title: N2 worms, day 7, day 6 lysates rep4 (small RNA-seq)

city: Beijing

first: Ying

last: Liu

address: 5 Summer Palace Road, Haidian District, Beijing

department: College of Future Technology

institute: Peking University

description: day6 lysates.miRNA.count.txt; day6 lysates.piRNA.count.txt; day6 lysates.22GRNA.count.txt; day6 lysates.26GRNA.count.txt

data_processing:
The raw sequence reads were cleaned from adapter sequences or low-quality sequences by SOAPnuke (developed by BGI) with the parameters "-n 0.001 -l 13 -q 0.1 --highA 1 --minReadLen 15 -- maxReadLen 44 --ada_trim". Quality control were conducted on both the raw and processed data using the FastQC tool (v.0.11.9, http://www.bioinformatics.babraham.ac.uk/projects/fastqc).
The cleaned reads were aligned to the Caenorhabditis elegans genome (Ensembl WBcel235/ce11 assembly) using Bowtie v.1.0.0 (http://bowtie-bio.sourceforge.net) with the parameters ‘-v 1 -M 1 --best --strata --tryhard --chunkmbs 512 -S’. The alignment outputs were then converted to sorted BAM files via Samtools v.1.3.1. Gene annotations in GTF format were downloaded from Ensembl (ftp://ftp.ensembl.org/pub/release-110/gtf/caenorhabditis_elegans/).
Structural reads, defined as reads mapping in the sense orientation to annotated rRNAs, tRNAs, snRNAs, or snoRNAs, were removed from further analyses using Bedtools v.2.30.0 (http://bedtools.readthedocs.io). Annotations for miRNA genes were derived from miRbase. miRNA reads were defined as those ranging from 21 to 24 bases that map in the sense orientation to the annotated miRNA genes. 21U reads were defined as 21-base reads beginning with T, which map in the sense orientation to piRNA genes, and these reads must align uniquely. Targets of piRNAs were predicted using piRTarBase. Gene-derived 22G-RNA were defined as reads ranging from 21 to 23 bases and 26G-RNA were 26-base reads. These reads were starting with G and mapping in the antisense orientation to annotated genes.
The read counts per gene were quantified using featureCounts/Subread v2.0.1. Reads were further extracted and filtered with Awk, Samtools and custom Python scripts. Filtered reads were then converted to BED files, and subsequently to BedGraph files using Bedtools v.2.30.0. For visualization, the BedGraph files were converted to BigWig files and displayed using the IGV tool (v.2.9.4).
Reads for each gene were normalized to the total mapped reads of individual gene class as reads-per-million (RPM). Differential expression analysis was conducted with DEseq2, with an adjusted p-value <0.05 set as the threshold for statistically significant differential expression for each gene class.
Assembly: Caenorhabditis elegans genome (Ensembl WBcel235/ce11 assembly)
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

organism: Caenorhabditis elegans

source_name: whole worms

growth_protocol: Worms were grown and maintained at 20 ºC and fed with E. coli OP50 on Nematode Growth Medium (NGM) (0.25% Bacto peptone, 0.3% sodium chloride, 1.7% agar, 5 ug/mL cholesterol, 25 mM potassium phosphate pH 6.0, 1 mM magnesium sulfate, 1 mM calcium chloride).

extract_protocol:
Synchronized worms were collected from the plates, washed at least three times with M9 buffer, and resuspended in TransZol Up reagent (TransGen Biotech, #ET111-01). Worm samples were frozen in liquid nitrogen and freeze-thawed for at least five times. Total RNA was isolated by chloroform extraction followed by isopropanol precipitation, washed with 75% (v/v) ethanol and dissolved in RNase-free water.
Small RNA libraries for small RNA seq were prepared by BGI Tech using DNBSEQ small RNA seq protocols.

treatment_protocol: To prepare mRNA-seq sample, approximately 1000 synchronized Day 7 N2 worms were treated with control, embryo lysates or day 6 worms lysates for 24h.

value: whole worms

value: day6 lysates


title: WTNC2

status: Public on Sep 07 2024

type: SRA

city: Hangzhou

first: Di

last: Wang

state: Zhejiang

address: Yuhgang Tang Rd No.866

department: School of Medicine

country: China

institute: Zhejiang University

library_source: transcriptomic

data_processing:
Raw reads were processed through quality control and genome mapping and further analyzed by the DESeq2 package (1.30.1). Differential expressed genes were determined with a cutoff of FDR smaller than 0.05. Normalized transcripts per million values (TPM) were used to plot heatmap using pheatmap package (1.0.12).
none provided by the submitter

molecule: total RNA

organism: Mus musculus

source_name: mice primary bone marrow-derived macrophages

growth_protocol: BMDMs were cultured with DMEM supplemented with 10% FBS, 1% AA.

extract_protocol:
Total RNA was extracted with RNA extraction kit following manufacturer's instructions
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Primary BMDMs from C57B6J mice were treated with B16F10 tumor cells conditioned medium supplemented with/without KCl or NaCl for 6 hours, and the final KCl and NaCl concentration was 40mM.

tag: strain

tag: treatment

value: Control group


title: N2 worms, day 7, day 6 lysates rep3 (small RNA-seq)

tag: tissue

tag: genotype

value: WT


title: N2 worms, day 7, day 6 lysates rep1 (small RNA-seq)


title: N2 worms, day 7, embryo lysates rep4 (small RNA-seq)

description: embryo lysates.miRNA.count.txt; embryo lysates.piRNA.count.txt; embryo lysates.22GRNA.count.txt; embryo lysates.26GRNA.count.txt

value: embryo lysates


title: N2 worms, day 7, embryo lysates rep1 (small RNA-seq)


title: N2 worms, day 7, day 6 lysates rep2 (small RNA-seq)


title: N2 worms, day 7, embryo lysates rep3 (small RNA-seq)


title: N2 worms, day 7, embryo lysates rep2 (small RNA-seq)


title: N2 worms, day 7, untreated rep3 (small RNA-seq)

description: untreated.miRNA.count.txt; untreated.piRNA.count.txt; untreated.22GRNA.count.txt; untreated.26GRNA.count.txt

value: untreated


title: N2 worms, day 7, untreated rep4 (small RNA-seq)


title: N2 worms, day 7, untreated rep2 (small RNA-seq)


title: N2 worms, day 7, untreated rep1 (small RNA-seq)


title: WTBK3

value: Treated with B16F10 TCM + KCl (Isotonic)


title: N2 worms, day 7, embryo lysates rep2

data_processing:
Sequencing quality evaluation prior to mapping was conducted using FastQC (version 0.11.9).
Subsequently, the reads were aligned to the Caenorhabditis elegans genome (Ensembl WBcel235/ce11 assembly) using HISAT2 (version 2.2.1) with default parameters. Only uniquely mapped reads were retained for further analysis. Gene annotations for WBcel235/ce11 in GTF format were downloaded from Ensembl (ftp://ftp.ensembl.org/pub/release-110/gtf/caenorhabditis_elegans/).
Gene count matrices were generated using Htseq-count from HTSeq (version 0.12.4).
To identify genes with differential expression levels between case and control groups, gene differential expression analysis was performed using the DESeq2 tool (version 1.26.0). Genes with low expression across all samples (FPKM < 0.5 in all samples) were excluded from the differential gene expression results. Genes with an adjusted p-value below 0.05 were identified as significantly differentially expressed.
KEGG enrichment analysis of the differentially expressed genes was performed using the clusterProfiler R package (version 4.10.0).
Assembly: Caenorhabditis elegans genome (Ensembl WBcel235/ce11 assembly)
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

extract_protocol:
Synchronized worms were collected from the plates, washed at least three times with M9 buffer, and resuspended in TransZol Up reagent (TransGen Biotech, #ET111-01). Worm samples were frozen in liquid nitrogen and freeze-thawed for at least five times. Total RNA was isolated by chloroform extraction followed by isopropanol precipitation, washed with 75% (v/v) ethanol and dissolved in RNase-free water.
RNA libraries for RNA seq were prepared by BGI Tech using DNBSEQ mRNA seq protocols.

treatment_protocol: To prepare mRNA-seq sample, approximately 500 synchronized Day 7 N2 worms were treated with control or embryo lysates for 24h.


title: N2 worms, day 7, embryo lysates rep4


title: N2 worms, day 7, embryo lysates rep1


title: N2 worms, day 7, untreated rep4


title: N2 worms, day 7, untreated rep3


title: N2 worms, day 7, untreated rep1


title: N2 worms, day 7, untreated rep2


title: rep2_MALAT1-ChIRP-DNA

city: Toronto

first: Juan

last: Zhang

state: Ontario

address: 25 Orde Street, Room 6-1001 MRS

country: Canada

institute: LTRI

library_source: genomic

data_processing:
the raw sequencing data were processed using bowtie2, then filtered using samtools to generate bam files.
The bam files were processed with deeptools bamCoverage to generate RPKM normalized, and blacklist filtered BigWigs with default 50bp bins.
The merged bam files were processed with macs3 to call LINE1 ChIRP peaks in BED files.
Assembly: hg38
Supplementary files format and content: bw
Library strategy: ChIRP-seq

molecule: genomic DNA

organism: Homo sapiens

growth_protocol: H9 hES cells were cultured in RSeT media (STEM CELL) following manual instruction. Cells were cultured in RSeT supplemented with 10 nM DZNep and 5nM TSA for 48 hours then collected for the ChIRP pulldown experiment.

extract_protocol:
ChIRP-DNAs after reverse crosslinking were purified using the MinElute PCR Purification Kit (QIAGEN #28004) following the instruction manuals. 40 ul of ChIRP-DNAs were eluted for each sample.
5 ul of purified ChIP-DNAs of each sample was used to prepare sequencing library. The library was prepared with NEBNextUltra II DNA Library Prep Kit for Illumina (NEB # E7645L), following the manual instruction. Library DNA were equally pooled at 8 nM for sequencing.

treatment_protocol: no treatment

tag: cell line

tag: cell type

value: Human embryonic stem cells

tag: fraction


title: N2 worms, day 7, embryo lysates rep3


title: rep2_L1-ChIRP-DNA


title: L1-ChIRP- input DNA

value: input


title: WTNC1


title: rep1_MALAT1-ChIRP-DNA


title: rep1_L1-ChIRP-DNA


title: UCMSC_2

city: Changsha, Hunan, China

first: Peiyun

address: 110 Xiangya Road

institute: Central South University

data_processing:
The clean reads were mapped to the reference genome using HISAT2.
FPKM of each gene was calculated and the read counts of each gene were obtained by HTSeq-count.
Assembly: GRCh38.p13
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: umbilical cord

growth_protocol: Induced mesenchymal stem cells (iMSCs) or umbilical cord-derived mesenchymal stem cells (UCMSCs) were maintained in  αMEM supplemented with 10% fetal bovine serum, 100 U/mL L-glutamine and 10 µg/mL basic fibroblast growth factor in humidified atmosphere with 5% CO2 at 37℃.

extract_protocol:
After harvesting cells, total RNA was extracted using the trizol reagent  (Invitrogen)  according to the manufacturer's protocol
The libraries were constructed using VAHTS Universal V6 RNA-seq Library Prep Kit according to the manufacturer's instructions.

value: umbilical cord

value: mesenchymal stem cell


title: OV749HG

first: Pamela

last: Ohashi

address: 610 University Ave

institute: Princess Margaret Cancer Centre

library_source: transcriptomic single cell

data_processing:
FASTQ files were aligned to GRCh38 and counts data was assembled using CellRanger v6.0 (10x Genomics). MTX sparse matrix files resulting from CellRanger processing were obtained.
Assembly: GRCh38
Supplementary files format and content: .mtx sparse matrix format

source_name: Ovarian

extract_protocol:
CD45+ and CD45- live cells were sorted from primary ovarian tumour resections (N=3) and mixed in a 1:1 ratio to ensure enough enrichment from both immune and tumour proportions.
Samples were prepared using Chromium Single Cell 5’ v2 Reagent Kit (Catalog no. PN-1000263, 10x Genomics) according to the manufacturer’s instructions. Library size was determined using Agilent High Sensitivity DNA Kit (5067-4626, Agilent Technologies). Samples were pooled and quantified using QubitTM dsDNA HS Assay Kit (Q32851, Qubit) on the QubitTM 2.0 Fluorometer. Pools were sequenced with an S2 flow cell on NovaSEq 6000 platform (Illumina) to a targeted depth of 50,000 reads per cell.

value: Ovarian

value: Sorted, mixed CD45- & CD45+ Cells


title: UCMSC_1


title: OV744HG


title: iMSC_2

source_name: urine-derived induced pluripotent stem cell

value: induced mesenchymal stem cell


title: OV348HG


title: UCMSC_3


title: H3K27me3_Primed_rep2

data_processing:
Adaptor sequences and low-quality score bases (Phred score < 33) were trimmed using Trimmomatic v.0.39.
The resulting reads were aligned to the GRCh38 genome assembly using the Burrows-Wheeler Aligner v.0.7.17.
Reads were filtered to keep only high-quality alignments (MAPQ score >20). Peak calling was performed with MACS2 v.2.2.7.1 using piling up of paired-end fragment mode (--format BAMPE) with q value <0.05. The BED files were then removed of blacklist regions and merged between replicates with bedtools intersection.
BigWig files were generated wtih deeptools bamCoverage (options --binSize 10 --normalizeUsing CPM and replicates merged with bigwigCompare.
Assembly: hg38
Supplementary files format and content: bw

growth_protocol: H9 hES cells were cultured in mTESR media (STEM CELL) and RSeT media (STEM CELL) following manual instruction for mainting primed and RSeT naive condition, respectively. For RSeT+DT hESCs, cells were cultured in RSeT supplemented with 10 nM DZNep and 5nM TSA until 48 hours later cells are collected.

