title: HEK293T cells, DMSO, rep1

city: Würzburg

first: Julian

last: Konig

address: Am Hubland

institute: Würzburg University

data_processing:
Quality control: FastQC (v0.11.8)
Trimming: Cutadapt (v1.18) with non-default parameters: cutadapt -a file:NexteraPE-PE.fa --minimum-length 50 (additional parameter used for C643, HEK293T, RPE1, male mESC samples: --cut 1)
Mapping: STAR (v2.7.3a) with non-default parameters: STAR --runMode alignReads --outFilterMismatchNoverLmax 0.04 --outFilterMismatchNmax 999 --outStd SAM --outSAMattributes NH HI AS nM MD --outSJfilterReads Unique --outSAMunmapped Within --runThreadN 4 --readFilesCommand zcat --sjdbOverhang READLENGTH-1
Filter/remove secondary hits: Samtools (v1.9) with parameters: samtools view -F 256
Counts per gene: Subread (v2.0.0) with non-default parameters: featureCounts --donotsort -s2 -t exon (default used for -g gene_id)
Assembly: human: GRCh38.p12 (Gencode release 31) (+ ERCC spike-ins in C643, HEK293T, RPE1)
Assembly: mouse: GRCm38.p6 (Gencode release M23) (+ ERCC spike-ins in male mESC)
Supplementary files format and content: tab-delimited text (.tsv) files include absolute read counts per gene for each sample

growth_protocol: For C643 and HEK293T: Cells were cultured in Dulbecco’s Modified Eagle Medium (DMEM, Life Technologies) supplemented with 10% fetal bovine serum (FBS, Life Technologies), 1% L-glutamine (Life Technologies) and 1% penicillin/streptomycin (P/S Life Technologies). For RPE1: Cells were cultured in DMEM/F12 (Life Technologies) supplemented with 10% foetal bovine serum (FBS, Life Technologies), 1% penicillin/streptomycin (P/S, Life Technologies), 1% L-Glutamin and 0.04% Hygromycin B (Life Technologies). Cells were grown at 37◦C with 5% CO2. For male and female mESC: Female mouse embryonic stem cells (mESC) were taken from a previous publication (PMID: 24506884). Single clones were picked and cultured until confluency. Male mESC were taken from a previous publication (PMID: 25569111).  Cells were cultured in 2i/LIF medium. Briefly, 500 ml medium was generated by adding 235 ml of each DMEM/F12 and neurobasal (Gibco; 21331020, 21103049), 7.5 ml BSA solution (7.5%, ThermoFisher; 11500496), 5 ml penicillin-streptomycin (Gibco; 15140-122), 2 mM L-Glutamin (ThermoSci; 25030024), 100 µM β-mercaptoethanol (Gibco; 21985023), 5 ml mM nonessential amino acids (Gibco; 11140050), 2.5 ml N2 supplement (Gibco; 17502048), 5 ml B27 supplement (Gibco; 17504044), 3 µM CHIR99021 (Sigma; SML1046), 1 µM PD 0325901 (Biomol; 13034-1), 10 ng/ml LIF (IMB Protein Production core facility). Cells were cultured at 37°C  with 5% CO2. Cell culture dishes were coated using 0.1% gelatin (Sigma; ES-006-B). The medium was exchanged every day and cells were passaged every second day.

extract_protocol:
For RNA extraction, cells were washed twice with ice cold 1x PBS and collected on ice. For total RNA isolation the RNeasy Plus Mini Kit (Qiagen) was used following the manufacturer’s instructions.
RNA-seq: All NGS library preps were performed with Illumina's Stranded mRNA Prep Ligation Kit following Stranded mRNA Prep Ligation Reference Guide (June 2020) (Document # 1000000124518 v00). For RNA-seq in HEK293T and C643 cells: Libraries were prepared with a starting amount of 350 ng for C643 samples and 1000 ng for HEK293T samples and amplified in 11 PCR cycles and 10 cycles respectively. For normalization, 2μl of a 1:300 dilution of ERCC spike-ins (Ambion) were added to the starting material for C643 samples and for HEK293T samples 2μl of a 1:100 dilution. Libraries were profiled in a DNA 1000 chip on a 2100 Bioanalyzer (Agilent technologies) and quantified using the Qubit dsDNA HS Assay Kit, in a Qubit 2.0 Fluorometer (Life technologies). All samples were pooled in equimolar ratio and sequenced on 1 NextSeq500 Highoutput FC, SR for 1x 80 cycles plus 10 cycles for the index read plus 1 dark cycle upfront Read 1. For RNAseq in male mESC cells upon 24 h of STM2457 treatment: Libraries were prepared with a starting amount of 1000 ng and amplified in 10 PCR cycles. For normalization, 2μl of a 1:100 dilution of ERCC spike-ins (Ambion) were added to the starting material. Libraries were profiled in a DNA 1000 chip on a 2100 Bioanalyzer (Agilent technologies) and quantified using the Qubit dsDNA HS Assay Kit, in a Qubit 2.0 Fluorometer (Life technologies). All samples were pooled in equimolar ratio and sequenced on 1 NextSeq500 Highoutput FC, SR for 1x 155 cycles plus 10 cycles for the index read and 1 dark cycle upfront Read 1. For RNAseq in RPE1 cells: Libraries were prepared with a starting amount of 1000 ng and amplified in 10 PCR cycles. For normalization, 2μl of a 1:100 dilution of ERCC spike-ins (Ambion) were added to the starting material. Libraries were profiled in a HS DNA chip on a 2100 Bioanalyzer (Agilent technologies) and quantified using the Qubit dsDNA HS Assay Kit, in a Qubit 2.0 Fluorometer (Life technologies). All samples were pooled in equimolar ratio and sequenced on 1 NextSeq500 Highoutput FC, SR for 1x 80 cycles plus 10 cycles for the index read and 1 dark cycle upfront Read 1. For RNAseq in male mESC upon STM2457 timecourse 3h-12 h: Libraries were prepared with a starting amount of 1000 ng and amplified in 10 cycles. For normalization, 2μl of a 1:100 dilution of ERCC spike-ins (Ambion) were added to the starting material. Libraries were profiled in a DNA 1000 chip on a 2100 Bioanalyzer (Agilent technologies) and quantified using the Qubit dsDNA HS Assay Kit, in a Qubit 2.0 Fluorometer (Life technologies). All samples were pooled in equimolar ratio and sequenced on 2 NextSeq500 Highoutput FC, SR for 1x 80 cycles plus 10 cycles for the index read plus 1 dark cycle upfront Read 1. For RNAseq in female mESC single clones: Libraries were prepared with a starting amount of 500 ng and amplified in 10 PCR cycles. Two post PCR purification steps were performed to exclude residual primer and adapter dimers. Libraries were profiled in a DNA 1000 chip on a 2100 Bioanalyzer (Agilent technologies) and quantified using the Qubit dsDNA HS Assay Kit, in a Qubit 2.0 Fluorometer (Life technologies). All 12 samples were pooled in equimolar ratio and sequenced on 1 NextSeq500 Highoutput FC, SR for 1x 79 cycles plus 10 cycles for the index read and 2 dark cycles upfront Read 1.

treatment_protocol: Cells were cultured in respective medium supplemented with Mettl3 inhibitor STM2457 or DMSO as negative control for 3h and up to 24h.

value: Human embryonic kidney 293T cell line

value: DMSO

tag: gender

value: female


title: p5_6neg

status: Public on Nov 18 2023

type: SRA

city: New York

first: Liora

middle: s

last: Katz

state: NY

address: One Gustave L. Levy Place, Box 1152, Atran building 5-17

country: USA

institute: Icahn School of Medicine at Mount Sinai

library_source: transcriptomic

data_processing:
Raw count data was pre-filtered to keep genes with CPM>1.0 for at least 60% of the samples.
Count data was normalized via the weighted-trimmed mean of M-Values, normalized counts were transformed into normally distributed expression values via the voom transformation using covariates model.
Statistical analysis was carried out using R language version 3.0.3
Assembly: GRCh38/hg38

molecule: total RNA

organism: Homo sapiens

source_name: Islets of Langerhans

extract_protocol:
Total RNA from ~100 human islets isolated using the RNAeasy micro kit (Qiagen) according to the manufacturer’s protocol.
Samples were submitted to the New York Genome Center and RNA was amplified via the NuGEN Ovation RNA-Seq System V2 prior to RNA sequencing. 35-40 million 2x50 bp paired-end reads were sequenced per sample on the HiSeq2500 instrument (Illumina)

tag: tissue

value: Islets of Langerhans

tag: donor

tag: treatment

value: 6mM glucose, 0nM T3


title: Donor Young-2, HSPC or CD34 enriched cells from BMMC, ATAC, sample 8

city: Boston

first: Chen

last: Weng

state: OH

address: 415 Main St, Cambridge

department: Genetics

institute: Broad Institute and Whitehead Institute

description: ATAC library (Cell barcodes are matchable with mRNA and mtDNA lib in sample 8): read1 file contains one end of accessible region; i5 file (1-24) contains cell barcodes, read2 file contains the other end of accessible region.

library_source: genomic single cell

data_processing:
The data preprocessing for the joint single-cell RNA and ATAC data was performed using 10X Genomics data preprocessing software Cell-ranger-arc.  The basic quality control analysis was as follows: RNA UMI: 1,000~25,000 transcripts per cell, unique ATAC fragment: 1,000 ~ 70,000, Fragment on peak minimum percentage: 10%, minimum mtDNA copies per position per cell: 10X. Finally, the possible doublets are removed by Amulet (using default parameter). Unsupervised community detection-based clustering was performed on weighted nearest neighbour (WNN) using Seurat. Cell types are firstly annotated by gene expression using the latest signature (van Galen under review) which was further validated by sorted bulk RNA-seq data (https://sankaranlab.shinyapps.io/geneExpression/). The ATAC unique fragments for each clustered cell type were further aggregated to generate pseudo-bulk ATAC tracks. The single cell motif analysis was performed using ChromVar using the JASPAR human transcription factor (TF) database. The deviation of the TF frequency was computed for each cell for the downstream analysis.
The mutation calling pipeline is in following steps using package redeemV: 1, Data Preprocessing and eUMI grouping. 2, Consensus filtering. 3, Strand bias removal. 4, Lineage informative variants identification
Assembly: hg38
Supplementary files format and content: 10x Genomics output files: filtered_feature_bc_matrix.h5, atac_fragments.tsv.gz
Supplementary files format and content: mtDNA mutation count matries (Cell-to-mito variants, MatrixMarket file)

