title: SX3678 young adults, 25oC, rep2

city: Cambridge

first: Miguel

middle: Vasconcelos

last: Almeida

address: Tennis Court Road

department: Department of Biochemistry

country: United Kingdom

institute: University of Cambridge

description:
rawCounts_25oC_YA.txt
DESEq2_25oC_YA.txt

data_processing:
Illumina adapters and reads with low-quality calls were filtered out using Trimmomatic v0.39 (Bolger et al., 2014) with options SLIDINGWINDOW:4:28 MINLEN:36.
Gene expression was quantified from trimmed reads using salmon v1.5.1 (Patro et al., 2017), with options --seqBias --gcBias - validateMappings -l A -1 -2 -o -i.
DESeq2 (Love et al., 2014) and custom scripts were used to calculate log-normalized and TPM counts, generate plots and conduct statistical tests on an R framework (R Core Team, 2021).
Assembly: WBcel235
Supplementary files format and content: Tab-delimited file includes raw counts for each sample of animals grown at 20oC.
Supplementary files format and content: Tab-delimited file includes raw counts for each sample of animals grown at 25oC.
Supplementary files format and content: Tab-delimited file includes DESeq2 results and normalized counts for each sample of animals grown at 20oC.
Supplementary files format and content: Tab-delimited file includes DESeq2 results and normalized counts for each sample of animals grown at 25oC.

organism: Caenorhabditis elegans

source_name: Whole animal

growth_protocol: N2 wild-type and fbxa-215(syb4404) animals grown at 20oC were synchronized by bleaching and overnight hatching in M9 buffer with gentle mixing. Synchronized L1 animals were brought onto HB101-seeded NGM plates the next day and grown at 20oC or at 25oC. Synchronized young adults were collected approximately 36 hours (batch grown at 25oC), or 48 hours (batch grown at 20oC) after plating. Animals were washed off plates with M9, further washed with M9, washed one last time in nuclease-free water, and frozen in dry ice.

extract_protocol:
Frozen worm aliquots were thawed, 300 µL of TRIzol (Life Technologies, 15596026) were added and mixed vigorously. Six freeze-thaw cycles were employed to dissolve animals, specifically by freezing tubes in liquid nitrogen for approximately 30 seconds, and subsequent thawing for approximately 3 minutes. After each cycle, tubes were mixed vigorously. After the sixth freeze-thaw cycle, samples were spun down at 20,000 G for 3 minutes and the supernatant was subsequently collected into a fresh tube. Next, 1 volume of 100% ethanol was added to the sample and mixed vigorously. Finally, the mixtures were loaded onto Direct-zol columns (Zymo Research, R2060) and manufacturer’s instructions were followed. In-column DNase I treatment was included.
Quality control of samples, library preparation (non-directional, with poly-A enrichment), and mRNA sequencing (Illumina, PE150) was performed by Novogene.

treatment_protocol: Animals were grown either at 20oC or 25oC.

value: Whole animal

value: young adult

value: Grown at 25oC


title: RNA_Tko_smc_rep1

status: Public on Dec 15 2024

type: SRA

city: Kyoto

first: Naomichi

last: Takemata

address: Kyoto University, Katsura, Nishikyo-ku

department: Synthetic Chemistry and Biological Chemistry

country: Japan

institute: Kyoto University

library_source: transcriptomic

data_processing:
Reads were counted using Salmon version 1.9.0 (Patro et al., 2017). Differentially expressed genes were identified using edgeR version 3.40.2 (Robinson et al., 2010).
Assembly: GCA_000009965.1
Supplementary files format and content: Tab-delimited tables showing Transcripts Per Million (TPM) values for each gene.

molecule: total RNA

organism: Thermococcus kodakarensis

extract_protocol:
Cells were grown to mid-to-late log phase and used for RNA extraction. 23S, 16S, and 5S rRNAs were removed using complementary DNA oligos and Rnase H.
Libraries were constructed NEBNext Ultra II Directional RNA Library Prep Kit for Illumina.

tag: cell line

tag: genotype

value: smc deletion


title: N_salina_Deplete_3

city: Los Alamos

first: Eric

middle: M

last: Small

state: New Mexico

address: Bikini Atoll Rd.

department: Earth and Environmental Sciences Division

country: USA

institute: Los Alamos National Laboratory

library_source: genomic

data_processing:
pod5 files generated by MinKNOW (via guppy) were re-basecalled using dorado 0.5.3 and the super-accuracy basecaller model (dna_r10.4.1_e8.2_400bps_sup@v4.3.0) on two NVIDIA RTX A4000 GPUs (dorado basecaller -batchsize 200 --modified-bases 6mA 5mC_5hmC --kit-name SQK-NBD114-96) (Oxford Nanopore Technologies, 2024a). Basecalled reads were demultiplex using dorado (dorado demux –no-classify). Reads were subsequently aligned to either the N. gaditana (accession #) or E. coli (accession #) genomes using the dorado implementation of minimap2 (dorado align {REFGENOME} {UBAM}) (Li, 2018). Aligned reads were subsequently passed to ModKit v0.6.2 to parse and count methylated bases (5mC, 5hmC and 6mA) (Modkit pileup --sampling-frac 1.0 –reference and Modkit summary –sampling-frac 1.0). Modified bed files were then split by base modification (5mC, 5hmC, or 6mA) and coerced into methylKit compatible files for methylKit analysis of differential methylation. ONT Modkit differential methylation analysis was performed at a base-pair resolution and gene resolution (modkit dmr pair -a -b –ref -o –base or modkit dmr multi -s –ref -o –base –regions). Hypermethylated adenines shared between all six replicates (light and dark) were combined, and motif analysis performed using MEME Suite (settings minimum width 4, maximum 6).
Raw fastq files were trimmed of adapters and poor-quality ends by trim galore v0.6.10. Reads were aligned using bismark v0.24.1 (to either the N. salina or N. gaditana genomes retrieved from JGI, accession #CCMP1776 and # CCMP1894 respectively) (Krueger and Andrews, 2011). Reads were deduplicated using Bismark (deduplicate_bismark). Aligned reads were parsed and methylated bases counted by methylDackel v0.3.0 (MethylDackel extract –methylKit –minDepth X –CHH, --CHG) (Ryan, 2024). Counts were taken as input for methylKit v1.28.0 analysis of differentially methylated bases (methylKit:: getMethylDiff()) (Akalin et al., 2012). Several permutations of statistical cutoffs were employed, with a linear regression model and SLIM multiple testing correction for statistical testing.
Assembly: E. coli genome was retrieved from genbank accession #U00096.3.   N. salina or N. gaditana genomes retrieved from JGI, accession #CCMP1776 and # CCMP1894 respectively
Supplementary files format and content: Data files are either methylDackel output for methylKit, or modKit calls for methylation.

molecule: genomic DNA

organism: Microchloropsis salina

extract_protocol:
Whole genome bisulfite sequencing was performed as previously described (Steadman 2020). Genomic DNA from N. salina and N. gaditana was isolated from three sets of cultures: nitrogen replete (full nutrients three days prior to nitrogen starvation), nitrogen starvation (the day nitrogen was not detectable in the media), and nitrogen depletion (three days after nitrogen starvation occurred). One ug of gNDA was digested with 1 unit of dsDNA Shearase Plus (Zymo catalog #E2018-50). Fragments were end-blunted, 3’-terminal-A extended, and purified using DNA Clean & Concentrator kit (Zymo catalog #D4003). Fragments were ligated to pre-annealed adapters containing methylated (5’-methyl) cytosine, filled in, and treated with sodium bisulfite using the EZ DNA Methylation-Lightning kit (Zymo catalog #D5003) . Illumina TruSeq indices were used for PCR; bisulfite treated fragment size and concentration were determined using an Agilent 2200 TapeStation (Agilent catalog #G2991BA). Fragments were sequenced on an Illumina HiSeq 2500.2x108 N. gaditana cells were processed using the Qiagen HW MagAttract kit (Qiagen catalog #67563 ) following the protocol for “gram (-) bacteria”. Prior to processing, cells were resuspended in buffer ATL and lysed by eight freeze thaw cycles -- 5 minutes on dry ice (-37c), followed by 5 minutes in a heat block at (37c) . DNA was eluted in 190uL ddH20 to prevent carryover of PCR inhibitors. To remove remaining RNA not removed by the kit, 400ug (4uL: 10mg/mL) RNASE A (ThermoFisher catalog #EN0531) was added with incubation at 37c for 1hr. Subsequently, to reduce polysaccharide contamination, 200uL 2X CTAB buffer was added to DNA solution (1.4 M NaCl, 20mM EDTA: pH 8.0, 2% CTAB w/v, 0.2% v/v β- mercaptoethanol, 100 mM Tris-Cl: pH 8.0), 400uL 25:24:1 Phenol:Chloroform:Isoamyl Alcohol buffered to pH 8.0 (Sigma Aldrich catalog #P2069) added, solution inverted 40X and phases separated by 5 minutes of centrifugation at 5000g. The aqueous phase was retained, taking care to avoid carryover of lipids or polysaccharides in the interphase. DNA was precipitated at -80c for 1hr by addition of 1/10 volume of NaACOH and ice-cold Ethanol (200 proof) (Thermo Fisher catalog #T036181000) to a final concentration of 75%, pelleted by centrifugation for 15 minutes at 7500g, washed with ice cold 75% ethanol, repelleted by 15 minutes centrifugation at 7500g, and air dried in the hood. DNA was resuspended in nuclease-free ddH20 and quantified using the Qubit 3.0 fluorometer and gDNA tapestation kit (Agilent catalog #5067-5366).
WBGS libraries were prepared using zymo kit #D5003. ONT libraries were constructed by: Libraries were prepared using the Native Barcoding DNA Ligation Kit K14 from nanopore (ONT catalog # SQK-NBD114.96). An E. coli DNA methylation null control was also prepared using the above ONT kit (Zymo catalog #D5016). Libraries were loaded onto a V11.4 Promethion flow cell (ONT catalog #FLO-PRO114M) with light shield (ONT catalog #SPR-FLS001P) and sequenced using MinKNOW with real-time basecalling set to fast and minimum length set to 200bp.
Bisulfite-seq and Oxford nanopore

tag: treatment

value: Deplete


title: 02CA1

city: Beijing

first: Wei

last: Ge

state: State...

address: 5 Dong Dan San Tiao, Dongcheng District

department: Department of Immunology

country: China

institute: Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences

data_processing:
Bowtie2 version 2.1.0 with the reference genome and the annotation GTF file downloaded from ENSEMBL (release 79, GRCH38), and the gene expression level was estimated using RSEM v1.2.15.
Assembly: Homo_sapiens.GRCh38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

organism: Homo sapiens

source_name: Hippocampus

extract_protocol:
Total RNA was extracted using an RNeasy Mini Kit (74106, Qiagen) following the manufacturer's instructions and RNA integrity was checked by using an Agilent Bioanalyzer 2100.
Total RNA sample preparation and sequencing were performed using the VAHTS Total RNA‐Seq Library PrepKit for Illumina.

tag: tissue

value: Hippocampus

tag: subfield

tag: group

value: NC


title: SX3678 young adults, 25oC, rep1

tag: developmental stage


title: RNA_Tko_KU216_rep3

value: Parental strain KU216


title: 01EC

value: EC


title: N_salina_Deplete_2


title: SX3678 young adults, 20oC, rep4

description:
rawCounts_20oC_YA.txt
DESEq2_20oC_YA.txt

value: Grown at 20oC


title: RNA_Tko_KU216_rep2


title: 01CA4


title: N_salina_Deplete_1


title: 02EC


title: N_salina_Starved_3

value: Starved


title: SX3678 young adults, 20oC, rep3


title: 01CA3


title: RNA_Tko_KU216_rep1


title: SX3678 young adults, 25oC, rep3


title: ChIP_Smc_IP_smc_rep2

data_processing:
Data were mapped using Bowtie 2 version 2.3.5.1 (Langmead & Salzberg, 2012). Low-quality alignments (MAPQ < 30) were removed using SAMtools version 1.9 (Li et al., 2009). Generated BAM files were processed using the bamCoverage function (version 3.5.1) of deepTools (Ramirez et al., 2016) to calculate Reads Per Kilobase region per Million mapped reads (RPKM) for genomic bins.
Assembly: GCA_000009965.1
Supplementary files format and content: bedgraph

extract_protocol:
Crosslinked cells were lysed by sonication, and the extract was clarified by centrifugation. Protein-DNA complexes were purified from the extract with antisera. After reversal of crosslinks, the DNA was extracted with phenol:chloroform:isoamyl alcohol and precipitated in ethanol.
Libraries were constructed using NEBNext Ultra II DNA Library Prep Kit for Illumina with Sample Purification Beads.

