Arabidopsis thaliana genome, TAIR10) with Bowtie for Illumina (Galaxy Version 1.1.2) for DNA sequencing on web https://usegalaxy.org/ with default setting, except that the paired-end was required.   MNase-seq data analyses were performed according to published methods86 with some modifications. In brief, raw reads were processed with cutadapt (version 3.4, -m 10) to remove adaptors. Secondly, the processed reads were mapped to the Arabidopsis thaliana genome (TAIR10) by Bowtie2 with default settings78. Thirdly, the nucleosome positions were determined by applying the improved nucleosome-positioning algorithm iNPS with default settings87. And then, the smoothed bigwig files across biological replicates were generated by using ‘dpos’ function in DANPOS388. Finally, MNase-seq data among samples were normalized by applying quantile normalization methods to normalize occupancy with ‘wiq’ function in DANPOS3.
MACS2 (Galaxy Version 2.1.1) was used for peak calling using the following parameters “gsize=119,667,750, bw=300, q=0.05, nomodel, extsize=200”.
The alignments were first converted to Wiggle (WIG) files and the bigwig files were generated using bamCoverage with “-bs 10”, “--normalizeUsing RPKM (reads per kilobase per million)” in DeepTools and then the data were imported into the Integrative Genomics Viewer (IGV) for visualization.
Assembly: TAIR10
Supplementary files format and content: bigwig files

extract_protocol:
Lysates were clarified from sonicated protein-DNA complexes were isolated with GFP antibody.
About 2 ng of ChIP DNA immuoprecipitated by anti-GFP antibody was used for ChIP-seq library construction. Blunting end, adapter ligation and amplification were carried out using Illumina Genomic DNA Sample Prep Kits according to the manufacturer's protocol. Novaseq was used for high-throughput sequencing of the ChIP-seq library.  The MNase assays were carried out as described previously85 with minor modifications. Approximately 0.4g of seedlings were used per sample. For MNase treatment, the prepared nuclei were resuspended in prewarmed MNase digestion buffer (20 mM Tris-HCl, pH 8.0, 5 mM NaCl, and 2.5 mM CaCl2), followed by the addition of 0.5 units of MNase (Takara, Cat. No. 2910A,) and incubation (10 min at 37◦C with periodic agitation). Finally, the mono-nucleosome DNA was isolated from 2% agarose gels and quantified by the Qubit dsDNA HS assay kit (ThermoFisher, Cat. No. Q32851).


title: Fbxo2GAP_C23


title: E11.5 hindlimb, wildtype, enhancer-capture HiC rep2

description: HL.ibed


title: ChIP_seq_BCL7B_IP2


title: Fbxo2GAP_C22


title: EGFP(R96Q)_mRNA_rep1


title: EGFP(R65)+Ser-tRNA_Arg(CCG)_mRNA_rep3

value: Transfected with EGFP(R65)-mCherry mistranslation reporter together with mc-tRNA Ser-tRNA_Arg(CCG) on a single plasmid


title: E11.5 face, wildtype, enhancer-capture HiC rep2

description: CF.ibed

source_name: face

value: face


title: ChIP_seq_BCL7B_IP1


title: EGFP(R65)+Ser-tRNA_Arg(CCG)_mRNA_rep1


title: ChIP_seq_BRM_IP1

description: BRM


title: EGFP(R65)+Ser-tRNA_Arg(CCG)_mRNA_rep2


title: ChIP_seq_BCL7A_brm-1_IP1


title: E11.5 face, wildtype, enhancer-capture HiC rep1

description: CF.ibed


title: Fbxo2GAP_C27


title: Fbxo2GAP_C21


title: ChIP_seq_BCL7A_IP2


title: E11.5 trunk, wildtype, enhancer-capture HiC rep1

description: TK.ibed

source_name: trunk

value: trunk


title: ChIP_seq_BCL7A_IP1


title: ChIP_seq_BCL7A_brm-1_IP2


title: bcl7a bcl7b brm-1 rep3

first: Yawen

last: Lei

description: brip3 brip4 brm-1 rep3

data_processing:
Sequencing separately at Novogene, using Illumina nova-seq (Sequencing method: Hiseq-PE150).
The paired-end RNA-seq reads were quantified by Salmon(Patro et al., 2017) (v1.5.1) with parameters -k 31 and --type quasi. Salmon index was generated using AtRTD2.fa as the reference transcriptome.
To analyze differential expression, the gene quantification files of all samples were used as inputs (TPM values) for differential gene expression analysis by DESeq2(Love et al., 2014) v3.10. To analyze differential gene expression in all samples, we used “parametric” Fit type, “ratio” method for estimate Size Factors and Wald significance test function provided by DESeq2.
Assembly: TAIR10
Supplementary files format and content: tab-delimited text files include TPM values for wt, brip3, brip4, brip3 brip4, brm-3, brm-1, brip3 brip4 brm-3 and brip3 brip4 brm-1.

extract_protocol:
Total RNA was extracted from 14-day-old Arabidopsis seedlings under short-day conditions using TRIzol reagent (Invitrogen) following the manufacturer's instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: condition

value: SD (short day)

tag: background

value: brip3 brip4 brm-1


title: EGFP(R65)_mRNA_rep1

value: Transfected with EGFP(R65)-mCherry mistranslation reporter


title: Fbxo2GAP_C20


title: Fbxo2GAP_C16


title: E11.5 tail, wildtype, enhancer-capture HiC rep1

description: TL.ibed

source_name: tail

value: tail


title: Fbxo2GAP_C19


title: E11.5 tail, wildtype, enhancer-capture HiC rep2

description: TL.ibed


title: Fbxo2GAP_C18


title: EGFP(R65)_mRNA_rep2

value: wt


title: Fbxo2GAP_C15


title: E11.5 heart, wildtype, enhancer-capture HiC rep2

description: HR.ibed

source_name: heart

value: heart


title: EGFP(R65)_mRNA_rep3


title: E11.5 heart, wildtype, enhancer-capture HiC rep1

description: HR.ibed


title: 276_Cre_pos_Treated

city: Birmingham

first: Nicholas

middle: R

last: Anderson

state: AL

address: 1824 S 6th Ave

institute: University of Alabama at Birmingham

data_processing:
Basecalls were performed using Illumina's bcl2fastq
Trim Galore (version 0.6.7) was used to trim primer adapters using parameters --paired --trim1
Trimmed sequences were then aligned with STAR (version 2.7.9a) using parameters --outReadsUnmapped Fastx --outSAMtype BAM SortedByCoordinate --outSAMattributes All
Transcript abundances were calculated with HTSeq-count (version 0.6.7) using parameters -m union -r pos -t exon -i gene_id -a 10 -s no -f bam
R package DESeq2 was used to normalize and perform differential expression following their vignette
Assembly: Gencode GRCm39 Release M26
Supplementary files format and content: tab delimited text file containing raw counts (transcript abundances) for each gene in each sample

source_name: Bone marrow

extract_protocol:
Qiagen Rneasy Plus Micro Kit
SMARTer Ultra Low Input RNA Kits for Sequencing (v4, TaKaRa Clontech) and Nextera XT DNA Library Preparation Kit (Illumina)

value: Bone marrow

tag: cell type

value: ST-HSC

value: CXCL12 KO

value: Cytarabine, doxorubicin, quizartinib


title: E11.5 trunk, wildtype, enhancer-capture HiC rep2

description: TK.ibed


title: TCR_PBMC_70_TCR_Alzheimers Disease

first: David

last: Gate

state: IL

address: 303 E Chicago Ave, Chicago, IL 60611

department: Neurology

institute: Northwestern University

description:
tcr_contigs_merged.csv
tcr_paired_clonotypes_merged.csv

data_processing:
Illumina RTA3 method for base-calling
10xGenomics cellranger pipeline for alignment and filtering (trimming 5' TSO sequence and 3' polyA tail, alignment with STAR, UMI counting, EmptyDrops method for empty droplet removal)
SoupX background contamination removal (S100A8 and S100A9 were used to estimate contamination fraction and counts were adjusted using SoupX::adjustCounts function)
DoubletFinder doublet removal (doublet formation rate of 5.4% based on 10xGenomics multiplet rate estimation, using 12 PCs and pN = 0.25)
Seurat filtering and normalization (filter out cells with >10% mitochondrial reads, retain cells with at least 200 mapped features, retain features with at least 3 mapped cells, counts were then normalized using Seurat's LogNormalize method)
Assembly: hg38
Supplementary files format and content: .rds object of raw gene count matrix for each gene and cell barcode
Supplementary files format and content: .rds object of log-normalized expression matrix for each gene and cell barcode
Supplementary files format and content: csv of BCR merged contigs
Supplementary files format and content: csv of BCR paired clonotypes
Supplementary files format and content: csv of TCR merged contigs
Supplementary files format and content: csv of TCR paired clonotypes
Library strategy: scV(D)J-seq (TCR)

source_name: Peripheral blood mononuclear cells

extract_protocol:
PBMCs were pelleted, frozen, and resuspended in PBS with 0.04% BSA before being sorted with Sytox blue live/dead dye
Chromium Next GEM Single Cell 5' v2 with immune profiling
scRNAseq + scV(D)J

value: Peripheral blood mononuclear cells

tag: Sex

value: female

tag: disease state

value: Alzheimers Disease


title: TCR_PBMC_947_TCR_Alzheimers Disease

value: male


title: TCR_PBMC_905_TCR_Healthy Control

value: Healthy Control


title: Fbxo2GAP_C17

value: cochlea

value: tamoxifen at 3 weeks, dissociation with Papain at 5 weeks.


title: bcl7a bcl7b brm-3 rep2

description: brip3 brip4 brm-3 rep2

value: SD (short day)

value: Seedling

value: brip3 brip4 brm-3


title: TCR_PBMC_970_TCR_Healthy Control


title: Fbxo2GAP_C12


title: 257_Cre_pos_Treated


title: bcl7a bcl7b brm-1 rep2

description: brip3 brip4 brm-1 rep2

value: brip3 brip4 brm-1


title: Fbxo2GAP_C14


title: bcl7a bcl7b brm-1 rep1

description: brip3 brip4 brm-1 rep1


title: Fbxo2GAP_C13


title: brm-1 rep3


title: 263_Cre_pos_Treated


title: bcl7a bcl7b brm-3 rep1

description: brip3 brip4 brm-3 rep1


title: TCR_PBMC_1236_TCR_Alzheimers Disease


title: Fbxo2GAP_C11


title: TCR_PBMC_1237_TCR_Alzheimers Disease


title: bcl7a bcl7b brm-3 rep3

description: brip3 brip4 brm-3 rep3


title: Fbxo2GAP_C09


title: Fbxo2GAP_C10


title: 262_Cre_neg_Treated

value: CXCL12 WT


title: brm-1 rep1


title: brm-1 rep2


title: 266_Cre_neg_Treated


title: 252_Cre_neg_Treated


title: brm-3 rep3


title: TCR_PBMC_836_TCR_Healthy Control


title: Fbxo2GAP_C08


title: TCR_PBMC_230_TCR_Alzheimers Disease


title: TCR_PBMC_921_TCR_Alzheimers Disease


title: TCR_PBMC_1200_TCR_Healthy Control


title: brm-3 rep2


title: 249_Cre_pos_Veh

value: Vehicle


title: 265_Cre_neg_Veh

value: Bone marrow


title: brm-3 rep1


title: TCR_PBMC_965_TCR_Alzheimers Disease


title: Fbxo2GAP_C06


title: TCR_PBMC_1010_TCR_Healthy Control


title: Fbxo2GAP_C07


title: bcl7a bcl7b rep3

description: brip3 brip4 rep3

value: brip3 brip4


title: Fbxo2GAP_C05


title: TCR_PBMC_989_TCR_Healthy Control


title: bcl7a bcl7b rep2

description: brip3 brip4 rep2


title: Fbxo2GAP_C04


title: TCR_PBMC_1162_TCR_Healthy Control


title: 240_Cre_neg_Veh

value: ST-HSC


title: Fbxo2GAP_C03


title: Sample_R21072416-aIgM-LPS-NAC-aIgM-LPS-NAC

city: shanghai

first: Ying

last: Fu

address: Dongan road

institute: Fudan university

library_source: other

data_processing:
Trimmomatic software were used to remove adapter and low quality reads.
Quality distribution plot and base content distribution were generated by FASTQC. [Andrews S (2012) FastQC: A Quality Control tool for High Throughput Sequence Data. Available: http://www.bioinformatics.babraham.ac.uk/projects/fastqc/]
Mapping of pair-end reads. Before read mapping, clean reads were obtained from the raw reads by removing the adaptor sequences. The clean reads were then aligned to reference genome mm10 sequences using the bwa program.
The bam file generated by the unique mapped reads as an input file, using macs2 software for callpeak with cutoff qvalue < 0.05.
Supplementary files format and content: processed data file include clean data for each Sample

molecule: other

source_name: Stimulated splenic B cell

extract_protocol:
Cell sample reference ‘ATAC-seq: A Method for Assaying Chromatin Accessibility genome-wide’ lysis of cells to obtain nuclei
Transposition reaction: 40000 cell nuclei were processed with Tn5 enzyme (Illumina) and the transposition reaction was processed. The DNA fragment after transposition was retrieved with MinElute PCR Purification Kit(Qiagen).  Database construction: 1X NEBNext High-Fidelity PCR Master Mix (New England Biolabs, MA) was used for PCR amplification. The amplification product was recovered by MinElute PCR Purification Kit (Qiagen).  Sequencing was performed with Illumina Novaseq 6000.