molecule: genomic DNA

source_name: Bone Marrow

extract_protocol:
Bone marrow was collected from healthy young or aged donors. Bone marrow aspirate was diluted with an equal volume of Wash Buffer (PBS, 2% FBS, 1mM EDTA). Ficoll medium was added to SepMateTM (Catalog #85460) tubes and then the diluted bone marrow sample was layered on top followed by centrifuging at 1200 g for 20 minutes at room temperature. The top layer, containing the mononuclear cells, was transferred to a new tube, which was then filled up by Wash Buffer. The mononuclear cells were centrifuged at 300 g for 8 minutes. The supernatant was discarded, and the cells were washed twice and resuspended in Wash Buffer for further enrichment or in Freezing buffer (10% DMSO in FBS). Starting with the BMMCs isolated from the previous step, we enriched CD34+ cells following EasySep™ Human Cord Blood CD34 Positive Selection Kit II (Catalog #17896). Briefly, EasySep™ Human CD34 Positive Selection Cocktail (Catalog #18096C) was added to BMMCs suspension to 100 ul/ml and incubated at room temperature for 10 minutes. EasySep™ Dextran RapidSpheres™ (Catalog #50100) was vortexed and added to each sample to 50 µl/ml.  The mix was incubated for 3 minutes at room temperature. Next, Wash Buffer (7 ml) was added to the tube, The cells were then washed 4 times in "The Big Easy" EasySep™ Magnet (Catalog #18001). Finally, cells were resuspended in Wash Buffer and were centrifuged at 300g for 10 min. The CD34+ positive cell pellet was then resuspended in a freezing buffer (10% DMSO in FBS).  To further enrich the hematopoietic stem cells (HSCs), an aliquot of the enriched CD34+ cells were stained by one of the following two antibody panels. 1) CD34 PerCP-Cy5.5 (Catalog #347222); CD45RA Alexa Fluor 488 (Catalog #304114); CD90 PE-Cy7 (Catalog #561558); and  DAPI (Catalog #D1306) as viability dye. Or 2) CD34 BV421 (Catalog #562577); CD45RA-APC-H7 (Catalog #560674); CD90 PE-Cy7 (Catalog #561558), and 7-AAD as viability dye(Catalog #559925). The cells were further sorted using BD FACSAriaTM for CD34+CD45RA-CD90+ to enrich HSCs. BMMCs, as well as enriched CD34+ and CD34+CD45RA-CD90+ cells were cryopreserved. After thawing, cells were immediately processed for experiment as soon as possible without any culturing.
RNA lib and ATAC lib prep:  After tagmentation, cells were immediately processed for GEM generation & barcoding following 10x Genomics Chromium Next GEM Single Cell Multiome ATAC + Gene Expression User Manual  (version CG000338 Rev A, 10x Genomics) with Step 2. Next, the Post GEM Incubation Cleanup and Pre-Amplification PCR were performed following the same User Manual with Step 3 and Step 4. The pre-amplified library was eluted in 100ul EB buffer instead of 160ul. For RNA library prep, we took an aliquot of 35 ul pre-amplified library and followed the same User Manual (version CG000338 Rev A, 10x Genomics) from Step 6 and Step 7. We developed an in-house protocol to generate the massive ATAC library with enough material for both direct sequencing and mtDNA hybridization. For each sample, 8 reactions of the following were performed (each in 50 ul). 5 μl pre-amplified product, 25 μl NEBnext mix (Catalog M0541L), 2.4 μl 10 μM Nextera N70X primer (Supplementary Data 2), 2.4 μl 10X SI PCR primer B (Catalog #PN2000128), 0.5 μl 100X SYBR Green (Catalog #S7563), and 14.7 μl water. The thermocycler program started with 98°C 45 s., followed by the 6-12 cycles of: 98°C for 10 s., 63°C for 30 s., and 72°C for 20 s.; The actual cycle numbers are determined using the amplification curve and the qPCR was stopped when the curve started to reach plateau. The qPCR products (50ul * 8 wells) were combined and purified using SPRI beads (Catalog #B23318) with size selection 0.4X~1.55X. The expected yield is 2,000 ng to 4,000 ng.
mtDNA lib prep: We designed 4 sets of DNA probes, with each probe set covering the whole mitochondrial genome and containing 138 biotinylated oligos that are 120 bp long. The 4 sets of probes ((v1, v2, v3, and v4) are staggered by 30 bp with each other and ensure good coverage on junction areas (Supplementary Data 2). The hybridization started with 500 ng ATAC library products for each probe set. In total, 4 independent reactions were performed in parallel and combined at the end (2,000ng input in total). The detailed incubation and wash methods largely followed the Tube Protocol in IDT xGen Hybridization Capture of DNA Libraries protocol.  Briefly, 500 ng input was combined with Cot DNA and purified by SPRI beads, which was eluted by hybridization mix that contains hybridization buffer, hybridization buffer enhancer, one of the probe set, as well as xGen™ Universal Blockers NXT (Catalog #1079584). The hybridization reaction was performed as below: 95C 30 seconds followed by 65C overnight.  The biotin-streptavidin Dynabeads purification was carried out on Day 2 using xGen Hybridization and Wash Kit. The Dynabeads after capturing and washing were used for final quick qPCR amplification (3-5 cycles). The reaction mix is as below: 20ul beads, 25ul KAPA HiFi HotStart ReadyMix (Catalog #KK2601), Primer 2.4ul P5 (Supplementary Data 2), Primer P7 (Supplementary Data 2), 0.5ul 100X SYBR Green (Catalog #S7563). The PCR program started with 98°C 45 s, followed by the 3-5 cycles of: 98°C for 10 s., 63°C for 30 s., and 72°C for 20 s. The final enriched mtDNA was purified by SPRI beads (1.6X)

value: Bone Marrow

tag: cell type

value: Hematopoietic Stem and progenitors (HSPC or CD34 enriched cells from BMMCs)


title: EGR1 inh rep1

city: Blacksburg

first: Xiguang

last: Xu

state: VA

address: 1015 Life Science Circle

department: Department of Biomedical Sciences and Pathobiology

institute: Virginia Tech

library_source: genomic

data_processing:
Sequencing adapters and low-quality bases were first trimed with cutadapt(v1.18) and trim_galore(v0.5.0) for all cun&run libraries. The retained reads were aligned to mouse genome(mm10) using bowtie2(v2.3.5) in pair-end mode with option “-N 1 -L 25”.
PCR duplications were removed using picard(v2.25.0) with the option “REMOVE_DUPLICATES=true”. Non-redundant reads were further filtered for minimal mapping quality (MAPQ ≥ 30) using samtools(v1.12) view with option “-q30”.
Peak calling for histone modifications was performed by MACS2(v2.2.5) using option “-p 0.05” for H3K27ac and H3K4me3, “--broad -p 0.05” for H3K4me1 and H3K27me3. The reproducible peaks between biological replicates was further identified following irreproducible discovery rate (IDR, v2.0.4.2) framework with parameters “--rank signal.value”.
Stricter parameters were adopted for EGR1 cun&run datasets peak calling to generate the reliable transcription factor binding sites，with option “-p 0.005” for  MACS2 and “--rank signal.value --idr-threshold 0.02” for IDR framework.
Assembly: mm10
Supplementary files format and content: narrowPeak, broad Peak
Library strategy: Cut&Run

organism: Mus musculus

source_name: whole brain

growth_protocol: Mice were maintained and bred in a 12-hour light/dark cycle under standard pathogen-free conditions.

extract_protocol:
Nuclei were isolated from adult mouse brain tissue and subjected to FACS-sorting. The FACS-sorted nuclei were used for Cut&Run with the CUTANA CUT&RUN Kit. The Cut&Run enriched DNA fragments were used for DNA library construction.
Cut&Run libraries were prepared using the NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB) following the manufacturer's instructions.

value: whole brain

value: inhibitory neuron

tag: genotype

value: Sun1 f/f | Emx1Cre (+)

tag: age

value: 8 weeks

tag: chip antibody


title: IS607_reRNA_sRNAseq

city: Berkeley

first: Marena

middle: Isabelle

last: Trinidad

state: CA

address: 2151 Berkeley Way

institute: Innovative Genomics Institute

data_processing:
NGS reads were merged using BBMerge using a normal merge rate and then mapped onto the TnpB containing locus using Geneious mapper at Low Sensitivity to identify reRNA boundaries (Geneious 2023.0.1 (https://www.geneious.com)).
Assembly: For each sample, a custom reference fasta was used for alignment, as described for each processed file below. Reference fastas are supplied under supplementary files.
Supplementary files format and content: MA_4_ISXfa1_IS607_Figure3A.bw was generated by aligning raw data from Figure_3A_IS607_sRNA to ISXfa1_IS607_Contig_Figure3A.fasta, then converted to BigWig Format with DeepTools (v3.5.1).
Supplementary files format and content: SFAV1_5dpi_sRNA.bw was generated by aligning raw data from Figure_5A_SFAV1_sRNA to AM398843_SFAV_IN_VIVO_2And5dpi_FIGURE_5_and_S5.fasta, then converted to BigWig Format with DeepTools (v3.5.1).
Supplementary files format and content: SFAV_2dpi.bw was generated by aligning raw data from Figure_S5A_SFAV1_sRNA to AM398843_SFAV_IN_VIVO_2And5dpi_FIGURE_5_and_S5.fasta, then converted to BigWig Format with DeepTools (v3.5.1).
Supplementary files format and content: sfav_baculo.bw was generated by aligning raw data from Figure_S5B_SFAV1_sRNA to SfAV-1_SF9_contig_FIGURE_S5.fasta, then converted to BigWig Format with DeepTools (v3.5.1).
Supplementary files format and content: hagv_sRNA.bw was generated by aligning raw data from Figure_S5B_HAGV1_sRNA to HAGv-1_SF9_contig_FIGURE_S5.fasta, then converted to BigWig Format with DeepTools (v3.5.1).
Supplementary files format and content: hvav.bw was generated by aligning raw data from Figure_S5B_HVAV1_sRNA to HvAV-1_SF9_contig_FIGURE_S5.fasta, then converted to BigWig Format with DeepTools (v3.5.1).

organism: Escherichia coli

extract_protocol:
The cell pellets were resuspended in 98% formamide and 10 mM EDTA and lysed at 70 °C for 10 min. The total RNA were then extracted from the lysate using Zymo Quick-RNA Miniprep Kit (Zymo Research) and used for small-RNA sequencing library preparation.
Following on-column DNAse treatment, total RNA was eluted using water. ~200 ng of total RNA was used for rRNA depletion reactions using NEBNext rRNA kit (bacteria) following manufacturer protocols. For eukaryotic samples, custom probes designed using NEBNext Custom rRNA depletion tool were used. The rRNA depleted RNA was purified using a Zymo-Spin IIC column, treated with T4 PNK using T4 PNK buffer (NEB) at 37 C for 30 minutes before spiking in ATP and further incubating. Further end treatment was performed using mRNA Decapping Enzyme (NEB) pre-mixed with its buffer directly into the PNK reaction and incubating at 37 C for 30 minutes. End-repaired RNA was purified using a Zymo-Spin IIC column, and used for Collibri small-RNA-seq library preparation reactions following manufacturer protocols (INVITROGEN). The resulting NGS adapter ligated cDNA was then amplified with KAPA HiFi HotStart ReadyMix using NGS indexing primers for 25 cycles (ROCHE). Amplified DNA fragments between 150~500nt were size selected by gel extraction purification following gel-electrophoresis in a 4% SYBR-GOLD E-GEL. Before loading into the sequencer, library concentrations were quantified using KAPA-QUANT qPCR kit (ROCHE).
Bulk RNA was subjected to rRNA depletion with NEBNext rRNA Kit for either bacteria or eukaryotes, depending on the biosample. The final library was prepared with the Collibri small-RNA-seq kit (INVITROGEN) according to manufacturer instructions.

tag: cell line

value: plasmid


title: EGR1 inh rep2


title: HEK293T_HA-SPINDOC, Flag-Spindlin1

city: Beijing

first: Fan

last: Zhao

address: 1 Qinghuayuan

country: China

institute: Tsinghua University

data_processing:
Raw data were aligned with Bowtie2 (version 2.2.5), and BAM files were further sorted by Samtools (version 1.11). Reads which were unmapped in reference genome were removed.
We filtered duplicates using Picard MarkDuplicates (version 2.26.6).
We called broad peak using MACS2 (version 2.2.7.1).
We used software bedGraphToBigWig (version 2.8) to transform the bedgraph files into BigWig files, which were applied for downstream analysis.
Assembly: hg38
Supplementary files format and content: bigWig

growth_protocol: DMEM, 10% fetal bovine serum, 2mM glutamine, 1*penicillin/streptomycin. Cells were cultured at 37°C at 5% CO2.

extract_protocol:
Cells were crosslinked with formaldehyde. After chromatin sonification and centrifugation, the supernatant was aliquoted and subjected to antibodies.
Libraries were prepared using the VAHTS Universal DNA Library Prep Kit (ND607). Briefly, DNA was subjected to end preparation, adapter ligation and library amplification.

treatment_protocol: Flag-Spindlin1 stably expressed, HA-SPINDOC overexpressed

value: Embryonic Kidney Cells

value: HA-SPINDOC

tag: antibody

value: Flag ChIP


title: ICR mice, Control1

city: Hangzhou

first: Sun

last: Peng

address: 260 Baichuan Street

institute: Zhejiang chinese medical University

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9)
We aligned reads of all samples to the research species reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.0.4) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome. And then by removing sequence-dependent bias and amplification noise using UMI-tools.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-1.3.4d) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Genes differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples). The genes with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change ≥ 2 were considered differentially expressed genes. Differentially expressed genes were then subjected to enrichment analysis of GO functions and KEGG pathways.
Assembly: mm9
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample ...
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: Submandibular gland

extract_protocol:
Total RNA was extracted usingTrizol reagent following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit, high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.
After total RNA was extracted, mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA). An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters, which including custom Unique Molecular Identifiers for minimizing sequence-dependent bias and amplification noise according to (Shiroguchi et al. 2012). Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys were 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina Novaseq™ 6000 following the vendor's recommended protocol.

value: Submandibular gland

value: WT


title: Donor Young-2, BMMCs, mRNA-derived cDNA, sample 7

description: 3' mRNA library (Cell barcodes are matchable with ATAC and mtDNA lib in sample 7): read1 (1-28nt) file contains cell barcode and UMI; read2 file contains transcript.