tag: chip antibody

value: Smc (custom)


title: 01CA2


title: N_salina_Starved_2


title: SX3678 young adults, 20oC, rep1


title: ChIP_Smc_IP_smc_rep1


title: 01CA1


title: N2 young adults, 25oC, rep4

value: wild-type


title: ChIP_Smc_input_smc_rep2


title: N2 young adults, 25oC, rep3


title: >48y

city: Guangzhou

first: Zhongchun

last: Tong

address: Lingyuan West Road 56#

department: Hosiptal of Stomatology

institute: Sun Yat- Sen University

library_source: transcriptomic single cell

data_processing:
The Seurat package was used to normalise data, dimensionality reduction, clustering, differential expression.
Gene Ontology (GO) enrichment analysis of marker genes was implemented by the clusterProfiler R package, in which gene length bias was corrected.
We used cluster Profiler R package to test the statistical enrichment of markergenes in KEGG pathways.
CellChat was used to compare cell-cell communication and infer ligand–receptor interactions in the young and aged dental pulp groups
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Dental Pulp

extract_protocol:
RNA from the barcoded cells was subsequently reverse-transcribed and sequencing libraries constructed with reagents from a Chromium Single Cell 3’ v2 reagent kit (10× Genomics) according to the manufacturer’s instructions.
Raw reads were demultiplexed and mapped to the reference genome by 10× Genomics Cell Ranger pipeline (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger) using default parameters. All downstream single-cell analyses were performed using Cell Ranger and Seurat

value: Dental Pulp

tag: age


title: N_salina_Replete_3

value: Replete


title: N_salina_Replete_2


title: 45y


title: SX3678 young adults, 20oC, rep2


title: ChIP_Smc_input_smc_rep1


title: N2 young adults, 25oC, rep2


title: ChIP_Smc_IP_trmBL2_rep2

value: trmBL2 deletion


title: N2 young adults, 25oC, rep1


title: 35y


title: ChIP_Smc_IP_trmBL2_rep1


title: N_salina_Replete_1


title: N2 young adults, 20oC, rep4


title: 26y


title: ChIP_Smc_input_trmBL2_rep2


title: DU145_control

city: Astana

first: Syed

middle: Hani

last: Abidi

address: 53, Kabanbay Batyr Ave

country: Kazakhstan

institute: Nazarbayev University

description:
Library name: DU145_sample
Illumina NovaSeq 6000

data_processing:
Raw data files in Fastq format were initially quality-checked using FastQC 16, while adapters were trimmed using the FASTP program 17,18. The trimmed reads were aligned to the human reference sequence (hg38) using HISAT2 19. Subsequently, Cufflinks was used to align reads with the transcripts to compare the differential gene expression across samples 20, while Cuffmerge was used to merge transcript assemblies generated by Cufflinks and remove overlapping transcripts. The differentially expressed genes (DEGs) were identified using Cuffdiff 21. The DEG data was exported into an MS Excel file, where statistically significant up- and down-regulated DEGs were identified using log2 fold change (log2FC) of >1 and <-1, respectively, and p< 0.05.
Assembly: Hg38
Supplementary files format and content: tab-delimited text file includes counts

source_name: Cell line

growth_protocol: Human prostate cancer cell lines, LNCaP and DU145 (originally purchased from ATCC; cat# CRL-1740 and HTB-81, respectively) were obtained from the stock cultures of the Aga Khan University and cultured/maintained in DMEM medium (Sigma, St. Louis, MO, USA) supplemented with 10% FBS, 1% L-glutamine, and 1% PenStrep at 37˚C in a humidified atmosphere of 5% CO2.

extract_protocol:
RNA Extraction: RNA extraction was performed using the Trizol-chloroform method as described previously 15. The total RNA concentration was calculated by Quant-IT RiboGreen (Invitrogen, cat#R11490). To assess the integrity of the total RNA, samples are run on the TapeStation RNA ScreenTape (Agilent, cat#5067-5576).
Only high-quality RNA preparations with RIN greater than 7.0 were used for RNA library construction. A library was independently prepared with 1μg of total RNA for each sample by Illumina TruSeq Stranded mRNA Sample Prep Kit (Illumina, Inc., San Diego, CA, USA, cat#20020595). The poly-A-containing mRNA molecules were purified using poly‐T‐attached magnetic beads, followed by mRNA fragmentation into small pieces using divalent cations under elevated temperature. The cleaved RNA fragments were copied into first-strand cDNA using SuperScript II reverse transcriptase (Invitrogen, cat#18064014) and random primers, and subsequently used for second-strand cDNA synthesis using DNA Polymerase I, RNase H, and dUTP. These cDNA fragments underwent an end-repair process by adding a single adenine (A) base and ligating the adapters. The products were purified and enriched with PCR to create the final cDNA library. The libraries were quantified using KAPA Library Quantification kits for Illumina Sequencing platforms according to the qPCR Quantification Protocol Guide (KAPA BIOSYSTEMS, #KK4854) and qualified using the TapeStation D1000 ScreenTape (Agilent Technologies, # 5067-5582). The indexed libraries were then submitted to an Illumina NovaSeq (Illumina, Inc., San Diego, CA, USA), and the paired-end (2×100 bp) sequencing, which was performed by Macrogen Inc., Korea. The experiments were run in duplicate, but cells were pooled at the library preparation step.

value: Cell line

tag: cell type

value: Cancer cell line


title: N_salina_Starved_1


title: 22y


title: LNCaP_Control

description:
Library name: LNCaP_sample
Illumina NovaSeq 6000

value: LNCAP


title: D003: siMAD2L1-2 transfected cell

city: Kagoshima

first: Yuya

last: Tomioka

institute: Kagoshima University

data_processing:
Sequencing adaptors, low quality reads, and bases were trimmed with Trimmomatic-0.39 tool.
The sequence reads were aligned to the Human reference genome (hg38) using STAR 2.7.10b.
The aligned reads were subjected to downstream analyses using StrandNGS 4.0 software (Agilent Technologies, Inc.).
The read counts allocated for each gene and transcript (RefSeq Database 2018.02.25) were quantified using a Transcripts Per Million (TPM) method.
The differentially expressed genes (DEGs) were estimated to be significant if FC (Fold Change) > 2.
Assembly: hg38
Supplementary files format and content: 24064_RNA-Seq_Quantified.xlsx

source_name: Lung

extract_protocol:
Total RNA was extracted using Trizol following the manufacturer's instructions.
Total RNA obtained from each sample was subjected to a sequencing library construction using TruSeq Stranded mRNA Library Prep Kit (Illumina, Inc., San Diego, CA) according to the manufacturer’s protocols. The equally pooled libraries of the samples were sequenced using NovaSeq 6000 (Illumina, Inc.) in 101-base-pair (bp) paired-end reads.

value: Lung

value: lung adenocarcinoma

value: WT


title: D002: siMAD2L1-1 transfected cell


title: N2 young adults, 20oC, rep2

value: Whole animal

value: young adult


title: N2 young adults, 20oC, rep1


title: N2 young adults, 20oC, rep3


title: ChIP_Smc_IP_KU216_rep1

value: Parental strain KU216


title: Genomic DNA from parental fibroblasts replicate 2

type: genomic

city: Solna

first: Gema

last: Sanz Santos

state: Stockholm

address: Nobels väg 16

country: Sweden

institute: Karolinska Institutet

description:
Parental fibroblasts with wildtype p53 sample
WT rep2

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridized to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: RnBeads web service

label: Cy5 and Cy3

source_name: Parental fibroblasts cell culture

label_protocol: Standard Illumina Protocol

growth_protocol: Fibroblasts stably expressing Cas9 were established and then transfected two times with p53 sgRNA.

extract_protocol: genomic DNA was extracted and purified from fibroblasts samples using Archive pure DNA cells/tissue kit (5 Prime) according to standard instructions

treatment_protocol: Enrichment of p53-deleted cells was performed by Nutlin treatment (10 µM) for 30 days.

value: fibroblast

tag: genotype/variation

value: p53 wild type


title: 18y


title: Genomic DNA from p53-null fibroblasts replicate 2

description:
p53-null fibroblasts sample
p53KO rep2

source_name: p53-null fibroblasts cell culture

value: p53 null


title: ChIP_Smc_input_KU216_rep2


title: siFAM111B-2 transfected cell

data_processing:
Sequencing adaptors, low quality reads, and bases were trimmed with Trimmomatic-0.39 tool.
The sequence reads were aligned to the Human reference genome (hg38) using STAR 2.7.10b.
The aligned reads were subjected to downstream analyses using StrandNGS 4.0 software (Agilent Technologies, Inc.).
The read counts allocated for each gene and transcript (RefSeq Database 2018.02.25) were quantified using a Transcripts Per Million (TPM) method.
The differentially expressed genes (DEGs) were estimated to be significant if FC (Fold Change) > 2.
Assembly: hg38
Supplementary files format and content: 24036_RNA-Seq_Quantified.xlsx


title: frontal hair follicles of androgenetic alopecia

first: Lian

middle: Shu

last: Wu

state: Guangdong

address: No.1838, North Guangzhou Avenue, Baiyun District

department: Department of Plastic and Aesthetic Surgery

institute: Nanfang Hospital of Southern Medical University

data_processing:
Hisat2 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence.
TPM(Transcripts Per Kilobase of Exon Model Per Million mapped reads) is the most commonly used method for estimating gene expression levels, considering the effect of sequencing depth and gene length on reads count. Bam files obtained by sequencing were mapped to GTF annotation files of reference species to obtain gene expression levels, and regional statistics of gene expression levels of genomes were carried out according to statistical methods to reflect the overall expression levels of samples. TPM density profile was used to investigate the gene expression pattern of samples.
Genome_build: mm9
Supplementary_files_format_and_content: gene expression data

source_name: hair follicles of androgenetic alopecia

extract_protocol:
After obtaining hair follicle tissues in the surgery, total RNA was isolated from the tissues using the Trizol (invitrogen) as soon as possible. RNA purity was assessed and each RNA sample had an A260:A280 ratio above 1.8 and A260:A230 ratio above 2.0. RNA integrity was evaluated using the Agilent 2200 TapeStation (Agilent Technologies, USA) and each sample had the RIN above 7.0. rRNAs were removed from Total RNA using EpicentreRibo-Zero rRNA Removal Kit (illumina, USA). Subsequently, the purified RNAs were subjected to first strand and second strand cDNA synthesis following by adaptor ligation and enrichment with a low- cycle. The purified l library products were diluted to 10 pM for cluster generation in situ on the pair-end flow cell followed by sequencing (2×150 bp) HiSeq3000.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: disease

value: androgenetic alopecia

value: hair follicles

tag: tissue source

value: frontal hair follicles


title: ChIP_Smc_IP_KU216_rep2

value: Smc (custom)


title: Genomic DNA from parental fibroblasts replicate 1

description:
Parental fibroblasts with wildtype p53 sample
WT rep1


title: SX3678 embryos, 25oC, rep3

description:
rawCounts_25oC_embryos.txt
DESEq2_25oC_embryos.txt

data_processing:
Illumina adapters and reads with low-quality calls were filtered out using Trimmomatic v0.39 (Bolger et al., 2014) with options SLIDINGWINDOW:4:28 MINLEN:36.
Gene expression was quantified from trimmed reads using salmon v1.5.1 (Patro et al., 2017), with options --seqBias --gcBias - validateMappings -l A -1 -2 -o -i.
DESeq2 (Love et al., 2014) and custom scripts were used to calculate log-normalized and TPM counts, generate plots and conduct statistical tests on an R framework (R Core Team, 2021).
Assembly: WBcel235
Supplementary files format and content: Tab-delimited file includes raw counts for each sample of embryos grown at 20oC.
Supplementary files format and content: Tab-delimited file includes raw counts for each sample of embryos grown at 25oC.
Supplementary files format and content: Tab-delimited file includes DESeq2 results and normalized counts for each sample of embryos grown at 20oC.
Supplementary files format and content: Tab-delimited file includes DESeq2 results and normalized counts for each sample of embryos grown at 25oC.