extract_protocol:
ChIP-DNAs were purified using the the ChIP-lysates True MicroChIP-Seq kit (Diagenode # C01011009) following the instruction manuals.
Cells were crossed-linked with 1% formaldehyde and lysed. Sonication of nuclei was then performed on a BioRuptor UCD-300 targeting 150-500 bp size. Immunoprecipitation of the histone marks was performed by using the Auto-ChIPmentation kit for Histones (Diagenode inc, cat# C01011009) according to the manufacturer’s instructions. The antibodies used in the immunoprecipitation were previously validated for ChIP-Seq applications by the manufacturers. These antibodies are H3K27me3 (Cell Signaling, cat# CST9733, 10.2 ug used), H3K27ac (Diagenode, cat # C15410196, 7 ug used)  and H3K9me3 (Abcam, cat# ab8898, 1 ug used). The libraries were size selected using Ampure XP Beads (Beckman Coulter, cat# A63880) and quantified using the KAPA Library Quantification kit - Universal (KAPA Biosystems, cat# KK4828).


title: iMSC_1

value: urine-derived induced pluripotent stem cell


title: H3K27me3_RSeT_rep1


title: H3K27me3_Primed_rep1


title: iMSC_3


title: H3K27ac_RSeT_rep2


title: H3K27ac_RSeT_rep1


title: H3K27me3_RSeT+DT_rep2


title: H3K27ac_Primed_rep1


title: H3K27me3_RSeT_rep2


title: H3K9me3_Primed_rep1


title: H3K27ac_RSeT+DT_rep2


title: H3K27ac_Primed_rep2


title: H3K9me3_RSeT_rep2


title: H3K9me3_Primed_rep2


title: H3K9me3_RSeT_rep1


title: Feline thyroid, hyperthyroid, rep10

city: Hatfield

first: Lucy

last: Davison

address: Hawkshead Lane

department: CSS

country: United Kingdom

institute: Royal Veterinary College

data_processing:
Adapters were trimmed from raw reads using PEAT v1.2.4.
Trimmed reads were aligned to the felCat9 reference genome (GCA_000181335.4) using STAR v2.6.0c.
Alignments were filtered to retain only uniquely mapped, properly paired reads using Samtools v1.9.
Gene-level read counts were obtained using featureCounts (from Rsubread v2.12.3) in R, and raw counts were TMM normalised and analysed with edgeR v3.40.2.
Assembly: Felis_catus_9.0 (GCA_000181335.4)
Supplementary files format and content: tab-delimited text file containing raw counts for each sample

organism: Felis catus

source_name: Thyroid

extract_protocol:
A 3-4 mm3 sample of each thyroid was dissected with scissors and washed with PBS prior to lysis in TRIzol reagent (Invitrogen). Where a distinct nodule or nodules were present in hyperthyroid cats, this area of tissue was prioritised for RNA-Seq. Phenol-chloroform extraction was used to isolate nucleic acids from the lysate, and RNA was purified from the resulting aqueous phase using a RNeasy Micro kit (Qiagen) with on-column DNase treatment to digest genomic DNA. Pure RNA was eluted with RNase-free water, and cleaned up using an RNA Clean & Concentrator-25 kit (Zymo Research). RNA integrity and concentration were determined using a Tapestation 4200 (Agilent) and Nanodrop ND-1000 (Thermo Scientific), respectively
RNA-seq libraries were prepared from total RNA by Oxford Genomics Centre (Wellcome Centre for Human Genetics, University of Oxford). Following ribodepletion with the NEBNext rRNA Depletion Kit v2 (NEB) to remove abundant rRNA species, stranded libraries were generated using a TruSeq Stranded Total RNA kit (Illumina).

value: Thyroid

tag: Sex

value: Male

tag: breed

value: Domestic short hair

tag: thyroid status

value: Hyperthyroid


title: H3K9me3_RSeT+DT_rep2


title: Feline thyroid, hyperthyroid, rep9

value: Domestic long hair


title: Feline thyroid, hyperthyroid, rep11

value: Female


title: H3K9me3_RSeT+DT_rep1


title: Feline thyroid, hyperthyroid, rep8


title: Feline thyroid, hyperthyroid, rep7


title: Primed_HESC_2

data_processing:
Adaptor sequences and low-quality score bases (Phred score < 33) were trimmed using Trimmomatic v.0.39.
The resulting reads were aligned to the GRCh38 genome assembly using STAR v.2.7.8a with Ensembl annotation (v104).
Raw counts of repetitive elements were obtained using the FeatureCounts function from the Subread package (v2.14.2).
Assembly: hg38
Supplementary files format and content: txt
Supplementary files format and content: csv

extract_protocol:
The RNA was extracted from 500K cells fixed in Trizol using the miRNeasy kit (QIAGEN, cat#217084), following the manufacturer instruction. RNA integrity was assessed with the Agilent 2100 Bioanalyzer System (Agilent Technologies).
RNA library preparations were carried out on 500 ng of RNA (RIN > 7) using the Illumina TruSeq Stranded Total RNA Sample preparation kit (Illumina, cat#20020596), according to manufacturer's protocol. The libraries were size-selected using Ampure XP Beads (Beckman Coulter, cat# A63880) and quantified using the KAPA Library Quantification kit - Universal (KAPA Biosystems, cat# KK4828).


title: Naive_HESC_RSeT_2


title: Feline thyroid, hyperthyroid, rep5


title: Primed_HESC_1


title: Naive_HESC_RSeT_DT_2


title: Feline thyroid, hyperthyroid, rep4


title: Feline thyroid, hyperthyroid, rep3


title: H3K27ac_RSeT+DT_rep1


title: rep2_ASO-L1KD, K27me3-ChIP

description: NovaSeq SP flowcell

data_processing:
the raw sequencing data were processed using bowtie2, then filtered using samtools to generate bam files.
The bam files were processed with deeptools bamCoverage to generate CPM normalized, and blacklist filtered BigWigs with default 50bp bins.
The merged bam files were processed with macs3 to call H3K27me3 ChIP peaks in BED files. Also, a restricted H3K27me3 peaks BED file was generated by intersecting for significantly H3K27me3 enriched peaks in both replicates.
BigWigs files were processed with MultiBigwigSummary to create a text output file for import in R.
Assembly: hg38
Supplementary files format and content: txt
Supplementary files format and content: bw

growth_protocol: H9 hES cells were cultured in RSeT media (STEM CELL) following manual instruction. Upon transfection performed, cells were cultured in RSeT supplemented with 10 nM DZNep and 5nM TSA until 48 hours later cells are collected.

extract_protocol:
ChIP-DNAs were purified using the the ChIP-lysates True MicroChIP-Seq kit (Diagenode # C01010132) following the instruction manuals. 20 ul of ChIP-DNAs were eluted for each sample.
10 ul of purified ChIP-DNAs of each sample was used to prepare sequencing library. The library was prepared with NEBNextUltra II DNA Library Prep Kit for Illumina (NEB # E7645L), following the manual instruction. Library DNA were equally pooled at 4 nM for sequencing.

treatment_protocol: Cells were transfected with 25 nM ASOs using 4ul Lipofectamine Stem Transfection Reagent (Thermo Fisher Scientific) per 6-well, following manual instruction. 0.7 uM Trans-ISRIB (Sigma # 5095840001) and 5 uM Emricasan (Sigma # SML2227) together with 10 uM ROCK inhibitor Y-27632 (Stemgent) were added to improve transfection efficiency and cell survival ability (Chen et al. 2021), and removed 24 hour later. 70,000 FAM+ transfected cells were collected by FACS for each ChIP pulldown.

tag: antibody


title: Feline thyroid, hyperthyroid, rep1


title: Feline thyroid, euthyroid, rep4

value: Euthyroid


title: rep2_ASO-CtrA, K27me3-ChIP

description: NovaSeq SP flowcell

value: ASO-CtrA


title: Feline thyroid, euthyroid, rep3


title: rep1_ASO-CtrA, K27me3-ChIP

description: NovaSeq SP flowcell


title: ASO-L1KD, 5% input

description: NovaSeq SP flowcell


title: Feline thyroid, euthyroid, rep1


title: lymphocytes+ PD-L2 KO exosomes 1

city: Nanjing

first: Shan

last: Gao

address: No. 2 Sipailou, Xuanwu District

institute: Southeast University

data_processing:
Raw FASTQ files were trimmed by fastp 0.23.2
Trimmed FASTQ files were aligned to hg38 genome by STAR 2.7.10a
BAM files were assemblyed by stringtie
Deseq2 was used to perform differential analysis
Assembly: hg38
Supplementary files format and content: exprSet.csv, csv format, containing the raw counts.

source_name: peripheral blood

growth_protocol: 786-O cell lines were maintained in RPMI1640 medium (Gibco) supplemented with 10% FBS. These cell lines except Renca were purchased from the Shanghai Cell Bank Type Culture Collection Committee (CBTCCC, Shanghai, China), verified by short tandem repeat assays for their identification, and cultured at 37°C in a humidified incubator with 5% CO2.

extract_protocol:
Total RNA isolated using RNAiso Plus (Takara).
RNA libraries for RNA-seq were prepared using Tru-seq Library Prep Kit following manufacturer's protocols

treatment_protocol: Lymphocytes cells purified from PBMC (5× 105 cells/ml in a 10 cm plate) were then stimulated by incubation with PMA (2 μg/ml) and Ionomycin (2 μg/ml) for 6h until CD69+ cell proportion up to over 75%. Exosomes isolated from 786-O CTR and PD-L2 KO culture supernatants of equal numbers of cells were feeded to stimulated lymphocytes isolated from peripheral blood lymphocytes in 10cm Petri dish for 72h.

value: peripheral blood

value: lymphocytes

value: PD-L2 KO exosome


title: Naive_HESC_RSeT_1

value: Human embryonic stem cells


title: ASO-CtrA, 5% input

description: NovaSeq SP flowcell


title: S5P_WT_siRNA_INTS8_rep3

city: Cambridge

first: Ana

last: Tufegdzic Vidakovic

state: Cambridge

address: Cambridge Biomedical Campus, Francis Crick Ave

institute: MRC-LMB

data_processing:
dxChIP-seq reads were trimmed and quality-filtered with Trim Galore using a quality threshold of 30.
Trimmed reads were aligned to the hg38 genome using Bowtie2 with default parameters, then PCR duplicates were marked and removed with Picard.
The correlation between replicates was checked using deepTools multiBamSummary, then replicates were merged.
Merged BAM files were converted into RPKM-normalised bigwigs using deepTools bamCoverage.
Assembly: GRCh38
Supplementary files format and content: bigWig

source_name: Flp-In T-REx HEK293

growth_protocol: DMEM (31966047), 10% fetal bovine serum, 1% penicillin/streptomycin. Cells were cultured at 37°C with 5% CO2.

extract_protocol:
Cells were fixed with 1.66 mM disuccinimidyl glutarate (DSG) for 15 minutes, followed by washing and fixing with 1% formaldehyde for 8 minutes at room temperature. After quenching and cell lysis, cells were sonicated using a Covaris E220 sonicator for 4 minutes.
dxChIP-seq samples were prepared using NEBNext Ultra II DNA Library prep kit and validated using tapestation HS D5000 kit.

treatment_protocol: Cells were transfected with control siRNA or siRNA targeting INTS8 48 h before collection.

value: Flp-In T-REx HEK293

value: Parental WT

tag: chip antibody


title: Feline thyroid, euthyroid, rep2


title: lymphocytes+ PD-L2 KO exosomes 2


title: Feline thyroid, hyperthyroid, rep6


title: lymphocytes+ CTR exosomes 2

value: CTR exosome


title: lymphocytes+ CTR exosomes 1


title: Feline thyroid, hyperthyroid, rep2


title: S5P_WT_siRNA_INTS8_rep1


title: c1434_3 0 µM

city: Milwaukee

first: Ulrich

last: Broeckel

state: WI

address: 8701 Watertown Plank Road

country: USA

institute: Medical College of Wisconsin

data_processing:
The raw reads in FASTQ format were aligned to the human hg19 reference genome using bwa mem with default parameters: bwa mem -M -t 8 -R "@RG\tID:SampleName\tPL:ILLUMINA\tSM:SampleName" -L 5
Gene quantification was done using HTSeq using the default parameters: htseq-count -f bam -r pos -s no Sorted.bam Transcriptome.rna_manifest.20190313.geneExpression.targets.gtf
Differential gene expression was analyzed using the DESeq2 (v.1.26.0) R/Bioconductor package as well as a generalized linear model procedure (proc glm) in SAS 9.4
Assembly: hg19, custom annotation GTF file for targeted transcripts (Transcriptome.rna_manifest.20190313.geneExpression.targets.gtf) received from the manufacturer
Supplementary files format and content: tab-delimite matrix table with raw gene counts (rows) for all AmpliSeq targets and sample names (columns)

source_name: human induced pluripotent stem cell (hiPSC) cardiomyocytes

growth_protocol: iPSC-CMs were purchased from FujiFilm Cellular Dynamics, Inc.(FCDI), and grown in according to the FCDI protocol of culturing iCell cardiomyocytes.