library_source: transcriptomic single cell

molecule: polyA RNA

value: Bone Marrow Mononuclear Cells (BMMCs)


title: p4_20neg

value: 20mM glucose, 0nM T3


title: P4_20pos

value: 20mM glucose, 10nM T3


title: EGR1 exc rep2

value: excitatory neuron


title: Donor Young-1, Timepoint2, HSC or CD34+CD45RA-CD90+ enriched cells from BMMC, ATAC, sample 6

description: ATAC library (Cell barcodes are matchable with mRNA and mtDNA lib in sample 6): read1 file contains one end of accessible region; i5 file (1-24) contains cell barcodes, read2 file contains the other end of accessible region.

value: Hematopoietic Stem cells (HSC or CD34+CD45RA-CD90+ enriched cells from BMMCs)


title: p4_6neg

value: Islets of Langerhans

value: 6mM glucose, 0nM T3


title: p1_20neg


title: Donor Young-1, Timepoint2, HSPC or CD34 enriched cells from BMMC, mitochondrial DNA, sample 5

description: mtDNA library (Cell barcodes are matchable with mRNA and ATAC lib in sample 5): read1 file contains one end of mitochondrial genomic region; i5 file (1-24) contains cell barcodes, read2 file contains the other end of mitochondrial genomic region.

data_processing:
The data preprocessing for the joint single-cell RNA and ATAC data was performed using 10X Genomics data preprocessing software Cell-ranger-arc.  The basic quality control analysis was as follows: RNA UMI: 1,000~25,000 transcripts per cell, unique ATAC fragment: 1,000 ~ 70,000, Fragment on peak minimum percentage: 10%, minimum mtDNA copies per position per cell: 10X. Finally, the possible doublets are removed by Amulet (using default parameter). Unsupervised community detection-based clustering was performed on weighted nearest neighbour (WNN) using Seurat. Cell types are firstly annotated by gene expression using the latest signature (van Galen under review) which was further validated by sorted bulk RNA-seq data (https://sankaranlab.shinyapps.io/geneExpression/). The ATAC unique fragments for each clustered cell type were further aggregated to generate pseudo-bulk ATAC tracks. The single cell motif analysis was performed using ChromVar using the JASPAR human transcription factor (TF) database. The deviation of the TF frequency was computed for each cell for the downstream analysis.
The mutation calling pipeline is in following steps using package redeemV: 1, Data Preprocessing and eUMI grouping. 2, Consensus filtering. 3, Strand bias removal. 4, Lineage informative variants identification
Assembly: hg38
Supplementary files format and content: 10x Genomics output files: filtered_feature_bc_matrix.h5, atac_fragments.tsv.gz
Supplementary files format and content: mtDNA mutation count matries (Cell-to-mito variants, MatrixMarket file)
Library strategy: mtDNA-seq

value: Bone Marrow

value: Hematopoietic Stem and progenitors (HSPC or CD34 enriched cells from BMMCs)


title: HEK293T_HA-SPINDOC, Input

value: Input


title: H3K27me3 inh rep1

value: whole brain

value: inhibitory neuron

value: Sun1 f/f | Emx1Cre (+)

value: 8 weeks


title: HEK293T_HA-SPINDOC, H3K4me3

value: Embryonic Kidney Cells

value: HA-SPINDOC

value: H3K4me3 ChIP


title: EGR1 exc rep1


title: H3K27me3 inh rep2


title: HEK293T, Flag ChIP

value: wildtype

value: Flag ChIP


title: P4_6pos

value: 6mM glucose, 10nM T3


title: p1_6pos


title: Donor Young-1, Timepoint2, HSPC or CD34 enriched cells from BMMC, ATAC, sample 5

description: ATAC library (Cell barcodes are matchable with mRNA and mtDNA lib in sample 5): read1 file contains one end of accessible region; i5 file (1-24) contains cell barcodes, read2 file contains the other end of accessible region.


title: Donor Young-1, Timepoint2, HSPC or CD34 enriched cells from BMMC, mRNA-derived cDNA, sample 5

description: 3' mRNA library (Cell barcodes are matchable with ATAC and mtDNA lib in sample 5): read1 (1-28nt) file contains cell barcode and UMI; read2 file contains transcript.


title: p1_20pos

value: 20mM glucose, 10nM T3


title: HEK293T, H3K9me3 ChIP

value: H3K9me3 ChIP


title: Donor Young-1, Timepoint2, HSC or CD34+CD45RA-CD90+ enriched cells from BMMC, mitochondrial DNA, sample 6

description: mtDNA library (Cell barcodes are matchable with mRNA and ATAC lib in sample 6): read1 file contains one end of mitochondrial genomic region; i5 file (1-24) contains cell barcodes, read2 file contains the other end of mitochondrial genomic region.

value: Hematopoietic Stem cells (HSC or CD34+CD45RA-CD90+ enriched cells from BMMCs)


title: Donor Young-1, Timepoint2, BMMCs, ATAC, sample 4

description: ATAC library (Cell barcodes are matchable with mRNA and mtDNA lib in sample 4): read1 file contains one end of accessible region; i5 file (1-24) contains cell barcodes, read2 file contains the other end of accessible region.

value: Bone Marrow Mononuclear Cells (BMMCs)


title: H3K27ac inh rep2


title: H3K27me3 exc rep2

value: excitatory neuron


title: Donor Young-1, Timepoint2, BMMCs, mitochondrial DNA , sample 4

description: mtDNA library (Cell barcodes are matchable with mRNA and ATAC lib in sample 4): read1 file contains one end of mitochondrial genomic region; i5 file (1-24) contains cell barcodes, read2 file contains the other end of mitochondrial genomic region.

value: Bone Marrow


title: HEK293T_HA-SPINDOC, H3K9me3


title: p1_6neg

value: Islets of Langerhans

value: 6mM glucose, 0nM T3


title: Donor Young-1, Timepoint2, HSC or CD34+CD45RA-CD90+ enriched cells from BMMC, mRNA-derived cDNA, sample 6

description: 3' mRNA library (Cell barcodes are matchable with ATAC and mtDNA lib in sample 6): read1 (1-28nt) file contains cell barcode and UMI; read2 file contains transcript.


title: H3K27ac exc rep2

value: whole brain


title: HEK293T, Input

value: Input


title: LIMK1 Cofilin Library Screen Replicate 3 Timepoint 2

city: New Haven

first: Ben

last: Turk

state: CT

address: 333 Cedar Street, SHM B386

department: Pharmacology Department

institute: Yale University

library_source: other

data_processing:
raw fastq files were trimmed, sorted using condition-specific barcodes, and matched to expected library sequences using the FASTX-Toolkit, Perl, and the shRNA_Screen_analysis_pipeline provided on the Ruddle HPC cluster by the Yale Center for Genome Analysis
Assembly: N/A. Data was aligned using known sequences within the cofilin library.
Supplementary files format and content: Table of raw counts is in .xslx format. It provides the total number of counts of each library component for different conditions, timepoints, and replicates

molecule: other

organism: Saccharomyces cerevisiae

extract_protocol:
After the screen was complete, plasmids were recovered from cell pellets using a QIAGEN Spin Miniprep kit. The N-terminal variable region of the plasmid pool was PCR amplified to attach sequencing adaptors and add barcodes.
To generate the cofilin-1 N-terminal mutagenesis library, an oligonucleotide pool spanning the region was synthesized with phosphoramidite trimer mixtures encoding all 20 amino acids at the sites encoding Ala2, Gly4 and Val5, and an ACC/AGC mixture (encoding a mix of Ser and Thr) in place of Ser3 (core DNA sequences encoding the four residues are provided in Dataset S1). Oligonucleotides were PCR amplified and inserted into pRS423-GPD-His6-cofilin-1 plasmid using the 5’ BamHI restriction site upstream of the start codon and a 3’ SalI restriction sites that was introduced by silent mutagenesis within the cofilin-1 coding sequence. Electrocompetent DH10β E. coli (Invitrogen ElectroMAX) were transformed with ligation products, providing at least 1000 transformants per library variant. Plasmid library DNA was recovered from the pool of transformed bacterial colonies, PCR amplified and sequenced on an Illumina NovaSeq instrument to confirm full representation of all variants.
Library plasmids were recovered by miniprep, the variable region was amplified, and the resulting oligos were submitted for Next Generation Sequencing

tag: strain


title: LIMK1 Cofilin Library Screen Replicate 3 Timepoint 3


title: LIMK1 Cofilin Library Screen Replicate 3 Timepoint 1


title: anti-BAF155 CUT&RUN, DN2 and DN3 thymocytes, Runx1 WT, rep 2

city: Chicago

first: Alexandra

last: Bradu

state: IL

address: 924 East 57th Street

department: Pathology

institute: University Of Chicago

data_processing:
Adaptor sequences were trimmed using SeqPurge (v2019_11).
Trimmed reads were mapped to mm10 mouse genome assembly using Bowtie2 (v2.2.9) with settings --local --very-sensitive-local –no-unal –no-mixed –no-discordant –phred33 -I 10 -X 700.
PCR duplicates were removed using Picard (v2.21.8) MarkDuplicates REMOVE_DUPLICATES=true VALIDATION_STRINGENCY=LENIENT.
Reads with MAPQ scores below 30 were purged using samtools (v1.9) view with settings -b -q 30 -f 2 -F 1804.
BedGraph files were generated using bedtools (v2.27.1) genomecov and normalized by the number of fragments intersecting nucleosome-depleted promoter regions (-300 bp to +100 bp) relative to transcriptional start-sites).
BedGraphs were converted to BigWig format using bedGraphToBigWig (v4)
Assembly: mm10
Supplementary files format and content: bigWig
Library strategy: CUT&RUN

source_name: bone marrow

extract_protocol:
CUT&RUN was performed as previously described (Skene et al., eLife, 2017) with minor modifications. Briefly, 500k cells were washed 3x in Wash Buffer (20 mM HEPES pH 7.5, 150 mM NaCl, 0.5 mM spermidine, 1x EDTA-free protease inhibitor cocktail (Roche)), then bound to Concanavalin-A beads (Bangs Laboratories) according to manufacturer’s instructions. Cells were incubated with 1:100 dilution of anti-BAF155 antibody (G. Crabtree) overnight at 4 °C in Digitonin Buffer (0.025% digitonin, 20 mM HEPES pH 7.5, 150 mM NaCl, 0.5 mM spermidine, 1x EDTA-free protease inhibitor cocktail) supplemented with 2 mM EDTA. Sample was then incubated with pA-MNase (S. Henikoff) at 1:200 dilution in Digitonin Buffer at 4 °C for 1h. Digestion was performed under high Ca2+/low salt conditions in Low-Salt Rinse Buffer (3.5 mM HEPES pH 7.5, 0.5 mM spermidine, 0.025% digitonin) at 4 °C for 15 min. The reaction was stopped by the addition of 4x Stop Buffer (final concentration 170 mM NaCl, 10 mM EDTA, 20 mM EGTA, 0.025% digitonin, 25 µg/mL glycogen, 25 µg/mL RNase A (Thermo Fisher)) and the sample was incubated at 37 °C for 30 min. Sample was centrifuged at 16,000g for 10 min at 4 °C, supernatant recovered, and proteins digested in 1x Stop Buffer with 0.1% SDS and 250 µg /mL Proteinase K (New England Biolabs) for 1 hour at 55 °C. CUT&RUN fragments were purified by phenol chloroform extraction.
CUT&RUN libraries were generated using NEBNext UltraII DNA Library Prep Kit for Illumina coupled with NEBNext Multiplex Oligos for Illumina (New England Biolabs) with modifications optimized for small fragments as detailed in dx.doi.org/10.17504/protocols.io.bagaibse.

value: bone marrow

value: 2-4 months

tag: Sex

value: male

value: DN23 thymocytes

tag: replicate

value: Runx1f/f; Rosa26nTnG/CreERT2

value: Ethanol


title: LIMK1 Cofilin Library Screen Replicate 3 Timepoint 0


title: Donor Young-1, HSC or CD34+CD45RA-CD90+ enriched cells from BMMC, mitochondrial DNA, sample 3

description: mtDNA library (Cell barcodes are matchable with mRNA and ATAC lib in sample 1): read1 file contains one end of mitochondrial genomic region; i5 file (1-24) contains cell barcodes, read2 file contains the other end of mitochondrial genomic region.


title: Donor Young-1, Timepoint2, BMMCs, mRNA-derived cDNA, sample 4

description: 3' mRNA library (Cell barcodes are matchable with ATAC and mtDNA lib in sample 4): read1 (1-28nt) file contains cell barcode and UMI; read2 file contains transcript.