source_name: Whole embryo

growth_protocol: N2 wild-type and fbxa-215(syb4404) animals grown at 20oC were synchronized by bleaching and overnight hatching in M9 buffer with gentle mixing. Synchronized L1 animals were brought onto HB101-seeded NGM plates the next day and grown at 20oC or at 25oC. Synchronized gravid adult worms were bleached approximately 47 hours (batch grown at 25oC), or 56 hours (batch grown at 20oC) after plating. After 2 washes in ice-cold M9 and a final wash in nuclease-free water, embryos were frozen in dry ice.

value: embryo (mixed stages)

value: Grown at 25oC


title: siFAM111B-1 transfected cell


title: Genomic DNA from p53-null fibroblasts replicate 1

description:
p53-null fibroblasts sample
p53KO rep1


title: D001: transfection reagent only 1


title: SX3678 embryos, 25oC, rep2


title: ChIP_Smc_input_KU216_rep1


title: occipital hair follicles of androgenetic alopecia

value: occipital hair follicles


title: 3C_Tko_TK0795_rep2

data_processing:
*library strategy: 3C-seq
Data were processed using HiC-Pro version 3.0.0 (Servant et al., 2015). Normalized contact matrices were generated with MAX_ITER = 500. LOW_COUNT_PERC was set to 0.006 for Thermococcus kodakarensis.
Assembly: GCA_000009965.1, GCA_000195915.1
Supplementary files format and content: Tab-delimited tables. The first and second columns indicate genomic bins. The third column indicate normalized interaction frequencies between the bins.

extract_protocol:
Cells were crosslinked, permeabilized, and treated with AluI and HaeIII to digest genomic DNA. The insoluble fraction was collected and used for proximity ligation. After reversal of crosslinks, the DNA was extracted with phenol:chloroform:isoamyl alcohol, precipitated in ethanol, and sonicated.
Libraries were constructed using NEBNext Ultra II DNA Library Prep Kit for Illumina with Sample Purification Beads.

value: TK0795 deletion


title: SX3678 embryos, 25oC, rep4


title: axillary hair follicles of androgenetic alopecia

value: axillary hair follicles


title: transfection reagent only 2

value: Lung

value: lung adenocarcinoma


title: SX3678 embryos, 25oC, rep1

value: Whole animal


title: beard hair follicles of androgenetic alopecia

value: beard hair follicles


title: siANLN-2 transfected cell

value: WT


title: Genomic DNA from p53-null fibroblasts replicate 3

description:
p53-null fibroblasts sample
p53KO rep3

value: fibroblast


title: Genomic DNA from parental fibroblasts replicate 3

description:
Parental fibroblasts with wildtype p53 sample
WT rep3

value: p53 wild type


title: 3C_Tko_TK0795_rep1


title: siANLN-1 transfected cell


title: IP m6A Rep 1

city: Santiago

first: Daniela

last: Toro Ascuy

state: Region Metropolitana

address: Av. Independencia 1027

department: Virology

country: Chile

institute: University of Chile

description:
IP m6A RNA
MAPPED_particle_peaks.xls

data_processing:
Read quality was evaluated with FastQC v0.11.8
Burrows-Wheeler Alignment Tool v0.7.17-r1188  (BWA -Mem) were used for mapping reads to the HIV-2 genome.
The Aligment data were analazed by MACS2 v2.1.1.20160309 to call peaks  with -f BAMPE  --nomodel --SPMR -q 0.05 options to generated viral peaks data, and to generated FPKM (Fragments Per Kilobase per Million mapped reads). Predicted peaks were sorted by average coverage.
For the adenosine conservation analysis, all the HIV-2 sequences present in HIV database were aligned with HIV Premade Aligments,ALL GENOME options, processed and classified with a inhouse script. Motif was analyzed by WebLogo v2.8.2
Genome_build: HIV-2 fasta sequence pRod10 vector
Supplementary_files_format_and_content: tab-delimited text files

source_name: embryonic kidney cells

growth_protocol: HEK293T was maintained in DMEM (Life Technologies) supplemented with 10% FBS (Hyclone) and antibiotics (Hyclone) at 37ºC and 5% CO2 atmosphere.

extract_protocol:
HEK-293T cells were transfected with the HIV-2 pROD10-ΔEnv molecular clone. At 24 hpt, total RNA was extracted and 70 microg were treated with kit TURBO DNA-free™ Kit and then used to obtain polyA RNA using the mRNA isolation kit (Sigma-Aldrich). PolyA RNA was fragmented using the RNA Fragmentation Reagent (Ambion), 500 ng were stored as the input and 2 microg were used for immunoprecipitation of the methylated mRNA (m6A-IP samples) using an anti-m6A antibody (0,5 mg/mL; Synaptic System #202003).
cDNA libraries preparations and RNAseq was performed as a service from Genoma Mayor. All the samples were sequenced in an Illumina HiSeq2000 platform with paired-end 150 bp read length. This was obtained as a  RNA Seq/TruSeq Stranded RNA + RiboMinus.
meRIP-seq

treatment_protocol: No treatments were performed

value: HEK293T, embryonic kidney cells

tag: antibody


title: IP m6A Rep 2

description:
IP m6A RNA
MAPPED_intracell_peaks.xls

value: m6A antibody (0,5 mg/mL; Synaptic System #202003)


title: SX3678 embryos, 20oC, rep4

description:
rawCounts_20oC_embryos.txt
DESEq2_20oC_embryos.txt

value: Grown at 20oC


title: 3C_Tko_trmBL2_rep2

value: trmBL2 deletion


title: Input (poliA) Rep 2

description:
total RNA
MAPPED_intracell_peaks.xls


title: SX3678 embryos, 20oC, rep3


title: 3C_Tko_trmBL2_rep1


title: transfection reagent only 1


title: SX3678 embryos, 20oC, rep2


title: 3C_Tko_dif_rep2

value: dif deletion


title: Input (poliA) Rep 1

description:
total RNA
MAPPED_particle_peaks.xls


title: A549 cells, miR-195-3p transfected

data_processing:
Sequencing adaptors, low quality reads, and bases were trimmed with Trimmomatic-0.39 tool.
The sequence reads were aligned to the Human reference genome (hg38) using STAR 2.7.10b.
The aligned reads were subjected to downstream analyses using StrandNGS 4.0 software (Agilent Technologies, Inc.).
The read counts allocated for each gene and transcript (RefSeq Database 2018.02.25) were quantified using a Transcripts Per Million (TPM) method.
The differentially expressed genes (DEGs) were estimated to be significant if FC (Fold Change) > 2.
Assembly: hg38
Supplementary files format and content: 23159_RNA-Seq_Quantified.xlsx

value: miR-195-3p transfected


title: SX3678 embryos, 20oC, rep1

value: embryo (mixed stages)


title: A549 cells, miR-195-5p transfected

value: miR-195-5p transfected


title: N2 embryos, 25oC, rep4

value: wild-type

value: Grown at 25oC


title: 3C_Tko_xerA_rep2

value: xerA deletion


title: G13_OM

city: Campinas

first: Luciana

middle: Souto

last: Mofatto

state: Sao Paulo

address: R. Carl Von Linaeus

department: Genetics, Evolution and Bioagents

country: Brazil

institute: Institute of Biology - University of Campinas

data_processing:
For RNA-seq data, quality of raw data was evaluated by FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
Data was filtered by quality using Perl scripts, with quality cut over 20. The adapters were removed with Cutadapt (Martin 2011) and trim galore (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/).
Filtered reads of RNA library were mapped against the human genome (GRCh38) using the pipeline Tophat2-Cufflinks (Trapnell et al. 2012).
Number of reads aligned per genes (read counts) and fragments per kilobase of transcript per million mapped reads (FPKM) were calculated by RSEM program (Li and Dewey 2011).
Genome_build: GRCh38
Supplementary_files_format_and_content: RSEM output file with transcript length, effective_length, expected_count, TPM, FPKM values for each Sample.

source_name: periodontal ligament

growth_protocol: Cell clones were cultivated in Dulbecco’s modified Eagle medium high glucose (DMEM) supplemented with 10% FBS, penicillin (100 U/ml) and streptomycin (100 mg/mL) (Gibco, USA)

extract_protocol:
TRIzol (Invitrogen, Carlsbad, CA, USA) was used to extract total RNA from confluent C-O and C-F clones when were cultivated during 14 days. Phenol-Chloroform protocol was used to extract RNA.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Each cell clone were seeded (2x105cells/well) in 24-well plates with medium that was composed by Dulbecco’s modified Eagle medium high glucose (DMEM) supplemented with 10% FBS, penicillin (100 U/ml) and streptomycin (100 mg/mL) (Gibco, USA) and incubated for 24 hours. After this period, cells were cultivated in osteogenic medium (OM) composed by  DMEM supplemented with 50 mg/mL ascorbic acid (Sigma-Aldrich, Cat #A4544, China) 10 mM b-glycerophosphate (Sigma-Aldrich, Cat #G9422, USA), and 10-8 M dexamethasone (Sigma-Aldrich, Cat #D2915, USA) for 14 days.

value: Periodontal Ligament Primary Cell Clone With Osteo/Cementoblastic Phenotype

tag: passage


title: N2 embryos, 25oC, rep3

value: Whole animal


title: 3C_Tko_smc_scpB_rep2

value: smc scpB deletion


title: G48_OM


title: A549 cells, transfection reagent only

value: Lung

value: lung adenocarcinoma

value: WT

value: transfection reagent only


title: Body (corpus), post-SG patient 21, scRNAseq

city: Jerusalem

first: Danny

last: Ben-Zvi

state: Israel

address: The Institute for Medical Research Israel Canada, The Faculty of Medicine

department: Department of Developmental Biology and Cancer Research

country: Israel

institute: The Hebrew University of Jerusalem

description: 10X Genomics

data_processing:
Alignment to the GRCh38 human reference genome and count matrix generation was carried out using Cellranger "count" command processes FASTQ files (6.1.2).
Analysis was carried out using Seurat (version 4.1.1) using as input the "raw_feature_bc_matrix.h5"
Barcodes were filtered for a minimum of 200 expressed genes per cell. SoupX (1.6.2) was applied to mitigate potential extracellular mRNA contamination during droplet-based library generation.
To identify potential doublets, we employed scDblFinder (1.10.0)
The corrected count matrices from SoupX of only the identified single cells of each sample were preprocessed to identify and remove low-quality and non-viable cells. Cells in each sample with a high percentage of mitochondrial genes, exceeding 20-25%, were considered dead and were consequently removed. Additionally, only cells with features between 800-6000 and total UMI counts between 2000-100,000 were selected for further analysis. Each sample was processed individually before merging the data.
SCTransform (0.3.5) normalization was independently applied to each of these samples. parameters used in this process included "method = 'glmGamPoi'" for efficiency, "variable.features.n = 3000" to determine variable features based on residual variance ranking, and "vars.to.regress = 'percent.mt'" to regress out mitochondrial percentage-related variations.
For corpal samples: To identify variable genes across cells for integration, we utilized SelectIntegrationFeatures function (Seurat 4.1.1), setting nfeatures=3000. PrepSCTIntegration (Seurat 4.1.1) was employed afterwards. RunPCA (Seurat 4.1.1) step was performed on each sample. The parameters in FindIntegrationAnchors function (Seurat 4.1.1) are (reduction = "rpca", k.filter=100, k.anchor=10). For the integration process, we used the IntegrateData function (Seurat 4.1.1) k.weight =90. For antral samples: To identify variable genes across cells for integration, we utilized SelectIntegrationFeatures function (Seurat 4.1.1), setting nfeatures=3000. PrepSCTIntegration (Seurat 4.1.1) was employed afterwards. The parameters in FindIntegrationAnchors function (Seurat 4.1.1) are (reduction = "cca"). For the integration process, we used the IntegrateData function (Seurat 4.1.1).
Initially dimensionality reduction using the RunPCA (Seurat 4.1.1) method to conduct Principal Component Analysis (PCA). Subsequently, clustering was executed utilizing the FindNeighbors (Seurat 4.1.1) method (with reduction = "pca", dims = 1:50), constructing a k-nearest neighbor (k-NN) graph based on the Euclidean distance within the PCA space. This graph served as the foundation for the clustering process. The FindClusters method (resolution = 0.77) (Seurat 4.1.1) was employed for clustering the cells, utilizing the shared nearest neighbor (SNN) clustering algorithm. To visualize the data in a lower dimension, we applied Uniform Manifold Approximation and Projection (UMAP) using the RunUMAP (Seurat 4.1.1) method (with dims = 1:50).
PreSCTFindMarkers (Seurat 4.1.1) is employed first. To categorize each cluster into specific cell types, we utilized the FindAllMarkers (Seurat 4.1.1) method from the Seurat package (with min.pct = 0.25, logfc.threshold = 0.25).
Assembly: GRCh38
Supplementary files format and content: Raw gene-barcode matrix (all valid barcodes from GEMs captured in the data)