value: Stimulated splenic B cell

value: WT

value: aIgM-LPS-NAC

tag: time


title: Fbxo2GAP_C02


title: bcl7a bcl7b rep1

description: brip3 brip4 rep1


title: TCR_PBMC_820_TCR_Healthy Control

value: Peripheral blood mononuclear cells


title: bcl7b rep2

description: brip4 rep2


title: Fbxo2GAP_C01


title: TCR_PBMC_953_TCR_Alzheimers Disease

value: male

value: Alzheimers Disease


title: 275_Cre_pos_Veh

value: CXCL12 KO


title: bcl7b rep3

description: brip4 rep3


title: TCR_PBMC_1282_TCR_Healthy Control

value: Healthy Control


title: Fbxo2_B96

value: cochlea

value: tamoxifen at 3 weeks, dissociation with Papain at 5 weeks.


title: bcl7b rep1

description: brip4 rep1

value: SD (short day)

value: Seedling


title: control3,day 28

city: Beijing

first: Lihui

last: Meng

address: Dongcheng Strict

institute: Peking Union Medical College Hospital

data_processing:
The image data measured by the high-throughput sequencer are converted into  sequence data (reads) by CASAVA base recognition. Raw data (raw reads) of fastq  format were firstly processed through in-house perl scripts. In this step, clean data  (clean reads) were obtained by removing reads containing adapter, reads containing N  base and low quality reads from raw data.
Reference genome and gene model annotation files were downloaded from  genome website directly. Index of the reference genome was built using Hisat2  (v2.0.5) and paired-end clean reads were aligned to the reference genome using  Hisat2 (v2.0.5).
featureCounts (v1.5.0-p3) was used to count the reads numbers mapped to each  gene. And then FPKM of each gene was calculated based on the length of the gene  and reads count mapped to this gene.
Assembly: mm10
Supplementary files format and content: the text file of gene count of each sample

source_name: retina

extract_protocol:
Total amounts and integrity of RNA were assessed using the RNA Nano 6000  Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
mRNA was purified from total RNA by using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase, then use RNaseH to degrade the RNA. Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and dNTP. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 370~420 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then PCR amplification, the PCR product was purified by AMPure XP beads, and the library was finally obtained.

value: retina

value: infusion with saline


title: 253_Cre_neg_Veh

value: Bone marrow

value: CXCL12 WT

value: Vehicle


title: TCR_PBMC_978_TCR_Healthy Control

value: female


title: Fbxo2_B95


title: control2,day 28

value: WT


title: Fbxo2_B94


title: bcl7a rep3

description: brip3 rep3


title: control1,day 28


title: bcl7a rep2

description: brip3 rep2


title: TCR_PBMC_912_TCR_Healthy Control


title: experiment3,day 28

value: infusion with Ang II


title: Sample_R21072415-aIgM-LPS-aIgM-LPS

value: Stimulated splenic B cell

value: aIgM-LPS


title: Fbxo2_B93


title: TCR_PBMC_656_TCR_Alzheimers Disease

value: Peripheral blood mononuclear cells

value: Alzheimers Disease


title: experiment4,day 28


title: bcl7a rep1

description: brip3 rep1


title: Sample_R21072414-aIgM-aIgM

value: aIgM


title: Fbxo2_B91

value: cochlea


title: Fbxo2_B92

value: tamoxifen at 3 weeks, dissociation with Papain at 5 weeks.


title: TCR_PBMC_781_TCR_Healthy Control

value: Healthy Control


title: biological replicate 2 of postnatal 5wks old mice

city: Shanghai

first: Fan

last: Yang

address: No. 1954, Huashan Road

department: Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders

institute: Bio-X Institutes, Shanghai Jiao Tong University

data_processing:
Fastp software used for filtering.
Hisat2 software used for alignment. GRCm38 was used as reference genome.
R packge ballgown was used for statistic analysis.
Genome_build: GRCm38
Supplementary_files_format_and_content: Comma seperated text file include FPKM of each gene in each sample.

source_name: smooth muscle tissue

growth_protocol: The mice were fed ad libitum with unrestricted access to water. The mice were maintained at 23 °C under a 12 h light/dark cycle. All the mice used in this study were age-matched (postnatal, 1-week-old (PW1), 3-week-old (PW3), and 5-week-old (PW5).

extract_protocol:
Mice were sacrificed with an overdose of isoflurane inhalation followed by cervical dislocation. The entire colons were quickly removed before stripping the mucosal layers by sharp dissection. When the whole colon was opened to expose the mucosa along the mesenteric border, the proximal colon displayed a characteristic thick mucosal fold. This thick mucosal fold section was used for proximal preparation (1 or 2 cm below the ileocecal sphincter). For the distal colon, we used muscle preparations to 2 cm above the internal anal sphincter. These preparations were subsequently rinsed with Krebs-Ringer bicarbonate (Krebs) solution before being frozen in liquid nitrogen. Total RNA was isolated from proximal and distal colon tissues using the Direct-zol RNA Purification Kit (Zymo Research, Irvine, CA, USA) following which, the quality of total RNAs was determined using NanoDrop 2000 (Thermo Scientific, Waltham, MA, USA).
Samples with an RNA integrity number (RIN) exceeding 8.5 were processed for preparation of libraries using a NEBNext Ultra II RNA Library Prep Kit from Illumina (Cat#E7770). RNA sequencing was performed using an Illumina NovaSeq 6000 platform at the DNA facility of Novogene Co. Ltd. (Beijing, China). Deep sequencing was conducted with 150 bp paired-end reads. Each biological replicate was considered as a separate sample.

treatment_protocol: no additional treatment.

value: postnatal 5wks old

value: smooth muscle tissue of colon

tag: strain

value: untreated


title: TCR_PBMC_1111_TCR_Healthy Control


title: TCR_PBMC_1147_TCR_Alzheimers Disease

value: male


title: Fbxo2_B90


title: Fbxo2_B89


title: TCR_PBMC_968_TCR_Healthy Control


title: experiment1,day 28

value: retina


title: Fbxo2_B88


title: TCR_PBMC_942_TCR_Alzheimers Disease


title: WT rep2

value: SD (short day)

value: Seedling


title: Fbxo2_B86


title: experiment2,day 28

value: WT


title: TCR_PBMC_1020_TCR_Healthy Control


title: biological replicate 1 of postnatal 5wks old mice


title: WT rep3


title: TCR_PBMC_780_TCR_Healthy Control

value: female


title: Long-20

type: RNA

city: SHEFFIELD

first: Rachel

last: Waller

state: South Yorkshire

address: SITraN, 385A Glossop Road

department: Neuroscience

country: United Kingdom

institute: The University of Sheffield

hyb_protocol: Post-hybridisation array washing, and staining were performed in the GeneChip Fluidics station and arrays scanned using the GeneChip 3000 7G scanner.

scan_protocol: standard Affymetrix protocol

data_processing: Individual sample .CEL files quantifying gene transcripts were uploaded into Expression Console (Thermo Fisher Scientific, UK) and several quality control (QC) parameters were checked for each sample including poly-A RNA labelling controls, hybridisation controls, positive vs. negative area under the curve (AUC) and signal intensity. Qlucore Omics Explorer (Qlucore, Lund, Switzerland) was used to identify differentially expressed genes between successfully QC’d samples with long vs. short disease duration (FC ≥ ±1.20, p-value 0.05). Both Metascape (http://metascape.org) 14 and Ingenuity Pathway Analysis (IPA) (Qiagen, UK) were used to interrogate the data further.

label: biotin

source_name: Lymphoblastoid cell line RNA

label_protocol: 300 ng of extracted RNA was processed using the Ambion Whole Transcript (WT) Expression Kit (Thermo Fisher Scientific, UK) producing fragmented biotin-labelled sense-stranded copy DNA that was hybridised onto Human Exon 1.0ST GeneChip microarrays

extract_protocol: For mRNA extraction, 75 µl LCL suspension containing approximately 5x10^6 cells was taken through the QIAGEN RNeasy Mini Kit protocol following the manufacturer’s instructions, with total RNA eluted in 40μL RNase-free water

tag: gender

value: Male


title: Fbxo2_B85


title: WT rep1


title: TCR_PBMC_802_TCR_Alzheimers Disease


title: biological replicate 3 of postnatal 5wks old mice


title: biological replicate 3 of postnatal 3wks old mice

value: postnatal 3wks old


title: TCR_PBMC_932_TCR_Alzheimers Disease

value: Peripheral blood mononuclear cells


title: biological replicate 3 of postnatal 1wk old mice

value: postnatal 1wk old


title: biological replicate 2 of postnatal 3wks old mice


title: TCR_PBMC_598_TCR_Healthy Control


title: Long-19

value: Female


title: Fbxo2_B83

value: cochlea


title: biological replicate 1 of postnatal 3wks old mice


title: TCR_PBMC_1279_TCR_Healthy Control


title: Fbxo2_B84

value: tamoxifen at 3 weeks, dissociation with Papain at 5 weeks.


title: Fbxo2_B81


title: biological replicate 1 of postnatal 1wk old mice


title: Fbxo2_B82


title: biological replicate 2 of postnatal 1wk old mice


title: Unstimulated_1

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

extract_protocol:
Total RNA was extracted using RNAsimple Total RNA Kit (TIANGEN, China).
The first step in the workflow involves purifying the poly-A containing mRNA molecules using poly-T oligo-attached magnetic beads. Following purification, the mRNA is fragmented into small pieces using divalent cations under elevated temperature. The cleaved RNA fragments are copied into first strand cDNA using reverse transcriptase and random primers. This is followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. These cDNA fragments then have the addition of a single 'A' base and subsequent ligation of the adapter. The products are then purified and enriched with PCR amplification. We then quantified the PCR yield by Qubit and pooled samples together to make a single strand DNA circle (ssDNA circle), which gave the final library.