extract_protocol:
Qiagen RNeasy 96 protocol that is automated on the Qiacube HT instrument
Targeted whole transcriptome sequencing was done using the AmpliSeq for Illumina Transcriptome Human Gene Expression Panel (Illumina, Inc) following manufacturer’s recommendations.

treatment_protocol: Drug treatment was conducted by following the recommednatiosn of Agilent/ACEA.

value: Ventricular hiSPC-CMs

tag: gender

tag: cohort

value: iCell

tag: doxcategory

value: Resistant

tag: flowcell


title: D8L4Y_WT_siRNA_INTS8_rep3


title: S5P_WT_siRNA_INTS8_rep2


title: c1254 0.3 µM

value: UTH


title: Input_WT_siRNA_INTS8_rep3


title: c1187_704 3 µM

value: Male

value: UAB

value: Sensitive


title: Input_WT_siRNA_INTS8_rep2


title: D8L4Y_WT_siRNA_INTS8_rep1


title: c1187_704 1 µM


title: S5P_WT_rep3

value: untreated


title: rep1_ASO-L1KD, K27me3-ChIP

description: NovaSeq SP flowcell


title: c1187_704 0.3 µM


title: S5P_WT_rep2


title: c1187_704 0 µM


title: c1078_717 3 µM

value: Female


title: S5P_WT_rep1


title: c1078_717 1 µM


title: Input_WT_rep2


title: Input_WT_rep1


title: c1078_717 0.3 µM


title: D8L4Y_WT_siRNA_INTS8_rep2


title: D8L4Y_WT_rep2


title: c1078_704 3 µM


title: c1078_704 1 µM


title: D8L4Y_WT_rep3


title: c1078_704 0 µM


title: c1078_704 0.3 µM


title: S5P_ARMC5_KO_siRNA_INTS8_rep3

value: ARMC5 KO


title: Input_ARMC5_KO_siRNA_INTS8_rep3


title: Naive_HESC_RSeT_DT_1


title: D8L4Y_ARMC5_KO_siRNA_INTS8_rep3


title: Input_ARMC5_KO_siRNA_INTS8_rep2


title: c1078_701 0.3 µM


title: Input_ARMC5_KO_siRNA_INTS8_rep1


title: c1078_701 1 µM


title: S5P_ARMC5_KO_siRNA_INTS8_rep1


title: c1066 3 µM


title: D8L4Y_ARMC5_KO_siRNA_INTS8_rep2


title: c1078_701 3 µM


title: Input_WT_rep3


title: c1078_701 0 µM


title: c1066 0.3 µM


title: c1066 0 µM


title: S5P_ARMC5_KO_rep2


title: D8L4Y_WT_rep1


title: S5P_ARMC5_KO_rep1


title: c1434_3 3 µM


title: Input_ARMC5_KO_rep2


title: Input_ARMC5_KO_rep1


title: c1308 3 µM


title: c1308 1 µM


title: D8L4Y_ARMC5_KO_rep3


title: c1308 0.3 µM


title: Input_ARMC5_KO_rep3


title: c1330 1 µM


title: D8L4Y_ARMC5_KO_rep1


title: Rep3, +UNC1999

data_processing:
RNA-seq reads were quality-checked and trimmed using Trim Galore! v0.4.0
The the trimmed reads were aligned to the hg19 with TopHat2 v2.0.13, which generated bam. files
FeatureCounts function from the subread package (v1.5.0) was applied to count reads of each gene to generate the raw counts table.
Assembly: hg19
Supplementary files format and content: txt

growth_protocol: H9 hES cells were cultured in RSeT media (STEM CELL) following manual instruction.

extract_protocol:
RNA extraction was performed using the Direct-zol RNA microprep Kits (Zymo), according to the manufacturer’s instructions.
200ng equal amount RNA each sample was used to prepare sequencing library. The cDNA library was prepared with NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB #  E7490S) and NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB # E7760L), following the manual instruction. Library cDNA were equally pooled at 10 nM for sequencing.

treatment_protocol: After 24 hours of cell passage, attached cells were cultured in RSeT supplemented with 10 nM DZNep and 5nM TSA, in combination with UNC1999 and UNC2400 added at 2.5 μM final concentration for the treatment and controls. 48 hours later ,cells are collected.


title: c1330 0 µM


title: c1066 1 µM


title: D8L4Y_ARMC5_KO_rep2


title: S5P_ARMC5_KO_rep3


title: Rep3, +UNC2400


title: Rep2, +UNC1999


title: c1330 0.3 µM


title: Rep2, +UNC2400


title: c1434_3 1 µM


title: c1297 0 µM


title: Rep1, +UNC1999


title: c1297 1 µM


title: c1297 3 µM


title: D8L4Y_ARMC5_KO_siRNA_INTS8_rep1


title: Rep3, SO-L1

growth_protocol: H9 hES cells were cultured in PXGL media (Guo et al. 2021). Upon transfection performed, cells were cultured in PXGL until 48 hours later cells are collected.

treatment_protocol: Cells were transfected with 25 nM ASOs using 4ul Lipofectamine Stem Transfection Reagent (Thermo Fisher Scientific) per 6-well, following manual instruction. 0.7 uM Trans-ISRIB (Sigma # 5095840001) and 5 uM Emricasan (Sigma # SML2227) together with 10 uM ROCK inhibitor Y-27632 (Stemgent) were added to improve transfection efficiency and cell survival ability (Chen et al. 2021), and removed 24 hour later. Transfected cells were collected directly without sorting for downstream analysis 48 hours post transfection.

tag: transfection


title: Rep3, ASO-L1


title: c1297 0.3 µM


title: c1273 0 µM


title: Rep2, ASO-L1


title: c1330 3 µM


title: c1308 0 µM


title: c1273 3 µM


title: Rep2, SO-L1


title: c1273 0.3 µM


title: Rep1, ASO-L1


title: Rep1, SO-L1


title: c1269 0 µM


title: c1269 3 µM


title: c1273 1 µM


title: Kidney organoids differentiated in UniMat

city: Ulsan

first: Tae-Eun

last: Park

address: 50, UNIST-gil, Eonyang-eup, Ulju-gun

department: Biomedical Engineering

country: South Korea

institute: Ulsan National Institute of Science and Technology (UNIST)

data_processing:
Alignment to the GRCh38 human reference genome, filtering, barcode counting, and UMI counting of FASTQ files were performed using the Cell Ranger (v6.1.2) pipeline (10X Genomics).
Assembly: GRCh38
Supplementary files format and content: Tab-separatedvalues (tsv) files and matrix files

source_name: hiPSC-derived kidney organoids

extract_protocol:
Kidney organoids were collected from both the AggreWell and UniMat using a pipette, and then dissociated into single cells using Accutase at 37 °C for 20 min. The single cells were resuspended in the basal differentiation medium containing 1.5% FBS.
samples were prepared following the manufacturer’s protocol (10X Genomics). The single-cell libraries were sequenced using the Chromium Next GEM Single Cell 3’ RNA library and gel bead v3.1 kit in HiSeqXten (Illumina).

value: hiPSC-derived kidney organoids


title: Kidney organoids differentiated in AggreWell


title: c1269 1 µM


title: Rep1, +UNC2400


title: RSeT_H9,L1KD Rep4, ASO-L1

description:
RSeT_H9,L1KD,raw_counts,rmDup.txt
RSeT_H9,L1KD-log2Nom_counts,cutoff=0.2_BatchCo.txt
RSeT_H9,ASO_sO-DEG,Cutoff=0.2.txt

data_processing:
RNA-seq reads were quality-checked and trimmed using Trim Galore! v0.4.0
The the trimmed reads were aligned to the hg19 with TopHat2 v2.0.13, which generated bam. files
FeatureCounts function from the subread package (v1.5.0) was applied to count reads of each gene to generate the raw counts table.
Assembly: hg19

growth_protocol: H9 hES cells were cultured in RSeT media (STEM CELL) following manual instruction. Cells were cultured in RSeT media until 48 hours later cells are collected.

extract_protocol:
RNA extraction was performed using the Direct-zol RNA microprep Kits (Zymo), according to the manufacturer’s instructions.
80-130ng equal volume RNA each sample was used to prepare sequencing library. The cDNA library was prepared with NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB #  E7490S) and NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB # E7760L), following the manual instruction. Library cDNA were equally pooled at 10 nM for sequencing.

treatment_protocol: Cells were transfected with 25 nM ASOs using 4ul Lipofectamine Stem Transfection Reagent (Thermo Fisher Scientific) per 6-well, following manual instruction. 0.7 uM Trans-ISRIB (Sigma # 5095840001) and 5 uM Emricasan (Sigma # SML2227) together with 10 uM ROCK inhibitor Y-27632 (Stemgent) were added to improve transfection efficiency and cell survival ability (Chen et al. 2021), and removed 24 hour later. Transfected cells were FACS collected for downstream analysis 48 hours post transfection.


title: c1254 0 µM


title: RSeT_H9,L1KD Rep4, sO-L1


title: RSeT_H9,L1KD Rep4, ASO-Ctr

value: ASO-Ctr


title: c1269 0.3 µM


title: c1434_3 0.3 µM


title: c1254 3 µM


title: RSeT_H9,L1KD Rep3, sO-L1


title: RSeT_H9,L1KD Rep3, ASO-L1


title: c1254 1 µM


title: RSeT_H9,L1KD Rep3, ASO-Ctr


title: c1194 0 µM


title: RSeT_H9,L1KD Rep2, ASO-L1


title: c1194 1 µM


title: c1194 3 µM


title: c1194 0.3 µM


title: RSeT_H9,L1KD Rep2, sO-L1


title: RSeT_H9,L1KD Rep2, ASO-Ctr


title: RSeT_H9,L1KD Rep1, ASO-L1


title: RSeT_H9,L1KD Rep1, sO-L1


title: c1159 0.3 µM


title: Rep3, ASO-L1+TPRX1-siRNA

description:
RSeT+DT_H9,hL1KD+siRNA,raw_counts,rmDup.txt
RSeT+DT_H9,hL1KD+siRNA,log2Nom_counts_BatchCo,cutoff=0.2.txt

growth_protocol: H9 hES cells were cultured in RSeT media (STEM CELL) following manual instruction. Upon transfection performed, cells were cultured in RSeT supplimented with 10 nM DZNep and 5nM TSA until 48 hours later cells are collected.

extract_protocol:
RNA extraction was performed using the RNeasy mini kit (QIAGEN), according to the manufacturer’s instructions.
32ng RNA each sample was used to prepare sequencing library. The cDNA library was prepared with NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB #  E7490S) and NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB # E7760L), following the manual instruction. Library cDNA were equally pooled at 10 nM for sequencing.

treatment_protocol: Cells were transfected with 25 nM ASOs and 40nM siRNAs using 4ul DharmaFECT 1 Transfection Reagent (Dharmacon # T-2001-02) per 6-well, following manual instruction. 0.7 uM Trans-ISRIB (Sigma # 5095840001) and 5 uM Emricasan (Sigma # SML2227) together with 10 uM ROCK inhibitor Y-27632 (Stemgent) were added to improve transfection efficiency and cell survival ability (Chen et al. 2021), and removed 24 hour later. Transfected cells were FASC collected for downstream analysis 48 hours post transfection.


title: RSeT_H9,L1KD Rep1, ASO-Ctr


title: Rep3, ASO-L1+NT-siRNA


title: c1139 0 µM


title: c1139 3 µM


title: c1139 0.3 µM


title: c1139 1 µM


title: Rep2, ASO-L1+TPRX1-siRNA


title: Rep2, ASO-L1+NT-siRNA

description:
RSeT+DT_H9,hL1KD+siRNA,raw_counts,rmDup.txt
RSeT+DT_H9,hL1KD+siRNA,log2Nom_counts_BatchCo,cutoff=0.2.txt
RSeT+DT_H9,L1KD.H3XYsi_L1KD.NT.siRNA_cutoff=0.2.txt


title: c1120 0 µM


title: Rep1, ASO-L1+TPRX1-siRNA

description:
RSeT+DT_H9,hL1KD+siRNA,raw_counts,rmDup.txt
RSeT+DT_H9,hL1KD+siRNA,log2Nom_counts_BatchCo,cutoff=0.2.txt
RSeT+DT_H9,L1KD.TP53si_CtrA.NTsi_cutoff=0.2.txt


title: c1120 1 µM


title: c1120 3 µM


title: RSeT H9, rep3  LMNB1-dam

data_processing:
the raw sequencing datas were processed using bwa, then filtered using samtools 1.10 (by “samtools view -b -F 4 -q 10”) to generate bam files.
The bam files were processed with Epic2 to call the LADs with parameters bin_size=10000, gap=10.
The final_LADs files were called if two of three applicated samples were called in the NADs.
Assembly: hg38
Supplementary files format and content: bed

growth_protocol: Naïve and primed H9 hES cells maintained in RSeT and mTeSR, respectively, following manual instruction.

extract_protocol:
genomic DNA was extracted the ISOLATE II Genomic DNA Kit (Bioline # BIO-52066) following manual instructions
Library construction mostly followed the DamID sequencing protocol by Leemans et al. 2019 with minor changed descried by van Schaik et al. 2020 in the pA-DamID sequencing protocol. More protocol details are described in the methods of this study.