molecule: polyA RNA

source_name: Gastric Body (corpus)

extract_protocol:
The biopsies were incubated with 0.5% DTT/HBSS w/o Ca & Mg [Roche #10197777001/Sartorius 02-018-1A] to reduce the mucus layer. Collagenase [Rosch #11213873001] at 1mg/ml was used for digestion in 20mM HEPES, 0.2% BSA in 1mM glucose DMEM [Roche #11213873001/Gibco 21885-025]. The biopsies were incubated twice for 15 min. at 37ºC. Crypts were dissociated to single cells with TrypLE/DNaseI [Gibco 12604-013/Roche 40276300] at 0.5mg/ml for 1-minute while pipetting, at room temperature. Cells were passed through a 30µm filter [MACS® smartstrainers]. Dead cells were removed using magnetic MicroBeads [Dead Cell Removal Kit Miltenyl #130-090-101] and then enriched for epithelial cells using magnetic MicroBeads [CD326 (EpCAM) MicroBeads Miltenyl #130-061-101].
Cells were separated into droplet emulsion using Chromium controller (10x genomics) and scRNAseq libraries were prepared and barcoded with UDIs using Chromium Next GEM Single Cell 3’ Kit v3.1 (10X Genomics), according to the manufacturer protocol. Sequencing was done using Illumina NextSeq 500 platform and Illumina NovaSeq 6000 platform with the following sequencing conditions: 28bp (Read1) and 54/56bp (Read2), and 28bp (Read1) and 90bp (Read2) respectevly.

tag: Sex

value: Female

value: Gastric Body (corpus)

value: Gastric Epithelium

value: Sleeve-Gastrectomy


title: Fundus (corpus), post-SG patient 21, scRNAseq

description: 10X Genomics

source_name: Gastric Fundus (corpus)

value: Gastric Fundus (corpus)


title: G23_OM

value: Periodontal Ligament Primary Cell Clone With Fibroblastic Phenotype


title: 3C_Tko_smc_scpB_rep1


title: N2 embryos, 25oC, rep1

value: embryo (mixed stages)


title: 3C_Tko_smc_scpA_rep2

value: smc scpA deletion


title: N2 embryos, 20oC, rep4

value: wild-type

value: Grown at 20oC


title: 3C_Tko_smc_scpA_rep1


title: G16_OM


title: C2

first: Jianwei

last: Jiao

state: Beijing

address: 1 Beichen West Road

department: State Key Laboratory of Reproductive Biology

institute: Institute of Zoology, Chinese Academy of Sciences

description: Library name: Sample 4

data_processing:
Illumina Casava1.7 software used for basecalling.
Raw Data was processed with Perl scripts to ensure the quality of data used in further analysis. The adopted filtering criteria are as follows：1) Remove the adaptor-polluted reads. (Reads containing more than 5 adapter-polluted bases were regarded as adaptor-polluted reads and would be filtered out; 2) Remove the low-quality reads. Reads with the number of low quality bases (phred Quality value less than 19) accounting for more than 15% of total bases are regarded as low-quality reads; 3) Remove reads with number of N bases accounting for more than 5 %.
Bowtie2 v2.2.3 was used for building the genome index, and Clean Data was mapped to the reference genome using TopHat v2.0.12.
The IGV (Integrative Genomics Viewer) was used to view the mapping result by the Heatmap, histogram, scatter plot or other stytle.
Reads Count for each gene in each sample was counted by HTSeq v0.6.0, and RPKM (Reads Per Kilobase Millon Mapped Reads) was then calculated to estimate the expression level of genes in each sample.
Assembly: mm9
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

organism: Mus musculus

source_name: Cerebral cortex

extract_protocol:
Total RNA was harvested by Trizol reagent.2 ug of total RNA was used to construct sequencing libraries.
RNA libraries sequencing  was performed using standard Illumina protocols

value: Cerebral cortex


title: C1

description: Library name: Sample 3


title: Fundus (corpus), post-SG patient 20, scRNAseq

description: 10X Genomics


title: Body (corpus), post-SG patient 20, scRNAseq

description: 10X Genomics


title: 3C_Tko_scpB_rep2

value: scpB deletion


title: 3C_Tko_dif_rep1

value: dif deletion


title: W1

description: Library name: Sample 1


title: 3C_Tko_scpB_rep1


title: Antrum, post-SG patient 20, scRNAseq

description: 10X Genomics

source_name: Gastric Antrum

value: Gastric Antrum


title: 3C_Tko_scpA_rep2

value: scpA deletion


title: N2 embryos, 20oC, rep1

value: Whole animal


title: Antrum, naive patient 11, scRNAseq

description: 10X Genomics

value: naive


title: Fundus (corpus), naive patient 11, scRNAseq

description: 10X Genomics

value: Female


title: N2 embryos, 25oC, rep2

value: Grown at 25oC


title: Body (corpus), naive patient 17, scRNAseq

description: 10X Genomics

value: Gastric Body (corpus)

value: Gastric Epithelium


title: 3C_Tko_scpA_rep1


title: AMKO AP5

city: Shanghai

first: Jingpiao

last: Bao

address: South Chongqing Road no. 227  Copyright © 2013 Shanghai jiaotong university school of medicine

institute: Shanghai Jiao Tong University School of Medicine

data_processing:
We applied the reads filtering towards the raw reads after sequencing to achieve the clean data following the criteria: a)10% base quality <15 b) 13% base quality <20.
Hisat2 2.0.4 mapping to reference genome
count counting
Genome_build: mm10
Supplementary_files_format_and_content: TXT file contain counts for each sample

source_name: Pancreas tissue

extract_protocol:
Total RNA was extracted from cell or animal tissue by Trizol reagent (Invitrogen) separately. The RNA quality was checked by Bioanalyzer 2200 (Aligent) and kept at -80℃.The RNA with RIN >8.0 is right for cDNA library construction.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Caerulein hyperstimulation pancreatitis was induced by ten hourly intraperitoneal injections of caerulein (100 μg/kg), then mice were sacrificed at 12 h after the first injection.

value: Pancreas

value: AMKO

value: post natal day 56


title: AMKO AP6


title: Fundus (corpus), post-SG patient 10, scRNAseq

description: 10X Genomics

value: Gastric Fundus (corpus)

value: Sleeve-Gastrectomy


title: Fundus (corpus), naive patient 17, scRNAseq

description: 10X Genomics


title: AMKO AP4


title: Antrum, post-SG patient 10, scRNAseq

description: 10X Genomics


title: W2

description: Library name: Sample 2


title: Fundus (corpus), post-SG patient 15, scRNAseq

description: 10X Genomics


title: Body (corpus), post-SG patient 10, scRNAseq

description: 10X Genomics


title: N2 embryos, 20oC, rep3

value: embryo (mixed stages)

value: wild-type

value: Grown at 20oC


title: 3C_Tko_smc_rep1

value: smc deletion


title: AMKO AP3


title: Body (antrum), post-SG patient 15, scRNAseq

description: 10X Genomics

source_name: Gastric Body (antrum)

value: Gastric Body (antrum)


title: AMKO AP2


title: Body (corpus), naive patient 9, scRNAseq

description: 10X Genomics


title: 3C_Tko_KU216_rep2

value: Parental strain KU216


title: Antrum, post-SG patient 15, scRNAseq

description: 10X Genomics

value: Gastric Antrum


title: AMKO AP1


title: 3C_Tko_KU216_rep1


title: Fundus (corpus), naive patient 7, scRNAseq

description: 10X Genomics

value: naive


title: 3C_Tko_smc_rep2


title: Body (corpus), naive patient 7, scRNAseq

description: 10X Genomics

value: Female


title: Fundus (corpus), naive patient 14, scRNAseq

description: 10X Genomics


title: WT AP6

value: wild type


title: Rvq110_rep3

city: Valencia

first: Jose

last: Leon

address: CPI Edificio 8E, Ingeniero Fausto Elio s/n

country: Spain

institute: IBMCP (CSIC-UPV)

data_processing:
Sequences mapped to the reference genome by using STAR software
The following steps were performed: 1) Remove the reads containing the adaptor(adaptor pollution); 2) Remove reads whose N content is greater than 5%; 3) Remove low-quality reads (we define reads with bases with a quality score less than 10 as the proportion of total bases in the reads that are greater than 20% as low-quality reads). 2) Remove reads whose N content is greater than 5%; 3) Remove low-quality reads (we define reads with bases with a quality score less than 10 as the proportion of total bases in the reads that are greater than 20% as low-quality reads). The filtered "Clean Reads" are saved in FASTQ format. 1) Remove the reads containing the adaptor(adaptor pollution); 2) Remove reads whose N content is greater than 5%; 3) Remove low-quality reads (we define reads with bases with a quality score less than 10 as the proportion of total bases in the reads that are greater than 20% as low-quality reads). The filtered "Clean Reads" are saved in FASTQ format.
The filtered "Clean Reads" are saved in FASTQ format.
Genomic reference used  TAIR10, and transcript annotation associated to that reference TAIR10.57 available by July 27,2023. la TAIR10.57 available in Ensembl date July27, 2023. Hierarchical Indexing for Spliced Alignment of Transcripts (HISTAT) is software for mapping RNA-seq reads.
Assembly: HISAT2 v2.0.4 (--sensitive --no-discordant --no-mixed -I 1 -X 1000 -p 8 --rna-strandness RF)
Supplementary files format and content: tab-delimited text files including AGI code and READ_COUNT values for each Sample were generate by using DESeq2

organism: Arabidopsis thaliana

source_name: whole seedlings

growth_protocol: Arabidopsis thaliana seedlings grown in MS medium supplemented with 1% sucrose under photoperiodic long-day conditions (16h ligh:8h darkness; 150 micromol photons m-2 s-1) and normoxic conditions (21% O2) for 14 days.

extract_protocol:
Total RNAs were extracted by the NucleoSpin Plant RNA kit (Macherey-Nagel) and the quality checked by Bioanalyzer with RIN > 8.  1 microgram of RNAs were used for the construction of sequencing libraries.
RNA libraries for RNA-Seq were prepared using a 5´random primer linked to a 6bp Unique Molecular Identifyer (UMI). Quality control of the libraries were analyzed by QIAxcel Advanced System (Qiagen). ),  compuesto por 6pb y separado del  primer por un separador de secuencia  conocida.
3´RNA-Seq

treatment_protocol: At ZT=4 of day 14 seedlings under standadrd normoxic conditions were harvested for subsequent total RNA isolation.