value: Stimulated splenic B cell

value: Unstimulated


title: TCR_PBMC_773_TCR_Alzheimers Disease

value: Alzheimers Disease


title: Long-16


title: TCR_PBMC_863_TCR_Alzheimers Disease


title: Fbxo2_B80


title: Long-17


title: Unstimulated_2


title: TCR_PBMC_917_TCR_Alzheimers Disease


title: TCR_PBMC_911_TCR_Healthy Control

value: Healthy Control


title: Long-14


title: Fbxo2_B78


title: Long-18


title: Long-13


title: αIgMLPS_2


title: TCR_PBMC_738_TCR_Alzheimers Disease


title: αIgMLPS_3


title: Fbxo2_B77


title: Long-12


title: Fbxo2_B79


title: Fbxo2_B76


title: TCR_PBMC_1180_TCR_Healthy Control


title: Fbxo2_B75


title: TCR_PBMC_696_TCR_Alzheimers Disease


title: Long-15


title: iROS_2


title: Long-9


title: TCR_PBMC_1273_TCR_Healthy Control

value: male


title: αIgMLPS_1


title: iROS_3


title: Fbxo2_B74


title: Long-10


title: Long-11


title: TCR_PBMC_1052_TCR_Alzheimers Disease


title: TCR_PBMC_516_TCR_Alzheimers Disease


title: Fbxo2_B73


title: αIgM_3

value: alpha-IgM


title: Long-8


title: αIgM_2


title: Fbxo2_B71


title: iROS_1


title: Fbxo2_B69


title: TCR_PBMC_1160_TCR_Alzheimers Disease


title: TCR_PBMC_254_TCR_Alzheimers Disease


title: Fbxo2_B68


title: αIgM_1


title: Fbxo2_B70


title: Long-6


title: Long-7


title: TCR_PBMC_1120_TCR_Alzheimers Disease


title: TCR_PBMC_1055_TCR_Alzheimers Disease


title: FAK ihibition of HCC7721 replication 3

city: Chong Qing

first: Xianfeng

last: Li

address: Da ping

department: Department of Gastroenterology, Daping Hospital

institute: Army Medical University (Third Military Medical University)

data_processing:
RNA-seq were filtered by fastp (version 0.20.1).
The cleaned reads of RNA-seq were aligned against the hg38 transcriptome using HISAT214 (version 2.1.0) and quantitated with featureCounts
The gene expression were normalized to TPM with our in-house scripts.
Low expression genes were filtered and raw count matrix was used for differential expression analysis using edgeR (version 3.28.1). Differential expressed genes (DEGs) were set as FDR < 0.05 and |log2 FoldChange| > 0.58.
The clusterProfiler package in R (version 3.6.1) was implemented to perform GO and KEGG pathway enrichment analyses of those DEGs.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include raw count for each Sample

extract_protocol:
The poly (A)(+) messenger RNA (mRNA)  was enriched by Oligo dT
And then quantiﬁed and quality controlled by Agilent Bioanalyzer 2100 system. After cDNA library construction, the library preparations were sequenced on BGISEQ500 platform (BGI)

value: Human liver cancer


title: Fbxo2_B66


title: Long-5


title: FAK ihibition of HCC7721 replication 1


title: TCR_PBMC_1034_TCR_Alzheimers Disease


title: TCR_PBMC_1092_TCR_Alzheimers Disease


title: Fbxo2_B67


title: Long-3


title: TCR_PBMC_906_TCR_Alzheimers Disease


title: Long-4


title: Long-2


title: Short-22


title: Long-1


title: TCR_PBMC_1241_TCR_Alzheimers Disease


title: Fbxo2_B64


title: Wild type of HCC7721 replication 3

value: DMSO


title: Short-20


title: TCR_PBMC_1028_TCR_Healthy Control


title: Fbxo2_B62


title: Fbxo2_B63


title: FAK ihibition of HCC7721 replication 2

value: WT


title: Wild type of HCC7721 replication 2


title: Wild type of HCC7721 replication 1


title: Short-21


title: Fbxo2_B61


title: Short-18


title: Short-22 R4S6-25

description:
Short-22
25 pM concentration per lane

data_processing:
Initial QC completed in Illumina Sequencing Analysis Viewer
Sequence data were converted from the generated image .bcl files to raw, demultiplexed sequencing data in the .fastq text file format using the Illumina developed bcl2fastq pipeline.
In OASIS 2.0, an online small RNA data analysis software package the Illumina TruSeq 3′adapter (TGGAATTCTCGGGTGCCAAGG) sequence was removed from the .fastq file of each sample’s reads and the read size filtered (15-32nt) with low abundance reads (<5 reads) discarded.
All remaining reads were mapped to the Human genome (Oasis 2.0: GRCh38 [hg38]). Differential miRNA expression using DESeq2 between patient samples with long disease duration and short disease duration were assessed.
Ingenuity Pathway Analysis (IPA) (Qiagen) was used to analyse the diseases and biological functions of the differentially expressed miRNA associated with disease duration.
Assembly: GRCh38 [hg38]
Supplementary files format and content: Tab-delimited text files include count values for each Sample

source_name: Human lymphoblastoid cell line

extract_protocol:
100 μL LCL suspension containing approximately 6.6 x106 cells was taken through the Maxwell 16 miRNA tissue kit protocol using the Maxwell 16MDX instrument following the manufacturer’s instructions, with miRNA eluted in 60 μL RNase-free water.
RNA libraries for small RNA-seq were prepared using the Illumina TruSeq Small RNA library preparation kit following a modified protocol as described previously (Waller et al 2017 doi:10.3389/fnins.2017.00731). For cluster generation 1000 pM of each barcoded cDNA library were pooled together and loaded onto two lanes of the flow cell at 20 pM and 25 pM concentration per lane.

value: Human lymphoblastoid cell line


title: Short-17

value: Male


title: Short-19


title: GEX_PBMC_905_GEX_Healthy Control

description:
rna_raw_counts.rds
rna_lognorm_expression.rds

data_processing:
Illumina RTA3 method for base-calling
10xGenomics cellranger pipeline for alignment and filtering (trimming 5' TSO sequence and 3' polyA tail, alignment with STAR, UMI counting, EmptyDrops method for empty droplet removal)
SoupX background contamination removal (S100A8 and S100A9 were used to estimate contamination fraction and counts were adjusted using SoupX::adjustCounts function)
DoubletFinder doublet removal (doublet formation rate of 5.4% based on 10xGenomics multiplet rate estimation, using 12 PCs and pN = 0.25)
Seurat filtering and normalization (filter out cells with >10% mitochondrial reads, retain cells with at least 200 mapped features, retain features with at least 3 mapped cells, counts were then normalized using Seurat's LogNormalize method)
Assembly: hg38
Supplementary files format and content: .rds object of raw gene count matrix for each gene and cell barcode
Supplementary files format and content: .rds object of log-normalized expression matrix for each gene and cell barcode
Supplementary files format and content: csv of BCR merged contigs
Supplementary files format and content: csv of BCR paired clonotypes
Supplementary files format and content: csv of TCR merged contigs
Supplementary files format and content: csv of TCR paired clonotypes


title: Fbxo2_B60


title: Short-16


title: GEX_PBMC_970_GEX_Healthy Control


title: Short-22 R4S6

description:
Short-22
20 pM concentration per lane


title: Fbxo2_B59


title: GEX_PBMC_70_GEX_Alzheimers Disease

value: female


title: Short-21 R4S5

description:
Short-21
20 pM concentration per lane


title: GEX_PBMC_947_GEX_Alzheimers Disease

value: Peripheral blood mononuclear cells


title: Short-20 R4S4

description:
Short-20
20 pM concentration per lane


title: Fbxo2_B57


title: Short-20 R4S4-25

description:
Short-20
25 pM concentration per lane


title: GEX_PBMC_1200_GEX_Healthy Control


title: Fbxo2_B58


title: Short-14


title: Fbxo2_B56


title: GEX_PBMC_1237_GEX_Alzheimers Disease


title: Fbxo2_B55


title: Short-19 R4S3-25

description:
Short-19
25 pM concentration per lane


title: Short-21 R4S5-25

description:
Short-21
25 pM concentration per lane


title: Short-15


title: Short-13


title: Fbxo2_B54


title: GEX_PBMC_1236_GEX_Alzheimers Disease


title: Short-19 R4S3

description:
Short-19
20 pM concentration per lane


title: Fbxo2_B53


title: Short-12


title: GEX_PBMC_836_GEX_Healthy Control


title: Short-18 R4S1

description:
Short-18
20 pM concentration per lane


title: GEX_PBMC_230_GEX_Alzheimers Disease


title: GEX_PBMC_921_GEX_Alzheimers Disease


title: Short-11


title: Fbxo2_B52


title: Fbxo2_B51


title: Short-17 R3S6

description:
Short-17
20 pM concentration per lane


title: Fbxo2_B50


title: Short-10


title: Short-9


title: GEX_PBMC_965_GEX_Alzheimers Disease


title: Short-16 R3S5-25

description:
Short-16
25 pM concentration per lane


title: Fbxo2_B49


title: Short-16 R3S5

description:
Short-16
20 pM concentration per lane


title: Short-18 R4S1-25

description:
Short-18
25 pM concentration per lane


title: GEX_PBMC_1010_GEX_Healthy Control


title: Fbxo2_B48


title: Short-5


title: Fbxo2_B47


title: GEX_PBMC_1162_GEX_Healthy Control


title: Short-17 R3S6-25

description:
Short-17
25 pM concentration per lane


title: Short-4


title: Fbxo2_B46


title: GEX_PBMC_953_GEX_Alzheimers Disease


title: Fbxo2_B45


title: WT_Y_50_IP

city: Fuzhou

first: Mengting

last: Chen

address: Fujian Medical University, 1 Xuefubei Road, Minhou, Fuzhou, Fujian province, China

institute: Fujian Medical University

description:
d_m6A_agingwt.xls
agingwt_DESeq2.xls
d_m6A_week28.xlsx
week28_DESeq2.xls

data_processing:
The raw MeRIP-seq data were aligned to genome reference sequences by Hisat2. The aligned reads were used for m6A-modification peak calling and the significant methylation was identified by exomepeak2 , and the m6A peak calling can be visualized by IGV software.
The MetaTX was used to examine the distribution pattern of epitranscriptome profiles. The STREME  was used to determine if the m6A peaks contained the consensus of m6A motif sequences.
For mRNA-seq, the mRNA expression level was analyzed by StringTie, and differentially expressed mRNAs were calculated by DEseq.
The substrates of m6A regulators were obtained from starBase v2.0.
The statistical enrichment analysis of Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway for differentially expressed genes (DEGs) and differentially methylated mRNAs were applied by DAVID and KOBAS.

source_name: liver

extract_protocol:
Total RNA was extracted according to manufacturer’s instruction.
The stranded RNA sequencing library was constructed by KC-DigitalTM Stranded mRNA Library Prep Kit for Illumina® (Catalog NO. DR08502, Wuhan Seqhealth Co., Ltd. China) following the manufacturer’s instruction. The kit eliminates duplication bias in PCR and sequencing steps, by using unique molecular identifier (UMI) of 8 random bases to label the pre-amplified cDNA molecules. The library products corresponding to 200-500 bps were enriched

treatment_protocol: Approximately 100 mg liver tissue was harvested and stored in 1 ml TRIzol reagent (Invitrogen, Carlsbad, CA, USA)

value: liver

value: 28 weeks

value: Animal organ cells


title: GEX_PBMC_1282_GEX_Healthy Control


title: Short-14 R3S3-25

description:
Short-14
25 pM concentration per lane


title: Fbxo2_B44

value: cochlea

value: tamoxifen at 3 weeks, dissociation with Papain at 5 weeks.