title: H3K27me3 exc rep1

value: Sun1 f/f | Emx1Cre (+)

value: 8 weeks


title: LIMK1 Cofilin Library Screen Replicate 2 Timepoint 3


title: H3K27ac exc rep1


title: HEK293T, H3K4me3 ChIP

value: Embryonic Kidney Cells

value: wildtype

value: H3K4me3 ChIP


title: anti-BAF155 CUT&RUN, DN2 and DN3 thymocytes, Runx1 WT, rep 1


title: H3K27ac inh rep1

value: inhibitory neuron


title: Donor Young-1, HSC or CD34+CD45RA-CD90+ enriched cells from BMMC, ATAC, sample 3

description: ATAC library (Cell barcodes are matchable with mRNA and mtDNA lib in sample 1): read1 file contains one end of accessible region; i5 file (1-24) contains cell barcodes, read2 file contains the other end of accessible region.

value: Bone Marrow

value: Hematopoietic Stem cells (HSC or CD34+CD45RA-CD90+ enriched cells from BMMCs)


title: LIMK1 Cofilin Library Screen Replicate 2 Timepoint 2


title: anti-BAF155 CUT&RUN, DN1 thymocytes, Runx1 WT, rep 2

value: DN1 thymocytes


title: H3K4me3 inh rep2

value: whole brain


title: anti-BAF155 CUT&RUN, DN1 thymocytes, Runx1 WT, rep 1


title: anti-BAF155 CUT&RUN, DN2 and DN3 thymocytes, Runx1 cKO, rep 2

value: Tamoxifen


title: H3K4me3 inh rep1


title: LIMK1 Cofilin Library Screen Replicate 2 Timepoint 0


title: anti-BAF155 CUT&RUN, DN2 and DN3 thymocytes, Runx1 cKO, rep 1

value: bone marrow


title: H3K4me3 exc rep2

value: excitatory neuron


title: LIMK1 Cofilin Library Screen Replicate 2 Timepoint 1


title: Donor Young-1, HSPC or CD34 enriched cells from BMMC, ATAC, sample 2

value: Hematopoietic Stem and progenitors (HSPC or CD34 enriched cells from BMMCs)


title: Donor Young-1, HSPC or CD34 enriched cells from BMMC, mitochondrial DNA, sample 2


title: H3K4me3 exc rep1


title: H3K4me1 inh rep2


title: Donor Young-1, HSPC or CD34 enriched cells from BMMC, mRNA-derived cDNA, sample 2

description: 3' mRNA library (Cell barcodes are matchable with ATAC and mtDNA lib in sample 1): read1 (1-28nt) file contains cell barcode and UMI; read2 file contains transcript.


title: LIMK1 Cofilin Library Screen Replicate 1 Timepoint 2


title: anti-BAF155 CUT&RUN, DN1 thymocytes, Runx1 cKO, rep 2

value: 2-4 months

value: male


title: Donor Young-1, HSC or CD34+CD45RA-CD90+ enriched cells from BMMC, mRNA-derived cDNA, sample 3


title: LIMK1 Cofilin Library Screen Replicate 1 Timepoint 3


title: Donor Young-1, BMMCs, ATAC, sample 1

value: Bone Marrow Mononuclear Cells (BMMCs)


title: LIMK1 Cofilin Library Screen Replicate 1 Timepoint 1


title: Donor Young-1, BMMCs, mitochondrial DNA , sample 1


title: H3K4me1 inh rep1

value: Sun1 f/f | Emx1Cre (+)


title: anti-BAF155 CUT&RUN, DN1 thymocytes, Runx1 cKO, rep 1

value: Runx1f/f; Rosa26nTnG/CreERT2


title: anti-BAF155 CUT&RUN, DN2 and DN3  thymocytes, Bcl11b WT, rep 4

source_name: thymus

value: thymus

value: 3-6 weeks

value: female

value: DN23 thymocytes

value: Bcl11bf/f; Vav1-Cre-/-


title: Donor Young-1, BMMCs, mRNA-derived cDNA, sample 1

value: Bone Marrow


title: anti-BAF155 CUT&RUN, DN2 and DN3  thymocytes, Bcl11b WT, rep 3


title: LIMK1 Cofilin Library Screen Replicate 1 Timepoint 0 Raffinose DOX


title: LIMK1 Cofilin Library Screen Replicate 1 Timepoint 0 Glucose


title: Donor Aged2, HSPC or CD34 enriched cells from BMMC, mitochondrial DNA, sample 13

description: mtDNA library (Cell barcodes are matchable with mRNA and ATAC lib in sample 13): read1 file contains one end of mitochondrial genomic region; i5 file (1-24) contains cell barcodes, read2 file contains the other end of mitochondrial genomic region.


title: anti-BAF155 CUT&RUN, DN2 and DN3  thymocytes, Bcl11b cKO, rep 4

value: Bcl11bf/f; Vav1-Cre-/+


title: anti-BAF155 CUT&RUN, DN2 and DN3 thymocytes, Bcl11b cKO, rep 3


title: Starting Cofilin Library


title: Donor Aged2, HSPC or CD34 enriched cells from BMMC, ATAC, sample 13

description: ATAC library (Cell barcodes are matchable with mRNA and mtDNA lib in sample 13): read1 file contains one end of accessible region; i5 file (1-24) contains cell barcodes, read2 file contains the other end of accessible region.


title: Donor Aged2, HSPC or CD34 enriched cells from BMMC, mRNA-derived cDNA, sample 13

description: 3' mRNA library (Cell barcodes are matchable with ATAC and mtDNA lib in sample 13): read1 (1-28nt) file contains cell barcode and UMI; read2 file contains transcript.


title: RL_3

first: Ye

last: Shen

state: Zhejiang

address: Qingchun Road 79th

institute: zhejiang university

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic b benchwork (paramet er- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath co ost: 2 insertion cost: 3 deletic
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

organism: Oryctolagus cuniculus

source_name: cornea

growth_protocol: Normal diet, 6 months old

extract_protocol:
RNA was harvested using Rneasy mini plus kit(Qiagen).1.3ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: light exposure for 6 weeks

value: cornea

value: RL


title: RL_2


title: C3

city: Yantai

first: Mengqi

last: Jiang

address: 346 Guanhai Road, Laishan District, Yantai City, Shandong Province, China

institute: Binzhou Medical University

data_processing:
Basecalls performed using SOAPnuke (v1.5.6).    Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to whole genome using bowtie HISAT2.    Each sample peaks and differentially enriched peaks were analyzed by DESeq2 (v1.4.5).
Assembly: GCF_000001405.39_GRCh38.p13

extract_protocol:
The whole RNA of two group of hiPSC-CMs  using Trizol reagent.Total RNA of the sample was subjected to test the RNA integrity using agarose gel.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample(KitKAPA Stranded mRNA-seq Kit). Including cDNA synthesis, add A in 3’end,

value: Cardiac myocytes differentiated from human multipotential stem cells

value: COX6A2 knockdown

value: Cardiomyocytes differentiated


title: ATAC-seq, DN3 thymocytes, Runx1 WT, rep 3

data_processing:
Adaptor sequences were trimmed using SeqPurge (v2019_11).
Trimmed reads were mapped to mm10 mouse genome assembly using Bowtie2 (v2.2.9) with settings --very-sensitive -X 2000.
PCR duplicates were removed using Picard (v2.21.8) MarkDuplicates REMOVE_DUPLICATES=true VALIDATION_STRINGENCY=LENIENT.
Reads with MAPQ scores below 30 were purged using samtools (v1.9) view with settings -b -q 30 -f 2 -F 1804.
Peaks were called for each sample using MACS2 (v2.2.7.1) with settings --shift -75 --extsize 150 --nomodel --call-summits --nolambda --keep-dup all -p 0.01 --min-length 100. For each sample, a 501 bp fixed-width peak set was generated by extending the MACS2 summits by 250 bp in both directions. Peaks were ranked by significance (MACS2 peak score) and overlapping peaks with lower peak scores were removed iteratively to create non-overlapping sample peak sets. To facilitate comparison of peaks across samples, each peak’s ‘score-per-million’ (SPM) was calculated by dividing the peak score by the sum of all peak scores in the sample, divided by 1 million. All sample peak sets were merged, less significant overlapping peaks removed, and remaining peaks were filtered for those that were observed in at least two samples with an SPM value > 5. We removed peaks mapping to chrY as well as any that spanned genomic regions containing “N” nucleotides. We then removed any peak that overlapped with those called in activated B cell samples to create a “Total T cell” merged peak set. To identify T effector-specific peaks, sample peak sets from only peripheral T effector samples were merged and processed as above for non-overlapping, robust, reproducible peaks purged of activated B cell peaks. To account for less robust but significant T effector peaks which were robustly accessible in early thymocyte development, we added filtered sample peaks from DN1-DN4 stages (reproducible, SPM > 5) that overlapped with reproducible T effector peaks at SPM > 2 to this initial filtered T effector merged set. This merged set was again filtered for non-overlapping, robust (SPM > 5), reproducible peaks purged of activated B cell peaks to generate the final union peak set referred to as “T effector loci”.
To generate peak-by-sample count matrices, ATAC fragment counts within each peak were normalized by the number of inserts intersecting nucleosome-depleted promoter regions (-300 bp to +100 bp relative to transcriptional start-sites).
Assembly: mm10
Supplementary files format and content: tab-delimited text file containing TSS-normalized fragment counts over all T effector loci (n = 65253) for each ATAC-seq sample

extract_protocol:
ATAC-seq was performed as described previously (Buenrostro et al., Nature Methods, 2013) with minor modifications. For nuclei isolation, 50,000-60,000 FACS-sorted cells were lysed in Thymocyte Hypotonic Buffer (25 mM HEPES, 5 mM MgCl2, 0.05 mM EDTA, 10% Glycerol, 0.1% NP40. Tagmentation reactions were performed for 30 minutes at 37 °C using reagents from Illumina Tagment DNA TDE1 Enzyme and Buffer Kit. Tagmented DNA samples were purified with DNA Clean & Concentrator-5 kit (Zymo Research).
Libraries were quantified by qPCR, amplified accordingly, and purified using DNA Clean & Concentrator kit (Zymo Research).

value: bone marrow

value: 2-4 months

value: DN3 thymocytes

value: Ethanol


title: RL_1


title: C2


title: GL_3

value: GL


title: ATAC-seq, DN2 thymocytes, Runx1 WT, rep 3

value: male

value: DN2a thymocytes

value: Runx1f/f; Rosa26nTnG/CreERT2


title: H3K4me1 exc rep2

value: whole brain

value: excitatory neuron

value: Sun1 f/f | Emx1Cre (+)

value: 8 weeks


title: C1


title: Donor Aged2, BMMCs, ATAC, sample 12

description: ATAC library (Cell barcodes are matchable with mRNA and mtDNA lib in sample 12): read1 file contains one end of accessible region; i5 file (1-24) contains cell barcodes, read2 file contains the other end of accessible region.

value: Bone Marrow

value: Bone Marrow Mononuclear Cells (BMMCs)


title: ATAC-seq, DN1 thymocytes, Runx1 WT, rep 3

value: DN1 thymocytes


title: Donor Aged2, BMMCs, mitochondrial DNA , sample 12

description: mtDNA library (Cell barcodes are matchable with mRNA and ATAC lib in sample 12): read1 file contains one end of mitochondrial genomic region; i5 file (1-24) contains cell barcodes, read2 file contains the other end of mitochondrial genomic region.


title: GL_2

value: cornea


title: ATAC-seq, DN3 thymocytes, Runx1 cKO, rep 3

value: Tamoxifen


title: WT3

value: Cardiac myocytes differentiated from human multipotential stem cells

value: WT

value: Cardiomyocytes differentiated


title: GL_1


title: H3K4me1 exc rep1


title: Donor Aged2, BMMCs, mRNA-derived cDNA, sample 12

description: 3' mRNA library (Cell barcodes are matchable with ATAC and mtDNA lib in sample 12): read1 (1-28nt) file contains cell barcode and UMI; read2 file contains transcript.


title: WT2


title: ATAC-seq, DN2 thymocytes, Runx1 cKO, rep 3

value: bone marrow

value: 2-4 months


title: Donor Aged1, HSPC or CD34 enriched cells from BMMC, mitochondrial DNA, sample 11

description: mtDNA library (Cell barcodes are matchable with mRNA and ATAC lib in sample 11): read1 file contains one end of mitochondrial genomic region; i5 file (1-24) contains cell barcodes, read2 file contains the other end of mitochondrial genomic region.