tag: cell state

value: Naïve

tag: protocol


title: c1120 0.3 µM


title: Rep1, ASO-L1+NT-siRNA

description:
RSeT+DT_H9,hL1KD+siRNA,raw_counts,rmDup.txt
RSeT+DT_H9,hL1KD+siRNA,log2Nom_counts_BatchCo,cutoff=0.2.txt
RSeT+DT_H9,L1KD.TPRX1si_CtrA.NTsi_cutoff=0.2.txt

value: Human embryonic stem cells


title: c1102 0 µM


title: RSeT H9, rep3   Dam-only

value: Dam-only


title: c1159 3 µM


title: c1159 1 µM


title: c1102 3 µM


title: Rep1, ASO-Ctr+NT-siRNA

description:
RSeT+DT_H9,hL1KD+siRNA,raw_counts,rmDup.txt
RSeT+DT_H9,hL1KD+siRNA,log2Nom_counts_BatchCo,cutoff=0.2.txt
RSeT+DT_H9,L1KD.NTsiRNA_CtrA.NTsi_cutoff=0.2.txt

value: ASO-Ctr+NT-siRNA


title: c1159 0 µM


title: RSeT H9, rep2  LMNB1-dam


title: c1102 0.3 µM


title: Rep3, ASO-Ctr+NT-siRNA


title: H3K27me3_RSeT+DT_rep1

tag: treatment


title: RSeT media Rep4, ASO-L1

description:
RSeT+DT_H9,hL1KD-raw_counts,rmDup.txt
RSeT+DT_H9,hL1KD-log2Nom_counts,cutoff=0.2_BatchCo.txt
RSeT+DT_H9,ASO_sO-L1intORF,DEG_cutoff=0.2.txt

extract_protocol:
RNA extraction was performed using the RNeasy mini kit (QIAGEN), according to the manufacturer’s instructions.
80-130ng equal volume RNA each sample was used to prepare sequencing library. The cDNA library was prepared with NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB #  E7490S) and NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB # E7760L), following the manual instruction. Library cDNA were equally pooled at 10 nM for sequencing.


title: RSeT H9, rep2  Dam-only


title: RSeT media Rep4, SO-L1


title: c1324 3 µM


title: c1324 0.3 µM


title: Rep2, ASO-Ctr+NT-siRNA

description:
RSeT+DT_H9,hL1KD+siRNA,raw_counts,rmDup.txt
RSeT+DT_H9,hL1KD+siRNA,log2Nom_counts_BatchCo,cutoff=0.2.txt
RSeT+DT_H9,L1KD.TP53si_L1KD.NT.siRNA_cutoff=0.2.txt


title: c1324 0 µM


title: RSeT H9, rep1  LMNB1-dam


title: c1302 3 µM


title: RSeT media Rep4, ASO-Ctr


title: RSeT H9, rep1  Dam-only


title: RSeT media Rep3, ASO-L1


title: c1302 0.3 µM


title: c1434_2 3 µM


title: Primed H9, rep3   LMNB1-dam

value: Primed


title: RSeT media Rep3, SO-L1


title: c1302 0 µM

value: Ventricular hiSPC-CMs


title: Primed H9, rep3  Dam-only


title: c1102 1 µM


title: c1434_2 0.3 µM

value: iCell


title: RSeT media Rep3, ASO-Ctr


title: c1434_2 1 µM

value: Resistant


title: Primed H9, rep2    LMNB1-dam


title: c1434_2 0 µM


title: c1324 1 µM

value: UTH


title: c1434_1 3 µM


title: RSeT media Rep2, ASO-L1


title: Primed H9, rep2 Dam-only


title: RSeT media Rep2, SO-L1


title: c1434_1 0.3 µM


title: c1434_1 1 µM


title: c1434_1 0 µM


title: RSeT media Rep2, ASO-Ctr


title: c1302 1 µM


title: c1060 3 µM


title: RSeT media Rep1, ASO-L1


title: Primed H9, rep1 Dam-only


title: c1060 1 µM


title: granulocyte-monocyte progenitors, sleep fragmentation+myocardial infarction, rep3

city: Shanghai

first: Peinan

last: Ju

address: 301 Middle Yanchang Road

department: Department of Cardiology,

institute: Shanghai Tenth People’s Hospital, School of Medicine, Tongji University

data_processing:
Illumina Casava1.7 software used for basecalling.
Raw reads of fastq format were firstly processed using fastp and the low quality reads were removed to obtain the clean reads.
The clean reads were mapped to the reference genome using HISAT2. FPKM of each gene was calculated and the read counts of each gene were obtained by HTSeq-count
Assembly: GRCm39
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

molecule: polyA RNA

source_name: bone marrow

extract_protocol:
Total RNA was extracted using the QIAGEN RNeasy Micro Kit (Hilden, Germany) according to the manufacturer’s protocol.
The libraries were constructed using VAHTS Universal V6 RNA-seq Library Prep Kit according to the manufacturer’s instructionsThe libraries were constructed using VAHTS Universal V6 RNA-seq Library Prep Kit according to the manufacturer’s instructions

tag: tissue

value: bone marrow

value: granulocyte-monocyte progenitors

tag: genotype

value: WT

value: sleep fragmentation + myocardial infarction


title: GWI Colon Tissue Replicate 8

city: College Station

first: Claudia

last: Collier

address: 3120 TAMU

institute: Texas A&M University

data_processing:
sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36.
Mapped to mus musculus (GRCm38) usign STAR aligner v.2.5.2b
Read counts and normalization was performed with DESeq2 (R package)
Assembly: GRCm38
Supplementary files format and content: tab-deliminating text file contains raw counts for each sample

source_name: Colon

extract_protocol:
RNA was extracted using Qiagen Rneasy extraction kit
RNA libraries for RNA-seq were prepared by Azenta life Sciecnes

treatment_protocol: C57BL/6 male mice (32-34 weeks old) were given 2mg/kg of PB oraly through drinking water for 7 days. Then after 7 days of PB exposure, PB was removed from the water and mice were maintained till 30 days.

value: Colon

value: GWI


title: granulocyte-monocyte progenitors, sleep fragmentation+myocardial infarction, rep2

tag: cell type


title: c1060 0 µM

value: Female


title: granulocyte-monocyte progenitors, sleep fragmentation+myocardial infarction, rep1


title: Primed H9, rep3  Nucleolar DNA

data_processing:
the raw sequencing datas were processed using bwa, then filtered using samtools 1.10 (by “samtools view -b -F 4 -q 10”) to generate bam files.
The bam files were processed with Epic2 to call the NADs with parameters bin_size=10000, gap=5.
The final_NADs files were called if two of three applicated samples were called in the NADs.
Assembly: hg38
Supplementary files format and content: bed
Library strategy: NAD-seq

extract_protocol:
DNA were extracted with the TakaRa NucleoBond AGX-20 columns (TakaRa # 740544) and corresponding NucleoBond® Buffer Set III (TakaRa # 740603), following the manual instructions.
Libraries were constructed using Illumina`s TruSeq DNA PCR-free Library Preparation kit (Illumina # 20015962), and 350 bp fragments were sonicated and size-selected by sample-purifying beads following manual instruction.
DNA PCR-free Library

tag: cell line

tag: fraction

value: nucleolar DNA


title: GWI Colon Tissue Replicate 7


title: Rep2, ASO-L1

description:
Primed_H9,hL1KD,raw_counts_rmDup.txt
Primed_H9,hL1KD,log2Nom_counts,cutoff=0.5_BatchCo.txt
Primed_H9,hL1KD,ASO_sO-DEG,Cutoff=0.5.txt

data_processing:
RNA-seq reads were quality-checked and trimmed using Trim Galore! v0.4.0
The the trimmed reads were aligned to the hg19 with TopHat2 v2.0.13, which generated bam. files
FeatureCounts function from the subread package (v1.5.0) was applied to count reads of each gene to get the raw counts table.
Assembly: hg19

growth_protocol: H9 hES cells were cultured in mTeSR media (STEM CELL) following manual instruction.Clls were transfected and maintained in mTeSR.

extract_protocol:
RNA extraction was performed using the Direct-zol RNA Miniprep Kits (Zymo), according to the manufacturer’s instructions.
80-130ng equal volum RNA each sample was used to prepare sequencing library. The cDNA library was prepared with NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB #  E7490S) and NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB # E7760L), following the manual instruction.

treatment_protocol: Cells were transfected with 25 nM ASOs using 4ul Lipofectamine Stem Transfection Reagent (Thermo Fisher Scientific) per 6-well, following manual instruction. 0.7 uM Trans-ISRIB (Sigma # 5095840001) and 5 uM Emricasan (Sigma # SML2227) together with 10 uM ROCK inhibitor Y-27632 (Stemgent) were added to improve transfection efficiency and cell survival ability (Chen et al. 2021), and remove 24 hour later. Transfected cells were collected for down stream analysis 48 hours post transfection.


title: GWI Colon Tissue Replicate 6


title: GWI Colon Tissue Replicate 5


title: Rep2, sO-L1


title: RSeT media Rep1, ASO-Ctr

value: ASO-Ctr


title: Primed H9, rep1  LMNB1-dam

value: Human embryonic stem cells


title: GWI Colon Tissue Replicate 4


title: Primed H9, rep3 Whole-cell DNA

value: whole-cell DNA


title: granulocyte-monocyte progenitors, control+myocardial infarction, rep1

value: myocardial infarction


title: granulocyte-monocyte progenitors, control+myocardial infarction, rep2


title: Primed H9, rep2 Nucleolar DNA

value: Primed


title: GWI Colon Tissue Replicate 3


title: Rep2, ASO-Ctr


title: granulocyte-monocyte progenitors, control+myocardial infarction, rep3


title: Primed H9, rep2   Whole-cell DNA


title: Rep1, ASO-L1


title: c1078_717 0 µM

value: Ventricular hiSPC-CMs

value: UAB

value: Sensitive


title: GWI Colon Tissue Replicate 2


title: c1060 0.3 µM

value: UTH

value: Resistant


title: Rep1, sO-L1


title: RSeT media Rep1, SO-L1


title: Liver, AAV-scramble, Con A 6h

first: Wenyu

last: Tian

address: No. 38 Xueyuan Road, Haidian District

description: 10x Genomics

data_processing:
The Cell ranger software pipeline (version 6.0.1) provided by 10xGenomics was used to demultiplex cellular barcodes,map reads to the transcriptome, control quality and generate quantitative matrix.
The R package Seurat (version 4.0.3) was used for generation of Seurat object.
The count matrix was normalized with NormalizeData function.
tSNE and UMAP were performed by R package Seurat (version 4.0.3).
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Liver

extract_protocol:
Single cells were mixed with Gel Beads, Partitioning Oil and glycerol, using for preparation of GEMs with ChromiumTM Next GEM Chip G Single Cell Kit. The GEMs were subjected to RT-PCR, and the products were purified with Dynabeads, followed by cDNA amplification.
RNA libraries were prepared with ChromiumTM Next GEM Single Cell 3' GEM, Library & Gel Bead Kit v3.1 according to the manufacturer's protocol.
10x scRNA-Seq

value: Liver

value: infection of AAV-scramble, ConA (i.v)


title: GWI Colon Tissue Replicate 1


title: Liver, AAV-shBicd2, Con A 6h

description: 10x Genomics

value: WT

value: infection of AAV-shBicd2, ConA (i.v)


title: Primed H9, rep1 Nucleolar DNA


title: Primed H9, rep1  Whole-cell DNA


title: RSeT H9, rep3 Nucleolar DNA

value: Naïve


title: FVB_SND1_KI_2

city: Houston

first: Bin

state: TX

address: 1515 Holcombe BLVD

department: epigenetics and molecular carcinogenesis

institute: University of Texas MD Anderson Cancer Center

data_processing:
Tophat2 and bowtie2 to map the raw reads to mouse reference (GRCm38)
read count for genes by featureCount
Assembly: GRCm38
Supplementary files format and content: excel file

growth_protocol: All mice were housed in modified-barrier and given normal chow with 12hr light cycles. Tissues were harvested together from male mice at 60 days old.

extract_protocol:
Total RNA was harvested using manufacture recommendations for TriZol reagent (Ambion, cat# 15596026), and subject to a second round of isopropanol cleanup to incrase RNA purity.
Library was prepared by Medgenome using Illumina TruSeq stranded mRNA kit.

value: hepatocyte

value: SND1 KI


title: FVB_SND1_KI_3


title: Control Colon Tissue Replicate 9

value: Colon

value: Control


title: Control Colon Tissue Replicate 8


title: RSeT H9, rep3   Whole-cell DNA

value: Human embryonic stem cells

value: whole-cell DNA


title: Rep1, ASO-Ctr

value: ASO-Ctr


title: organoids from caRANKvil-Tg_4

city: Vienna

first: Maria

last: Novatchkova

address: Dr Bohrgasse

country: Austria

institute: IMP/IMBA

data_processing:
RNA-seq reads were trimmed using BBDuk v38.06 (ref=polyA.fa.gz,truseq.fa.gz k=13 ktrim=r useshortkmers=t mink=5 qtrim=r trimq=10 minlength=20) and reads mapping to abundant sequences included in the iGenomes Ensembl GRCm38 bundle (mouse rDNA, mouse mitochondrial chromosome, phiX174 genome, adapter) were removed using bowtie2 v2.3.4.1 alignment.
Remaining reads were analyzed using genome and gene annotation for the GRCm38/mm10 assembly obtained from Mus musculus Ensembl release 94. Reads were aligned to the genome using star v2.6.0c and reads in genes were counted with featureCounts (subread v1.6.2) using strand-specific read counting for QuantSeq experiments (-s 1).
Assembly: mm10
Supplementary files format and content: tab-delimited text files with per gene counts

source_name: intestine

extract_protocol:
Total RNA isolation was performed using the RNA isolation kit (VBCF, Vienna) which uses a lysis step based on guanidine thiocyanate and magnetic beads applied on the KingFisher instrument.
Equivalent quantities of total RNA were used for library preparation using the Lexogen QuantSeq 3′ mRNA-Seq Library Prep Kit FWD for Illumina.
Libraries were pooled at an equimolar ratio and sequenced on an Illumina HiSeq 2500 instrument using the single-read 50-read mode.