title: Short-8


title: GEX_PBMC_989_GEX_Healthy Control


title: Short-14 R3S3

description:
Short-14
20 pM concentration per lane


title: GEX_PBMC_978_GEX_Healthy Control


title: Short-3


title: WT_Y_50_Input


title: Fbxo2_B43


title: Short-13 R3S1-25

description:
Short-13
25 pM concentration per lane


title: GEX_PBMC_820_GEX_Healthy Control


title: Short-6


title: Short-15 R3S4-25

description:
Short-15
25 pM concentration per lane


title: GEX_PBMC_912_GEX_Healthy Control


title: Short-2


title: WT_Y_30_IP


title: Short-15 R3S4

description:
Short-15
20 pM concentration per lane


title: Short-13 R3S1

description:
Short-13
20 pM concentration per lane


title: Short-1

value: Female


title: Fbxo2_B42


title: GEX_PBMC_656_GEX_Alzheimers Disease

value: Alzheimers Disease


title: Fbxo2_B41


title: Short-6 R2S6-25

description:
Short-6
25 pM concentration per lane


title: Short-7


title: WT_Y_1_IP


title: GEX_PBMC_1111_GEX_Healthy Control

value: Healthy Control


title: Short-6 R2S6

description:
Short-6
20 pM concentration per lane


title: Fbxo2_B39


title: GEX_PBMC_781_GEX_Healthy Control


title: Short-11 R2S5-25

description:
Short-11
25 pM concentration per lane


title: WT_Y_1_Input


title: Fbxo2_B38


title: Fbxo2_B37


title: GEX_PBMC_1147_GEX_Alzheimers Disease

value: male


title: WT_Y_30_Input


title: WT_Y_68_Input

description:
d_m6A_agingwt.xls
agingwt_DESeq2.xls
d_m6A_week8.xls
week8_DESeq2.xls

value: 8 weeks


title: Fbxo2_B36


title: Fbxo2_B34


title: GEX_PBMC_942_GEX_Alzheimers Disease


title: WT_Y_67_IP


title: Short-10 R2S4

description:
Short-10
20 pM concentration per lane


title: Short-10 R2S4-25

description:
Short-10
25 pM concentration per lane


title: GEX_PBMC_1020_GEX_Healthy Control


title: GEX_PBMC_968_GEX_Healthy Control


title: Short-9 R2S3-25

description:
Short-9
25 pM concentration per lane


title: Fbxo2_B33


title: WT_Y_67_Input


title: WT_Y_66_Input


title: WT_Y_66_IP


title: GEX_PBMC_802_GEX_Alzheimers Disease


title: Short-9 R2S3

description:
Short-9
20 pM concentration per lane


title: Fbxo2_B32


title: GEX_PBMC_780_GEX_Healthy Control


title: WT_Y_68_IP


title: Short-8 R2S2-25

description:
Short-8
25 pM concentration per lane


title: KO_44_IP

description:
d_m6A_agingKO.xls
agingKO_DESeq2.xls
d_m6A_week28.xlsx
week28_DESeq2.xls

value: ApoF gene knockout


title: Fbxo2_B30


title: Fbxo2_B29


title: GEX_PBMC_932_GEX_Alzheimers Disease


title: Short-11 R2S5

description:
Short-11
20 pM concentration per lane


title: Short-8 R2S2

description:
Short-8
20 pM concentration per lane


title: KO_44_Input


title: GEX_PBMC_917_GEX_Alzheimers Disease


title: Fbxo2_B27


title: GEX_PBMC_598_GEX_Healthy Control


title: KO_8_IP


title: Fbxo2_B26


title: Fbxo2_B25


title: KO_8_Input


title: Short-7 R2S1

description:
Short-7
20 pM concentration per lane


title: Short-12 R1S6-25

description:
Short-12
25 pM concentration per lane


title: KO_3_IP


title: Fbxo2_B23


title: GEX_PBMC_773_GEX_Alzheimers Disease


title: Short-12 R1S6

description:
Short-12
20 pM concentration per lane


title: GEX_PBMC_863_GEX_Alzheimers Disease


title: KO_3_Input


title: KO_52_IP

description:
d_m6A_agingKO.xls
agingKO_DESeq2.xls
d_m6A_week8.xls
week8_DESeq2.xls


title: Fbxo2_B22


title: Short-5 R1S5

description:
Short-5
20 pM concentration per lane


title: Short-5 R1S5-25

description:
Short-5
25 pM concentration per lane


title: GEX_PBMC_1180_GEX_Healthy Control


title: Fbxo2_B20


title: KO_52_Input


title: Short-4 R1S4-25

description:
Short-4
25 pM concentration per lane


title: Fbxo2_B21


title: Short-7 R2S1-25

description:
Short-7
25 pM concentration per lane


title: KO_51_IP


title: GEX_PBMC_738_GEX_Alzheimers Disease


title: GEX_PBMC_1279_GEX_Healthy Control


title: Short-4 R1S4

description:
Short-4
20 pM concentration per lane


title: GEX_PBMC_1273_GEX_Healthy Control


title: KO_51_Input


title: Fbxo2_B18


title: KO_19_IP


title: GEX_PBMC_696_GEX_Alzheimers Disease


title: Fbxo2_B17


title: GEX_PBMC_911_GEX_Healthy Control


title: KO_19_Input


title: Short-3 R1S3-25

description:
Short-3
25 pM concentration per lane


title: GEX_PBMC_516_GEX_Alzheimers Disease


title: Short-2 R1S2-25

description:
Short-2
25 pM concentration per lane


title: GEX_PBMC_1052_GEX_Alzheimers Disease


title: Fbxo2_B16


title: WT_ATAC_sublib_53

city: Hangzhou

first: Fang

last: Ye

state: Zhejiang

address: 866 Yuhangtang Rd

institute: Zhejiang University

description: Mixed library of multiple tissues from normal mouse, scATAC-seq

data_processing:
Raw reads for scRNA-seq were pre-processed with customed scripts. The 6-nt UMI (6 nucleotides(nt)long) and the 18-nt long cell-specific barcodes in each Read1 and 10-nt long preindex barcodes in each Read2 were extracted using umi-tools (version 1.1.2). We used STAR (version 2.5.2a) with default parameters to align  reads from mouse were aligned to GRCm38/mm10 reference genome. Paired GTF annotation files were used to tag aligned reads. A list of two rounds of cell barcode oligo sequences was used to correct the extracted cellular barcodes extracted from Read1. Finally, the digital expression matrices were obtained using Drop-seq tools (version 2.5.1). For scATAC-seq, reads from mouse were converted to Fastq format and aligned to mm10 reference genome using bwa (version 0.7.15). 18-nt long cell-specific barcodes and 10-nt long preindexs were directly extracted from Read1. One mismatched barcode in alignment were corrected by the same list of barcode oligo sequences used in the RNA processing procedure. Fragments were obtained from aligned BAM files by SnapTools (version 1.4.8) and customed python scripts. To save time and space, we only kept top 20,000 barcodes (10, 000 for primary tumor mouses) with highest unique fragments for downstream analysis. Cells with reads less than 3,000 were defined as low quality cells, and with percentage of unique mapped reads for either genome above 80% was regarded as species-specific cells, while the remaining cells were labeled collisions. For each fragment file, a 5,000 trunk size cell-bin matrix was generated using ArchR (version 1.0.2) for dimension reduction and UMAP visualization.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Multiple tissues

extract_protocol:
Mouse fresh tissues were cut and ground in liquid nitrogen using a tamping tank. Cold tissue powder was rapidly transferred into a 1.5-ml centrifuge tube. Cell pellet was lysed in 1 ml ice-cold lysis buffer (RNA experiment: 10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% Tween-20, 1% Murine RNase inhibitor (Vazyme Biotech), 0.1% IGEPAL CA-630, 1 mM DTT; ATAC experiment: 10 mM Tris-HCl, pH 8.0, 10 mM NaCl, 3 mM MgCl2, 0.1% Tween-20, 0.1% IGEPAL CA-630, 0.01% Digitonin (Promega), 1× Protease inhibitor (Sangon Biotech)) and incubated on ice for 2 minutes. Then, 5 ml ice-cold RSBT buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% Tween-20) was added to quench the lysis reaction. The medium was then filtered using a 40μm strainer. The nuclei were centrifuged at 500 g for 5 min at 4 ℃ and washed with 1 ml cold RSBT buffer.
For scRNA-seq, nuclei were resuspended in 100 ul RSBT buffer and 10 ml ice-cold 4% paraformaldehyde was then added carefully. Nuclei were fixed in 4 ℃ for 30 minutes and 1.5 ml 2.5 M glycine (Sangon Biotech) was added to quench the fixation. Fixed nuclei were washed twice with 1 ml RSBT buffer (centrifuged at 500 g for 5 minutes at 4 ℃). Nuclei were resuspended in reverse transcription buffer mix (each well: 0.5 µl 10 mM dNTPs, 0.5 µl 10% Triton X-100, 1.5 µl PEG8000 (Sigma-Aldrich), 3.6 µl fixed nuclei (10,000 nuclei) in RSB buffer without Tween-20,) and split into 4 96-well plate. Then, 1 µl 10 µM 384 barcoded random primers was added into each well. The plates were incubated at 55 ℃ for 5 minutes and immediately placed on ice. Then, 3 µl reverse transcription enzyme mix (2 µl 5× RT buffer (31 mM Tris-HCl, pH 8.0, 37.5 mM NaCl, 3.1 mM MgCl2, 10 mM DTT), 0.5 µl Murine RNase inhibitor, 0.5 µl Maxima H Minus RTase (Thermo Fisher)) was added into each well. The in situ reverse transcription reaction was performed as follows: ten cycles of 8 °C for 12 s, 15 °C for 30 s, 20 °C for 45 s, 25 °C for 1 minutes, 30 °C for 1 minutes, 42 °C for 2 minutes followed by a final step at 42 °C for 30 minutes. After reverse transcription, 96-well plates were placed on ice for 2 minutes to stop the reaction. Then, 3 µl of Exonuclease I mix (1.3 µl 10X Exonuclease I Reaction Buffer (NEB), 1.5 µl nuclease-free water, 0.2 µl Exonuclease I (NEB) was added into each well. The plates were slowly rotated at 37 ℃ for 30 minutes in incubator. After Exonucleases I treatment, nuclei were pooled and washed twice with RSBT. Then, nuclei were resuspended in poly-A tailing mix (20 µl nuclei in RSB buffer, 56 µl nuclease-free water, 2 µl Murine RNase inhibitor, 10 µl 10X Terminal Transferase Reaction Buffer (NEB), 10 µl 10× CoCl2 (NEB), 1 µl 100 mM dATP (Sangon Biotech), 1 µl Terminal Transferase (NEB)). The tube was slowly rotated at 37 ℃ for 30 minutes in incubator. After dA-tailing reaction, the nuclei were washed 1 ml 3× SSC-T (3× SSC, 0.05% Tween-20) and twice with 1 ml RSB. The nuclei were resuspended in RSB before loading on the chips. Around 30,000 nuclei and 30,000 barcoded beads were loaded on one chip. Beads was washed twice with RSB buffer before use. Nuclei and beads were resuspended in loading mix and 11 µl loading mix with nuclei and beads (6 µl nuclease-free water, 5 µl KAPA HiFi HotStart ReadyMix (Roche)). Chip was taken out using a flat mouth tweezers. Loading mix with nuclei and beads was pipetted few times and quickly added into the chip surface using flat mouth pipette tip. After all the liquid were drawn into the chip (5-10 second), another 5 µl loading enzyme mix (0.8 µl Bsu DNA Polymerase, Large Fragment (NEB), 0.6 µl RNase H (NEB), 0.6 µl USER enzyme (NEB), 3 µl KAPA HiFi HotStart ReadyMix) was added into the chip. For scATAC-seq, Nuclei were washed with RSBT buffer and counted. 2× TD buffer (20 mM Tris-HCl, pH7.4, 10 mM MgCl2, 20% dimethylformamide (Sigma-Aldrich)) was prepared and stored in 4 °C before tagmentation. Then, nuclei were resuspended in tagmentation mix (25 µl for each well: 12.5 µl 2× TD buffer, 8 µl 1× PBS, 0.25 µl 10 % Tween-20, 0.25 µl 1% digitonin, 2 µl assembled Tn5, 2 µl nuclease-free water) and split into 4 96-well plate (10,000 nuclei in each well). The tagmentation reaction was performed at 55 °C for 30 minutes. The plates were then placed on ice for 5 minutes to stop the reaction. Nuclei were pooled and washed twice with RSB buffer before loading on the chips. Loading procedures of ATAC-seq were the same as RNA-seq. Loading mix with nuclei and beads: 2 µl 5× KAPA HiFi Fidelity buffer (Roche, catalog no. KB2500), 1 µl 10mM KAPA dNTP mix, 7 µl 50mM EDTA, 3.7 µl RSB with nuclei and beads, 0.3 µl µM 100ATAC_SpikeIn_oligos. After all the liquid were drawn into the chips (5-10 second), chips were put back into tubes and lids were covered. The tubes were put into a 50 °C incubator for 30 minutes to release the DNA fragments from nuclei. Then, another 6.6 µl loading enzyme mix (2 µl 5× KAPA HiFi Fidelity buffer, 1 µl nuclease-free water, 1 µl 1U µl-1 KAPA HiFi HotStart DNA Polymerase (Roche, catalog no. KE2502), 2 µl 400 mM MgCl2, 0.6 µl USER enzyme) was added into the chip. For both scRNA-seq and scATAC-seq, 150 µl sealing oil was carefully added along the tube wall to seal the chip. The beads oligo cleavage and linear amplification reaction in chip was performed as follows: 37 °C for 1 hour, 72 °C for 30 minutes, 98 °C for 10 minutes; then ten cycles of 98 °C for 3 minutes, 55 °C for 3 minutes, 72 °C for 4 minutes followed by a final step at 72 °C for 30 min. Sealing oil were gently removed after preamplification. 80 µl nuclease-free water with 6× DNA loading dye (Thermo Fisher) were directly added into the chips. The tubes with chip inside were put into a high-speed bench top centrifuge and centrifuged for 5 minutes to collect all the liquid in the chips. Liquid with loading dye color were separated from remaining oil and transferred to another new PCR strip tubes, the tubes were placed on the magnetic stand to remove all the beads. For each chip, preamplification was purified using 1.5× VAHTS DNA cleaning beads. Then, 18 μl of purified pre-amplificated library was mixed with 1 μl MGI_P5_primer, 1 μl MGI_P7_primer and 20 μl KAPA HiFi HotStart ReadyMix. PCR was performed as follows: 72 °C for 5 min, 98 °C for 3 min; twelve cycles of 98 °C for 20 s, 60 °C for 30 s, 72 °C for 1 min; one cycle of 72 °C for 5 min; then hold at 10 °C. Final RNA library was purified using 1.2× VAHTS DNA cleaning beads. Final ATAC library was purified using two rounds size selection: 0.55× VAHTS DNA cleaning beads for first round, collect the supernatant and discard beads; 1.0× VAHTS DNA cleaning beads for second round purification. The concentration of final library was quantified using Qubit 3.0 fluorometer. The purified linear DNA library was circularized into single-stranded DNA (ssDNA) library using VAHTS Circularization Kit for MGI (Vazyme Biotech). The ssDNA library was amplified using a DNBSEQ DNB preparation kit (MGI). Amplified DNA nanoballs (DNBs) were sequenced on MGI DNBSEQ-T7 using pair-end 150 mode. Custom TM (Tn5 modified) sequencing primers were adopted.