extract_protocol:
Bone marrow was collected from healthy young or aged donors. Bone marrow aspirate was diluted with an equal volume of Wash Buffer (PBS, 2% FBS, 1mM EDTA). Ficoll medium was added to SepMateTM (Catalog #85460) tubes and then the diluted bone marrow sample was layered on top followed by centrifuging at 1200 g for 20 minutes at room temperature. The top layer, containing the mononuclear cells, was transferred to a new tube, which was then filled up by Wash Buffer. The mononuclear cells were centrifuged at 300 g for 8 minutes. The supernatant was discarded, and the cells were washed twice and resuspended in Wash Buffer for further enrichment or in Freezing buffer (10% DMSO in FBS). Starting with the BMMCs isolated from the previous step, we enriched CD34+ cells following EasySep™ Human Cord Blood CD34 Positive Selection Kit II (Catalog #17896). Briefly, EasySep™ Human CD34 Positive Selection Cocktail (Catalog #18096C) was added to BMMCs suspension to 100 ul/ml and incubated at room temperature for 10 minutes. EasySep™ Dextran RapidSpheres™ (Catalog #50100) was vortexed and added to each sample to 50 µl/ml.  The mix was incubated for 3 minutes at room temperature. Next, Wash Buffer (7 ml) was added to the tube, The cells were then washed 4 times in "The Big Easy" EasySep™ Magnet (Catalog #18001). Finally, cells were resuspended in Wash Buffer and were centrifuged at 300g for 10 min. The CD34+ positive cell pellet was then resuspended in a freezing buffer (10% DMSO in FBS).  To further enrich the hematopoietic stem cells (HSCs), an aliquot of the enriched CD34+ cells were stained by one of the following two antibody panels. 1) CD34 PerCP-Cy5.5 (Catalog #347222); CD45RA Alexa Fluor 488 (Catalog #304114); CD90 PE-Cy7 (Catalog #561558); and  DAPI (Catalog #D1306) as viability dye. Or 2) CD34 BV421 (Catalog #562577); CD45RA-APC-H7 (Catalog #560674); CD90 PE-Cy7 (Catalog #561558), and 7-AAD as viability dye(Catalog #559925). The cells were further sorted using BD FACSAriaTM for CD34+CD45RA-CD90+ to enrich HSCs. BMMCs, as well as enriched CD34+ and CD34+CD45RA-CD90+ cells were cryopreserved. After thawing, cells were immediately processed for experiment as soon as possible without any culturing.
RNA lib and ATAC lib prep:  After tagmentation, cells were immediately processed for GEM generation & barcoding following 10x Genomics Chromium Next GEM Single Cell Multiome ATAC + Gene Expression User Manual  (version CG000338 Rev A, 10x Genomics) with Step 2. Next, the Post GEM Incubation Cleanup and Pre-Amplification PCR were performed following the same User Manual with Step 3 and Step 4. The pre-amplified library was eluted in 100ul EB buffer instead of 160ul. For RNA library prep, we took an aliquot of 35 ul pre-amplified library and followed the same User Manual (version CG000338 Rev A, 10x Genomics) from Step 6 and Step 7. We developed an in-house protocol to generate the massive ATAC library with enough material for both direct sequencing and mtDNA hybridization. For each sample, 8 reactions of the following were performed (each in 50 ul). 5 μl pre-amplified product, 25 μl NEBnext mix (Catalog M0541L), 2.4 μl 10 μM Nextera N70X primer (Supplementary Data 2), 2.4 μl 10X SI PCR primer B (Catalog #PN2000128), 0.5 μl 100X SYBR Green (Catalog #S7563), and 14.7 μl water. The thermocycler program started with 98°C 45 s., followed by the 6-12 cycles of: 98°C for 10 s., 63°C for 30 s., and 72°C for 20 s.; The actual cycle numbers are determined using the amplification curve and the qPCR was stopped when the curve started to reach plateau. The qPCR products (50ul * 8 wells) were combined and purified using SPRI beads (Catalog #B23318) with size selection 0.4X~1.55X. The expected yield is 2,000 ng to 4,000 ng.
mtDNA lib prep: We designed 4 sets of DNA probes, with each probe set covering the whole mitochondrial genome and containing 138 biotinylated oligos that are 120 bp long. The 4 sets of probes ((v1, v2, v3, and v4) are staggered by 30 bp with each other and ensure good coverage on junction areas (Supplementary Data 2). The hybridization started with 500 ng ATAC library products for each probe set. In total, 4 independent reactions were performed in parallel and combined at the end (2,000ng input in total). The detailed incubation and wash methods largely followed the Tube Protocol in IDT xGen Hybridization Capture of DNA Libraries protocol.  Briefly, 500 ng input was combined with Cot DNA and purified by SPRI beads, which was eluted by hybridization mix that contains hybridization buffer, hybridization buffer enhancer, one of the probe set, as well as xGen™ Universal Blockers NXT (Catalog #1079584). The hybridization reaction was performed as below: 95C 30 seconds followed by 65C overnight.  The biotin-streptavidin Dynabeads purification was carried out on Day 2 using xGen Hybridization and Wash Kit. The Dynabeads after capturing and washing were used for final quick qPCR amplification (3-5 cycles). The reaction mix is as below: 20ul beads, 25ul KAPA HiFi HotStart ReadyMix (Catalog #KK2601), Primer 2.4ul P5 (Supplementary Data 2), Primer P7 (Supplementary Data 2), 0.5ul 100X SYBR Green (Catalog #S7563). The PCR program started with 98°C 45 s, followed by the 3-5 cycles of: 98°C for 10 s., 63°C for 30 s., and 72°C for 20 s. The final enriched mtDNA was purified by SPRI beads (1.6X)
For each sample, all three libraries were sequenced on Illumina NovaSeq S4 300 cycle kit. The sequencing length was as below. Read1: 149nt, i7: 8nt, i5: 24nt, Read2: 149nt. We expected to sequence 20,000~30,000 raw reads per cell for RNA libraries and ATAC libraries, while 50,000~60,000 raw reads for enrich mtDNA libraries.

value: Hematopoietic Stem and progenitors (HSPC or CD34 enriched cells from BMMCs)


title: Ctrl_3

value: Ctrl


title: Donor Aged1, HSPC or CD34 enriched cells from BMMC, ATAC, sample 11

description: ATAC library (Cell barcodes are matchable with mRNA and mtDNA lib in sample 11): read1 file contains one end of accessible region; i5 file (1-24) contains cell barcodes, read2 file contains the other end of accessible region.


title: WT1


title: ATAC-seq, DN1 thymocytes, Runx1 cKO, rep 3

value: male

value: Runx1f/f; Rosa26nTnG/CreERT2


title: Ctrl_2


title: Donor Aged1, HSPC or CD34 enriched cells from BMMC, mRNA-derived cDNA, sample 11

description: 3' mRNA library (Cell barcodes are matchable with ATAC and mtDNA lib in sample 11): read1 (1-28nt) file contains cell barcode and UMI; read2 file contains transcript.


title: HVAV1_reRNA_SF9_sRNAseq

organism: Spodoptera frugiperda

value: recombinant baculovirus


title: Donor Aged1, BMMCs, mitochondrial DNA , sample 10

description: mtDNA library (Cell barcodes are matchable with mRNA and ATAC lib in sample 10): read1 file contains one end of mitochondrial genomic region; i5 file (1-24) contains cell barcodes, read2 file contains the other end of mitochondrial genomic region.


title: Ctrl_1


title: BL_3

value: blue light


title: ca-Acvr1 mutant NP rep 1

city: Wuhan

first: Lingxin

last: Zhu

state: Hubei

address: 237 Luoyu Road, Hongshan District, School and Hospital of Stomatology, Wuhan University

institute: Wuhan University

data_processing:
Data were aligned using the STAR aligner and featureCounts v1.6.4 software, and reads per kilobase of transcript per million mapped read values on gene level were estimated for ensemble transcriptome.
DESeq2 was used to estimate significance between any two experimental groups.
Assembly: mm10

source_name: E11.5 nasal process tissues

extract_protocol:
Trizol extraction of total RNA was performed according to the manufacturer's instructions.
The construction of libraries was generated using QuantSeq 3’ mRNA-Seq Library Prep Kit (Lexogen) according to the manufacturer’s instructions.

value: E11.5 nasal process tissues


title: HAGV1_reRNA_SF9_sRNAseq


title: ca-Acvr1 mutant NP rep 2


title: SFAV1_reRNA_SF9_sRNAseq


title: BL_2


title: Control NP rep 2


title: BL_1


title: Donor Aged1, BMMCs, ATAC, sample 10

description: ATAC library (Cell barcodes are matchable with mRNA and mtDNA lib in sample 10): read1 file contains one end of accessible region; i5 file (1-24) contains cell barcodes, read2 file contains the other end of accessible region.

value: Bone Marrow


title: SFAV1_reRNA_5dpi_hemolymph_sRNAseq

source_name: Hemolymph

value: Hemolymph

value: wild-type ascovirus


title: SFAV1_reRNA_2dpi_hemolymph_sRNAseq


title: PC-3 cells, shRNA LPIN1 KD Target B, passage 19

status: Public on Nov 17 2023

city: Athens

first: Brian

middle: Scott

last: Cummings

state: Georgia

address: 302 College of Pharmacy South, Pharmaceutical and Biomedical Sciences

institute: University of Georgia

data_processing:
Galaxy was used for RNA bioinformatic analysis
Cutadapt within Galaxy was used to remove low quality reads with < 20 nt and PHRED scores of < 20.
FastQC was used to assess the quality of reads before and after trimming.
Results were mapped to the human genome (hg38) with splice junctions using the RNA Spliced Transcripts Alignment to a Reference (STAR) software within Galaxy.
Read Distribution was used to assess the success of mapping reads over the human genome.
featureCounts was used to measure gene expression before DESeq2 was used to determine the differentially expressed genes (DEGs) from the count tables.
Assembly: hg38
Supplementary files format and content: tabular files contain featureCounts for each sample

growth_protocol: The human PCa cell line PC-3 was cultured in RPMI-1640 media supplemented with 10% FBS and 1% penicillin-streptomycin in an incubator at 37 °C with 5% CO2.

extract_protocol:
Total RNA was harvested using RNeasy® Plus Mini Kit (Qiagen, Hilden, Germany) according to the manufacturer’s protocol with a selection of 30 μL of RNase-free water added directly to the spin column membrane. Total RNA samples were diluted to 1 μg RNA in 40 μL RNase-free water.
Libraries were generated using the Kapa Biosystems Stranded RNA-Seq kit following the manufacturer's instructions

value: bone metastasis of a grade IV prostatic adenocarcinoma from a 62-year-old, White, male

value: shRNA LPIN1 KD Target B


title: PC-3 cells, shRNA LPIN1 KD Target B, passage 20


title: PC-3 cells, shRNA LPIN1 KD Target B, passage 15


title: PC-3 cells, shRNA LPIN1 KD Target B, passage 16


title: PC-3 cells, shRNA LPIN1 KD Target B, passage 17


title: PC-3 cells, shRNA LPIN1 KD Target A, passage 17

value: shRNA LPIN1 KD Target A


title: PC-3 cells, shRNA LPIN1 KD Target A, passage 16


title: PC-3 cells, shRNA Control, passage 20

value: shRNA Control


title: PC-3 cells, shRNA LPIN1 KD Target A, passage 20


title: PC-3 cells, shRNA LPIN1 KD Target A, passage 19


title: PC-3 cells, shRNA LPIN1 KD Target A, passage 18


title: PC-3 cells, shRNA Control, passage 18


title: PC-3 cells, shRNA Control, passage 16


title: PC-3 cells, shRNA Control, passage 17


title: PC-3 cells, shRNA Control, passage 19


title: Control NP rep 1


title: Donor Aged1, BMMCs, mRNA-derived cDNA, sample 10

description: 3' mRNA library (Cell barcodes are matchable with ATAC and mtDNA lib in sample 10): read1 (1-28nt) file contains cell barcode and UMI; read2 file contains transcript.