value: intestine

value: organoids

value: caRANKvil-Tg


title: organoids from caRANKvil-Tg_3


title: FVB_SND1_KI_1


title: FVB_SND1_KO_3

value: SND1 KO


title: RSeT H9, rep2  Nucleolar DNA

value: nucleolar DNA


title: Control Colon Tissue Replicate 6


title: RSeT H9, rep1  Nucleolar DNA


title: FVB_SND1_KO_2

value: Liver


title: Control Colon Tissue Replicate 5


title: organoids from caRANKvil-Tg_1


title: Control Colon Tissue Replicate 7


title: control_organoids_4

value: control


title: RSeT H9, rep2   Whole-cell DNA


title: Control Colon Tissue Replicate 4


title: FVB_SND1_KO_1


title: RSeT H9, rep1  Whole-cell DNA


title: Control Colon Tissue Replicate 3


title: FVB_SND1_WT_3

value: WT


title: control_organoids_2


title: control_organoids_3


title: Control Colon Tissue Replicate 2


title: FVB_SND1_WT_1


title: SO_L1

data_processing:
the raw sequencing datas were processed using Cell Ranger (v7.1.0) with default parameters.
Assembly: hg38
Supplementary files format and content: mtx

extract_protocol:
6-FAM (Fluorescein) labeled ASOs were transfected in RSeT cultured ES cells with DT adding, as described above. 48 hours post transfection, single cells were suspended in sorting buffer (HBSS+2% FBS+ 25 mM HEPES) with DAPI, and immediately processed to Fluorescence-activated cell sorting (FACS) at the Sony MA900 machine. 100,000 FAM+ cells (SO-L1 and ASO-L1 transfected, respectively) were sorted to the HBSS+2%FBS buffer and kept on ice during the sorting. The sorted cells were spin-pelleted at 500x g for 4 min and resuspended with 100 ul  HBSS+2%FBS buffer, and then immediately processed on theChromium for barcoding on each sample separately, with the 10x Genomics Single Cell 3’ v3 RNA-seq kit and targeting a yield of 12,000 cells. Final libraries were sequenced on a NovaSeq6000 S1 flow cell (Illumina) and achieved for an average depth of >65,000 reads/cell.
10x Genomics Single Cell 3' v3 RNA-seq

treatment_protocol: Cells were transfected with 25 nM ASOs using 4ul Lipofectamine Stem Transfection Reagent (Thermo Fisher Scientific) per 6-well, following manual instruction. 0.7 uM Trans-ISRIB (Sigma # 5095840001) and 5 uM Emricasan (Sigma # SML2227) together with 10 uM ROCK inhibitor Y-27632 (Stemgent) were added to improve transfection efficiency and cell survival ability (Chen et al. 2021), and removed 24 hour later. Cells were collected 48 hours post transfection.


title: control_organoids_1


title: Control Colon Tissue Replicate 1


title: FVB_SND1_WT_2


title: organoids from caRANKvil-Tg_2


title: HEK293, Prm1 positive DAPI high, Hi-C

status: Public on Sep 06 2024

city: Haifa

first: Noam

last: Kaplan

address: Efron 1

country: Israel

institute: Technion - Israel Institute of Technology

data_processing:
readpair fastq files were processed using distiller-nf v0.34 to create interaction maps in mcool format.
Assembly: hg38
Supplementary files format and content: mcool, separately pooled for all Prm1 positive and all Prm1 negative samples

growth_protocol: HEK293 cells were cultured under standard conditions. Cells were maintained in Dulbecco’s Modified Eagle Medium (DMEM) supplemented with 10% fetal bovine serum (FBS) and 1% penicillin-streptomycin. Cultures were kept at 37°C in a humidified atmosphere containing 5% CO2. Cells were passaged every 2-3 days to maintain exponential growth. Cell density was monitored to ensure optimal confluency of 70-80% before transfection experiments.

extract_protocol:
Hi-C libraries were prepared using FLIE Hi-C protocol. Cells were crosslinked with 2% formaldehyde. The cells were lysed in cold lysis buffer (10 mM Tris-HCl, pH 8.0, 10 mM NaCl, 0.2% Igepal CA-630) to permeabilize the nuclei. The nuclei were digested with DpnII restriction enzyme, following by end-filling with biotin-14-dATP, dCTP, dGTP, and dTTP with Klenow. Blunt ends were ligated with T4 DNA ligase, and the formaldehyde crosslinking was reversed by proteinase K (10 mg/ml). DNA was purified using phenol-chloroform and ethanol precipitation, sonicated to an average size of 200 bp, and biotin was removed from non-ligated DNA ends with T4 polymerase. Biotinylated chimeric DNA strands were pulled down using streptavidin beads (Dynabeads C1).
Libraries were prepared using the NEBNext Ultra II DNA Library Prep Kit for Illumina according to the manufacturer’s instructions.

treatment_protocol: HEK293 cells were plated 24 hours before transfection in 10 mm plates. They were then transfected with Prm1-mCherry plasmid and incubated for 72 hours before proceeding with the Hi-C sample preparation.


title: HEK293, Prm1 positive DAPI low, Hi-C


title: UGA

city: Blacksburg

last: Sharakhova

state: VIRGINIA

address: 360 West Campus Drive

department: Entomology

institute: Virginia polytechnic institute and state university

data_processing:
The sequence quality assessment was performed using FastQC software v.0.12.1
Juicer Pipeline was used to build the contact matrices and Hi-C heatmaps
Assembly: AaegL5
Supplementary files format and content: hic files include contact meatices and Hi-C heatmaps
Supplementary files format and content: text files include experiment description for hic files

organism: Aedes aegypti

source_name: 2-5 day Adult

extract_protocol:
The proximally-ligated DNA is prepared with Arima-HiC+ for High Coverage kit (Arima Genomics)
Libraries are prepared with Arima-HiC+ for High Coverage kit (Arima Genomics)

value: 2-5 day Adult

tag: strain

value: UGA

tag: Sex

value: male


title: RU3

source_name: 15-18h Embryonic tissue

value: 15-18h Embryonic tissue

value: pooled male and female


title: PKT

value: PKT


title: SHM

value: SHM


title: T51


title: MONT

value: MONT


title: ORL

value: ORL


title: MIN

value: MIN


title: NGO

value: NGO


title: M69


title: OHI

value: OHI


title: OGD

value: OGD


title: LVP

value: LVP


title: ASO_L1

value: Human embryonic stem cells


title: KAK

value: KAK


title: K27


title: K2


title: GUER

value: GUER


title: FCV

value: 2-5 day Adult

value: FCV


title: C62

value: male


title: F54


title: TPW 60blood

type: genomic

city: New York

first: Michael

last: Corley

state: NY

address: 413 East 69th Street

department: Medicine, Division of Infectious Diseases

institute: Weill Cornell Medicine

description: BuffyCoat/DNA

hyb_protocol: Samples were processed according to the Illumina Infinium HumanMethylationEPIC BeadChip (Illumina) protocol.

scan_protocol: Illumina Infinium HumanMethylationEPIC protocol. Scanned using Illumina HiScan System.

data_processing:
IDAT Data loaded into R using The Chip Analysis Methylation Pipeline (ChAMP) and normalized using BMIQ method.
The NHLBIPowell.csv contains normalized average beta values.

label: Cy5 and Cy3

source_name: Buffy Coat

label_protocol: Illumina Infinium protocol. Cy5 and Cy3

extract_protocol: Genomic DNA was extracted from FACS sorted cells in RLT buffer using the Qiagen Allprep Universal DNA/RNA kit according to manufacturer's instructions. DNA was bisulfite converted using the Zymo EZ DNA methylation kit.

value: Female

value: BuffyCoat

tag: disease state

value: Control

tag: group


title: TPW 59blood

description: BuffyCoat/DNA


title: AWK

value: AWK


title: TPW 57blood

description: BuffyCoat/DNA


title: TPW 55blood

description: BuffyCoat/DNA


title: TPW 56blood

description: BuffyCoat/DNA


title: TPW 54blood

description: BuffyCoat/DNA


title: TPW 53blood

description: BuffyCoat/DNA


title: TPW 58blood

description: BuffyCoat/DNA


title: TPW 52blood

description: BuffyCoat/DNA


title: TPW 48blood

description: BuffyCoat/DNA


title: TPW 47blood

description: BuffyCoat/DNA


title: TPW 50blood

description: BuffyCoat/DNA


title: TPW 46blood

description: BuffyCoat/DNA


title: TPW 40blood

description: BuffyCoat/DNA


title: TPW 45blood

description: BuffyCoat/DNA


title: TPW 44blood

description: BuffyCoat/DNA


title: TPW 42blood

description: BuffyCoat/DNA


title: TPW 43blood

description: BuffyCoat/DNA


title: TPW 49blood

description: BuffyCoat/DNA


title: TPW 51blood

description: BuffyCoat/DNA


title: TPW 38blood

description: BuffyCoat/DNA


title: TPW 39blood

description: BuffyCoat/DNA


title: B53


title: TPW 35blood

description: BuffyCoat/DNA


title: TPW 34blood

description: BuffyCoat/DNA

value: Male


title: TPW 36blood

description: BuffyCoat/DNA


title: TPW 37blood

description: BuffyCoat/DNA


title: TPW 33blood

description: BuffyCoat/DNA


title: TPW 31blood

description: BuffyCoat/DNA


title: TPW 28blood

description: BuffyCoat/DNA


title: TPW 27blood

description: BuffyCoat/DNA


title: TPW 29blood

description: BuffyCoat/DNA


title: TPW 30blood

description: BuffyCoat/DNA


title: TPW 26blood

description: BuffyCoat/DNA


title: TPW 25blood

description: BuffyCoat/DNA


title: TPW 23blood

description: BuffyCoat/DNA


title: TPW 20blood

description: BuffyCoat/DNA


title: TPW 24blood

description: BuffyCoat/DNA


title: TPW 21blood

description: BuffyCoat/DNA


title: TPW 41blood

description: BuffyCoat/DNA


title: TPW 18blood

description: BuffyCoat/DNA


title: TPW 17blood

description: BuffyCoat/DNA


title: TPW 14blood

description: BuffyCoat/DNA


title: TPW 13blood

description: BuffyCoat/DNA


title: TPW 15blood

description: BuffyCoat/DNA


title: TPW 16blood

description: BuffyCoat/DNA


title: TPW 12blood

description: BuffyCoat/DNA


title: TPW 10blood

description: BuffyCoat/DNA


title: TPW 9blood

description: BuffyCoat/DNA


title: TPW 11blood

description: BuffyCoat/DNA


title: TPW 6blood

description: BuffyCoat/DNA


title: TPW 32blood

description: BuffyCoat/DNA


title: TPW 8blood

description: BuffyCoat/DNA


title: TPW 7blood

description: BuffyCoat/DNA


title: TPW 4blood

description: BuffyCoat/DNA


title: TPW 3blood

description: BuffyCoat/DNA


title: TPW 2blood

description: BuffyCoat/DNA


title: TPW 22blood

description: BuffyCoat/DNA


title: TPW 1blood

description: BuffyCoat/DNA


title: Hap1, 10000 cells, Hi-C

data_processing:
readpair fastq files were processed using distiller-nf v0.34 to create interaction maps in mcool format.
Assembly: hg38, mm10
Supplementary files format and content: mcool for 5k hap1, 10k hap1, 4x50k mouse neurons (pooled), 1x50 mouse neurons (WT4/Rep1)

treatment_protocol: Mouse forebrain was dissected and minced using homogenizer in 5 ml homogenization buffer (0.25M sucrose, 25mM KCl, 5mM MgCl2, 20mM Tricine-KOH, 1mM DTT, 0.15mM spermine, 0.5mM spermidine), 7 µl RNase Inhibitor (Promega N2611) and 300 µl 5% IGEPAL. The sample was filtered through a 40 µm strainer, mixed with 5 ml of 50% iodixanol (Sigma D1556), underlaid with a gradient of 30% and 40% iodixanol, and centrifuged at 4,600g for 1 hour in a swinging bucket centrifuge at 4°C. Nuclei were collected at the 30%-40% interface. The nuclei were transferred to a 2 ml tube and centrifuged 10 min at 1,000g and 4°C. Nuclei were then FACS-sorted into 4 tubes of 50,000 nuclei each. Finally, nuclei were transferred to freezing buffer (0.32M sucrose, 5mM CaCl2, 0.1mM EDTA, 10mM tris HCl, 3mM Mg(Ac)2) and frozen in -80°C.  5,000 and 10,000 Hap1 human haploid cells (Horizon Discovery) were FACS-sorted to ensure accurate cell counts following formaldehyde crosslinking and quenching as described in the FLIE Hi-C protocol.