value: Multiple tissues

tag: library type

value: DNA


title: Fbxo2_B14


title: WT_ATAC_sublib_54


title: Short-2 R1S2

description:
Short-2
20 pM concentration per lane

value: Human lymphoblastoid cell line


title: Short-3 R1S3

description:
Short-3
20 pM concentration per lane

value: Male


title: GEX_PBMC_254_GEX_Alzheimers Disease


title: Short-1 R1S1-25

description:
Short-1
25 pM concentration per lane


title: Fbxo2_B13


title: Fbxo2_B19


title: Fbxo2_B15


title: WT_ATAC_sublib_52


title: Short-1 R1S1

description:
Short-1
20 pM concentration per lane


title: WT_ATAC_sublib_51


title: GEX_PBMC_1120_GEX_Alzheimers Disease

value: female


title: Fbxo2_B12


title: Long-18 R4S10-25

description:
Long-18
25 pM concentration per lane


title: WT_ATAC_sublib_50


title: GEX_PBMC_1092_GEX_Alzheimers Disease

value: Peripheral blood mononuclear cells


title: Long-18 R4S10

description:
Long-18
20 pM concentration per lane


title: GEX_PBMC_1055_GEX_Alzheimers Disease


title: WT_ATAC_sublib_49


title: Fbxo2_B10


title: GEX_PBMC_1034_GEX_Alzheimers Disease


title: Fbxo2_B09


title: WT_ATAC_sublib_48


title: Fbxo2_B08


title: Long-16 R3S12-25

description:
Long-16
25 pM concentration per lane


title: WT_ATAC_sublib_47


title: GEX_PBMC_906_GEX_Alzheimers Disease


title: GEX_PBMC_1241_GEX_Alzheimers Disease


title: Fbxo2_B07


title: WT_ATAC_sublib_45


title: Fbxo2_B06


title: GEX_PBMC_1028_GEX_Healthy Control


title: Long-15 R3S11-25

description:
Long-15
25 pM concentration per lane


title: Long-16 R3S12

description:
Long-16
20 pM concentration per lane


title: PBMC_905_Healthy Control

description:
atac_cd4_raw_peaks.rds
atac_noncd4_raw_peaks.rds
atac_cd4_TFIDF_peaks.rds
atac_noncd4_TFIDF_peaks.rds

data_processing:
Illumina RTA3 method for base-calling
10xGenomics cellranger atac pipeline for alignment and filtering (alignment with BWA-MEM, UMI counting, EmptyDrops method for empty droplet removal)
Filtered to retain fragments between 10 and 2000 bp and with TSS enrichment > 10 , and cells with between 1e3 and 1e5 fragments
LSI reduction and UMAP generation with nNeighbors = 20 and minDist = 0.1
peak calling and matrix creation using MACS2 within ArchR using default parameters
conversion of ArchR project to Seurat objects using ArchR2Signac
Assembly: hg38
Supplementary files format and content: .rds file of raw peaks matrix in CD4+ T Cells
Supplementary files format and content: .rds file of raw peaks matrix in non-CD4+ T Cells
Supplementary files format and content: .rds file of TF-IDF normalized peaks matrix in CD4+ T Cells
Supplementary files format and content: .rds file of TF-IDF normalized peaks matrix in non-CD4+ T Cells

extract_protocol:
PBMCs were pelleted, frozen, and resuspended in PBS with 0.04% BSA before being sorted with Sytox blue live/dead dye. Live PBMCs were lysed using 10x Genomics protocols to isolate nuclei.
Chromium Next GEM Single Cell ATAC v1.1


title: Fbxo2_B11


title: Long-15 R3S11

description:
Long-15
20 pM concentration per lane


title: WT_ATAC_sublib_43


title: Fbxo2_B05


title: GEX_PBMC_1160_GEX_Alzheimers Disease


title: Fbxo2_B04


title: Long-17 R4S8-25

description:
Long-17
25 pM concentration per lane


title: Long-14 R3S10-25

description:
Long-14
25 pM concentration per lane


title: WT_ATAC_sublib_42


title: Fbxo2_B03


title: Long-17 R4S8

description:
Long-17
20 pM concentration per lane


title: WT_ATAC_sublib_46


title: PBMC_254_Alzheimers Disease


title: WT_ATAC_sublib_41


title: PBMC_70_Alzheimers Disease


title: WT_ATAC_sublib_40


title: PBMC_947_Alzheimers Disease


title: WT_ATAC_sublib_44


title: Long-13 R3S9

description:
Long-13
20 pM concentration per lane


title: Fbxo2_B01


title: PBMC_1236_Alzheimers Disease


title: Fbxo2_A96


title: PBMC_836_Healthy Control


title: PBMC_970_Healthy Control


title: WT_ATAC_sublib_38


title: Fbxo2_A95


title: WT_ATAC_sublib_39


title: Long-12 R3S7-25

description:
Long-12
25 pM concentration per lane


title: PBMC_960_Healthy Control


title: Fbxo2_A94


title: Long-14 R3S10

description:
Long-14
20 pM concentration per lane


title: WT_ATAC_sublib_36


title: Long-11 R2S12-25

description:
Long-11
25 pM concentration per lane


title: PBMC_230_Alzheimers Disease


title: Fbxo2_A93


title: WT_ATAC_sublib_35


title: Fbxo2_A91


title: PBMC_921_Alzheimers Disease


title: Fbxo2_A92


title: Fbxo2_B02


title: Long-9 R2S9-25

description:
Long-9
25 pM concentration per lane


title: Long-13 R3S9-25

description:
Long-13
25 pM concentration per lane


title: PBMC_1010_Healthy Control


title: WT_ATAC_sublib_32


title: Long-9 R2S9

description:
Long-9
20 pM concentration per lane


title: Fbxo2_A89


title: Long-10 R2S10

description:
Long-10
20 pM concentration per lane


title: PBMC_1162_Healthy Control


title: PBMC_965_Alzheimers Disease


title: Long-10 R2S10-25

description:
Long-10
25 pM concentration per lane


title: Fbxo2_A90


title: WT_ATAC_sublib_34


title: PBMC_989_Healthy Control


title: WT_ATAC_sublib_37


title: WT_ATAC_sublib_31


title: WT_ATAC_sublib_30


title: Long-8 R2S8-25

description:
Long-8
25 pM concentration per lane


title: Fbxo2_A88


title: Fbxo2_A87


title: Long-11 R2S12

description:
Long-11
20 pM concentration per lane


title: Long-12 R3S7

description:
Long-12
20 pM concentration per lane


title: PBMC_820_Healthy Control


title: Long-8 R2S8

description:
Long-8
20 pM concentration per lane


title: WT_ATAC_sublib_33


title: WT_ATAC_sublib_29


title: PBMC_1282_Healthy Control


title: Long-7 R2S7-25

description:
Long-7
25 pM concentration per lane


title: Fbxo2_A84


title: WT_ATAC_sublib_28


title: Long-7 R2S7

description:
Long-7
20 pM concentration per lane


title: Fbxo2_A85


title: PBMC_656_Alzheimers Disease


title: Long-6 R1S12-25

description:
Long-6
25 pM concentration per lane


title: WT_ATAC_sublib_27


title: Long-6 R1S12

description:
Long-6
20 pM concentration per lane


title: PBMC_912_Healthy Control


title: PBMC_978_Healthy Control


title: PBMC_781_Healthy Control


title: WT_ATAC_sublib_24


title: Fbxo2_A83


title: WT_ATAC_sublib_25


title: Long-5 R1S11-25

description:
Long-5
25 pM concentration per lane


title: Fbxo2_A81


title: Fbxo2_A82


title: Long-5 R1S11

description:
Long-5
20 pM concentration per lane


title: PBMC_1147_Alzheimers Disease


title: WT_ATAC_sublib_23


title: Fbxo2_A86


title: PBMC_968_Healthy Control


title: PBMC_942_Alzheimers Disease


title: Long-4 R1S10-25

description:
Long-4
25 pM concentration per lane


title: WT_ATAC_sublib_22


title: Fbxo2_A79


title: Fbxo2_A78


title: Long-4 R1S10

description:
Long-4
20 pM concentration per lane


title: WT_ATAC_sublib_26


title: WT_ATAC_sublib_20


title: PBMC_802_Alzheimers Disease


title: WT_ATAC_sublib_21


title: PBMC_780_Healthy Control


title: PBMC_1020_Healthy Control


title: Fbxo2_A76


title: WT_ATAC_sublib_18


title: Long-2 R1S8

description:
Long-2
20 pM concentration per lane


title: PBMC_659_Healthy Control


title: Long-2 R1S8-25

description:
Long-2
25 pM concentration per lane


title: Fbxo2_A77


title: Long -1 R1S7

description:
Long -1
20 pM concentration per lane


title: WT_ATAC_sublib_17


title: Long -1 R1S7-25

description:
Long -1
25 pM concentration per lane


title: PBMC_932_Alzheimers Disease


title: Fbxo2_A74


title: Fbxo2_A73


title: WT_ATAC_sublib_14


title: PBMC_1279_Healthy Control


title: Fbxo2_A80


title: WT_ATAC_sublib_16


title: Fbxo2_A70


title: PBMC_917_Alzheimers Disease


title: PBMC_863_Alzheimers Disease


title: WT_ATAC_sublib_12


title: Control_subject_time_t0 [US83400190_257015618091_S01_miRNA_1200_Jun14_2_4]

city: Roma

first: Ivan

last: Arisi

address: viale Regina Elena 295

department: Bioinformatics Facility

country: Italy

institute: European Brain Research Institute

description: miRNA expression microarray from PBMCs extracted from peripheral blood of control subjects

hyb_protocol: Samples were then dried through a vacuum concentrator, and a 45 µl hybridization solution was added to each one. At last, samples were hybridized to the Agilent Human miRNA Microarrays chip 8x60K (Agilent PN G4870-60530, grid ID 070156), containing 2549 human miRNAs. The glasses were incubated in the Agilent Hybridization Oven at 55°C, at 10 RPM, for 20 hours.

scan_protocol: Post-hybridization image acquisition was accomplished using the Agilent Scanner G2564C. Data extraction from the 20 bits TIFF images was accomplished by Agilent Feature Extraction (FE)  ver 12.1  software using the standard Agilent one-color miRNA expression extraction protocol (version miRNA_1200_Jun14).