value: Bone Marrow Mononuclear Cells (BMMCs)


title: Hepatocyte fraction obtained at the first step of liver perfusion from mouse2

first: Pushpinder

last: Bawa

state: Massachusetts

address: 670 Albany St

department: Boston University Medical Campus

institute: Center for Regenerative Medicine

data_processing:
The sample was processed using the standard Cellranger v.3 pipeline
Reads were mapped to GRCm38 supplemented with sequences for eYPF reporter sequence
Downstream analysis and QC done on Seurat
Differential expression using MAST models
Assembly: GRCm38
Supplementary files format and content: the processed files are the standard output from the cellranger count pipeline: count matrices compressed in the HDF5  format

source_name: Liver

extract_protocol:
Cells were resuspended in buffer at a concentration of 1000 cells/ul and captured using a 10X chromium instrument (10X Chromium, Pleasanton, CA), following standard Chromium 10x guidelines.
Libraries were prepared using a Chromium Single Cell 3' v3 kit (10x Genomics) and loaded on a NextSeq 2000 system (Illumina) aiming for sequencing depth of approximately 50,000 reads/cell

value: Liver

value: Liver cells

value: Male Krt19-CreERT, R26LSLtdTomato


title: Non-parenchymal cells obtained in the later steps of liver perfusion obtained from mouse2


title: Non-parenchymal cells obtained in the later steps of liver perfusion obtained from mouse1


title: D6, KO, Rep3

city: Cincinnati

first: Konrad

last: Thorner

address: 3333 Burnet Ave

institute: Cincinnati Children's Hospital Medical Center

data_processing:
Aligned and quantified using Bowtie2 + RSEM
Assembly: mm10
Supplementary files format and content: tab-delimited file of raw counts
Supplementary files format and content: tab-delimited file of TPMs

growth_protocol: Control or Runx1KO C2C12 cells were grown in growth media (20% FBS) or differentiation media (2% horse serum) for indicated amount of time

extract_protocol:
RNA isolated using Purolink kit following manufacturer's instructions
PolyA_Oligo dT

value: Differentiation media


title: D6, WT, Rep2

value: WT


title: D6, WT, Rep1


title: Old MuSCs, SAM, 1

city: Los Angeles

first: Jengmin

last: Kang

address: 615 Charles E Young Dr S

institute: University of California, Los Angeles

data_processing:
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using a TruSeq PE Cluster Kit v3-cBot-HS (Illumina) according to the manufacturer’s instructions.
Nextera adaptor sequences were trimmed from the reads using skewer (0.2.2).
Reads were aligned to a reference genome using BWA, with standard parameters.
Reads were then filtered for high quality (MAPQ ≥ 13), non-mitochondrial DNA, and properly paired reads (longer than 18 nt).
All peak calling was performed with macs2 using ‘macs2 callpeak --nomodel --keepdup all --call-summits’.
Assembly: ensembl_mus_musculus_grcm38_p6_gca_000001635_8
Supplementary files format and content: BigWig

source_name: limb muscle

growth_protocol: MuSCs were isolated from mouse hindlimbs as previously described (Liu et al., 2015).

extract_protocol:
ATAC-seq libraries were generated using an ATAC-seq kit (Active Motif; #53150)
The tagmented DNA was amplified in the presence of a different combination of i7/i5 indexed primers which are based on Illumina’s Nextera adapters.

treatment_protocol: Mice were injected intraperitoneally with 200 μmol/kg of MCHA (Sigma Aldrich; #CDS019932) or 5 mg/kg of SAM (New England Biolabs; B9003S) which are dissolved in sterile PBS daily for 3 weeks.

value: limb muscle

value: Muscle stem cells

value: Freshly-isolated, in vivo SAM


title: Old MuSCs, SAM, 2


title: Old MuSCs, MCHA , 2

value: Freshly-isolated, in vivo MCHA


title: Old MuSCs, 2

value: Freshly-isolated


title: D6, WT, Rep3


title: Old MuSCs, MCHA , 1


title: Hepatocyte fraction obtained at the first step of liver perfusion from mouse1


title: Young MuSCs, 2


title: D6, KO, Rep2


title: Ovary ERB Knockout ChIP-Seq rep 1

city: Stockholm

first: Rajitha

last: Indukuri

state: Sweden

address: Tomtebodavägen 23a, Solna

country: Sweden

institute: Scilifelab

data_processing: ChIP-Seq reads were mapped to the mouse reference genome assembly mm10 using STAR and reads which assigned to multiple locations were discarded. ERβ binding sites were identified by HOMER applying a false dis-covery rate (FDR) less than 0.001 and four-fold enrichment over control (Input) cut-off. Peaks present in at least 2 out of 3 replicates were considered for further analysis. HOMER was used to perform De novo motif analysis of identified binding sites.

source_name: ovary

growth_protocol: Fresh ovaries were collected from female C57BL/6J mice.

extract_protocol:
Cells were incubated with LB1, LB2 buffers to separate nuclear chormatin fractions and immunoprecipitated with ERβ anitbody.
The libraries of ChIP DNA were prepared by using the kit NEB Next Ultra II DNA Library Prep Kit for Illumina following user instrcutions

treatment_protocol: Ovaries were cross-linked for 15 min with 1% formaldehyde and uncross-linked with 0.125M of glycine. Cells were collected from ovaries using a Dounce homogenizer and frozen at -80°C.

value: cat no:PPZ0506, lot no:A2, mouse monoclonal, R&D systems

value: Deleted ERBeta

value: ovary


title: Ovary Input 2

data_processing:
ChIP-Seq reads were mapped to the mouse reference genome assembly mm10 using STAR and reads which assigned to multiple locations were discarded. ERβ binding sites were identified by HOMER applying a false dis-covery rate (FDR) less than 0.001 and four-fold enrichment over control (Input) cut-off. Peaks present in at least 2 out of 3 replicates were considered for further analysis. HOMER was used to perform De novo motif analysis of identified binding sites.
Assembly: mm10

value: endogenously express ERBeta


title: Young MuSCs, 1


title: D6, KO, Rep1


title: Ovary Input 1


title: smRNA-seq of C. elegans: adult day 5 alg-2(ok304) hermaphrodites (rep5)

city: Cambridge

first: Laura

last: Chipman

state: MA

address: 1 Portland St

institute: Pfizer

data_processing: Adapter sequences were removed using Cutadapt, and smRNA reads were mapped to the annotated C. elegans genome (WS266) using Bowtie-build to first create indices and miRDeep2 to align and quantify reads (Friedländer et al. 2012; Langmead et al. 2009). Differential expression analysis was performed by first normalizing reads to library size (read counts per million) and then measuring the log2foldchange of mutants to WT strains within replicates. MiRNAs were called significantly misregulated if they exhibited an absolute mean log2foldchange greater than 1.5 and a padj less than 0.05.

organism: Caenorhabditis elegans

source_name: whole organism

growth_protocol: Adult C. elegans were separated from eggs and progeny daily by washing plates with M9 into conical tubes and allowing the adults to settle by gravity for a few minutes on a bench top. The supernatant containing larvae and eggs was then removed, and this process was repeated 3-15 times until eggs and larvae were no longer visible.

extract_protocol: Small RNA sequencing was performed on five independent replicates of synchronized wildtype (N2), alg-1(gk214), and alg-2(ok304) strains collected on day 5 of adulthood. Strains were cultured at 20°C to day five of adulthood and collected for RNA isolation. Eggs and progeny were separated from adult worms through daily washes with M9 solution, followed by gravity separation of pelleted adult worms from the supernatant containing eggs and progeny. The supernatant was aspirated and M9 washed, this was repeated until the M9 remained clear. Total RNA was isolated and smRNA libraries were then prepared from 1 μg of total RNA using the Illumina TruSeq Small RNA Library Prep Kit. Once prepared, smRNA libraries were sent for single-end sequencing on an Illumina HiSeq 4000.

value: whole organism

tag: developmental stage

value: adult day 5

tag: fraction

value: small RNA


title: smRNA-seq of C. elegans: adult day 5 alg-2(ok304) hermaphrodites (rep4)


title: D3, WT, Rep3


title: Ovary ERB ChIP-Seq rep 3


title: D3, WT, Rep2


title: smRNA-seq of C. elegans: adult day 5 alg-2(ok304) hermaphrodites (rep1)


title: smRNA-seq of C. elegans: adult day 5 alg-2(ok304) hermaphrodites (rep2)


title: Ovary ERB Knockout ChIP-Seq rep 2


title: Ovary ERB ChIP-Seq rep 2


title: Old MuSCs, 1


title: Ovary ERB ChIP-Seq rep 1


title: smRNA-seq of C. elegans: adult day 5 alg-1(gk214) hermaphrodites (rep3)


title: D3, KO, Rep3


title: smRNA-seq of C. elegans: adult day 5 alg-1(gk214) hermaphrodites (rep2)


title: smRNA-seq of C. elegans: adult day 5 alg-1(gk214) hermaphrodites (rep4)


title: smRNA-seq of C. elegans: adult day 5 N2 hermaphrodites (rep4)


title: smRNA-seq of C. elegans: adult day 5 N2 hermaphrodites (rep5)


title: PEC-5FU

type: genomic

city: Frankfurt am Main

first: Ria

last: Winkelmann

address: Theodor-Stern-Kai 7

country: Germany

institute: Dr. Senckenberg Institute of Pathology Frankfurt am Main

hyb_protocol: Affymetrix Oncoscan Array Protocol

scan_protocol: Affymetrix Oncoscan Array Protocol

data_processing: Raw CEL files were converted to OSCHP files using Chromosome Analysis Suite (v4.2.0.80). The TuScan algorithm provided by the Chromosome Analysis Suite was used to calculate copy numbers.

label: Biotin

label_protocol: Affymetrix Oncoscan Array Protocol

growth_protocol: Cell lines were grown according to standard conditions.

extract_protocol: For DNA isolation from formalin-fixed, paraffin-embedded (FFPE) patient tumor tissue and FFPE-processed primary parental cells and the adapted chemo-resistant sublines were used. Areas with high tumor content were marked on hematoxylin and eosin (H&E)-stained slides with a 2 μm tissue section by experienced pathologists (RW). Afterwards, tissue cores (1.0 mm diameter) from FFPE blocks were taken from the marked area. DNA was isolated using the truXTRAC FFPE total NA Kit (Covaris, Woburn, MA, USA) based on focused ultrasonification and column purification according to the manufacturer's instructions. The DNA was eluted in 50 μL nuclease-free water and stored at −20°C. The DNA was quantified using the Quantus™ Fluorometer and ONE dsDNA Assay Kit (Promega Corporation, Madison, Wisconsin, USA). Additionally, samples have been screened for fragment length using Bioanalyzer 2100 (Agilent Technologies, Santa Clara, California, USA) and Agilent DNA 7500 Kit (Agilent Technologies, Santa Clara, California, USA) in order to include samples with fragments larger than 150 bp for subsequent Copy-number variation analysis.     For DNA isolation from formalin-fixed, paraffin-embedded (FFPE) patient tumor tissue and FFPE-processed primary parental cells and the adapted chemo-resistant sublines were used. Areas with high tumor content were marked on hematoxylin and eosin (H&E)-stained slides with a 2 μm tissue section by experienced pathologists (RW). Afterwards, tissue cores (1.0 mm diameter) from FFPE blocks were taken from the marked area. DNA was isolated using the truXTRAC FFPE total NA Kit (Covaris, Woburn, MA, USA) based on focused ultrasonification and column purification according to the manufacturer's instructions. The DNA was eluted in 50 μL nuclease-free water and stored at −20°C. The DNA was quantified using the Quantus™ Fluorometer and ONE dsDNA Assay Kit (Promega Corporation, Madison, Wisconsin, USA). Additionally, samples have been screened for fragment length using Bioanalyzer 2100 (Agilent Technologies, Santa Clara, California, USA) and Agilent DNA 7500 Kit (Agilent Technologies, Santa Clara, California, USA) in order to include samples with fragments larger than 150 bp for subsequent Copy-number variation analysis.

treatment_protocol: 5-FU and CDDP, as well as both

value: squamous cell carcinoma of the penis


title: smRNA-seq of C. elegans: adult day 5 N2 hermaphrodites (rep3)


title: PEC-CDDP

source_name: PEC-CDDP


title: D3, KO, Rep1


title: smRNA-seq of C. elegans: adult day 5 N2 hermaphrodites (rep2)


title: smRNA-seq of C. elegans: adult day 5 alg-2(ok304) hermaphrodites (rep3)


title: D1, WT, Rep3


title: smRNA-seq of C. elegans: adult day 5 N2 hermaphrodites (rep1)


title: smRNA-seq of C. elegans: adult day 5 alg-1(gk214) hermaphrodites (rep5)


title: UKF-PEC untreated

source_name: UKF-PEC untreated


title: D3, WT, Rep1


title: Microglia from male WT;ATTAC mouse

city: Rochester

first: Cheng

last: Zhang

state: MN

address: 200 1st street SW

institute: Mayo Clinic

data_processing:
reads were mapped to the reference genome using 10X Genomics cellranger v3.0.2
Assembly: mm10
Supplementary files format and content: feature-barcode matrix file

source_name: Cortex and hippocampus

extract_protocol:
Single cell dissociation with accutase, myelin removal, CD11b selection
Cells were first counted and measured for viability using the Vi-Cell XR Cell Viability Analyzer (Beckman-Coulter, Brea, CA). The barcoded Gel Beads were thawed from -80°C and the cDNA master mix was prepared according to the manufacture’s instruction for Chromium Next GEM Single Cell 3’ Library and Gel Bead Kit (10x Genomics, Pleasanton, CA). A per sample concentration of 400,000 cells per milliliter was required for the targeted cell recovery of approximately 10,000 cells. The cell suspension and master mix, thawed Gel Beads and partitioning oil were added to a Chromium Single Cell G chip. The filled chip was loaded into the Chromium Controller, where each sample was processed and the individual cells within the sample were partitioned into uniquely labeled GEMs (Gel Beads-In-Emulsion). The GEMs were collected from the chip and taken to the bench for reverse transcription, GEM dissolution, and cDNA clean-up. The resulting cDNA contained a pool of uniquely barcoded molecules. A portion of the cleaned and measured pooled cDNA continued to library construction, where standard Illumina sequencing primers and a 10x Genomics unique i7 Sample index were added to each cDNA pool. All cDNA pools and resulting libraries were measured using Qubit High Sensitivity assays (Thermo Fisher Scientific, Waltham, MA) and Agilent Bioanalyzer High Sensitivity chips (Agilent, Santa Clara, CA). Libraries are sequenced at between 40,000 and 50,000 fragment reads per cell following Illumina’s standard protocol using the Illumina cBot and HiSeq 3000/4000 PE Cluster Kit (Illumina, San Diego, CA). The flow cells were sequenced as 100 X 2 paired end reads on an Illumina HiSeq 4000 HD using HiSeq 3000/4000 sequencing kit and HCS v3.4.0.38 collection software. Base-calling was performed using Illumina’s RTA version 2.7.7.