title: TPW 19blood

description: BuffyCoat/DNA


title: Hap1, 5000 cells, Hi-C


title: Sample_30_AD

city: Stanford

first: JAUME

last: FORES MARTOS

state: California

address: 300 Pasteur Drive

department: Pathology

institute: Stanford

data_processing:
The paired-end raw sequence reads were preprocessed using the Kallisto bustools package (kbpython:0.26.0). An alignment index was constructed based on the human reference pre-mRNA (GRCh38, Ensembl 105).  Using the Lamanno workflow, we generated separate count matrices for spliced and unspliced transcripts. These matrices were then merged to obtain the total nucleus count matrix. Downstream analysis, including quality control, integration, cell type annotation, and differential gene expression, was performed using the nuclear transcript counts. Empty droplets were removed by comparison with ambient RNA levels using the DropletUtils package. Droplets with FDR <0.05 were removed, and 80,864 non-empty droplets were retained. To identify potential doublets, we used the DoubletFinder package version 4.2. An average doublet rate of 2.53% per sample was detected. The identified doublets were labeled and retained during batch correction and data integration. Following clustering and major cell type annotation, we identified two clusters of doublets based on high doublet scores and the presence of markers specific to more than one major cell type. These clusters, containing 721 nuclei, were excluded from downstream analysis. Four additional clusters driven by low gene count nuclei, containing 15,668 nuclei, were also excluded from the analysis. We used Scanpy version 3.9.1 to analyze raw count data. First, nuclei expressing less than 100 genes were removed from the analysis. Counts were normalized and log transformed. Highly variable genes were identified using default parameters and a dispersion threshold of 0.5. Principal Component Analysis (PCA) was applied to reduce dimensionality, and the first 50 principal components were computed. Samples were integrated using Harmony with the Donor used as batch effect. After integration, the neighborhood graph was computed employing 20 PCs and 15 neighbors. Clustering was carried out employing the Leiden algorithm with a resolution parameter of 1.0. Marker genes for each cluster were determined using the Wilcoxon rank sum test with a significance threshold of adjusted p-value (padj) < 0.05. We then applied a more stringent cutoff of 400 for the minimum number of UMIs per nuclei. The final integrated dataset included 58,447 nuclei (8,724 neuronal and 49,723 non-neuronal) for downstream analysis.
Assembly: GRCh38, release-105
Supplementary files format and content: Raw counts, normalized counts, metadata, dimensionality reduction, integration and clustering, cell-type annotations

source_name: Prefrontal cortex

extract_protocol:
We isolated nuclei from fresh-frozen brain tissue blocks obtained from the ALSP donor (white and gray matter from prefrontal cortex, and white matter from medial temporal lobe, parietal cortex, and occipital cortex), and controls (white and gray matter from prefrontal cortex). The gray or white matter was dissected under a stereomicroscope, and then chopped it into small pieces (< 1 mm³) with a chilled razor blade. For tissue homogenization, a Kimble Kontes all-glass tissue grinder was utilized (Kimble, 885300-0007). Each tissue sample was dissociated using 2.4 mL of homogenization buffer containing 10 mM Tris pH 8, 5 mM MgCl2, 25 mM KCl, 250 mM sucrose, 1 μM DTT, 0.5x protease inhibitor (cOmplete, Roche #4693159001), 0.2 U/μL RNase inhibitor, and 0.1% Triton X-100. The homogenates were subsequently filtered through a 40-μm cell strainer, transferred into 1.5-mL Eppendorf tubes, and centrifuged at 1000 ×g for 8 minutes at 4°C. The supernatant was aspirated and discarded, and the pellets were resuspended in 450 μL of cold homogenization buffer. Further clean-up was carried out using iodixanol gradient centrifugation. An equal volume (450 μL) of 50% v/v iodixanol solution (41.25 mM sucrose, 24.75 mM KCl, 4.95 mM MgCl2, 9.9 mM Tris pH 8, 50% w/v iodixanol) was added to the homogenate and gently mixed with a pipette. The mixture was then transferred to a 2-mL Eppendorf tube containing 900 μL of cold 29% iodixanol solution (129.17 mM sucrose, 77.5 mM KCl, 15.5 mM MgCl2, 31 mM Tris pH 8, and 29% w/v iodixanol) by slow layering on the top. The tubes were centrifugated at 13,500 ×g for 20 minutes at 4°C, resulting in the sedimentation of nuclei at the bottom. The supernatant and top layer of myelin and cell debris were removed and discarded. The nuclei pellets were then detached with a small amount (~50 μL) of immunostaining buffer (0.1 M PBS; pH 7.4, 0.5% bovine serum albumin [BSA], 5 mM MgCl2, 2 U/mL DNAse I, 0.2 U/μL RNase inhibitor), transferred to clean tubes, and gently resuspended in a total volume of 200 μL of immunostaining buffer. After a 15-minute incubation with immunostaining buffer at 4°C, with gentle rocking, primary antibodies (NeuN; 1:1000, Millipore cat#MAB377; and/or PAX6; 1:500, Biolegend, 901301) were added, and the suspension was further incubated for 40 minutes at 4°C with gentle rocking. Subsequently, an equal volume (500 μL) of immunostaining buffer was added, and the tubes were inverted several times before being centrifuged at 500 ×g for 5 minutes at 4°C. The supernatant was removed, and the pellets resuspended in 600 μL of immunostaining buffer. Secondary antibodies (Alexa Fluor 488, Alexa Fluor 647) and a nuclear stain (Hoechst 34580; 1:1,000 of 2.5 mg/ml stock, Invitrogen cat# H21486) were subsequently added, and the solutions incubated for 30 minutes at 4°C with gentle rocking. Microscopic evaluation of the number and morphology of the nuclei was conducted after each critical step and immediately before FANS. FANS was employed to enrich single nuclei from glia. We used a Sony SH800 cell sorter with a 100-μm microfluidics sorting chip. The primary laser, at 488 nm, was utilized for the generation of forward scatter (FSC) and back scatter (BSC). Secondary lasers emitting at 405, 488, and 638 nm were utilized to detect Hoechst 34580, Alexa Fluor 488, and Alexa Fluor 647, respectively. The FSC versus BSC gates were set with permissive limits, discarding the smallest debris and largest particles. Hoechst 34580 fluorescence was used to discriminate single nuclei from doublets and clumps. We sorted Hoechst 34580 positive singlets from ALSP white matter. For ALSP gray matter, we sorted non-neuronal (NeuN-negative) nuclei. For healthy and AD control tissue, we sorted the PAX6-positive, NeuN-negative population singlets. Nuclei were collected in collection buffer (0.1 M PBS pH 7.4, 0.1 U/μL RNase inhibitor, 1% BSA) into BSA-coated Eppendorf tubes.
snRNAseq of postmortem human brain nuclei was conducted using the 10x Genomics Chromium Single Cell 3’ v3 assay. The input single nuclear suspensions were centrifuged at 400 ×g for 5 min at 4°C to achieve a concentration of ~350 nuclei per μL, determined using a hemocytometer. On average, ~12,500 nuclei were loaded to capture around 5,000 nuclei per sample, with an expected capture efficiency of ~40%. cDNA amplification and library construction were performed following the manufacturer’s instructions. The paired-end libraries were sequenced on Novaseq 6000. A total of 12 samples were sequenced in 3 batches. For each sequencing batch, the concentration of each sample was normalized to the total number of nuclei to ensure similar numbers of reads per nucleus. Nuclei were sequenced to a depth of ~75,000 reads per nucleus.

tag: assay

tag: donor

tag: brain region

value: Prefrontal cortex

value: gm/wm

tag: rin

tag: sort

value: III

value: Diffuse plaques

tag: age


title: Sample_108_Control


title: Sample_112_Control

value: I


title: Sample_116_Control


title: THP-1, H37Rv, hour2

city: Wuhan

first: Xianglin

last: Peng

address: No.215, Zhongshan Road, Qiaokou District

department: Department of Orthopedics

institute: Huazhong University of Science and Technology

data_processing:
DESeq R package (1.8.3)
Mapped small RNA tags were used to looking for known miRNA. miRBase20.0 was used as reference, modified software mirdeep2 (Friedlander et al., 2011) and srna-tools-cli were used to obtain the potential miRNA and draw the secondary structures. Custom scripts were used to obtain the miRNA counts 3 as well as base bias on the first position of identified miRNA with certain length and on each position of all identified miRNA respectively.
The characteristics of hairpin structure of miRNA precursor can be used to predict novel miRNA. The available software miREvo (Wen et al., 2012) and mirdeep2 (Friedlander et al., 2011) were integrated to predict novel miRNA through exploring the secondary structure, the Dicer cleavage site and the minimum free energy of the small RNA tags unannotated in the former steps. At the same time, custom scripts were used to obtain the identified miRNA counts as well as base bias on the first position with certain length and on each position of all identified miRNA respectively.
For the samples with biological replicates:  Differential expression analysis of two conditions/groups was performed using  the DESeq R package (1.8.3). The P-values was adjusted using the Benjamini  & Hochberg method. Corrected P-value of 0.05 was set as the threshold for  significantly differential expression by default.
For the samples without biological replicates:  Differential expression analysis of two samples was performed using the  DEGseq (2010) R package. P-value was adjusted using qvalue (Storey et al,  2003). qvalue < 0.01 and |log2(foldchange)| > 1 was set as the threshold  forsignificantly differential expression by default.
Assembly: ensembl_109_homo_sapiens_grch38_toplevel
Supplementary files format and content: Readcount_TMP contains readcounts and TPM normalized values for both sets of samples
Supplementary files format and content: AvsB.Differential_analysis_results contains the normalized readcount and P values

growth_protocol: THP-1 cells were obtained from the China Center for Type Culture Collection (CCTCC, GDC0100) and cultured in RPMI-1640 medium (Gibco, Thermo Fisher Scientific, USA) containing 10% fetal bovine serum (FBS) (Gibco, Thermo Fisher Scientific, USA) at 37°C with 5% CO2 for passaging.

extract_protocol:
Total RNA was used as input material for the RNA sample preparations.
Sequencing libraries were generated using NEB Next® Multiplex Small RNA Library Prep Set for Illumina® （NEB  E7300L）.

treatment_protocol: THP-1 were added to 6-well plates and cultured for 24 h, they were washed three times with phosphate buffer solution (PBS), and bacterial suspensions at Multiplicity of infection (MOI) = 10 were added dropwise to each well (H37Rv-to-cell ratio of 10:1), and incubated at 37°C with 5% CO2. Cells were collected after H37Rv infection for 2h replacing the complete medium supplemented with gentamicin and continuing the culture for 24h.

value: WT


title: Sample_100_Control


title: Sample_94_Control


title: Sample_46_AD

value: IV


title: NHR2del fusion positive megakaryoblasts in vitro culture replicate 1

city: Palo Alto

first: Tanja

middle: A

last: Gruber

state: CA

address: 1000 Welch Road Suite 300

department: Pediatrics

institute: Stanford University

description: NHR2del fusion positive megakaryoblasts in vitro culture rabbit IgG IP

data_processing:
(DNA) Raw CUT&RUN-seq FASTQ files were aligned using Basepair (aligner Bowtie and reference genome hg19). MACS2 (v2.2.71) was used to call peaks (using parameters --shift 0 -m 5 50 -g 2700000000 --pvalue 1e-3 --call-summits -B --SPMR) against IgG control for each Sample. (Samples lines 29 - 48)
(RNA) RNA-seq reads in BAM format (aligned to hg19 using STAR v2.3.0e) were converted to raw counts uing HTSeq (htseq-count, v0.11.2). Raw counts were processed for differential expression testing using DESeq2 (v1.32.0) R package installed in R v4.1, using default settings. (Sample lines 55-83)
(RNA) For RNA-seq reads from the NHR2del experiment, raw RNA-seq reads in FASTQ format were pre-processed (trimmed using Trimmomatic v0.39) before aligned to hg38 using STAR (v2.7.1a). Raw counts were processed for differential expression testing using DESeq2 (v1.32.0) R package installed in R v4.1, using default settings. (Sample lines 49 - 54)
Assembly: hg19, hg38
Supplementary files format and content: (DNA) tab-delimited MACS2 output for each Sample / (RNA) tab-delimited raw gene counts for each Sample
Library strategy: CUT & RUN

source_name: Megakaryoblasts

extract_protocol:
EpiCypher CUTANA ChIC/CUT&RUN Kit (DNA) / Trizol extraction (RNA)
CUT&RUN sequencing was performed according to the manufacturer's instructions using the DNA library prep (NEBNext/ChIPSeq) kit / RNA sequencing was performed according to the manufacturer's instructions using the low input RNA (Ovation/NEB) library prep kit

value: Megakaryoblasts


title: NHR2del fusion positive megakaryoblasts in vitro culture replicate 3

description: NHR2del fusion positive megakaryoblasts in vitro culture TY IP biological replicate 2


title: TPW 5blood

description: BuffyCoat/DNA


title: NHR2del fusion positive megakaryoblasts in vitro culture replicate 2

description: NHR2del fusion positive megakaryoblasts in vitro culture TY IP biological replicate 1


title: sk-mel-2 cell, regorafenib-3

city: wuhan

first: xiu

middle: yun

last: xuan

address: 1095 Emancipation Avenue

department: Department of Dermatology

institute: Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology

data_processing:
Illumina Casava2.19 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using hisat2 v2.0.5 with parameters hisat2 [options]* -x <hisat2-idx> {-1 <m1> -2 <m2> | -U <r> | --sra-acc <SRA accession number>} [-S <hit>]
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Trapnell,Cole et al., Transcript assembly and quantification by RNA-seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat. Biotechnol, 2010. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: homo_sapiens_Ensembl_97
Supplementary files format and content: gene_count.txt
Supplementary files format and content: gene_fpkm.txt

source_name: skin

growth_protocol: sk-mel-2 cell was maintained in RPMI supplemented wth 10% fetal bovine seum (FBSl and antbioics in humidifed almosphere with 5% C02 at 37℃

extract_protocol:
Total amounts and integrity of RNA were assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system
mRNA was purified from total RNA by using poly-T oligo-attached magnetic beads. Then PCR amplification, the PCR product was purified by AMPure XP beads, and the library was finally obtained.