data_processing: Samples were processed according to the standard experimental Agilent procedure. The “gTotalGeneSignal” data column of the Feature Extraction *_GeneView.txt output files was used as expression value for miRNAs. Data analysis was performed using R-Bioconductor (Seattle, WA, USA). Samples were normalized by the median alignment method and Log2 transformed. Control non biological probes were excluded from the analysis. Only miRNAs with expression values >0.0 in every sample were included in the analysis.

source_name: PBMCs from peripheral blood

label_protocol: MicroRNA expression profiling was performed according to the standard “Agilent miRNA Microarray System, miRNA Complete Labelling, and Hyb Kit” protocol (Agilent Technologies, Version 3.1.1, 2015). After a phosphatase treatment and a denaturation process via DMSO, 100 ng of RNA, extracted from each sample, were labelled with 3-pCp Cyanine (Cy3).

growth_protocol: Some patients were treated by other drugs before this study (characteristics: Previous drug treatment = YES), while others were naive to any drug therapy for MS (characteristics: Previous drug treatment = NO). For control subjects this information is not available (characteristics: Previous drug treatment = NA).

extract_protocol: Patients and healthy subjects peripheral blood samples were collected in Vacutainer tubes containing EDTA. 15 ml of PBS (without Ca2+, Mg2+) and 7.5 ml of Ficoll were added to 10 ml of blood from each sample and left to settle. After a 30 min centrifugation (18-20 °C) at 1800rpm, tubes exhibited 4 different layers, containing: plasma, lymphocytes and monocytes, Ficoll, granulocytes and erythrocytes, respectively from top to bottom. The lymphocytes/monocytes layer was accurately collected in clean tubes; cells were then pelleted (1400rpm for 10 min at 18-20 °C) and washed with PBS. The dry pellet was finally stored at -80°C. RNA extraction was performed according to the miRNeasy Tissue/Cells Advanced Mini Kit (QIAGEN) instructions: cells were suspended in 500μl of RTL buffer + beta mercaptoethanol, incubated at 37°C for 10 min and homogenized. Samples passed through two different spin columns, the gDNA Eliminator spin column to remove all DNA, and the RNeasy spin column to select RNA molecules. The miRNeasy Tissue/Cells Advanced Kits enabled efficient RNA’s enrichment down to approximately 18 nucleotides in size. All RNA samples were again stored at -80°C. RNA purity and concentration quality control included the evaluation of absorbance at 260 nm by NanoDrop ND-1000 (Labtech International, Ringmer, UK). To assess the RNA integrity, samples were analyzed through the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA) via the Eukaryote total RNA 6000 nano kit (Agilent Technologies, Santa Clara, CA, USA) and the Small RNA kit (Agilent Technologies, Santa Clara, CA, USA). The Bioanalyzer assessed each sample’s RNA integrity number (RIN). Samples displaying an under-threshold RIN value of 8.0 were excluded.

treatment_protocol: CLA drug tablets were administered to the selected relapsing-remitting MS patients with a dosage of 1.75 mg/kg given for five days.-  OCRE drug was administered to the other relapsing-remitting MS patients by infusion with a dosage of 300 mg, twice in two weeks. Control subjects were not treated.

value: peripheral blood

value: lymphocytes and monocytes

tag: time point

tag: drug treatment

value: untreated


title: WT_ATAC_sublib_15

tag: tissue

tag: age


title: PBMC_598_Healthy Control

tag: genotype


title: Control_subject_time_t0 [US83400190_257015618091_S01_miRNA_1200_Jun14_2_1]

value: F

tag: age at time t0 in years

tag: previous drug treatment


title: Control_subject_time_t0 [US83400190_257015618091_S01_miRNA_1200_Jun14_1_4]


title: Fbxo2_A71

data_processing:
The fastq files of read 1 were mapped to the reference transcriptome by using STAR.
The reads were assigned to genes by using htseq-count.
The UMI sequences were extracted from read 2 (the first five bases).
The reads with the same UMI were collapsed. The number of UMIs of each gene were counted.
Assembly: mm10
Supplementary files format and content: Tab-separated UMI count matrix; Files: Exon_UMI_matrix.txt

source_name: cochlea

value: cochlea

tag: treatment

value: tamoxifen at 3 weeks, dissociation with Papain at 5 weeks.


title: WT_ATAC_sublib_11


title: Control_subject_time_t0 [US83400190_257015618091_S01_miRNA_1200_Jun14_1_3]


title: Fbxo2_A69


title: WT_ATAC_sublib_13


title: PBMC_1180_Healthy Control


title: WT_ATAC_sublib_19


title: Fbxo2_A67


title: Fbxo2_A68


title: Fbxo2_A75


title: PBMC_773_Alzheimers Disease

value: Alzheimers Disease


title: WT_ATAC_sublib_10


title: WT_ATAC_sublib_9


title: PBMC_911_Healthy Control

value: Healthy Control


title: Fbxo2_A65


title: Control_subject_time_t0 [US83400190_257015618091_S01_miRNA_1200_Jun14_2_2]

value: M


title: Control_subject_time_t0 [US83400190_257015618091_S01_miRNA_1200_Jun14_2_3]


title: WT_ATAC_sublib_8

value: 8 weeks


title: PBMC_738_Alzheimers Disease


title: Fbxo2_A66


title: Fbxo2_A64


title: Control_subject_time_t0 [US83400190_257015618091_S01_miRNA_1200_Jun14_1_2]


title: OCRE_treated_MS_patient_Time_t1 [US83400190_257015618090_S01_miRNA_1200_Jun14_2_2]

description: miRNA expression microarray from PBMCs extracted from peripheral blood of MS patients 6 months post treatment by OCRE

value: OCRE

value: YES


title: Control_subject_time_t0 [US83400190_257015618091_S01_miRNA_1200_Jun14_1_1]


title: Fbxo2_A62


title: WT_ATAC_sublib_5

value: Multiple tissues

value: DNA


title: WT_ATAC_sublib_7

value: Male


title: PBMC_1160_Alzheimers Disease

value: male


title: Fbxo2_A61


title: OCRE_treated_MS_patient_Time_t0 [US83400190_257015618090_S01_miRNA_1200_Jun14_1_2]

description: miRNA expression microarray from PBMCs extracted from peripheral blood of MS patients before treatment by OCRE


title: Control_subject_time_t0 [US83400190_257015618089_S01_miRNA_1200_Jun14_2_4]


title: PBMC_1120_Alzheimers Disease

value: Peripheral blood mononuclear cells

value: female


title: WT_ATAC_sublib_4


title: Fbxo2_A60


title: Control_subject_time_t0 [US83400190_257015618089_S01_miRNA_1200_Jun14_2_2]

value: peripheral blood

value: lymphocytes and monocytes


title: PBMC_516_Alzheimers Disease


title: PBMC_1055_Alzheimers Disease


title: WT_ATAC_sublib_2


title: WT_ATAC_sublib_3


title: Fbxo2_A58


title: Control_subject_time_t0 [US83400190_257015618089_S01_miRNA_1200_Jun14_1_4]

value: untreated

value: F


title: Fbxo2_A59

value: cochlea

value: tamoxifen at 3 weeks, dissociation with Papain at 5 weeks.


title: Control_subject_time_t0 [US83400190_257015618089_S01_miRNA_1200_Jun14_2_1]


title: Control_subject_time_t0 [US83400190_257015618089_S01_miRNA_1200_Jun14_1_3]


title: Fbxo2_A63


title: PBMC_1034_Alzheimers Disease

value: Alzheimers Disease


title: PBMC_1052_Alzheimers Disease


title: WT_ATAC_sublib_6


title: WT_ATAC_sublib_1


title: WT_RNA_sublib_28

description: Mixed library of multiple tissues from normal mouse, scRNA-seq

value: mRNA


title: PBMC_1092_Alzheimers Disease


title: Control_subject_time_t0 [US83400190_257015618089_S01_miRNA_1200_Jun14_1_2]

value: M


title: Control_subject_time_t0 [US83400190_257015618089_S01_miRNA_1200_Jun14_1_1]


title: PBMC_906_Alzheimers Disease


title: Fbxo2_A57


title: Fbxo2_A56


title: PBMC_1241_Alzheimers Disease


title: WT_RNA_sublib_27

value: 8 weeks


title: Fbxo2_A54


title: Fbxo2_A55


title: PBMC_1154_Alzheimers Disease


title: PBMC_1081_Healthy Control

value: Healthy Control


title: WT_RNA_sublib_26

value: Multiple tissues


title: WT_RNA_sublib_25


title: PBMC_1200_Healthy Control


title: PBMC_1086_Healthy Control


title: PBMC_1028_Healthy Control


title: Fbxo2_A53


title: OCRE_treated_MS_patient_Time_t0 [US83400190_257015618065_S01_miRNA_1200_Jun14_2_4]

value: OCRE

value: YES


title: OCRE_treated_MS_patient_Time_t0 [US83400190_257015618065_S01_miRNA_1200_Jun14_2_2]

value: NO


title: WT_RNA_sublib_21

value: Male


title: WT_RNA_sublib_24


title: Fbxo2_A51


title: Fbxo2_A52


title: OCRE_treated_MS_patient_Time_t1 [US83400190_257015618065_S01_miRNA_1200_Jun14_2_1]


title: OCRE_treated_MS_patient_Time_t0 [US83400190_257015618065_S01_miRNA_1200_Jun14_1_3]


title: OCRE_treated_MS_patient_Time_t1 [US83400190_257015618065_S01_miRNA_1200_Jun14_2_3]


title: Fbxo2_A50


title: JGG01-E2-4-OHT-06

city: Rennes

first: Raphaël

last: Métivier

address: Campus de Beaulieu

country: France

institute: CNRS UMR 6290

data_processing:
Sequencing was carried out on Paired End (2x150 bp) on Illumina NovaSeq at Azenta Life Sciences facility (GENEWIZ Germany, Leipzig).
Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36. The trimmed reads were mapped to the Homo sapiens GRCh38 reference genome available on ENSEMBL using the STAR aligner v.2.5.2b generating .bam files.
Unique gene hit counts were calculated from the generated .bam files containing aligned reads by using featureCounts from the Subread package v.1.5.2. The hit counts were summarized and reported using the gene_id feature in the annotation file. Only unique reads that fell within exon regions were counted.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files that includes  the number of reads aligned on Ensembl GRCh38-hg38 annotated genes.

source_name: TeloHAEC hERα-WT

extract_protocol:
RNA was isolated from TeloHAEC through the phenol-chloroform method using TRIzol (Ambion) reagent. The resulting RNA quality was determined using a Fragment Analyzer Instrument and all samples had RNA integrity numbers above 8.
RNA sequencing libraries were prepared according to the Genewiz/Azenta company platform.

value: aortic endothelial cell

value: 6 hours


title: OCRE_treated_MS_patient_Time_t1 [US83400190_257015618065_S01_miRNA_1200_Jun14_1_4]

value: peripheral blood

value: lymphocytes and monocytes


title: OCRE_treated_MS_patient_Time_t0 [US83400190_257015618065_S01_miRNA_1200_Jun14_1_1]

value: F


title: WT_RNA_sublib_20


title: JGG01-E2-4-OHT-03


title: Fbxo2_A49

extract_protocol:
After tissue dissociation, single cells are sorted into 96-well plate by FACS.
Libraries were constructed by following SMART-MATQ protocol.

value: cochlea


title: WT_RNA_sublib_19


title: OCRE_treated_MS_patient_Time_t1 [US83400190_257015618065_S01_miRNA_1200_Jun14_1_2]


title: WT_RNA_sublib_22


title: CLA_treated_MS_patient_Time_t0 [US83400190_257015618064_S01_miRNA_1200_Jun14_2_4]

description: miRNA expression microarray from PBMCs extracted from peripheral blood of MS patients before treatment by CLA

value: CLA


title: WT_RNA_sublib_23


title: Fbxo2_A48

value: tamoxifen at 3 weeks, dissociation with Papain at 5 weeks.