value: Cortex and hippocampus

value: Microglia

value: Male


title: Primary tumor sample

source_name: Primary tumor sample


title: D3, KO, Rep2

value: Differentiation media


title: D1, WT, Rep1

value: WT


title: IMR90_PW3_VEH24H

city: Durham

first: Shaun

middle: David

last: McCullough

state: NC

address: 3040 E. Cornwallis Rd., PO Box 12194

department: Exposure & Protection

institute: RTI International

data_processing:
bcl2fastq ver 2.20.0 used for basecalls
Mapping of sequence reads to the human genome (GRCh38) was performedbySTAR (version 2.5)
Mapped read counts per gene were collected by Subread featureCounts (version 1.5.0-0-p1). Genes with a minimum average of normalized mapped read counts > 50 in at least one category were selectedfor differential gene expression analysis.
Assembly: hg38
Supplementary files format and content: raw gene counts for each sample and gene

source_name: Human lung fibroblast

growth_protocol: Cells were seeded on 12mm cell culture wells with dpHBECs on cell culture inserts above them

extract_protocol:
RNA was isolated according to standard protocol for the Thermo PureLink RNA Mini Kit.  Purified RNA was stored at -80°C until core submission
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The overyling dpHBECs were left exposed to air or had 250 uL of StemCell Pneumacult Medium applied

value: fetal lung fibroblast cell line

value: Lung fibroblast

value: Medium application to overyling dpHBEC for 24 hours


title: PEC_5FU_CDDP


title: IMR90_PW3_VEH6H

value: Medium application to overyling dpHBEC for 6 hours


title: smRNA-seq of C. elegans: adult day 5 alg-1(gk214) hermaphrodites (rep1)


title: IMR90_PW2_VEH6H


title: IMR90_PW3_PRE

value: Overlying dpHBEC maintained at ALI


title: D1, KO, Rep3


title: IMR90_PW1_VEH24H


title: IMR90_PW2_VEH24H


title: IMR90_PW1_VEH6H


title: D1, KO, Rep2


title: IMR90_PW2_PRE


title: IMR90_PW1_PRE


title: Microglia from female WT;ATTAC mouse

value: Female


title: Microglia from male tau mouse


title: D1, WT, Rep2


title: Microglia from female tau mouse


title: D0, WT, Rep2

value: Growth media


title: D1, KO, Rep1


title: sv40-rep4

city: Villeneuve d'ascq

first: Tristan

last: Cardon

state: haut de france

address: Bât SN3, 1er étage, porte 109

country: France

institute: INSERM U1192 Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM)

data_processing:
Demultiplexing was performed using bcl2fastq v2.20.0.422. Subsequent fastq trimming utilized trimmomatic v0.39 with parameters MINLEN:35 and AVGQUAL:20.
The mapping and counting steps were executed using RSEM v1.3.1 along with STAR v2.7.3a, referencing genome version hg38 and GTF from Gencode v39.
Assembly: hg38 and GTF from Gencode v39
Supplementary files format and content: tab-delimited text files includes raw counts and RPKM for each samples

molecule: protein

growth_protocol: Human PEO-4 ovarian cancer cells were cultured in Roswell Park Memorial Institute (RPMI) 1640 medium (Thermo Fisher Scientific), supplemented with 10% fetal bovine serum (Thermo Fisher Scientific), 2 mM L-glutamine (Thermo Fisher Scientific) and 100 U/mL penicillin-streptomycin (Thermo Fisher Scientific). Human SKOV-3 ovarian cancer cells were cultured in McCoy's 5A (modified) medium (Thermo Fisher Scientific), supplemented with 10% fetal bovine serum and 100 U/mL penicillin-streptomycin. Human immortalized ovarian epithelial cells SV-40 (T1074) were cultured in Prigrow I medium (Applied Biological Materials), supplemented with 10% fetal bovine serum and 100 U/mL penicillin-streptomycin. The three cell lines were grown in a humidified air incubator at 37 °C under an atmosphere of 5% CO2. Aliquots of three million cells were harvested by trypsin-EDTA (0.05%, phenol red) (Thermo Fisher Scientific), centrifuged at 100 x g for 5 min at 20 °C and washed three times with DPBS (Thermo Fisher Scientific).

extract_protocol:
RNA was extracted from four replicates of three million cells from each cell line employing the NucleoSpin RNA Mini kit for RNA purification (MACHEREY-NAGEL), following the vendor’s protocol.
1 µg of RNA was utilized for library preparation using RiboNaut rRNA Depletion Kit and Rapid Directional RNAseq Kit 2.0 (PerkinElmer). Nine cycles of PCR were performed during this preparation. Library sequencing was carried out using the NovaSeq6000 sequencing platform (Illumina; SP flow cell) following a 2x75 paired-end mode.

value: Ovarian Epithelial Cells


title: sv40-rep3


title: sv40-rep2


title: Microglia from male tau;ATTAC mouse


title: sv40-rep1


title: D0, WT, Rep1


title: skov3-rep4

value: Ovarian serous cystadenocarcinoma


title: Microglia from female tau;ATTAC mouse


title: D0, KO, Rep2


title: skov3-rep3


title: peo4-rep4

value: Ovarian cystadenocarcinoma


title: skov3-rep2


title: D0, KO, Rep3


title: skov3-rep1


title: peo4-rep2


title: D0, KO, Rep1


title: peo4-rep3


title: GM, WT Rep2

data_processing:
Processed using nf-core/atacseq v2.0
Specified parameters --narrow-peak and –read-length = 100
Assembly: mm10
Supplementary files format and content: bigwig

growth_protocol: Control or Runx1KO C2C12 cells were grown in triplicate in growth (20% FBS) media

extract_protocol:
Cells were lysed and nuclei isolated in lysis buffer (10mM Tris-HCl (pH 7.4), 10 mM NaCl, 3 mM MgCl2, 0.5% NP-40) and tagmented using Tn5 transposase from Vanzyme
Libraries were made using Illumina's TruePrep DNA Library Prep Kit V2

tag: time

value: 0 day

value: growth media


title: REH_TK

city: Kuopio

first: Merja

last: Heinäniemi

address: Yliopistonranta 1 E

department: School of Medicine

country: Finland

institute: University of Eastern Finland

description: Cell line experiment in REH comparing two drugs targeting ETS-factors at 72 h. TK216 (800 nM) sample.

data_processing:
Data was aligned with Cell Ranger 3.1.0 to combined human (hg19) and mouse (mm10) genome as reference from 10x Genomics with default parameters.
Cells were filtered with Cell Ranger 3.1.0 following alignment. The mouse cells were left out by filtering cells which cellranger characterized as mouse or doublet cells or had more than 500 counts assigned to mouse genes
The mouse genes were filtered out from the count matrix.
Assembly: hg19
Supplementary files format and content: barcode annotation: 10x Cell Ranger filtered barcode list; feature annotation: 10x Cell Ranger feature list; count matrix: 10x Cell Ranger filtered UMI count matrix

source_name: REH pre-B-ALL cell line

growth_protocol: The E/R+ REH cell line (ACC-22, DSMZ, Germany) was maintained in RPMI 1640 (Gibco, Thermo Fisher) supplemented with 10% FBS (Gibco, Thermo Fisher), 2 mM L-glutamine (Gibco, Thermo Fisher), penicillin (100 U/ml), and streptomycin (100 mg/ml) (Sigma-Aldrich).

extract_protocol:
Viability was checked using Trypan blue with Cellometer Mini Automated Cell Counter (Nexcelom Bioscience) and Dead Cell Removal Kit (#130-090-101, MACS miltenyi Biotech) was used. Viable cells were eluted by rinsing twice with 1 ml binding buffer. Subsequently 0.42-0.5 million cells were methanol fixated according to 10X Genomics Methanol Fixation of Cells for Single Cell RNA Sequencing protocol User guide CG000136 Rev E, using a mix of two RNAse inhibitors (RNase Inhibitor, Thermo Fisher, Carlsbad, CA, USA and RNasin® Plus RNase Inhibitor, Promega, Madison, WI, USA). Samples were stored < 6 weeks before proceeding with Chromium run.
Cells were thawn following the MetOH fixation protocol and processed for loading following the Chromium Single Cell 3´Reagent Kits v3 User guide CG000183 Rev C. REH cells were prepared into pools together with mouse cells (not this study) and human cell singlets separated in data analysis step. Loading concentration of 2100-2200 cells/uL was used. Using 10X GemCode Technology, the poly-A transcripts are barcoded with an Illumina R1 sequence, a 16 bp 10X barcode and a 10 bp Unique Molecular Identifier (UMI). 13 cycles of PCR were used to amplify the cDNA.

treatment_protocol: REH cells were seeded into 6-well plates (0.6 milion/ml concentration) and treated with XRP44X (Sigma-Aldrich) (1 µM), TK216 (MedChemExpress, NJ USA) (800 nM), Vincristine (1nM) (Abmole), Dexamethasone (10nM) or DMSO for 72 h.

value: REH pre-B-ALL cell line

tag: construct


title: peo4-rep1


title: REH_DMSO

description: Cell line experiment in REH comparing two drugs targeting ETS-factors at 72 h. DMSO control sample.

value: DMSO


title: 11 - Control

city: Fuzhou

first: Kaiyang

last: Lin

state: Please Select

address: No. 134, East Street, Gulou District

institute: Fujian province hospital

data_processing:
The image processing and base calling are performed using Solexa pipeline version 1.8 (Off-Line Base Caller software, version 1.8).
Assembly: GRCh37

source_name: Plasma

extract_protocol:
After enrichment using oligo dT (rRNA depletion), the total RNA sample is processed.1-2 μg of total RNA is used for constructing RNA sequencing libraries.
RNA libraries for RNA-Seq were prepared using KAPA Stranded RNA-Seq Library Prep Kit（Illumina） following manufacturer‘s protocol.

value: Plasma

tag: disease state

value: without contrast-induced acute kidney injury (CI-AKI)

value: male

value: percutaneous coronary intervention (PCI)

tag: clinical data

value: The 64-year-old male did not develop contrast-induced acute kidney injury (CA-AKI) after the emergency PCI procedure. He belongs to the control group. His baseline estimated glomerular filtration rate (eGFR) was 79.141 ml/min. He has hypertension but does not have diabetes, atrial fibrillation, or heart failure.


title: 14 - Control

tag: tissue

value: The 80-year-old male did not develop contrast-induced acute kidney injury (CA-AKI) after the elective PCI procedure. He belongs to the control group. His baseline estimated glomerular filtration rate (eGFR) was 54.785 ml/min. He has hypertension but does not have diabetes, atrial fibrillation, or heart failure.


title: 13 - Control

tag: treatment

value: The 80-year-old male did not develop contrast-induced acute kidney injury (CA-AKI) after the elective PCI procedure. He belongs to the control group. His baseline estimated glomerular filtration rate (eGFR) was 48.706 ml/min. He has hypertension but does not have diabetes, atrial fibrillation, or heart failure.


title: 15 - Control

value: The 56-year-old male did not develop contrast-induced acute kidney injury (CA-AKI) after the elective PCI procedure. He belongs to the control group. His baseline estimated glomerular filtration rate (eGFR) was 42.582 ml/min. He has hypertension and diabetes but does not have atrial fibrillation or heart failure.


