title: Fibroblasts-2

city: Zhenjiang

first: Liping

last: Liu

state: Jiangsu

address: No.438 Jiefang Road

department: Department of Dermatology

institute: Affiliated Hospital of Jiangsu University

data_processing:
Sequenced reads were trimmed for adaptor sequence using trimmomatic, then mapped to hg38 genome using hisat2. The raw reads counts were extracted by stringtie.
The raw reads count matrix was normalized by DESeq2 for downstream analysis, including PCA, differently gene expression analysis and GO terms enrichment analysis.
Genome_build: hg38 from GENECODE
Supplementary_files_format_and_content: Matrix table with raw gene counts for each gene and each sample

source_name: skin

growth_protocol: Amniotic epithelial stem cells were isolated form fullterm amnion using 0.05% Trypsin-EDTA solution and cultured in the AESC medium, which contained 10 ng/ml epidermal growth factor, 5 µg/ml insulin, 0.5 µg/ml epinephrine, 36 ng/ml hydrocortisone, 5 µg /ml transferrin, 4 pg/ml triiodo-L-thyronine, and 5% fetal bovine serum. Keratinocytes were cultured in dishes treated with iMatrix 511 (Matrixome) and Epilife medium (Gibco) was used. Fibroblasts were cultured in high-glucose DMEM containing 10% FBS.

extract_protocol:
Total RNA was extracted using TRIzol reagent from AESCs, KCs, and fibroblasts.
RNA sequencing was performed by Eurofins Genomics K.K. (Tokyo, Japan) who used the Illumina HiSeq 2500 (Illumina, San Diego, CA, United States).

tag: cell type

value: Fibroblasts

value: adult


title: Qiaseq_plasma_Rep04

status: Public on Jan 20 2022

type: SRA

city: Wien

first: Andreas

middle: B

last: Diendorfer

address: Leberstraße 20

country: Austria

institute: TAmiRNA GmbH

library_source: transcriptomic

data_processing:
fastQC (v0.11.8) quality control
cutadapt (v2.3) adapter trimming and filtering
bowtie (v1.2.2) genome alignment
miRDeep2 (v2.0.1.2) miRNA quantification
edgeR (v3.28) differential expression
Genome_build: GRCh38.p12
Supplementary_files_format_and_content: miRNA raw reads and RPM (based on total library size and total amount of mapped miRNA reads)

molecule: total RNA

organism: Homo sapiens

source_name: Plasma

extract_protocol:
Maxwell RSC miRNA Tissue kit (Promega, AS1460); miRNeasy Mini kit  (Qiagen,Cat. 217004)
NEXTFLEX Small RNA-Seq kit v3 for Illumina platforms (Cat. NOVA-5132-06, PerkinElmer), QIAseq miRNA Library kit (Cat. 331502, Qiagen), CleanTag small RNA library prep kit (Cat. 040L-3206-24, TriLink Biotechnologies) and RealSeq-Biofluids NGS library preparation kit for miRNAs and small RNAs for total RNA samples from biofluids (Cat. 600-00012-SOM, RealSeq Biosciences, protocol 20181220_RealSeq-BF_CL)
small RNA sequencing with various library preparation kits focusing on miRNAs

tag: tissue

value: Plasma

tag: protocol

value: Qiaseq

tag: disease

value: NHV

value: No

tag: operator

value: Operator 1


title: Qiaseq_plasma_Rep02


title: Smooth muscle cell - D91_Proliferative

city: Charlottesville

first: Mete

last: Civelek

state: Virginia

address: 21 Hospital Drive, Old Medical School Room 3836

department: Biomedical Engineering

country: USA

institute: University of Virginia

description: Proliferative.tsv

data_processing:
RNA-seq reads trimmed the with low average Phred scores (<20) using Trim Galore
Reads were mapped to the hg38 version of the human reference genome using the STAR Aligner in two-pass mode
Only uniquely mapped read pairs were kept.
Expression values were calculated as transcripts per million (TPM) for each gene using RNA-SeQC based on GENCODE v32 transcript annotations
Genome_build: grch38
Supplementary_files_format_and_content: Transcript per Million Gene Expression Quiescent SMCs
Supplementary_files_format_and_content: Transcript per Million Gene Expression Proliferative SMCs

source_name: Smooth Muscle Cell

growth_protocol: SMCs were grown till 80% confluence

extract_protocol:
RNeasy Mini Kit (Qiagen) and the RNase-free DNase Set
Illumina TruSeq Stranded mRNA Library Prep Kit

treatment_protocol: proliferative SMCs were grown in the presence of 5% FBS while quiescent SMCs were cultered without FBS for 24 hours