title: JGG01-E2-4-OHT-04


title: Fbxo2_A47


title: Fbxo2_A46


title: WT_RNA_sublib_17

value: mRNA


title: JGG01-E2-4-OHT-02


title: OCRE_treated_MS_patient_Time_t1 [US83400190_257015618064_S01_miRNA_1200_Jun14_2_3]


title: WT_RNA_sublib_18


title: JGG01-E2-4-OHT-05


title: WT_RNA_sublib_16


title: JGG01-E2-4-OHT-01


title: JGG01-4-OHT-06


title: CLA_treated_MS_patient_Time_t0 [US83400190_257015618064_S01_miRNA_1200_Jun14_2_2]


title: JGG01-4-OHT-05


title: Fbxo2_A45


title: WT_RNA_sublib_14


title: Fbxo2_A44


title: Fbxo2_A42


title: JGG01-4-OHT-04


title: Fbxo2_A43


title: Fbxo2_A41


title: JGG01-4-OHT-03


title: WT_RNA_sublib_15


title: CLA_treated_MS_patient_Time_t1 [US83400190_257015618064_S01_miRNA_1200_Jun14_1_4]

description: miRNA expression microarray from PBMCs extracted from peripheral blood of MS patients 6 months post treatment by CLA


title: CLA_treated_MS_patient_Time_t1 [US83400190_257015618064_S01_miRNA_1200_Jun14_2_1]


title: JGG01-4-OHT-02


title: Fbxo2_A39


title: OCRE_treated_MS_patient_Time_t0 [US83400190_257015618064_S01_miRNA_1200_Jun14_1_3]


title: JGG01-4-OHT-01


title: CLA_treated_MS_patient_Time_t0 [US83400190_257015618064_S01_miRNA_1200_Jun14_1_1]


title: CLA_treated_MS_patient_Time_t1 [US83400190_257015618064_S01_miRNA_1200_Jun14_1_2]


title: Fbxo2_A38


title: WT_RNA_sublib_10


title: JGG01-E2-05


title: Fbxo2_A36


title: WT_RNA_sublib_13


title: JGG01-E2-06


title: WT_RNA_sublib_8


title: WT_RNA_sublib_12


title: Fbxo2_A37


title: CLA_treated_MS_patient_Time_t1 [US83400190_257015618063_S01_miRNA_1200_Jun14_2_3]


title: Fbxo2_A35


title: CLA_treated_MS_patient_Time_t0 [US83400190_257015618063_S01_miRNA_1200_Jun14_2_4]


title: Fbxo2_B87


title: JGG01-E2-04


title: WT_RNA_sublib_7


title: JGG01-E2-03


title: WT_RNA_sublib_6


title: WT_RNA_sublib_11


title: Fbxo2_A34


title: WT_RNA_sublib_5


title: Fbxo2_A32


title: JGG01-E2-02


title: Fbxo2_A33


title: CLA_treated_MS_patient_Time_t0 [US83400190_257015618063_S01_miRNA_1200_Jun14_2_2]


title: CLA_treated_MS_patient_Time_t1 [US83400190_257015618063_S01_miRNA_1200_Jun14_2_1]


title: CLA_treated_MS_patient_Time_t1 [US83400190_257015618063_S01_miRNA_1200_Jun14_1_4]

value: M


title: WT_RNA_sublib_4

value: 8 weeks


title: CLA_treated_MS_patient_Time_t0 [US83400190_257015618063_S01_miRNA_1200_Jun14_1_3]


title: JGG01-E2-01


title: WT_RNA_sublib_9


title: WT_RNA_sublib_3


title: CLA_treated_MS_patient_Time_t1 [US83400190_257015618063_S01_miRNA_1200_Jun14_1_2]


title: JGG01-DMSO-04

value: Vehicle


title: JGG01-DMSO-06


title: Fbxo2_A30


title: Fbxo2_A29


title: WT_RNA_sublib_2

value: Multiple tissues


title: JGG01-DMSO-05


title: Tumor_ATAC_sublib_10

description: Mixed library of four tumor tissues from normal agin mouse, scATAC-seq

source_name: Liver, lung, stomach and subcutaneous tumor

value: 18 months

value: DNA


title: CLA_treated_MS_patient_Time_t0 [US83400190_257015618063_S01_miRNA_1200_Jun14_1_1]

value: YES


title: OCRE_treated_MS_patient_Time_t0 [US83400190_257015617916_S01_miRNA_1200_Jun14_2_4]

value: OCRE


title: Fbxo2_A26


title: CLA_treated_MS_patient_Time_t0 [US83400190_257015617916_S01_miRNA_1200_Jun14_2_2]

value: NO


title: WT_RNA_sublib_1

value: Male


title: Fbxo2_A27


title: OCRE_treated_MS_patient_Time_t1 [US83400190_257015617916_S01_miRNA_1200_Jun14_2_3]

value: peripheral blood


title: Tumor_ATAC_sublib_8

value: Liver, lung, stomach and subcutaneous tumor


title: JGG01-DMSO-01

value: aortic endothelial cell

value: 6 hours


title: Fbxo2_A25

value: cochlea


title: Tumor_ATAC_sublib_9


title: JGG01-DMSO-02


title: Scramble-treated Sample 8

city: Dublin 2

first: Kelvin

middle: E How

last: Lau

state: Dublin

address: York House, 31A, York Street, Dublin 2

department: Medical Physics & Physiology

country: Ireland

institute: Royal College of Surgeons in Ireland (RCSI)

data_processing:
Base Calling using Casava 1.8
Filtering (removal): reads containing adapters, reads containing more than 10% of uncertain nucleotides (N > 10%), and reads with Q Score (< 5) in more than 50% of the reads
Alingment to hg38 genome using HISAT2 v2.0.5
Quantification of gene expression using featureCounts v1.5.0-p3
Fragments per Kilobase of transcript sequence per Millions base pairs sequenced (FPKM) calculated using a protocol by Trapnell et al. Nature Biotechnology 2010
Assembly: hg38
Supplementary files format and content: .txt and .csv  files containing matrices with raw count and FPKM values corresponding to each gene and sample

source_name: human-iPSC

growth_protocol: Human-iPSC derived neurons were differentiated and maintained for at least 30 days in neural differentiation medium supplemented with BDNF, GDNF, AA, cAMP salts, laminin and antibiotics in humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
Trizol-chloroform RNA extraction
Standard Illumina Protocol

treatment_protocol: Cells were treated with 300 nM of anta-N, anta-E or scr for 48 hours before RNA extraction and transcriptome analysis.

tag: cell line

value: human-iPSC

value: Neurons

value: Scramble


title: Tumor_ATAC_sublib_7


title: OCRE_treated_MS_patient_Time_t1 [US83400190_257015617916_S01_miRNA_1200_Jun14_2_1]

value: lymphocytes and monocytes

value: M


title: JGG01-DMSO-03

value: Vehicle


title: OCRE_treated_MS_patient_Time_t0 [US83400190_257015617916_S01_miRNA_1200_Jun14_1_3]


title: Scramble-treated Sample 7


title: Tumor_ATAC_sublib_6

value: 18 months


title: Fbxo2_A22

value: tamoxifen at 3 weeks, dissociation with Papain at 5 weeks.


title: Fbxo2_A21


title: Scramble-treated Sample 5


title: Tumor_ATAC_sublib_5

value: DNA


title: Fbxo2_A20


title: Scramble-treated Sample 6


title: Tumor_ATAC_sublib_4


title: Scramble-treated Sample 4


title: Scramble-treated Sample 3


title: Tumor_ATAC_sublib_3


title: Fbxo2_A23


title: CLA_treated_MS_patient_Time_t1 [US83400190_257015617916_S01_miRNA_1200_Jun14_1_2]

value: CLA


title: OCRE_treated_MS_patient_Time_t1 [US83400190_257015617916_S01_miRNA_1200_Jun14_1_4]

value: OCRE

value: F

value: YES


title: OCRE_treated_MS_patient_Time_t0 [US83400190_257015617915_S01_miRNA_1200_Jun14_2_4]

value: peripheral blood

value: NO


title: OCRE_treated_MS_patient_Time_t1 [US83400190_257015617915_S01_miRNA_1200_Jun14_2_3]


title: Scramble-treated Sample 2


title: Tumor_ATAC_sublib_2

value: Liver, lung, stomach and subcutaneous tumor

value: Male


title: Fbxo2_A15

value: cochlea


title: Tumor_ATAC_sublib_1


title: OCRE_treated_MS_patient_Time_t0 [US83400190_257015617915_S01_miRNA_1200_Jun14_2_2]


title: OCRE_treated_MS_patient_Time_t0 [US83400190_257015617916_S01_miRNA_1200_Jun14_1_1]


title: OCRE_treated_MS_patient_Time_t1 [US83400190_257015617915_S01_miRNA_1200_Jun14_2_1]


title: Fbxo2_A16


title: Scramble-treated Sample 1

value: human-iPSC

value: Neurons


title: Fbxo2_A28


title: Fbxo2_A14


title: Fbxo2_A13


title: Tumor_RNA_sublib_20

description: Mixed library of four tumor tissues from normal agin mouse, scRNA-seq

value: mRNA


title: Tumor_RNA_sublib_18


title: Fbxo2_A18


title: OCRE_treated_MS_patient_Time_t1 [US83400190_257015617915_S01_miRNA_1200_Jun14_1_4]

value: lymphocytes and monocytes


title: Fbxo2_A19


title: OCRE_treated_MS_patient_Time_t1 [US83400190_257015617915_S01_miRNA_1200_Jun14_1_2]


title: OCRE_treated_MS_patient_Time_t0 [US83400190_257015617915_S01_miRNA_1200_Jun14_1_3]


title: Antago-N-miR-376a-3p-treated Sample 7


title: OCRE_treated_MS_patient_Time_t0 [US83400190_257015617915_S01_miRNA_1200_Jun14_1_1]


title: Tumor_RNA_sublib_19


title: Antago-N-miR-376a-3p-treated Sample 6


title: Fbxo2_A12


title: OCRE_treated_MS_patient_Time_t1 [US83400190_257015617914_S01_miRNA_1200_Jun14_2_4]

value: M


title: Fbxo2_A11


title: Antago-N-miR-376a-3p-treated Sample 8


title: Antago-N-miR-376a-3p-treated Sample 4


title: Antago-N-miR-376a-3p-treated Sample 5


title: Fbxo2_A10


title: Antago-N-miR-376a-3p-treated Sample 3


title: Tumor_RNA_sublib_17

value: 18 months


title: OCRE_treated_MS_patient_Time_t0 [US83400190_257015617914_S01_miRNA_1200_Jun14_2_2]


title: CLA_treated_MS_patient_Time_t1 [US83400190_257015617914_S01_miRNA_1200_Jun14_2_1]


title: Tumor_RNA_sublib_15


title: Tumor_RNA_sublib_14


title: Tumor_RNA_sublib_13


title: CLA_treated_MS_patient_Time_t0 [US83400190_257015617914_S01_miRNA_1200_Jun14_2_3]


title: Tumor_RNA_sublib_12


title: Tumor_RNA_sublib_11


title: Antago-N-miR-376a-3p-treated Sample 2


title: Antago-E-miR-376a-3p-treated Sample 7

value: Antago-Edited miR-376a-3p


title: Fbxo2_A04

value: tamoxifen at 3 weeks, dissociation with Papain at 5 weeks.


title: Fbxo2_A09


title: Antago-E-miR-376a-3p-treated Sample 6


title: H4-del MNase

city: Frederick

first: Wilfried

middle: Marie Francis

last: Guiblet

state: MD

address: 8560 Progress Drive

institute: Frederick National Laboratory for Cancer Research

data_processing:
Raw FASTQ read pairs were trimmed with cutadapt
Trimmed read pairs were assembled with PEAR to obtain nucleosome-size fragments (-p 0.0001)
The resulting fragments were then mapped with Bowtie2 (34, parameter -x), using the sequence of the BRCA1 gene (from human genome hg19) as a reference
Fragments with samtools flag 260 (unmapped/not primary alignment) were filtered out.
The MNase-seq DNA fragments with the lengths 147-149 bp for W-T, H2A and H4-del datasets, and 146-148 bp for H4-glob dataset were selected. The centers of MNase-seq fragments were assumed to represent the nucleosome DYADs. The numbers of DYADs at each position of hBRCA1 gene (the DYAD occurrences) were saved in ".occur" files.
hg19
Supplementary files format and content: For each library, a 147-9bp.DYADs.sorted file

organism: Escherichia coli

growth_protocol: Transformed E. coli with TAR/BAC containing full length hBRCA1 gene (BRCA1-TAR/YAC/BAC) was obtained from V. Larionov (30). It was first placed on agar plates supplemented with chloramphenicol as a selective agent (0.5 ml of 25 g/ml stock solution per 1 L of LB media). Cells were transferred into filtered LB media supplemented with 10 g yeast extract, 10 g NaCl, 2 g bactotryptone, 0.5 ml of 25 mg/ml of chloramphenicol and 0.4 ml of 5 M NaOH per 1 L of media and grown overnight at 37°C on platform shaker.