title: 9 - Disease

value: postoperative contrast-induced acute kidney injury (CI-AKI)

value: female

value: The 78-year-old female was diagnosed with contrast-induced acute kidney injury (CA-AKI) after an elective PCI procedure. Her baseline estimated glomerular filtration rate (eGFR) was 66.537 ml/min. She has diabetes, hypertension, and atrial fibrillation but does not have heart failure.


title: GM, WT, Rep1

value: WT


title: 8 - Disease

value: The 55-year-old female was diagnosed with contrast-induced acute kidney injury (CA-AKI) after an elective PCI procedure. Her baseline estimated glomerular filtration rate (eGFR) was 45.348 ml/min. She has diabetes, hypertension, and atrial fibrillation but does not have heart failure.


title: GM, KO, Rep3

value: 0 day


title: 5 - Disease

value: The 71-year-old male was diagnosed with contrast-induced acute kidney injury (CA-AKI) after PCI. His baseline estimated glomerular filtration rate (eGFR) was 35.637 ml/min. He does not have diabetes or heart failure, but he has hypertension and atrial fibrillation. The CA-AKI occurred after the emergency PCI procedure.


title: GM, WT, Rep3

value: growth media


title: SNU-668 Erastin-resistant cells, IP

city: shanghai

first: Ming

middle: zhe

last: Ma

email: mmz666@163.com, mmz666@shca.org.cn

address: Dongan Road 270

department: Department of gastric surgery

institute: Fudan university shanghai cancer center

data_processing:
Basecalls were performed using bcl2fastq v2.17 for Novaseq output.
ChIP-seq reads were trimmed from 3' end until the final base had a quality score > 30, using Trimmomatic v0.33, discarding reads left with < 20 bp
ChIP-seq reads were aligned to the UCSC hg38 genome using Bowtie version 1.1.2. Only uniquely mapping reads with at most two mismatches were retained.
To create ChIP-seq coverage plots, the locations of the mapped ChIP-seq reads were extended to 150 bp to represent sequenced fragments, renormalized (to reads per million, rpm) and reformatted in the bigWig file format.
Peaks were called using MACS v2.1.0 with the significance cut-off q-value <=0.01. bigWig files were generated using the genomicRanges R package. Score represents the normalized coverage of DNA fragments at a given genomic coordinate. narrowPeak files were generated using MACS v2 with default settings.
Assembly: hg19
Supplementary files format and content: Peak files

growth_protocol: SNU-668 Erastin-resistant cells were routinely generated by re-plating d 4 in DMEM supplemented with 10% FBS

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated using a E220 focused-ultrasonicator (Covaris).
ChIP-seq libraries were prepared using the KAPA HTP Library Preparation Kit complemented with NEXTflex DNA Barcodes from Bioo Scientific. 10 ng of DNA was used as starting material for input and ip samples. Libraries were amplified using 13 cycles on the thermocycler. Post amplification libraries were size selected at 250-450bp in length using Agencourt AMPure XP beads from Beckman Coulter. Libraries were validated using the Agilent High Sensitivity DNA Kit.

tag: cell type

value: gastric cancer cell line

value: SOX13 (proteintech,#18902-1-AP)


title: SNU-668 Erastin-resistant cells, Input

tag: genotype


title: Human_KDOAM25_3PN.8cell_embryos

city: GuangZhou

first: Teng

last: Wang

address: jingxiStreet

institute: Southern Medical University

description: STRT-seq

data_processing:
TrimGalore (version 0.6.5) and BS-Seeker2 (version 2.1.1)
For RNA-part data, reads in R2 were grouped according to specific cell barcode35 (8 bp), then UMI information was used to extract the corresponding R1 reads. Raw sequencing reads were trimmed to remove the template switch oligo (TSO) sequence, polyA tail and low-quality bases. Next, the clean R1 reads were aligned to human reference genome (hg38, UCSC) using STAR (version 2.7.9) with the default parameters, HTSeq (version 0.12.4) was used to quantify gene expression level. The number of distinct UMIs (unique molecular identifiers) for each gene was counted as the transcript copy number and normalized to TPM (transcripts per million) value. Gene expression level was shown as log2(TPM+1).
For DNA-part data, reads were trimmed with TrimGalore71 (version 0.6.5) to remove adaptor sequences, low-quality bases and 6 bp random primers. Only reads with length more than 50 bp were retained. Reads passed quality control were then aligned to the reference genome (hg38, UCSC)68 using BS-Seeker272 (version 2.1.1) under both end-to-end and local alignment mode. Duplicated reads generated from PCR amplification were removed by Samtools73 (version 1.10). Only the unique alignments were used for the following analysis. The cells that passed four strict quality control criteria (mapping ratio of DNA-part data higher than 30%; bisulfite conversion rate higher than 98%; more than 1,000,000 WCG sites and 8,000,000 GCH sites covered; the ratio of genome coverage higher than 5%) were retained.
Assembly: hg38
Supplementary files format and content: text file
Supplementary files format and content: WCG.txt and GCH.txt files include the read counts of cytosines in WCG and GCH context respectively. The columns in WCG.txt or GCH.txt files represent "chr" "position" "unmethylated read counts" "methylated read counts". TPM.txt files include the expression matrix normalized to TPM (transcripts per million) value.

molecule: cytoplasmic RNA

source_name: embryo

extract_protocol:
Here we performed single-cell multi-omics libraries referring to the methods of STRT-seq and scCOOL-seq. A mouth pipette was used to pick blastomeres and transferred into the 2.5 μl cell lysis buffer containing 4 U RNase inhibitor (Takara, Cat. 2313B), 0.25% IGEPAL CA-630 (Sigma, Cat. I3021), and in vitro methylation mix (1× GC reaction buffer, 160 μM S-adenosylmethionine and 2 U M.CviPI (NEB, Cat. M0227L). After gently vortexed for about 15 seconds, the lysate was incubated at 37°C for 20 mins and then at 65°C for 25 mins. To isolate DNA and RNA of the single cells, a 3 μl nuclear separation mixture containing 0.2 µl of Dynabeads Myone Carboxylic Acid (Invitrogen, Cat. 65011), 0.2% Tween-20 (Sigma, Cat. P1379), 1% Triton X-100 (Sigma, Cat. T8787), 4 U RNase inhibitor, 50 mM DTT and 2 µl of 5× Superscript II first-strand buffer (Invitrogen, Cat. 18064071), was added to above 2.5 μl cell lysis. The tube was placed on the magnet after mixing by vortexing and brief centrifugation. The nuclei (DNA) wrapped with magnetic beads and the cytoplasm in the supernatant were separated for subsequent use.
For the RNA-part, the supernatant containing cytoplasm was used to construct the single-cell/embryo library following STRT-seq method. Briefly, the separated supernatant was added into the 4.5 µl reverse transcription mix containing 100 U SuperScript II reverse transcriptase (Invitrogen, 18064071), 4 U RNase inhibitor, 3 µM 8bp-barcoded primer, 1 mM dNTP (Takara, 4019), 1 M Betaine (Sigma-Aldrich, B0300), 6 mM MgCl2, 10 µM TSO primer. The mixture was incubated at 25 °C for 5 min, 42 °C for 60 min, 50 °C for 30 min and then 70 °C for 10 min. The cDNA was subsequently amplified using KAPA HiFi HotStart ReadyMix PCR Kit (Roche, KK2631) and purified twice using 0.8× AMPure XP beads (Beckman, A63882). Biotin PCR was performed subsequently and the products were enriched using Dynabeads Myone Streptavidin C1 (Invitrogen, 65001). The cDNA library was finally prepared in accordance with the guidelines of KAPA Hyper Prep Kits for PCR Library Amplification/Illumina series (KAPA, KK8504).For the DNA-part, the magnetic beads containing cell nuclei were added with digestion buffer containing 2.5 µl M-digestion buffer (Zymo Research, D5021), 10 µg protease K (Qiagen, 19155), 2 µl H2O and were incubated for another 60 min at 50 °C to release the genomic DNA. Then the genomic DNA was treated with EZ-96 DNA Methylation-Direct MagPrep kit (Zymo Research, D5044) to perform the bisulfite conversion and purification. The purified DNA was amplified by Klenow exo- (TIANGEN, NG202-02) and scBS-seq-P5-N6-oligo1 (CTACACGACGCTCTTCCGATCTNNNNNN) in four rounds. After purified by 0.8× AMPure XP beads, the products were used to construct the second strand synthesization using Klenow exo- and scBS-seq-P7-N6-oligo2 (AGACGTGTGCTCTTCCGATCTNNNNN). Then, the DNA library was constructed with KAPA HiFi HotStart ReadyMix PCR Kit and index primers. Lastly, the samples were purified twice with 0.8× AMPure XP beads. For the preparation of the single-cell/embryo RNA-seq library, the whole cell or embryo was picked to perform library preparation using STRT-seq method as described above. All high-quality libraries were sequenced with 150 bp pair-end reads on Illumina NovaSeq 6000 platform (Haplox).

value: embryo

tag: age

tag: condition

value: Human 3PN 8-cell embryos from control and KDOAM25 treatment group

value: KDOAM25 treatment


title: GM, KO Rep2

tag: cell line


title: GM, KO, Rep1


title: Human_siYY1_3PN.8cell_embryos

description: STRT-seq

value: human 3PN 8-cell embryos from YY1 knockdown and negative control group

value: YY1 knockdown


title: DNA_AURKA_zygote_emb9

description: scCOOL-seq

value: Human arrested zygote (3PN) from AURKA inhibited group

value: AURKA inhibition


title: Human_Arrested.embryos

description: STRT-seq

value: Human arrested zygote to 8-cell embryos


title: Human_AURKA_3PN.zygote

description: STRT-seq

value: female

value: Human arrested zygote (3PN) from control and AURKA inhibited group


title: D2, WT, Rep3

value: WT

value: 2 day

value: differentiation media


title: Du145-DtxR, siRNA-BRPF1, Replica #3

city: Istanbul

first: Hamzah

last: Syed

address: Rumelifeneri Yolu

country: Turkey

institute: Koç University

description:
brpf1-III
counts2.xlsx

data_processing:
STAR was used to align Fastq files to the latest human reference transcriptome
Salmon was used for quantification
Tximport and DEseq2 used for normalisation of counts
Assembly: GRCh38
Supplementary files format and content: XLSX files of all sample counts

source_name: Docetaxel Resistant Du145 cell line

growth_protocol:
Du145-Docetaxel Resistant cells were cultured in RPMI 1640 medium supplemented with 10% FBS, 1% penicillin-streptomycin, and incubated at 37°C with 5% CO2 in a humidified environment.
Du145-Parental and Resistant cells were cultured in RPMI 1640 medium supplemented with 10% FBS, 1% penicillin-streptomycin, and incubated at 37°C with 5% CO2 in a humidified environment.

extract_protocol: Total RNA was extracted with NucleoSpin™ RNA Plus Isolation Kit (Macherey Nagel, 740984.50)

treatment_protocol:
The Docetaxel-resistant Du145 cells were plated on 6-well plates with a density of 170,000 cells (60% confluency). After 24 h, the cells underwent treatment with siControl and siBRPF1. Subsequently, after an additional 24 h, the media containing the siRNA was aspirated, and fresh medium was added. Total RNA isolation was carried out 48 h later. The efficiency of knockdown was tested, revealing a knockdown efficiency greater than 80%.
Du145 (ATCC no. HTB-81) cells were maintained in RPMI-1640 medium (Gibco, 11875093) supplemented with 10% fetal bovine serum (Biowest, S1810) and 1% penicillin/streptomycin (Biowest, L0022). Cells were grown at 37°C in a humidified atmosphere with 5% CO2. Resistant clones were selected by culturing cells with docetaxel (Sigma-Aldrich, 01885) and/or cabazitaxel (Sigma-Aldrich, SML2487) for 72 h. A dose-escalation strategy was implemented, beginning at 1 nM, and doubled to reach 125 nM. After waiting for approximately 1-2 weeks for the remaining survived cells to recover, they underwent a passage before proceeding with the new dose. Cell viability experiments were set up to assess the establishment of resistance at two dose increments. Parental cells were passaged alongside as an age-matched appropriate control.

value: Docetaxel Resistant Du145 cell line

value: BRPF1 Knockdown

value: siRNA BRPF1


title: DNA_AURKA_zygote_emb8

description: scCOOL-seq


title: DNA_AURKA_zygote_emb7

description: scCOOL-seq


title: DNA_AURKA_zygote_emb6

description: scCOOL-seq


title: DNA_AURKA_zygote_emb5

description: scCOOL-seq