value: whole seedlings

value: Normoxia


title: Antrum, naive patient 7, scRNAseq

description: 10X Genomics

value: Gastric Epithelium


title: Body (corpus), naive patient 14, scRNAseq

description: 10X Genomics

value: Gastric Body (corpus)


title: WT AP5

value: Pancreas

value: post natal day 56


title: WT AP4


title: Antrum, naive patient 14, scRNAseq

description: 10X Genomics


title: Rvq110_rep1


title: Rvq110_rep2


title: 3C_Tko_KU216_rep3


title: Fundus (corpus), naive patient 6, scRNAseq

description: 10X Genomics

value: Gastric Fundus (corpus)


title: Fundus (corpus), naive patient 12, scRNAseq

description: 10X Genomics


title: Antrum, post-SG patient 21, scRNAseq

description: 10X Genomics

value: Sleeve-Gastrectomy


title: Body (corpus), naive patient 6, scRNAseq

description: 10X Genomics


title: Body (corpus), naive patient 12, scRNAseq

description: 10X Genomics


title: WT AP3


title: Antrum, naive patient 6, scRNAseq

description: 10X Genomics


title: ChIP_Smc_input_trmBL2_rep1

value: trmBL2 deletion


title: Col-0_rep2

value: wt Col-0


title: Antrum, naive patient 12, scRNAseq

description: 10X Genomics


title: genomic DNA from NC_149

status: Public on Dec 14 2024

city: Jinan

first: chuanxin

last: wang

address: 247 Beiyuan Street, Jinan 250033, Shandong, China,

institute: The Second Hospital of Shandong University

description: normal PBMCs sample

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation850 Beadchip using standard Illumina protocol

scan_protocol: standard Illumina protocol

data_processing: Average Beta

label: Cy5, Cy3

extract_protocol: genomic DNA was extracted and purified from PBMC samples using Qiagen DNeasy Kit according to standard instructions

tag: gender

value: Male

tag: sample type

value: PBMCs

tag: disease state

value: normal


title: WT AP1


title: Fundus (corpus), post-SG patient 5, scRNAseq

description: 10X Genomics

tag: treatment


title: Col-0_rep1

tag: tissue

tag: genotype


title: WT AP2


title: genomic DNA from NC_214

description: normal PBMCs sample


title: genomic DNA from NC_210

description: normal PBMCs sample


title: genomic DNA from NC_195

description: normal PBMCs sample


title: genomic DNA from NC_215

description: normal PBMCs sample


title: genomic DNA from NC_206

description: normal PBMCs sample


title: genomic DNA from NC_188

description: normal PBMCs sample


title: Col-0_rep3


title: genomic DNA from NC_192

description: normal PBMCs sample


title: genomic DNA from Nc_62

description: normal PBMCs sample


title: genomic DNA from NC_65

description: normal PBMCs sample


title: genomic DNA from NC_155

description: normal PBMCs sample


title: genomic DNA from NC_185

description: normal PBMCs sample


title: genomic DNA from NC_49

description: normal PBMCs sample


title: genomic DNA from NC_61

description: normal PBMCs sample


title: genomic DNA from NC_58

description: normal PBMCs sample


title: genomic DNA from NC_54

description: normal PBMCs sample


title: genomic DNA from NC_56

description: normal PBMCs sample


title: genomic DNA from NC_52

description: normal PBMCs sample


title: genomic DNA from NC_38

description: normal PBMCs sample


title: genomic DNA from NC_36

description: normal PBMCs sample


title: genomic DNA from NC_69

description: normal PBMCs sample


title: genomic DNA from NC_67

description: normal PBMCs sample


title: genomic DNA from NC_50

description: normal PBMCs sample


title: genomic DNA from NC_213

description: normal PBMCs sample


title: genomic DNA from NC_202

description: normal PBMCs sample


title: genomic DNA from NC_35

description: normal PBMCs sample


title: genomic DNA from NC_20

description: normal PBMCs sample


title: genomic DNA from NC_184

description: normal PBMCs sample


title: genomic DNA from NC_21

description: normal PBMCs sample


title: genomic DNA from NC_37

description: normal PBMCs sample


title: genomic DNA from NC_19

description: normal PBMCs sample


title: genomic DNA from NC_46

description: normal PBMCs sample


title: genomic DNA from NC_57

description: normal PBMCs sample


title: genomic DNA from NC_42

description: normal PBMCs sample


title: genomic DNA from NC_45

description: normal PBMCs sample


title: genomic DNA from NC_34

description: normal PBMCs sample


title: genomic DNA from NC_44

description: normal PBMCs sample


title: genomic DNA from NC_43

description: normal PBMCs sample


title: genomic DNA from NC_32

description: normal PBMCs sample


title: genomic DNA from NC_53

description: normal PBMCs sample


title: genomic DNA from NC_30

description: normal PBMCs sample


title: genomic DNA from NC_24

description: normal PBMCs sample


title: genomic DNA from NC_27

description: normal PBMCs sample


title: genomic DNA from NC_17

description: normal PBMCs sample


title: genomic DNA from NC_47

description: normal PBMCs sample


title: genomic DNA from NC_5

description: normal PBMCs sample


title: genomic DNA from L_135

description: LUAD PBMCs sample

value: LUAD


title: genomic DNA from L_169

description: LUAD PBMCs sample


title: genomic DNA from NC_3

description: normal PBMCs sample


title: genomic DNA from NC_7

description: normal PBMCs sample


title: genomic DNA from L_20

description: LUAD PBMCs sample


title: genomic DNA from LC_46

description: LUAD PBMCs sample


title: genomic DNA from LC_61

description: LUAD PBMCs sample


title: genomic DNA from LC_55

description: LUAD PBMCs sample


title: genomic DNA from LC_85

description: LUAD PBMCs sample


title: genomic DNA from NC_41

description: normal PBMCs sample


title: genomic DNA from LC_28

description: LUAD PBMCs sample


title: genomic DNA from LC_11

description: LUAD PBMCs sample


title: genomic DNA from LC_44

description: LUAD PBMCs sample


title: genomic DNA from LC_58

description: LUAD PBMCs sample


title: genomic DNA from L_10

description: LUAD PBMCs sample


title: genomic DNA from LC_69

description: LUAD PBMCs sample


title: genomic DNA from LC_57

description: LUAD PBMCs sample


title: genomic DNA from LC_83

description: LUAD PBMCs sample


title: genomic DNA from LC_33

description: LUAD PBMCs sample


title: genomic DNA from LC_48

description: LUAD PBMCs sample


title: genomic DNA from LC_32

description: LUAD PBMCs sample


title: genomic DNA from NC_11

description: normal PBMCs sample


title: genomic DNA from LC_4

description: LUAD PBMCs sample


title: Antrum, naive patient 17, scRNAseq

description: 10X Genomics

value: Gastric Antrum

value: naive


title: genomic DNA from L_136

description: LUAD PBMCs sample


title: genomic DNA from L_96

description: LUAD PBMCs sample

value: Female


title: genomic DNA from L_88

description: LUAD PBMCs sample


title: genomic DNA from L_120

description: LUAD PBMCs sample


title: genomic DNA from L_38

description: LUAD PBMCs sample


title: genomic DNA from L_157

description: LUAD PBMCs sample


title: genomic DNA from LC_97

description: LUAD PBMCs sample


title: genomic DNA from LC_96

description: LUAD PBMCs sample


title: genomic DNA from L_117

description: LUAD PBMCs sample


title: genomic DNA from LC_17

description: LUAD PBMCs sample


title: genomic DNA from LC_16

description: LUAD PBMCs sample


title: N2 embryos, 20oC, rep2

extract_protocol:
Frozen worm aliquots were thawed, 300 µL of TRIzol (Life Technologies, 15596026) were added and mixed vigorously. Six freeze-thaw cycles were employed to dissolve animals, specifically by freezing tubes in liquid nitrogen for approximately 30 seconds, and subsequent thawing for approximately 3 minutes. After each cycle, tubes were mixed vigorously. After the sixth freeze-thaw cycle, samples were spun down at 20,000 G for 3 minutes and the supernatant was subsequently collected into a fresh tube. Next, 1 volume of 100% ethanol was added to the sample and mixed vigorously. Finally, the mixtures were loaded onto Direct-zol columns (Zymo Research, R2060) and manufacturer’s instructions were followed. In-column DNase I treatment was included.
Quality control of samples, library preparation (non-directional, with poly-A enrichment), and mRNA sequencing (Illumina, PE150) was performed by Novogene.

value: Whole animal

value: embryo (mixed stages)

value: wild-type

value: Grown at 20oC


title: Th1_cells, TMEM11KO, Day4, biorep3

city: Los Angeles

first: Yousang

last: Gwack

state: CA

address: 10833 Le Conte Ave, 53-159 CHS

department: Physiology

institute: Uuniversity of California Los Angeles

description:
Library name: Sample6
Column names in raw_count file: TMEM11KO_3-1_Raw_Read_Counts, TMEM11KO_3-2_Raw_Read_Counts (technical replicates)

data_processing:
Data quality check was done on Illumina SAV. Demultiplexing was performed with Illumina Bcl2fastq v2.19.1.403 software
The reads were mapped by STAR 2.7.9a and read counts per gene were quantified using the mouse Ensembl GRCm39.105 GTF file.
In Partek Flow, read counts were normalized by CPM +1.0E-4.
Assembly: mm10
Supplementary files format and content: tab-delimited files include RAW and CPM normalized counts for each sample

source_name: Lymph nodes, Spleen

growth_protocol: Naive CD4+ T-cells were isolated and purified from either wild-type or TMEM11 KO mice. Naïve CD4+ T cells were enriched by magnetic sorting from single-cell suspensions generated by mechanical disruption of spleens and lymph nodes of adult mice using MagniSort naïve CD4+ T cell enrichment kit (catalog # 8804-6824-74,ThermoFisher Scientific). For effector T cell differentiation, cells were stimulated with anti-CD3 antibody (1452C11, Bio X Cell) and anti-CD28 antibody (Clone 37.51, Bio X Cell) for 48 hours on a plate coated with rabbit anti-hamster antibody (MP Biomedicals). After 48 h, cells were taken off the plate and cultured in medium containing 10 U/ml recombinant human IL-2 (NCI Preclinical repository, for Th1 cells) for two days. At day 4 post isolation, ~3 million control and Tmem11−/− Th1 cells were stimulated with anti-CD3 and anti-CD28 antibodies for 5 h and harvested in TriZol reagent (Invitrogen) for RNA preparation

extract_protocol:
~3 million control and Tmem11−/− Th1 cells were harvested in TriZol reagent (Invitrogen) for RNA preparation. RNA was isolated using RNA purification kit (ThermoFisher Scientific), quantified and used for purification of mRNA, cDNA synthesis and library preparation using  KAPA stranded RNA seq-kit Sample following manufacturer’s instructions.
Libraries for RNA-Seq were prepared with KAPA Stranded RNA-Seq Kit. The workflow consists of depletion of rRNA by hybridization of complementary DNA oligonucleotides, followed by treatment with RNase H and DNase and RNA fragmentaion. First strand cDNA synthesis using random priming followed by second strand synthesis converting cDNA:RNA hybrid to double-stranded cDNA (dscDNA), and incorporates dUTP into the second cDNA strand. cDNA generation is followed by A-tailing, adaptor ligation and PCR amplification. Different adapters were used for multiplexing samples in one lane. Sequencing was performed on Illumina HiSeq3000 for a SE 1x50 run. Data quality check was done on Illumina SAV. Demultiplexing was performed with Illumina Bcl2fastq v2.19.1.403 software.

treatment_protocol: Wild-type vs TMEM11 Knock-Out (Genetic System)

value: Lymph nodes, Spleen

value: knock-out (TMEM11)

tag: batch


title: Th1_cells, Control, Day4, biorep2

description:
Library name: Sample2
Column names in raw_count file: Control_2-1_Raw_Read_Counts, Control_2-2_Raw_Read_Counts (technical replicates)

value: Wild-type


title: Th1_cells, Control, Day4, biorep1

description:
Library name: Sample1
Column names in raw_count file: Control_1-1_Raw_Read_Counts, Control_1-2_Raw_Read_Counts (technical replicates)


title: Th1_cells, TMEM11KO, Day4, biorep1

description:
Library name: Sample4
Column names in raw_count file: TMEM11KO_1-1_Raw_Read_Counts, TMEM11KO_1-2_Raw_Read_Counts (technical replicates)


title: genomic DNA from LC_7

description: LUAD PBMCs sample


title: Th1_cells, Control, Day4, biorep3

description:
Library name: Sample3
Column names in raw_count file: Control_2-1_Raw_Read_Counts, Control_2-2_Raw_Read_Counts (technical replicates)


title: genomic DNA from L_167

description: LUAD PBMCs sample


title: Chelonus formosanus,female,head,day1

city: haikou

first: qiujiu

last: cai

address: No. 14 Xingdan Road

institute: Institute of Plant Protection, Hainan Academy of Agricultural Sciences, China

description: Library name: sampleA-1

data_processing:
All assembled Unigenes were aligned against the non-redundant (Nr) protein database (http://www.ncbi.nlm.nih.gov/),Gene ontology (GO)(http://www.geneontology.org), SwissProt(http://www.expasy.ch/sprot/), Kyoto Encyclopedia of Genes and Genomes (KEGG)(http://www.genome.jp/kegg/) and eggNOG(http://eggnogdb.embl.de/) databases using DIAMOND with a threshold of Evalue<0.00001.
Assembly: No genome construction/assembly was used
Supplementary files format and content: processed data.xlsx files include Fold Change values for each Sample

organism: Chelonus formosanus

source_name: head

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 1000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0. Poly(A) RNA is purified from total RNA(5ug) using poly-T oligo-attached magnetic beads using two rounds of purification. Following purification, the mRNA is fragmented into smallpieces using divalent cations under elevated temperature. Then the cleaved RNA fragments werereverse-transcribed to create the final cDNA library in accordance with the protocol for the mRNASeq sample preparation kit (Illumina, San Diego, USA), the average insert size for the paired-endlibraries was 300 bp (±50 bp). And then we performed the paired-end sequencing on an Illumina Novaseq™ 6000 at the (LC Sceiences,USA) following the vendor’s recommended protocol.
Firstly, Cutadapt and perl scripts in house were used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases. Then sequence quality was verified using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). including the Q20, Q30 and GC-content of the clean data. All downstream analyses were based on clean data of high quality. De novo assembly of the transcriptome was performed with Trinity 2.4.0. Trinity groups transcripts into clusters based on shared sequence content. Such a transcript cluster is very loosely referred to as a 'gene'. The longest transcript in the cluster was chosen as the 'gene' sequence (aka Unigene).