treatment_protocol: sk-mel-2 cell was treated regorafenib (10μM) for 24h

value: skin

value: melanoma cells

value: regorafenib


title: sk-mel-2 cell, regorafenib-2


title: sk-mel-2 cell, DMSO-3

value: DMSO


title: sk-mel-2 cell, regorafenib-1


title: THP-1, Control, hour2


title: Heart_2_bulkRNA-seq Patient_18

city: Aachen

first: Tore

last: Bleckwehl

address: Pauwelsstrasse 30

department: Klinik fuer Nieren- und Hochdruckkrankheiten, rheumatologische und immunologische Erkrankungen (Medizinische Klinik II)

country: Germany

institute: RWTH Uniklinik

data_processing:
Sequencing reads from bulkRNA-seq were aligned with STAR to the same reference genome used for the single-cell RNA-seq and variants were called with freebayes using the following parameters: -iXu --min-mapping-quality 30 --min-base-quality 10 --min-coverage 5.
Assembly: hg38
Supplementary files format and content: VCF files with called SNPs

source_name: Heart

extract_protocol:
For snap frozen tissue samples, samples were shredded in RNeasy lysis buffer in a Mixer Mill prior RNA Isolation. For PBMC samples were lysed with RNeasy lysis buffer. Subsequently, RNA was extracted for both tissue and PBMC samples using the RNeasy Mini Kit (74106, Qiagen) according to the manufacturer’s instructions.
RNA libraries were prepped with the NEBNext Ultra II Directional RNA Library Prep Kit (NEB, E7760L) according to the manufacturer's instructions.

value: Heart


title: Kidney_bulkRNA-seq_Patient_21

source_name: Kidney

value: Kidney


title: Pooled scRNA-seq Kidney

description: Pooled 10X Genomics Library

data_processing:
For the demultiplexing of CellPlex and Hashtag based sample labeling, sequencing reads were mapped to the reference genome GRCh38-2020-A applying the the cellranger multi pipeline (version 7.1.0) with default setting and the used sample barcodes for the corresponding tagging method
Assembly: GRCh38-2020-A
Supplementary files format and content: raw_feature_bc_matrix, multiplexing_assignment_tables

extract_protocol:
For PBMC isolation blood was collected from patients into EDTA-tubes and mixed 1:1 with PBS. EDTA-blood was then carefully layered on to Ficoll-Paque Plus (1:1,5) and centrifuged (400 G, 40 min, RT). After centrifugation the PBMC-Layer was aspirated, resuspended in FACS-Buffer (PBS, 2% FCS, 2mM EDTA) and centrifuged (300 G, 10 min, RT). The supernatant was discarded and cells were resuspended in 300 µl FACS Buffer. At this step, PBMC were counted and ~0.5x106 cells were taken for each Bulk-RNA sequencing and WES. The remaining cells were stained with CD14-PE, CD16-APC, CD4-FITC, CD8-PE Cy7 and CD19-BB700 (30 min, 4°C, protected from light). Afterwards, cells were washed once with FACS Buffer (400 g, 5 min, 4°C) before staining PBMC with a unique CellPlex-Oligo (100 µl, 5 min, RT) for each patient. Subsequently cells were washed twice, before sorting a unique PBMC population for each patient (CD14 Monocytes, CD16 Monocytes, CD4 T-Cells, CD8 T-Cells, CD19 B-Cells) using a BD FACSMelody Cell Sorter. For lymphocytes Dapi, CD16 and CD14 positive cells were excluded to avoid dead cell and monocyte contamination. For monocytes Dapi, CD4 and CD8 positive cells were excluded to avoid dead cell and lymphocyte contamination. After sorting, PBMC were pooled and immediately loaded onto a Chromium Next GEM Chip G for snRNA-seq (10x, 3’ v3.1). For heart samples, Snap frozen tissue was crushed using a mortar and pestle, resuspended in 500 µl nuclei lysis Buffer (NLB, EZ lysis Buffer NUC101, Sigma-Aldrich with 1 Tab/10 ml  of Complete Protease Inhibitor, Roche and 10 µl/ml Recombinant RNase Inhibitor 2313A, Takara Bio and 10µl/ml Superase In RNase Inhibitor, Thermofisher) and homogenized with dounce tissue grinder pestles. The homogenized solution was spun down, supernatant discarded and the pellet resuspended in 4 ml nuclei resuspension buffer (NRB, PBS, 1% BSA, 10 µl/ml Protector RNase Inhibitor, Rochel). The suspension was then filtered via a 40 µm cell strain and centrifuged (500 G, 4°C, 5 min). Supernatant was discarded, and cells resuspended in 200 µl Nuclei resuspension Buffer (NRB, PBS, 1% BSA, 10 µl/ml Protector RNase Inhibitor, Rochel) with 3 µl of a unique TotalSeq anti-Nuclear Pore Complex Antibody Hashtag-Antibody for each sample (4°C, 20 min). Subsequently samples were washed with 1 ml NRB, centrifuged (500 G, 4°C, 5 min) and resuspended in 100 µl of a unique CellPlex Oligo for each sample (RT, 5 min). Cells were washed once more with NRB (500 G, 4°C, 5 min) before proceeding to Fluorescent-activated Nuclei-sorting of DAPI positive nuclei with a Sony SH800S. 5 minutes prior to sorting nuclei were stained with DAPI (Sigma-Aldrich). After sorting, nuclei were pooled and immediately loaded onto a Chromium Next GEM Chip G for snRNA-seq (10x, 3’ v3.1).
Single cell RNA (3’ v3.1, Dual Index) and 3’ CellPlex library preparation was performed according to the manufacturer's instructions. Hashtag-Libraries were prepared as described by Stoeckius et al.


title: Kidney_bulkRNA-seq_Patient_19


title: Kidney_bulkRNA-seq_Patient_20


title: Pooled scRNA-seq Heart_2

description: Pooled 10X Genomics Library


title: Heart_2_bulkRNA-seq Patient_17


title: Kidney_bulkRNA-seq_Patient_22


title: Heart_2_bulkRNA-seq Patient_16


title: Heart_2_bulkRNA-seq Patient_14


title: Heart_2_bulkRNA-seq Patient_15


title: Heart_2_bulkRNA-seq Patient_12


title: scRNA_seq_KMT2D-KO line#1-batch3 + hWNT3A

city: Guangzhou

first: Yingying

last: Zhao

address: Kaiyuan Avenue

department: Chinese Academy of Sciences Guangzhou Branch

institute: Guangzhou Institutes of Biomedicine and Health

description: Single Cell RNA seq of KMT2D-SET-KO cell-induced organoid at D21(hWNT3A treatment)

data_processing:
The gene expression level of RNA-seq data was calculated by using  RSEM.
CUT&Tag reads were aligned to the hg38 genome using Bowtie2. Duplicate reads were removed with the function MarkDuplicates from Picard. The .bw files were generated by deepTools.
The gene expression level of scRNA-seq data was calculated by using  STAR.
The fragment files of scATAC-seq data was generated by using  Cell Ranger ATAC.
Assembly: hg38
Supplementary files format and content: .genes.results files contain the gene expression level of RNA-seq data
Supplementary files format and content: .bw files contain the CUT&Tag data that will be displayed in the Genome Browser, a web-based tool used to display a requested portion of a genome at any scale.
Supplementary files format and content: _data.tar.tar files contain the gene expression level of scRNA-seq data
Supplementary files format and content: _fragments.tsv.gz files contain the fragments of scATAC-seq data

source_name: brain organoid

growth_protocol: Cerebral organoids were generated according to the previously published protocols with dual smad inhibitors (Lancaster and Knoblich, 2014).

extract_protocol:
RNA-seq: To extract the total RNAs, organoids were collected and lysed with 1 ml TRIzol reagent (MRC, TR118-200), followed by adding 200 μL chloroform. After centrifugation (14,000 ×g for 10 min at 4°C), the total RNAs in the supernatant were precipitated with isopropanol. 1ug RNAs were subjected to RNA-seq library construction. CUT&Tag: Brain organoids at D21 were dissociated into a single-cell suspension using the Worthington Papain Dissociation System kit (Worthington, LK003153). CUT&Tag assay was performed according to the Hyperactive In-Situ ChIP Library Prep Kit for Illumina (TD901-TD902, Vazyme). scRNA-seq: Brain organoids at D21 and D30 were dissociated into a single-cell suspension using the Worthington Papain Dissociation System kit (Worthington, LK003153). snATAC-seq: Brain organoids at D21 were dissociated into a single-cell suspension using the Worthington Papain Dissociation System kit (Worthington, LK003153). Nuclei were extracted from organoid-derived single cells following Demonstrated Protocol of Nuclei Isolation for Single Cell ATAC Sequencing (10X GENOMICS).
RNA-seq: RNA Sequencing libraries were prepared according to the VAHTS mRNA-seq V3 Library Prep Kit for Illumina (NR611, Vazyme).  CUT&Tag: Library amplification was prepared using TruePrep Amplify Enzyme (TAE, Vazyme) followed by PCR purification (Vazyme). scRNA-seq: 3'-library was constructed using Chromium Single Cell Reagent Kits v2 (10X GENOMICS). snATAC-seq:Isolated nuclei were preceded to Tn5-mediated transposition, single cell barcoding, and library construction using Chromium Single Cell ATAC Reagent Kits (10X GENOMICS).

treatment_protocol: For rescue experiments, 1μM CHIR99021 (ChemBest Research Laboratories Ltd.) or PBS equivalent was added during D10 and D14

tag: time

tag: library strategy

value: scRNA-seq

tag: library source

value: TRANSCRIPTOMIC SINGLE CELL


title: scRNA_seq_HN4-batch4

description: Single Cell RNA seq of HN4 cell-induced organoid at D21

tag: genotype

tag: treatment

value: untreated


title: E7_9_9 (smallseq)

city: Stockholm

first: Cheng

address: Solnavägen 1, 171 77 Solna

department: Department of Clinical Science

country: Sweden

institute: Karolinska institute

data_processing:
SncRNA reads were processed using a modified version of the Small-Seq pipeline. First, the UMIs (8bp associated with the unique molecular identifiers) were removed from sequence reads and appended to the reads' name using umi_tools (v0.4.4). Then, cutadapt (v1.17) was used to remove adapter and polyA sequences (parameters: -e 0.1 -o 3 -m 18 -M 81 -u 2). The setting of "-M 81" was chosen because our small RNA sequencing had a maximum read length of 101 base pairs. Additionally, at least 10-base pair trimming of adapter or polyA sequences was performed to ensure that the reads originated from short transcripts.  The resulting clean reads were aligned to GRCh38-3.0.0  using bowtie (v1.0.0) with the following parameters: "-a --best --strata -v 2 -m 50 -S -q -p 2".  To avoid false positive mapping, reads with a length less than 20 base pairs and with one or more mismatches were excluded and reads with lengths between 20 and 40 base pairs and two mismatches were also filtered out. Mismatches located at the last base pair of reads were disregarded, considering the "CCA" addition in tRNA maturation and miRNA modification dynamics. In addition, unmapped reads underwent recursive soft clipping by 1 nucleotide from the 3' end and were then mapped to the reference genome using Bowtie with parameters ”-a --best --strata -v 1 -m 50 “ until the soft-clipped read length reached 3 nucleotides, the same procedure for 5’ end of reads was subsequently performed.  Any reads with a  mapping length of less than 17 base pairs were discarded. PCR amplicons were collapsed, and RNA molecules were counted using UMI-tools with the "dedup --method directional" option. Deduplicated soft-clipped reads were remapped onto the genome using the same procedure as above to recover multiple mapping information dampened by the "dedup" process. Annotation coordinates on the genome were then extracted from Mirbase V22 (miRNA), Gencode V39 (snoRNA, snRNA, rRNA, and others),  GtRNAdb V19 (tRNA), piBase V3.0 to assign the reads to their corresponding categories. The reads were assigned to each category in a hierarchical manner based on their overlap with the above annotations. If a read was mapped to more than one category, we assigned it to only one category based on the following order of priority: miRNA, rRNA, snoRNA, snRNA, tRNA, piRNA, and other types of transcripts. Subsequently, cell quality filtering was implemented based on three criteria: First, each cell required a minimum of 0.5 million sequenced reads. Second, the proportion of mitochondrial associated UMIs was required to be less than 25%. Third, the number of expressed miRNA molecules per cell was required to be more than 100. Data generated using Co-seq were only used for data integration and were excluded from downstream analysis to minimise introduction of batch differences from library preparation and as such introduce technical errors.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: embryo