extract_protocol:
Plasmids were prepared using Qiagen Large-construct kit (cat. # 12462) according to the manufacturer’s instruction, and then cleaned with phenol chloroform extraction, precipitated, and resuspended in 10 mM Tris pH 8.0, 0.2 mM EDTA.
Reconstituted BRCA1-TAR/YAC/BAC arrays were assembled using Xenopus histone octamers with wild-type (W-T) and H2A/H4 N-tailless histones obtained from Histone Source, Protein Expression and Purification Facility at Colorado State University. Reconstitution was performed as described earlier (31). Briefly, core histone octamers and purified DNA were combined in a final mixture containing 2 M NaCl and 1 mM PMSF. Samples were kept on ice for 1 hour following dialysis in 3500 MWCO membranes against buffer (2 M NaCl, 10 mM Tris, 0.2 mM EDTA, 0.1% NP-40, 5 mM β-mercaptoethanol, pH=8.0) for 2 h. Samples were transferred to 1.5 M NaCl buffer and dialyzed for 2 h, followed by dialysis against 1 M NaCl and 0.75 M NaCl buffers, 3 hours each, and 0.5 M NaCl buffer overnight (all other buffer component were kept constant). Reconstitutes were next dialyzed against a buffer containing 5 mM NaCl, 10 mM Tris, 0.2 mM EDTA, 0.1% NP-40, 5 mM β-mercaptoethanol, pH 8.0, for 3 h. Samples were dialyzed in the buffer with 5 mM NaCl, 10 mM Tris, 0.025% NP-40 and no EDTA for additional 3 h.
Reconstituted chromatin (1 µg in 60 µl) in buffer containing 50 mM NaCl, 10 mM Tris 0.025% NP-40, 20% Ficoll, and 0.7 mM CaCl2 was digested with 0.2 units MNase  for 10 min at 20°C. Reaction was stopped by addition of 20 mM EDTA and cooled on ice. Digested samples were treated with SDS and proteinase K for 2 h at 55°C and cleaned with Promega Wizard SV Gel and PCR Clean-Up System (cat. # A9282). Nucleosomal DNA fragments were subjected to paired-end sequencing on Illumina platform.

tag: histone


title: Tumor_RNA_sublib_9


title: Fbxo2_A08


title: Antago-N-miR-376a-3p-treated Sample 1

tag: cell type


title: H4-glob MNase


title: Fbxo2_A07


title: Fbxo2_A02


title: H2A-tailless MNase


title: Antago-E-miR-376a-3p-treated Sample 3


title: Fbxo2_A01


title: Wild-type MNase

value: Wild-type


title: Tumor_RNA_sublib_6

tag: Sex


title: Antago-E-miR-376a-3p-treated Sample 8


title: OCRE_treated_MS_patient_Time_t0 [US83400190_257015617914_S01_miRNA_1200_Jun14_1_4]

value: OCRE


title: CLA_treated_MS_patient_Time_t1 [US83400190_257015617914_S01_miRNA_1200_Jun14_1_3]

value: CLA


title: Tumor_RNA_sublib_16


title: Fbxo2_A06


title: Fbxo2_A05


title: Antago-E-miR-376a-3p-treated Sample 1


title: Tumor_RNA_sublib_10


title: Fbxo2_A03


title: Tumor_RNA_sublib_8


title: Antago-E-miR-376a-3p-treated Sample 4


title: human pluripotent stem cell-derived aggregates, Day5

city: Sakyo-ku

first: Yusuke

last: Seto

state: Kyoto

address: 53 Shogoin Kawara-cho

country: Japan

institute: Kyoto University

data_processing:
Cellranger mkfastq v5.0.1 to generate FASTQ
Cellranger count v5.0.1 to generate count matrix
Seurat v4.1.0 for downstream analyses
Assembly: human NCBI genomme build 38
Supplementary files format and content: Cellranger output files including tab-separated value files (barcodes.tsv, features.tsv), and Matrix Market file (matrix.mtx)
Supplementary files format and content: Rds files which contain single cell data processed with Seurat

growth_protocol: Aggregates of human pluripotent stem cells were cultured in NCC inductino medium (DMEM/F-12 with GlutaMAX supplemented with 1x B-27 minus vitamin A and 5 mg/ml bovine serum albumin.

extract_protocol:
Aggregates were dissociated using TrypLE Express. Dissociated single cells were used in library construction using v3 Chromium Single Cell 3′ Reagent Kit (10X Genomics)
10x Genomics Chromium 3’ v3 Single Cell Gene Expression Kit

value: differentiation day4


title: Tumor_RNA_sublib_7


title: Med1313lfl_UNT_HIC_rep2

city: Utrecht

first: Robin H.

last: van der Weide

state: Utrecht

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institute

data_processing:
Hi-C sequencing data was mapped to GRCm38.p6 and processed with Hi-C-Pro 2.9.
Further data analysis was performed with GENOVA (github.com/deWitLab/GENOVA).
Genome_build: mm10
Supplementary_files_format_and_content: validPairs files, containing the genomic position and strand of the two pairs of a Hi-C ligation

source_name: Mouse embryonic stem cells, untreated control, Med13/13l fl/fl Hi-C

growth_protocol: Mouse embryonic stem cells were grown on gelatin-coated plates at 37°C and 5% CO2, in Dulbecco’s Modified Eagle Medium (DMEM) supplemented with 15% fetal bovine serum (Labtech), 2 mM L-glutamine (Life Technologies), 1x penicillin-streptomycin solution (Life Technologies), 1x non-essential amino acids (Life Technologies), 0.5 mM beta-mercaptoethanol (Life Technologies), and 10 ng/mL leukemia inhibitory factor. HEK293T celles were grown in EC-10 medium (DMEM supplemented with 10% fetal bovine serum (Labtech), 2 mM L-glutamine (Life Technologies), 1x penicillin-streptomycin solution (Life Technologies), 1x non-essential amino acids (Life Technologies), 0.4 mM beta-mercaptoethanol (Life Technologies), and 10 ng/mL leukemia inhibitory factor). Drosophila S2 (SG4) cells were grown adhesively at 25°C in Schneider’s Drosophila Medium (Life Technologies), supplemented with 1x penicillin-streptomycin solution (Life Technologies) and 10% heat-inactivated fetal bovine serum (Labtech).

extract_protocol:
In-situ Hi-C in Med13/13lfl/fl ESCs was performed in biological duplicates as described in Haarhuis et al. (2017).
Hi-C libraries were sequenced on Illumina NextSeq 500 platform as 51bp or 40bp paired-reds.

treatment_protocol: Med13/13lfl/fl ERT2-Cre ESCs were treated with 800nM 4-hydroxytamoxifen (Sigma) for 96 hours. Pcgf4-/-/Pcgf2fl/fl ERT2-Cre ESCs were treated with 800nM 4-hydroxytamoxifen (Sigma) for 72 hours. For RA differentiation, ESCs were treated with 1µM retinoic acid (Sigma-Aldrich) for 48h.

value: Med13;Med13l flfl

value: untreated

tag: treatment time


title: Antago-E-miR-376a-3p-treated Sample 2


title: Med1313lfl_TAM_HiC_rep2

source_name: Mouse embryonic stem cells, tamoxifen treated, Med13/13l fl/fl Hi-C

value: tamoxifen


title: SM22-∆Ogt-1

city: Xin Xiang

first: xiwen

last: xiong

address: 602 Jinsui Road

department: School of Forensic Medicine

institute: Xinxiang Medical University

data_processing:
Basecalls performed using CASAVA version 1.8
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using FASTX-Toolkit  version 0.0.13 and Perl version 5.8.8.
Paired-end sequence files (fastq) were mapped to the reference genome GRCm39.108 using Hisat2 (Hierarchical Indexing for Spliced Alignment of Transcripts, version 2.0.5). The output SAM (sequencing alignment/map) files were converted to BAM (binary alignment/map) files and sorted using SAMtools (version 1.3.1).
Gene abundance measurements were generationed and normalized  using Cufflink version 2.0.2.Linux_x86_64. The normalized standard were Fragments Per Kilobase of exon per Megabase of library size (FPKM).
Differential expression analysis for mRNA was performed using R package edgeR.
Assembly: GRCm39.108
Supplementary files format and content: Tab-delimited text file representing FPKMs and counts

source_name: Aorta

extract_protocol:
Total RNA was isolated using RNeasy mini kit (Qiagen, Germany).
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: Aorta

value: Ogt SMC specific knockout


title: SM22-∆Ogt-3


title: SM22-Ctrl-3

value: LoxP


title: Tumor_RNA_sublib_2

value: Liver, lung, stomach and subcutaneous tumor

value: Male


title: Tumor_RNA_sublib_1

value: mRNA


title: Tumor_RNA_sublib_5


title: SM22-Ctrl-2


title: OCRE_treated_MS_patient_Time_t1 [US83400190_257015617914_S01_miRNA_1200_Jun14_1_2]

value: peripheral blood

value: lymphocytes and monocytes

value: F

value: YES


title: Med1313lfl_TAM_HiC_rep1


title: Antago-E-miR-376a-3p-treated Sample 5

value: human-iPSC

value: Neurons

value: Antago-Edited miR-376a-3p


title: SM22-∆Ogt-2


title: Tumor_RNA_sublib_4

value: 18 months


title: Tumor_RNA_sublib_3


title: CLA_treated_MS_patient_Time_t0 [US83400190_257015617914_S01_miRNA_1200_Jun14_1_1]

value: CLA


title: SH_Col_96hr

status: Public on Jan 02 2024

first: Chuanwei

address: 2005 Songhu Road, Yangpu District

department: school of life sciences

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Tair 10 whole genome using bowtie
Differential gene expression analysis was done using R package
Genome_build: Tair 10

source_name: shoot

growth_protocol: Seeds were germinated on solid agar MS plates without sucrose. After stratification, plates were incubated in growth chambers under continuous white light (30-50 μE·m -2 ·s -1, R:FR ratio of 1.2) for 3 d at 22°C.

extract_protocol: RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Three-day-old seedlings grown under white light were treated with or without low R:FR (LED light, R: 13 μE·m -2 ·s -1;  Blue: 1.23 μE·m -2 ·s -1 and FR light: 20 μE·m -2 ·s -1, 22°C) for 1 h and 4 d.  Shoot tissue were collected

tag: genotype/variation

value: shoot

value: 7-day old seedlings

value: 3d white light+ 96hr low R:FR


title: SH_pil1hfr1_96h


title: Med1313lfl_TAM_HiC_rep0

value: Med13;Med13l flfl

tag: strain

value: tamoxifen


title: Med1313lfl_UNT_HIC_rep1

value: untreated


title: human pluripotent stem cell-derived aggregates, Day2

tag: time

value: differentiation day2


title: WL_Col

value: 7d white light


title: SM22-Ctrl-1

value: Aorta

value: LoxP


title: GPNMB- GAL-3-MT Immu cells

first: qiudong

last: zhao

address: 225 Changhai Road

department: Tumor Immunology and Gene Therapy Center

institute: Shanghai Eastern Hepatobiliary Surgery Hospital

description: DN

data_processing:
The sequencing reads were automatically uploaded and evaluated for quality using Illumina BaseSpace Onsite Computing platform.
Fastq sequence files were generated and analysis was performed using applications available on BaseSpace Onsite Computing platform
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated.
Clustering and correlation analysis were carried out using Metaboanalyst 3.0 software analysis package (http://www.metaboanalyst.ca).
Assembly: Rnor6
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample.Matrix table with raw gene counts for every gene and every sample.

organism: Rattus norvegicus

extract_protocol:
The total RNA  was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-2501) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: liver

value: DEN up to 16 weeks


title: Med1313lfl_UNT_HIC_rep0


title: human pluripotent stem cell-derived aggregates, Day4

value: differentiation day3