value: female

value: head


title: Chelonus formosanus,female,head,day1,rep3

description: Library name: sampleA-3


title: Chelonus formosanus,male,head,day1

description: Library name: sampleB-1

value: male


title: genomic DNA from L_80

description: LUAD PBMCs sample

value: Male


title: Chelonus formosanus,female,head,day1,rep2

description: Library name: sampleA-2


title: Chelonus formosanus,male,head,day1,rep2

description: Library name: sampleB-2


title: genomic DNA from L_60

description: LUAD PBMCs sample

value: PBMCs


title: genomic DNA from LC_2

description: LUAD PBMCs sample


title: Chelonus formosanus,male,head,day1,rep3

description: Library name: sampleB-3


title: RNA seq, Leaf surface wash, replicate 1

city: Davis

first: Patricia

last: Baldrich Gonzalez

address: 451 Health Sciences Dr., Davis, CA 95616

department: Genome Center

institute: University of California - Davis

description: Library name: RNAseq_LSW_R1

data_processing:
We sent all sRNA and RNAseq libraries for sequencing to the University of Delaware Sequencing and Genotyping Center, where they were sequenced on a NovaSeq2000 instrument using 50-bp single-end reads for sRNA and 75-bp paired-end reads for RNAseq.
For sRNA libraries we first trimmed the adaptors using Cutadapt version 1.16 using a minimum insert size of 10 nt and no maximum. We assessed sequence quality using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/ fastqc/). We aligned clean reads to the Arabidopsis genome (TAIR version 10) and all subsequent analyses were performed using the software Bowtie2. For miRNA analyses, we used the latest version of miRBase (version 22).
For RNA-seq libraries were analyzed using HiSat2 and Stringtie pipeline, and the TAIR10 available annotation file.
Assembly: Arabidopsis genome (TAIR version 10)
Supplementary files format and content: small RNA seq.: microRNA count files
Supplementary files format and content: RNAseq.: gtf count files

source_name: Leaf

growth_protocol: Arabidopsis thaliana Col-0 seeds were grown in a temperature-controlled room under a 9 h light/15 h dark photoperiod with 150 μmol ms photosynthetic photon fl ux density.

extract_protocol:
Total leaf RNA (cell lysate) was extracted from 100 mg of leaf tissue using TRIzol Reagent (Thermo Fisher Scientifi c™, Waltham, MA)
sRNA libraries were constructed using the RealSeq-AC kit version 2 (Realseq Biosciences, Santa Cruz, CA, catalog no. 500-00048;) as per the manufacturer’s instructions. For RNAseq libraries, we used NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs, catalog no. E7760L) protocol.

value: Leaf

value: Columbia 0


title: RNA seq, Cell lysate, not ribodepleted, replicate 2

description: Library name: RNAseq_CL_NT_R2


title: Th1_cells, TMEM11KO, Day4, biorep2

description:
Library name: Sample5
Column names in raw_count file: TMEM11KO_2-1_Raw_Read_Counts, TMEM11KO_2-2_Raw_Read_Counts (technical replicates)


title: RNA seq, Cell lysate, not ribodepleted, replicate 3

description: Library name: RNAseq_CL_NT_R3


title: RNA seq, Leaf surface wash, replicate 2

description: Library name: RNAseq_LSW_R2


title: RNA seq, Leaf surface wash, replicate 3

description: Library name: RNAseq_LSW_R3


title: RNA seq, Cell lysate, not ribodepleted, replicate 1

description: Library name: RNAseq_CL_NT_R1


title: RNA seq, Cell lysate, ribodepleted, replicate 2

description: Library name: RNAseq_CL_R2


title: RNA seq, Apoplastic washing fluid, replicate 2

description: Library name: RNAseq_AWF_R2


title: RNA seq, Cell lysate, ribodepleted, replicate 3

description: Library name: RNAseq_CL_R3


title: RNA seq, Apoplastic washing fluid, replicate 1

description: Library name: RNAseq_AWF_R1


title: RNA seq, Apoplastic washing fluid, replicate 3

description: Library name: RNAseq_AWF_R3


title: RNA seq, Cell lysate, ribodepleted, replicate 1

description: Library name: RNAseq_CL_R1


title: small RNA seq, Cell lysate, replicate 3

description: Library name: sRNAseq_CL_R3


title: small RNA seq, Cell lysate, replicate 2

description: Library name: sRNAseq_CL_R2


title: small RNA seq, Cell lysate, replicate 1

description: Library name: sRNAseq_CL_R1


title: small RNA seq, Apoplastic washing fluid, replicate 3

description: Library name: sRNAseq_AWF_R3


title: small RNA seq, Leaf surface wash, replicate 1

description: Library name: sRNAseq_LSW_R1


title: small RNA seq, Apoplastic washing fluid, replicate 2

description: Library name: sRNAseq_AWF_R2


title: small RNA seq, Leaf surface wash, replicate 2

description: Library name: sRNAseq_LSW_R2


title: Flood, H2O keep 1" above the soil level , 28°C, biol rep1

city: Serdang

first: Sime Darby

middle: Plantation

last: Technology Centre

state: Selangor

address: 1st Floor, Block B, UPM-MTDC, Universiti Putra Malaysia

department: Biotechnology & Breeding

country: Malaysia

institute: Sime Darby Plantation Technology Centre Sdn Bhd

description:
fpkm_flood.txt
readcount_flood.txt

data_processing:
Clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Clean reads were mapped onto oil palm reference genome using TopHat2 algorithm with a maximum mismatch set at 2.
Gene expression level was quantified using fragments per kilobase of transcript over million mapped reads (FPKM) method and analysed using HTSeq software
Assembly: PRJNA192219
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample
Supplementary files format and content: tab-delimited text files include raw counts for each Sample

organism: Elaeis guineensis

source_name: leaves

extract_protocol:
Total RNA of oil palm leaves was extracted from control and treated seedlings using MN Nucleospin RNA Plant Kit (Macherey-Nagel, Germany) according to the manufacturer's instructions.
A total amount of 3 μg RNA per sample was used for sequencing libraries generation using NEBNext® Ultra™ RNA Library Prep Kit from Illumina® (NEB, USA) following the manufacturer’s recommendations.

value: leaves

value: wildtype

value: Flood


title: Cold, 200 mL H2O, 10°C, biol rep1

description:
fpkm_cold.txt
readcount_cold.txt

value: Cold


title: Heat, 200 mL H2O, 40°C, biol rep3

description:
fpkm_heat.txt
readcount_heat.txt

value: Heat


title: Flood, H2O keep 1" above the soil level , 28°C, biol rep3

description:
fpkm_flood.txt
readcount_flood.txt


title: Cold, 200 mL H2O, 10°C, biol rep2

description:
fpkm_cold.txt
readcount_cold.txt


title: Heat, 200 mL H2O, 40°C, biol rep2

description:
fpkm_heat.txt
readcount_heat.txt


title: Flood, H2O keep 1" above the soil level , 28°C, biol rep2

description:
fpkm_flood.txt
readcount_flood.txt


title: Cold, 200 mL H2O, 10°C, biol rep3

description:
fpkm_cold.txt
readcount_cold.txt


title: Salinity, 200 mL 0.2M NaCl, 28°C, biol rep1

description:
fpkm_NaCl.txt
readcount_NaCl.txt

value: Salinity


title: Salinity, 200 mL 0.2M NaCl, 28°C, biol rep2

description:
fpkm_NaCl.txt
readcount_NaCl.txt


title: Heat, 200 mL H2O, 40°C, biol rep1

description:
fpkm_heat.txt
readcount_heat.txt


title: Drought, 0 mL H2O, 28°C, biol rep1

description:
fpkm_dro.txt
readcount_dro.txt

value: Drought


title: small RNA seq, Leaf surface wash, replicate 3

description: Library name: sRNAseq_LSW_R3


title: Control, 200 mL H2O, 28°C, biol rep3

description:
fpkm_ctrl.txt
readcount_ctrl.txt

value: Control


title: Control, 200 mL H2O, 28°C, biol rep2

description:
fpkm_ctrl.txt
readcount_ctrl.txt


title: Drought, 0 mL H2O, 28°C, biol rep2

description:
fpkm_dro.txt
readcount_dro.txt


title: Control, 200 mL H2O, 28°C, biol rep1

description:
fpkm_ctrl.txt
readcount_ctrl.txt


title: Salinity, 200 mL 0.2M NaCl, 28°C, biol rep3

description:
fpkm_NaCl.txt
readcount_NaCl.txt


title: Tha2P4M(MOI 0.5)_Rep_A

city: Portland

first: Arpiar

middle: B

last: Saunders

state: OR

address: 3232 SW Research Dr

institute: Vollum Institute (Oregon Health and Sciences University)

description:
Library name: A_2P4M_05
Chromium Next GEM Single Cell 3ʹ Kit v3.1 (10x Genomics)

data_processing:
CellRanger (10x Genomics; v5.0.1)
Assembly: GRCh38 & Tha RABV
Supplementary files format and content: H5 Digital Gene Expression (DGE) Matrix

source_name: hNSC-derived astrocytes/neurons; hiPSC-derived microglia

extract_protocol:
Chromium Next GEM Single Cell 3ʹ Kit v3.1 (10x Genomics)
Chromium Next GEM Single Cell 3ʹ Kit v3.1 (10x Genomics)

tag: cell line

value: hNSC, EnStem-A SCC003, Millipore; Human induced macrophage-like cells (Takata et al. 2017)

value: neurons/astrocytes/microglia

value: Tha2P4M(MOI 0.5) RABV


title: Drought, 0 mL H2O, 28°C, biol rep3

description:
fpkm_dro.txt
readcount_dro.txt


title: Tha(MOI 0.5)_Rep_C

description:
Library name: C_Tha_05
Chromium Next GEM Single Cell 3ʹ Kit v3.1 (10x Genomics)

value: hNSC-derived astrocytes/neurons; hiPSC-derived microglia

value: Tha(MOI 0.5) RABV


title: Tha2P4M(MOI 0.5)_Rep_B

description:
Library name: B_2P4M_05
Chromium Next GEM Single Cell 3ʹ Kit v3.1 (10x Genomics)


title: Tha(MOI 5)_Rep_A

description:
Library name: A_Tha_5
Chromium Next GEM Single Cell 3ʹ Kit v3.1 (10x Genomics)

value: Tha(MOI 5.0) RABV


title: Tha(MOI 0.5)_Rep_B

description:
Library name: B_Tha_05
Chromium Next GEM Single Cell 3ʹ Kit v3.1 (10x Genomics)


title: Tha(MOI 5)_Rep_B

description:
Library name: B_Tha_5
Chromium Next GEM Single Cell 3ʹ Kit v3.1 (10x Genomics)


title: No Infection_Rep B

description:
Library name: B_NI_0
Chromium Next GEM Single Cell 3ʹ Kit v3.1 (10x Genomics)

value: No RABV


title: No Infection_Rep C

description:
Library name: C_NI_0
Chromium Next GEM Single Cell 3ʹ Kit v3.1 (10x Genomics)


title: Tha(MOI 0.5)_Rep_A

description:
Library name: A_Tha_05
Chromium Next GEM Single Cell 3ʹ Kit v3.1 (10x Genomics)


title: small RNA seq, Apoplastic washing fluid, replicate 1

description: Library name: sRNAseq_AWF_R1

value: Leaf


title: No Infection_Rep A

description:
Library name: A_NI_0
Chromium Next GEM Single Cell 3ʹ Kit v3.1 (10x Genomics)


title: PB2-p95HER2 tumor 648, day 22

city: Pittsburgh

first: Dong

last: Hu

address: 530 45th Street

institute: University of Pittsburgh

data_processing:
RNA-seq fastq files were aligned to the mouse reference genome mm10. VIPER pipeline was used for data QC and processing. Briefly, STAR (v2.4.2a) was used for alignment and converted to raw counts. Genes with 0 counts across all samples were filtered out. Differentially expressed genes were identified using DESeq2 with raw counts as input.
Assembly: mm10
Supplementary files format and content: CSV file includes CPMs for each sample

source_name: Breast cancer

extract_protocol:
RNA was harvested using RNeasy mini plus kit (Qiagen).
Directional mRNA library preparation (poly A enrichment)

value: Breast cancer


title: PB2-p95HER2 tumor 646, day 22


title: ES2_Combination

city: Wenzhou

first: Kejie

last: Chen

state: Zhejiang

address: Chashan

institute: Wenzhou Medical University

description:
Library name: sample8
with Annonacin and Carboplation

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9). We aligned reads of all samples to the research species reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.2.1) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-2.1.6) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Genes differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples). The genes with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change ≥ 2 were considered differentially expressed genes. Differentially expressed genes were then subjected to enrichment analysis of GO functions and KEGG pathways.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: Human ovarian cancer cells A2780

growth_protocol: Cells were incubated at 37 ℃ in 5% CO2 and maintained in 5A medium with 10% FBS and 100 U/mL penicillin and streptomycin.