extract_protocol:
Supernumerary human embryos donated to research by patients attending CReATe Fertility Centre, with study approval by Veritas IRB (protocol number 16580) and regional ethics board (2018/691-31 and 20.126) were utilised. Embryos were thawed using the Vit Kit-Thaw (FujiFilm). A total of 87 embryos were cultured from embryonic days 3-7 in a SAGE 1-step medium. Embryos were then dissociated into single cells as previously described using TrypLE enzyme solution and micromanipulation with glass capillaries. Cells were manually collected into individual 8-strip PCR tubes containing 2 uL of lysis buffer (0.13% Triton X-100, 1.33 U/ul Recombinant RNase inhibitor, 2.0 uM 5.8S rRNA-masking oligonucleotide) and stored at -80°C until further processing. To identify embryonic lineages based on transcriptomic signatures, single-cell mRNA-sncRNA Co-seq was performed as previously described and validated on mouse embryos. Briefly, individual cells were collected into 4uL of lysis buffer. After cell lysis at 72°C for 20 minutes, lysates were split into two equal 2 µL halves, with one half allocated to sncRNA sequencing and the other to SmartSeq. Each half was prepared following the original Small-seq and SmartSeq2 protocols, using 22 amplification cycles during the first PCR of SmartSeq2. This approach enabled the association of mRNA markers of cell lineage with corresponding sncRNA profiles.
Small-seq Library Preparation and Sequencing:The remaining, non-Coseq sncRNA libraries were generated using the Small-seq protocol as previously described. Briefly, cells were thawed and incubated at 72°C for 20 minutes followed by 3’ adapter ligation at 30°C for 6h followed by 4°C for 10h. Free adapters were then removed by 5’ deadenylation followed by digestion of RT primer-3’ adapter duplexes by lambda exonuclease. The 5’ adapter was ligated at 37°C for 1h, followed by reverse transcription with Superscript II (ThermoFisher Scientific) at 42°C for 1h. Two PCRs were performed, first to amplify the cDNA products (12 cycles) and second to barcode the libraries for multiplexing (12 cycles). The resulting pooled libraries (~150 nt) were processed with the DNA Clean & Concentrator (Zymo) at a 7x buffer:DNA ratio, eluted in 50 uL, analysed by 2100 Bioanalyzer (Agilent) and quantified by Qubit DNA High Sensitivity (ThermoFisher Scientific). Libraries were sequenced on either NovaSeq or NextSeq 550 100 bp SE or PE for a sequencing depth of 2 million reads per cell. During the following analysis, only the forward read was used from PE data. Co-seq to capture sncRNA and mRNA from a single-cell: Briefly, individual cells were collected into 4uL of lysis buffer. After cell lysis at 72°C for 20 minutes, lysates were split into two equal 2 µL halves, with one half allocated to sncRNA sequencing and the other to SmartSeq. Each half was prepared following the original Small-seq and SmartSeq2 protocols, using 22 amplification cycles during the first PCR of SmartSeq2. This approach enabled the association of mRNA markers of cell lineage with corresponding sncRNA profiles.

tag: tissue

value: embryo

tag: developmental stage

value: embryo in vitro day E7


title: scRNA_seq_KMT2D-KO line#1-batch3

description: Single Cell RNA seq of KMT2D-SET-KO cell-induced organoid at D21


title: sk-mel-2 cell, DMSO-2

tag: cell line

tag: cell type


title: sk-mel-2 cell, DMSO-1


title: E7_9_28 (smallseq)


title: E7_9_30 (smallseq)


title: E7_9_31 (smallseq)


title: E7_9_32 (smallseq)


title: E7_9_23 (smallseq)


title: E7_9_27 (smallseq)


title: E7_9_24 (smallseq)


title: E7_9_26 (smallseq)


title: E7_9_22 (smallseq)


title: Heart_2_bulkRNA-seq Patient_13


title: E7_9_20 (smallseq)


title: E7_9_16 (smallseq)


title: E7_9_14 (smallseq)


title: E7_9_18 (smallseq)


title: Heart_2_bulkRNA-seq Patient_11


title: E7_9_12 (smallseq)


title: E7_9_13 (smallseq)


title: E7_9_11 (smallseq)


title: E7_9_10 (smallseq)


title: E7_6_8 (smallseq)


title: E7_6_5 (smallseq)


title: E7_6_6 (smallseq)


title: E7_6_3 (smallseq)


title: E7_6_2 (smallseq)


title: E7_6_16 (smallseq)


title: E7_9_25 (smallseq)


title: E7_6_15 (smallseq)


title: E7_6_13 (smallseq)


title: E7_6_12 (smallseq)


title: E7_4_9 (smallseq)


title: E7_6_14 (smallseq)


title: E7_4_8 (smallseq)


title: E7_6_10 (smallseq)


title: E7_9_17 (smallseq)


title: E7_6_11 (smallseq)


title: E7_9_15 (smallseq)


title: E7_4_7 (smallseq)


title: E7_9_19 (smallseq)


title: E7_4_4 (smallseq)


title: E7_4_3 (smallseq)


title: E7_4_22 (smallseq)


title: E7_4_6 (smallseq)


title: E7_4_25 (smallseq)


title: E7_4_5 (smallseq)


title: E7_4_21 (smallseq)


title: E7_6_9 (smallseq)


title: E7_4_26 (smallseq)


title: E7_6_4 (smallseq)


title: E7_4_19 (smallseq)


title: E7_4_2 (smallseq)


title: E7_4_18 (smallseq)


title: E7_4_16 (smallseq)


title: E7_4_14 (smallseq)


title: E7_4_13 (smallseq)


title: E7_4_15 (smallseq)


title: E7_4_11 (smallseq)


title: E7_4_10 (smallseq)


title: E7_3_7 (smallseq)


title: E7_3_9 (smallseq)


title: E7_4_1 (smallseq)


title: E7_3_6 (smallseq)


title: E7_3_40 (smallseq)


title: E7_3_4 (smallseq)


title: E7_3_39 (smallseq)


title: E7_3_5 (smallseq)


title: E7_3_34 (smallseq)


title: E7_3_33 (smallseq)


title: E7_3_31 (smallseq)


title: E7_3_32 (smallseq)


title: E7_3_37 (smallseq)


title: E7_3_26 (smallseq)


title: E7_3_28 (smallseq)


title: E7_3_17 (smallseq)


title: E7_3_3 (smallseq)


title: E7_3_15 (smallseq)


title: E7_3_16 (smallseq)


title: E7_3_13 (smallseq)


title: E7_3_14 (smallseq)


title: E7_2_7 (smallseq)


title: E7_3_11 (smallseq)


title: E7_2_8 (smallseq)


title: E7_3_1 (smallseq)


title: E7_2_9 (smallseq)


title: E7_3_12 (smallseq)


title: E7_2_6 (smallseq)


title: E7_2_5 (smallseq)


title: E7_2_27 (smallseq)


title: E7_2_26 (smallseq)


title: E7_2_4 (smallseq)


title: E7_3_27 (smallseq)


title: E7_2_2 (smallseq)


title: E7_3_22 (smallseq)


title: E7_2_18 (smallseq)


title: E7_2_15 (smallseq)


title: E7_2_14 (smallseq)


title: E7_2_11 (smallseq)


title: E7_2_13 (smallseq)


title: E7_2_10 (smallseq)


title: E7_2_17 (smallseq)


title: E7_13_47 (smallseq)


title: E7_13_44 (smallseq)


title: E7_13_51 (smallseq)


title: E7_2_1 (smallseq)


title: E7_13_43 (smallseq)


title: E7_13_38 (smallseq)


title: E7_13_41 (smallseq)


title: E7_13_40 (smallseq)


title: E7_13_39 (smallseq)


title: E7_13_37 (smallseq)


title: E7_2_3 (smallseq)


title: E7_13_36 (smallseq)


title: E7_2_23 (smallseq)


title: E7_2_28 (smallseq)


title: E7_13_34 (smallseq)


title: E7_13_33 (smallseq)


title: E7_13_31 (smallseq)


title: E7_13_30 (smallseq)


title: E7_13_26 (smallseq)


title: E7_13_27 (smallseq)


title: E7_13_19 (smallseq)


title: E7_13_23 (smallseq)


title: E7_13_2 (smallseq)


title: E7_13_12 (smallseq)


title: E7_13_21 (smallseq)


title: E7_12_9 (smallseq)


title: E7_13_13 (smallseq)


title: E7_12_5 (smallseq)


title: E7_13_11 (smallseq)


title: E7_12_4 (smallseq)


title: E7_12_21 (smallseq)


title: E7_12_26 (smallseq)


title: E7_12_20 (smallseq)


title: E7_12_18 (smallseq)


title: E7_12_16 (smallseq)


title: E7_13_35 (smallseq)


title: E7_12_28 (smallseq)


title: E7_2_12 (smallseq)


title: E7_12_29 (smallseq)


title: E7_13_25 (smallseq)


title: E7_12_12 (smallseq)


title: E7_12_6 (smallseq)


title: E7_12_10 (smallseq)


title: E7_11_7 (smallseq)


title: E6_9_7 (smallseq)

value: embryo in vitro day E6


title: E7_11_3 (smallseq)


title: E7_12_30 (smallseq)


title: E6_9_6 (smallseq)


title: E6_9_47 (smallseq)


title: E6_9_46 (smallseq)


title: E6_9_45 (smallseq)


title: E6_9_9 (smallseq)


title: E6_9_42 (smallseq)


title: E6_9_44 (smallseq)


title: E6_9_4 (smallseq)


title: E6_9_43 (smallseq)


title: E6_9_38 (smallseq)


title: E6_9_35 (smallseq)


title: E6_9_40 (smallseq)


title: E6_9_36 (smallseq)


title: E6_9_33 (smallseq)


title: E7_12_13 (smallseq)


title: E6_9_39 (smallseq)


title: E6_9_34 (smallseq)


title: E6_9_31 (smallseq)


title: E7_11_8 (smallseq)


title: E6_9_32 (smallseq)


title: E6_9_30 (smallseq)


title: E6_9_29 (smallseq)


title: E6_9_28 (smallseq)


title: E6_9_27 (smallseq)


title: E6_9_26 (smallseq)


title: E6_9_24 (smallseq)


title: E6_9_21 (smallseq)


title: E6_9_25 (smallseq)


title: E6_9_2 (smallseq)


title: E6_9_18 (smallseq)


title: E6_9_17 (smallseq)


title: E6_9_41 (smallseq)


title: E6_9_16 (smallseq)


title: E6_9_15 (smallseq)


title: E6_9_13 (smallseq)


title: E6_9_14 (smallseq)


title: E6_9_12 (smallseq)


title: E6_8_3 (smallseq)


title: E6_8_5 (smallseq)


title: E6_9_11 (smallseq)


title: E6_8_7 (smallseq)


title: E6_8_9 (smallseq)


title: E6_9_10 (smallseq)


title: E6_8_8 (smallseq)


title: E6_8_20 (smallseq)


title: E6_8_19 (smallseq)


title: E6_8_18 (smallseq)


title: E6_8_2 (smallseq)


title: E6_8_15 (smallseq)


title: E6_9_23 (smallseq)


title: E6_8_14 (smallseq)


title: E6_8_13 (smallseq)


title: E6_8_10 (smallseq)


title: E6_8_12 (smallseq)


title: E6_7_4 (smallseq)


title: E6_7_5 (smallseq)


title: E6_7_6 (smallseq)


title: E6_8_11 (smallseq)


title: E6_7_3 (smallseq)


title: E6_7_29 (smallseq)


title: E6_7_9 (smallseq)


title: E6_7_28 (smallseq)


title: E6_7_26 (smallseq)


title: E6_7_24 (smallseq)


title: E6_7_25 (smallseq)


title: E6_7_2 (smallseq)


title: E6_7_27 (smallseq)


title: E6_7_22 (smallseq)


title: E6_7_23 (smallseq)


title: E6_7_20 (smallseq)


title: E6_7_19 (smallseq)


title: E6_7_21 (smallseq)


title: E6_7_17 (smallseq)


title: E6_7_15 (smallseq)


title: E6_7_14 (smallseq)


title: E6_7_12 (smallseq)


title: E6_7_13 (smallseq)


title: E6_7_18 (smallseq)


title: E6_7_11 (smallseq)


title: E6_7_10 (smallseq)


title: E6_7_1 (smallseq)


title: E6_6_9 (smallseq)


title: E6_6_6 (smallseq)


title: E6_6_7 (smallseq)


title: E6_6_8 (smallseq)


title: E6_6_54 (smallseq)


title: E6_6_52 (smallseq)


title: E6_6_53 (smallseq)


title: E6_6_5 (smallseq)


title: E6_6_49 (smallseq)


title: E6_6_46 (smallseq)


title: E6_7_16 (smallseq)


title: E6_6_47 (smallseq)


title: E6_6_48 (smallseq)


title: E6_6_51 (smallseq)


title: E6_6_44 (smallseq)


title: E6_6_45 (smallseq)


title: E6_6_39 (smallseq)


title: E6_6_41 (smallseq)


title: E6_6_43 (smallseq)


title: E6_6_42 (smallseq)


title: E6_6_40 (smallseq)


title: E6_6_38 (smallseq)


title: E6_6_33 (smallseq)


title: E6_6_4 (smallseq)


title: E6_6_32 (smallseq)


title: E6_6_37 (smallseq)


title: E6_6_31 (smallseq)


title: E6_6_29 (smallseq)


title: E6_6_27 (smallseq)


title: E6_6_24 (smallseq)


title: E6_6_26 (smallseq)


title: E6_6_25 (smallseq)


title: E6_6_21 (smallseq)


title: E6_6_22 (smallseq)


title: E6_6_18 (smallseq)


title: E6_6_16 (smallseq)


title: E6_6_20 (smallseq)


title: E6_6_14 (smallseq)


title: E6_6_17 (smallseq)


title: E6_6_13 (smallseq)


title: E6_5_8 (smallseq)


title: E6_5_9 (smallseq)


title: E6_5_23 (smallseq)


title: E6_6_11 (smallseq)


title: E6_5_22 (smallseq)


title: E6_6_10 (smallseq)


title: E6_5_16 (smallseq)