extract_protocol:
Total RNA was extracted using Trizol reagent (thermofisher, 15596018) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA, 5067-1511) , high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.
mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA). An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys were 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina NovaseqTM 6000 following the vendor's recommended protocol.

treatment_protocol: A2780 and ES2 cells (3 × 105 cells/well in 6-well plates) were treated with Annonacin or carboplatin or the combination of Annonacin and carboplatin for 48 h. After treatment, the cells were collected, and total RNA from each group was extracted using TRIzol (TaKaRa, Japan). Paired-end sequencing was ultimately carried out on an Illumina HiSeq 4000 platform at LC-BIO Technologies (Hangzhou, China).

value: Human ovarian cancer cells A2780

value: Epithelial cell

value: WT

value: total RNA

value: paired-end


title: ES2_Carboplation

description:
Library name: sample7
with Carboplation


title: ES2_Annonacin

description:
Library name: sample6
with Annonacin


title: ES2_Control-untreated

description:
Library name: sample5
without any drugs


title: A2780_Combination

description:
Library name: sample4
with Annonacin and Carboplation


title: PB2-p95HER2 tumor 602, day 22


title: A2780_Carboplation

description:
Library name: sample3
with Carboplation


title: A2780_Annonacin

description:
Library name: sample2
with Annonacin


title: PB2-p95HER2 tumor 601, day 22


title: A2780_Control-untreated

description:
Library name: sample1
without any drugs


title: PB2-p95HER2 tumor 600, day 22


title: PB2-p95HER2 tumor 593, day 22


title: PB2-p95HER2 tumor 591, day 22


title: PB2-p95HER2 tumor 598, day 22


title: PB2-p95HER2 tumor 586, day 10


title: PB2-p95HER2 tumor 585, day 10


title: PB2-p95HER2 tumor 582, day 10


title: PB2-p95HER2 tumor 583, day 10


title: PB2-p95HER2 tumor 580, day 10


title: PB2-p95HER2 tumor 577, day 10


title: PB2-p95HER2 tumor 605, day 22


title: PB2-p95HER2 tumor 584, day 10


title: PB2-FL-HER2 tumor 624, day 22


title: PB2-FL-HER2 tumor 647, day 22


title: PB2-p95HER2 tumor 578, day 10


title: PB2-FL-HER2 tumor 620, day 22


title: PB2-FL-HER2 tumor 619, day 22


title: PB2-FL-HER2 tumor 614, day 22


title: PB2-FL-HER2 tumor 612, day 22


title: PB2-FL-HER2 tumor 613, day 22


title: PB2-p95HER2 tumor 604, day 22


title: PB2-FL-HER2 tumor 618, day 22


title: PB2-FL-HER2 tumor 6363, day 10


title: PB2-FL-HER2 tumor 639, day 10


title: PB2-FL-HER2 tumor 64042, day 10


title: PB2-FL-HER2 tumor 635, day 10


title: PB2-FL-HER2 tumor 60834, day 10


title: PB2-p95HER2 tumor 588, day 10


title: PB2-p95HER2 tumor 590, day 10


title: PB2-FL-HER2 tumor 60744, day 10


title: PB2-FL-HER2 tumor 60643, day 10


title: muscle, cums, rep3

first: Jiayao

last: Zhang

address: NO.1239, Republican New Road

institute: Stomatological Hospital and Dental School of Tongji University

data_processing:
Raw data (raw reads) of fastq format were firstly processed through custom perl and python scripts.Then, chose a certain range of length from clean reads to do all the downstream analyses. The small RNA tags were mapped to reference sequence by Bowtie (0.12.9) (Langmead et al., 2009) without mismatch to analyze their expression and distribution on the reference.
Mapped small RNA tags were used to looking for known miRNAs. miRBase20.0 was used as the reference, and the modified software mirdeep2 (0.0.5) and sRNA-tools-cli were used to obtain the potential miRNA and draw the secondary structures. The software miREvo (v1.1) and mirdeep2 were integrated to predict novel miRNAs.
miRNA expression levels were estimated by TPM (transcript per million) through the following criteria (Zhou et al., 2010):Normalization formula: Normalized expression = mapped readcount/Total reads*1000000
For the samples with biological replicates:Differential expression analysis of two conditions/groups was performed using the DESeq R package (3.0.3). 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.
Gene Ontology (GO) enrichment analysis was used on the target gene candidates of differentially expressed miRNAs.We used KOBAS (Maoet al., 2005) software to test the statistical enrichment of the target gene candidates in KEGG pathways.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes TPM values for each Sample

source_name: femur

extract_protocol:
Total RNA was extracted from M-exos and HM-exos using the Trizol reagent (Takara Biotechnology, Japan; 9109), and RNA integrity was assessed using a 2100 bioanalyzer (Agilent Technologies, CA, USA).
An Illumina TruSeq Small RNA kit (Illumina, San Diego, CA, USA) was used to construct the library, and a high-throughput sequencing platform was used to sequence the enriched 18–32 nt Small RNA fragments.

value: femur

value: CUMS


title: PB2-FL-HER2 tumor 623, day 22


title: muscle, cums, rep2


title: muscle, cums, rep1


title: muscle, control, rep2

value: CON


title: muscle, control, rep1


title: PB2-p95HER2 tumor [P1959]

description: Directional mRNA library preparation

data_processing:
Data processing service was provided by Novogene who also did RNA-seq.
STAR (v2.5) was used for read mapping.
HTSeq v0.6.1 was used to count the read numbers mapped of each gene.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include raw counts for each Sample

source_name: Tumor

growth_protocol: PB2 cells were maintained in DMEM/F12 supplemented with 10% adult bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37ºC.

extract_protocol:
RNA was harvested using RNeasy mini plus kit (Qiagen).
RNA libraries for RNA-seq were prepared using NEBNext Ultra II Directional RNA Library Prep Kit for Illumina following manufacturer's protocols.
mRNA enrichment and directional RNA library preparation.

treatment_protocol: Mice were placed under doxycycline diet DOX625.

value: Tumor

value: Mouse breast cancer cells

value: Doxycycline diet DOX625


title: 7822-JF-9

city: Ann Arbor

first: Poulami

last: Dey

address: 1301 Catherine St

institute: Michigan Medicine

data_processing:
For bulk RNA-seq, tissue was processed, RNA was isolated as previously described by our group (38), and 150bp paired-end reads were generated. The reads were adapter trimmed and aligned to the human genome hg38, with only the uniquely mapped reads used for expression level quantification. DESeq2 was used to perform read normalization and differential expression analyses.
Assembly: hg38
Supplementary files format and content: gene by sample count matrix

source_name: skin

extract_protocol:
Fresh frozen tissue via 3 mm punch biopsies were collected from LP lesional skin and normal appearing skin for bulk RNA-sequencing.
RNA sequencing was performed by the U-M Advanced Genomics Core on the Novaseq 6000 platform

value: skin


title: PB2-p95HER2 tumor [P1957]

description: Directional mRNA library preparation


title: PB2-p95HER2 tumor [P1960]

description: Directional mRNA library preparation


title: PB2-p95HER2 tumor [P1954]

description: Directional mRNA library preparation


title: PB2-p95HER2 tumor [P1955]

description: Directional mRNA library preparation


title: PB2-FL-HER2 tumor 63032, day 10


title: 7822-JF-7


title: 7822-JF-6


title: PB2-p95HER2 tumor [P1576]

description: Directional mRNA library preparation


title: PB2-FL-HER2 tumor 60929, day 10


title: PB2-FL-HER2 tumor 62633, day 10


title: PB2-p95HER2 tumor [P1947]

description: Directional mRNA library preparation


title: PB2-EV tumor [E1973]

description: Directional mRNA library preparation

value: EV


title: 7822-JF-49


title: 7822-JF-8


title: 7822-JF-5


title: PB2-EV tumor [E1971]

description: Directional mRNA library preparation


title: PB2-p95HER2 tumor [P1952]

description: Directional mRNA library preparation


title: 7822-JF-50


title: 7822-JF-4


title: 7822-JF-47


title: PB2-EV tumor [E1970]

description: Directional mRNA library preparation


title: Notch 2 ICD Stage 38 Sample 1

city: Williamsburg

first: Margaret

middle: S

last: Saha

state: Virginia

address: 540 Landrum Drive

department: Biology

institute: College of Wiliam & Mary

description:
Illumina- NovaSeq S1 - PE 150 Cycle
Column 1: gene symbol, Column 2: Counts

data_processing:
Quality checks were performed on the raw data using FASTQC . If adapters were present, the sequences were trimmed with Trim Galore
Sequences were aligned to the reference Xenopus laevis genome using HISAT2 and sorted by name
Ran HTSeq counts program on terminal to obtain counts for genes
Assembly: Xenopus laevis 10.1 genome (NCBI)
Supplementary files format and content: tab delimited text file that includes the HTSeq counts for each sample along with gene symbols

organism: Xenopus laevis

source_name: Xenopus laevis embryos (neurula, tailbud, swimming tadpole stages)

extract_protocol:
RNA was extracted with 4-bromoanisole and purified using the RNeasy Mini Kit (Qiagen)
RNA libraries for RNA-seq were prepared using Illumina Truseq Stranded mRNA Prep Kit following manufacturer's protocols.

tag: time

value: Stage 38 (swimming tadpole stage)

value: ICD treatment


title: Notch 2 ICD Stage 38 Sample 2

value: Xenopus laevis embryos (neurula, tailbud, swimming tadpole stages)


title: PB2-EV tumor [E1968]

description: Directional mRNA library preparation


title: Notch 2 ICD Stage 28 Sample 3

value: Stage 28 (tailbud stage)


title: 7822-JF-48


title: PB2-EV tumor [E1967]

description: Directional mRNA library preparation


title: Notch 2 ICD Stage 38 Sample 3


title: 7822-JF-44


title: 7822-JF-46


title: Notch 2 ICD Stage 28 Sample 2


title: Notch 2 ICD Stage 18 Sample 3

value: Stage 18 (neurula stage)


title: PB2-EV tumor [E1965]

description: Directional mRNA library preparation


title: Notch 2 ICD Stage 18 Sample 1


title: Notch 2 ICD Stage 18 Sample 2


title: 7822-JF-43


title: PB2-EV tumor [E1963]

description: Directional mRNA library preparation


title: Notch 2 GFP Stage 38 Sample 3

value: GFP treatment


title: PB2-EV tumor [E1962]

description: Directional mRNA library preparation


title: Notch 2 GFP Stage 38 Sample 2


title: 7822-JF-42


title: 7822-JF-41


title: Ctrl, Heart failure, Visium

city: Tsukuba

first: Yu

last: Yamada

state: Ibaraki

address: 1-1-1 Tennoudai

department: Cardiovascular

institute: University of Tsukuba

description: 10x Genomics

data_processing:
Library strategy: Spatial Transcriptomics (Visium)
10X Genomics' Spaceranger v1.0.0 pipeline was used to perform sample demultiplexing, reads alignment, and to generate feature-spot matrices. The reads were aligned to the mm10/GRCm38 reference transcriptome. The H&E staining image was supplemented to Spaceranger for tissue detection, fiducial detection, and alignment of the spatial position of sequenced data points.
Assembly: mm10
[slide information]  A_Ctrl:slide=V11Y10-334,area=A1; C_TTg_HF:slide=V11Y10-334,area=C1; D_Ctrl_HF:slide=V11Y10-334,area=D1
[sample Slide Serial Number]  AreaTIFA_CtrlV11Y10-334A1220207_HE_x10_A_Ctrl.tifC_TTg_HFV11Y10-334C1220207_HE_x10_C_TTg_HF.tifD_Ctrl_HFV11Y10-334D1220207_HE_x10_D_Ctrl_HF.tif
Supplementary files format and content: h5 format: Matrix with raw counts for every gene and every spot, filtered to include spots under tissue
Supplementary files format and content: Hematoxylin and Eosin (HE) image in TIF format
Supplementary files format and content: High resolution Hematoxylin and Eosin (HE) image in PNG format
Supplementary files format and content: Low resolution Hematoxylin and Eosin (HE) image in PNG format
Supplementary files format and content: Table with array and pixel coordinates
Supplementary files format and content: Scalefactors in json format

source_name: heart transverse section

extract_protocol:
Mice were sacrificed by CO2 inhalation, and hearts were immediately cannulated and perfused with cold PBS. Remove the hearts, create formalin-fixed, paraffin-embedded (FFPE) blocks. Heart FFPE blocks were sectioned (5μm) and placed on the already barcoded spots on the glass slide.
cDNA libraries were prepared for sequencing following the 10x Genomics Visium protocol

treatment_protocol: The HFpEF (Heart failure with preserved ejection fraction) model was induced by administering a high-fat diet (HFD, 60% kilocalories from fat) and Nω-Nitro-L-arginine methyl ester hydrochloride (L-NAME, Sigma, Cat# N5751-25G) for 15 weeks. L-NAME was dissolved in drinking water (1.0 g/L）. Tamoxifen (2 mg/day; Sigma, T5648) was administered intraperitoneally for 5 consecutive days at week 5.

value: heart transverse section

tag: strain

value: hybrid of C57BL/6 and ICR

value: Tcf21iCre/R26 tdTomato

value: male

value: LNAME+High fat diet, tamoxifen i.p. at week 5

tag: group


title: Notch 2 ICD Stage 28 Sample 1


title: 7822-JF-40


title: Notch 2 GFP Stage 18 Sample 3


title: Notch 2 GFP Stage 28 Sample 1


title: 7822-JF-3


title: TTg, Heart failure, Visium

description: 10x Genomics

value: Tcf21iCre/R26 tdTomato/MGTH2A


title: PB2-EV tumor [E1974]

description: Directional mRNA library preparation

value: Tumor

tag: cell type


title: 7822-JF-39


title: Notch 2 GFP Stage 18 Sample 1


title: Notch 2 GFP Stage 18 Sample 2


title: Notch 2 GFP Stage 28 Sample 3


title: Tpex KO rep1

city: Clayton

first: Wei

last: Shi

state: Victoria

address: 15 Innovation Walk

department: Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute

country: Australia

institute: Monash University

data_processing:
The libraries were aligned to the GRCm38/mm10 genome using Rsubread_2.10.2; only uniquely mapped read-pairs were allowed. The mapped read-pairs in each library were assigned to the NCBI RefSeq gene annotation for mm10 (build 38.1) by using featureCounts.
Genes were excluded from downstream analysis if they failed to achieve a CPM (counts per million mapped reads) value of at least 0.5 in at least 2 libraries. Counts were quantile normalized, precision weighted with the “voom” function of the limma package and converted to log2 counts per kilobase per million(log2 FKPM).
A linear model was fitted to each gene, and empirical Bayes moderated t-statistics were used to assess differences in expression. Genes were called differentially expressed if they achieved a false discovery rate of 15% or less.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include normalized log2-FPKM values for each library. The supplementary file, Supp_Raw_Counts.tsv, includes raw read counts for genes in all the libraries.

extract_protocol:
RNA extraction from sorted P14 T cells was performed following the manufacturer's protocol using the RNeasy Plus Mini Kit (Qiagen).
Libraries were generated following the manufacturer's protocol using the TruSeq RNA Library Preparation Kit (Illumina, San Diego, USA).

value: Tpex

value: spleen

tag: infection

value: Doc

tag: collection date


title: Tpex KO rep2


title: 7822-JF-38

value: skin


title: Tex KO rep2

value: Tex


title: 7822-JF-37


title: Tpex het rep1


title: Notch 2 GFP Stage 38 Sample 1

value: Stage 38 (swimming tadpole stage)


title: Ctrl, Heart failure, replicate2, scRNA-seq

description: 10x Genomics

data_processing:
Raw sequence reads were processed from 10X Genomics' Cell Ranger v.5.0.0 pipeline and generated fastq files. In brief, the demultiplexed fastq files were aligned to a custom reference genome with the tdTomato sequence added to the mm10/GRCm38 reference transcriptome, and the gene expression matrix was counted using the Cellranger count program.
Assembly: mm10
Supplementary files format and content: h5 format: Contains the per molecule read information from Cell Ranger.

source_name: whole ventricle

extract_protocol:
The isolation of non-CMs from the murine heart was performed as previously described with some modifications (Forte et al., 2020). In brief, mice were sacrificed by CO2 inhalation, and hearts were immediately cannulated and perfused with cold PBS. Remove the heart, separate the atria and valves from the heart, and cut the ventricular myocardium into 1 mm pieces on a bacterial Petri dish on ice. Transfer to a 10 ml tube containing 3 ml of enzyme solution and incubate in a water bath at 37°C for 45 min, trituration every 15 min. The enzyme solution contained 2 mg/ml collagenase type IV (Worthington Biochemical, CLS-4) and 1.2 U/ml Dispase II (Sigma, 255-914-4). After the final trituration, the enzyme/tissue mixture is filtered through a 40 μm cell strainer, FACS buffer and dead cell removal solution (Miltenyi Biotec, 130-109-398) is added, and debris is removed after centrifugation. Further, use RBC lysis buffer (pluriSelect, 60-00050-11) to remove red blood cells, then dye the cell suspension with Live/Dead (Invitrogen, L34975, 1:1000), Calcein Violet Working solution (BioLegend, 425203, 0.1μM). Using FACS instruments, cells with intact cell membranes and metabolically active cells (Live/Dead-, Calcein+) were sorted while minimizing pressure on the cells.
Libraries from non-CMs suspensions were generated with a Chromium controller from 10X Genomics according to the manufacturer's instructions. Approximately 8, 000 whole cells were loaded into each channel and processed using the Chromium Single Cell 3' v3.1 reagent kit (10X Genomics).

value: whole ventricle

value: non-CMs from whole ventricle


title: TTg, Heart failure, replicate1, scRNA-seq

description: 10x Genomics


title: Tpex het rep2


title: PB2-EV tumor [E1972]

description: Directional mRNA library preparation

value: Mouse breast cancer cells

value: EV

value: Doxycycline diet DOX625


title: Tex KO rep1


title: 7822-JF-36


title: Tex het rep2


title: Notch 2 GFP Stage 28 Sample 2

value: Xenopus laevis embryos (neurula, tailbud, swimming tadpole stages)

value: Stage 28 (tailbud stage)

value: GFP treatment


title: 7822-JF-35


title: Ctrl, Heart failure, replicate1, scRNA-seq

description: 10x Genomics

value: hybrid of C57BL/6 and ICR

value: Tcf21iCre/R26 tdTomato

value: male

value: LNAME+High fat diet, tamoxifen i.p. at week 5


title: Tex het rep1

value: spleen


title: 7822-JF-34


title: Ctrl, normal chow, Visium

description: 10x Genomics

value: heart transverse section

value: normal chow, tamoxifen i.p. at week 5

value: Ctrl


title: Notch 1 ICD Stage 38 Sample 2

description:
Illumina Hi-Seq High-Ouput v3 - PE 50 Cycle
Column 1: gene symbol, Column 2: Counts

value: Stage 38 (swimming tadpole stage)

value: ICD treatment


title: Ctrl, normal chow, replicate1, scRNA-seq

description: 10x Genomics

value: whole ventricle

value: non-CMs from whole ventricle


title: Notch 1 ICD Stage 38 Sample 1


title: Ctrl, normal chow, replicate2, scRNA-seq

description: 10x Genomics


title: TTg, Heart failure, replicate2, scRNA-seq

description: 10x Genomics

value: Tcf21iCre/R26 tdTomato/MGTH2A


title: 7822-JF-33

value: skin


title: 7822-JF-32


title: ATACseq of D30 hiPSC-CMs Rep2

city: Boston

first: Seong Won

last: Kim

state: MA

address: 77 Ave Louis Pasteur

department: Genetics

institute: Harvard Medical School

description:
Library name: hiPSC D30 rep2
PGP1_D30_ATAC_hg38_nolocal_bb.bb
PGP1_D30_ATAC_hg38.bigWig

data_processing:
Sequencing reads were aligned to the hg38 reference genome using BWA-MEM. Biological replicates were merged, and peaks were called using HOMER .
Assembly: hg38
Supplementary files format and content: Biological replicates were merged, and HOMER was used to generate bigwig and bigbed files, which are linked to the corresponding rep1 sample records.

extract_protocol:
50,000 cells were harvested and lysed to isolate nuclei, which were treated with Tn5 transpose (Nextera DNA Sample Prep Kit, Illumina).
Fragmented DNA was amplified using barcoded PCR primers, and pooled libraries were sequenced to a depth of 10 million reads per sample (Illumina Next-Seq).

value: hiPSC-CM


title: keratin + trace-elements; T. rubrum STRB012; rep VI [12_A_VI]

city: Nanchang

first: Oliver

last: Blechert

address: Fusheng Road 666

institute: Affiliated Hospital of Jiangxi University of Chinese Medicine

data_processing:
mRNA fragments mapped with hisat2
assigned to gene IDs and counted with htseq-count
normalized to counts per million (CPM)
Assembly: Trichophyton  rubrum assembly ASM15142v1
Supplementary files format and content: xls file with data normalized to counts per million (CPM)

organism: Trichophyton rubrum

source_name: hyphae

growth_protocol: The fungus has been pre-cultured in liquid keratin medium (2 g keratin, 1.8g KH2PO4 and 0.1g MgSO4 per liter; pH 5.8) for two weeks at 28°C with 140rpm.

extract_protocol:
RNA extraction kit for plants from Tiangen, Beijing
NEBNext Ultra RNA Library Prep Kit for Illumina

treatment_protocol: After pre-culture, the fungus has been aliquot to keratin medium (1 g keratin, 1.8g KH2PO4 and 0.1g MgSO4), keratin medium with trace-elements (1.0 mM CaCl2, 1.0 mM MnCl2, 1.0 mM ZnSO4, 0.2 mM CoCl2, 0.2 mM NiCl2, 0.1 mM H3BO3, 0.1 mM CuSO4, 0.1 mM FeCl3, 0.1 mM KI, 0.1 mM Na2MoO4) and keratin medium with glucose (20g/l).

value: hyphae

value: WT

value: trace-elements


title: ATACseq of D30 hiPSC-CMs Rep3

description:
Library name: hiPSC D30 rep3
PGP1_D30_ATAC_hg38_nolocal_bb.bb
PGP1_D30_ATAC_hg38.bigWig


title: ATACseq of D30 hiPSC-CMs Rep4

description:
Library name: hiPSC D30 rep4
PGP1_D30_ATAC_hg38_nolocal_bb.bb
PGP1_D30_ATAC_hg38.bigWig


title: Notch 1 ICD Stage 28 Sample 3

value: Xenopus laevis embryos (neurula, tailbud, swimming tadpole stages)

value: Stage 28 (tailbud stage)


title: keratin + trace-elements; T. rubrum STRB012; rep V [12_A_V]


title: Notch 1 ICD Stage 28 Sample 2


title: 7822-JF-31


title: ATACseq of D30 hiPSC-CMs Rep1

description:
Library name: hiPSC D30 rep1
PGP1_D30_ATAC_hg38_nolocal_bb.bb
PGP1_D30_ATAC_hg38.bigWig


title: ATACseq of D17 hiPSC-CMs Rep4

description:
Library name: hiPSC D17 rep4
PGP1_D17_ATAC_hg38_nolocal_bb.bb
PGP1_D17_ATAC_hg38.bigWig