value: ascending aorta

tag: treatment

value: Proliferative


title: Smooth muscle cell - D89_Quiescent

description: Quiescent.tsv

value: Quiescent


title: Qiaseq_plasma_Rep01


title: Smooth muscle cell - D88_Quiescent

description: Quiescent.tsv


title: Fibroblasts-1

country: China

tag: age


title: Smooth muscle cell - D88_Proliferative

description: Proliferative.tsv


title: Smooth muscle cell - D89_Proliferative

description: Proliferative.tsv


title: Smooth muscle cell - D96_Proliferative

description: Proliferative.tsv


title: Keratinocytes-2

value: Keratinocytes


title: Smooth muscle cell - D87_Quiescent

description: Quiescent.tsv


title: Smooth muscle cell - D87_Proliferative

description: Proliferative.tsv


title: Smooth muscle cell - D93_Proliferative

description: Proliferative.tsv


title: Amniotic epithelial stem cells-2

source_name: amnion

value: Amniotic epithelial stem cells

value: fullterm


title: RealSeq_plasma_Rep01

value: RealSeq


title: FGSC_CTCF_rep2

city: Shanghai

first: Ji

last: Wu

address: No.800, Dongchuan Road, Minhang District

institute: Shanghai Jiao Tong University

library_source: genomic

data_processing:
For ChIP pair-end raw data, we first trimmed the adaptor sequences and low-quality reads with BBmap (version 38.16), then aligned to the mm9 reference genome using bowtie2 (version 2.3.4.1)(Langmead and Salzberg, 2012) with default parameters.
PCR duplicates were removed using Samtools (version 2.0.1) (Li et al., 2009) and generated normalized genome coverage tracks from uniquely mapping reads (MAPQ>10) using deepTools2 (version 3.1).
Genome_build: mm9

molecule: genomic DNA

organism: Mus musculus

source_name: FGSC

growth_protocol: SSCs were cultured on mitomycin C (MMC)-treated mouse embryonic fibroblast (MEF) feeder cells with SSC culture medium. FGSCs were cultured on mitotically inactivated STO (SIM mouse embryo-derived thioguanine- and ouabain-resistant) cell feeders in minimum essential medium alpha (MEMa; Invitrogen) supplemented with 10% fetal bovine serum (FBS) (Life Technologies), 10 ng/mL mouse leukemia inhibitory factor (Santa Cruz Biotechnology), 20 ng/mL mouse epidermal growth factor (EGF) (PeproTech), 10 ng/mL basic fibroblast growth factor (bFGF) (PeproTech), 10 ng/mL mouse glial cell line-derived neurotrophic factor (GDNF) (PeproTech), 1mM non-essential amino acids (NEAA) (Life Technologies), 2 mM L-glutamine (Sigma), 30 mg/mL pyruvate (Amresco) and 50 mM -mercaptoethanol (Biotech).The primary NSCs was seeded onto poly-l-ornithine (Sigma-Aldrich) and laminin (Invitrogen) coated dishes, cultured as monocultures. Neural basal medium with 20ng/ml EGF (PeproTech), 20ng/ml bFGF(PeproTech), 20ng/ml Hepairn (Sigma-Aldrich) and 2% B27 (Invitrogen) was used as NSC proliferation medium. STOs were maintained in Dulbecco’s modified Eagle’s medium (DMEM) with high-glucose (Life Technologies), 10% FBS (Life Technologies), 1% non-essential amino acids (Life Technologies), 2mM glutamine (Sigma) and Penicillin (100U/ml, Sigma)/streptomycin (0.1mg/ml, Sigma).

extract_protocol:
Cells were crosslinked with 1% formaldehyde for 5 min at room temperature and quenched with 125mM glycine. Cells were then put on ice, resuspended in cold cell lysis buffer (140mM NaCl, 1mM EDTA pH 8.0, 1% TritonX-100 and 0.1% SDS and Protease Inhibitors (Roche)). Nuclei were sonicated into 200-1000 bp. The chromatin fragments were pre-cleared and then immunoprecipitated with Protein A+G Magnetic beads coupled with anti-H3K4me3 (ab8580, Abcam), anti-H3K27ac (ab4729, Abcam), anti-H3K27me3 (07-449, Milipore).After reverse crosslinking, immunoprecipitated DNAs and input DNAs were end-repaired and ligated adapters to the DNA fragments using NEBNext Ultra End-Repair/dA-Tailing Module (E7442, NEB) and NEBNext Ultra Ligation Module (E7445, NEB). High-throughput sequencing of the ChIP fragments was performed using Illumina NextSeq 500 following the manufacturer's protocols.
Library was prepared with NEBNext Ultra End-Repair/dA-Tailing Module (E7442, NEB) and NEBNext Ultra Ligation Module (E7445, NEB). High-throughput sequencing of the ChIP fragments was performed using Illumina NextSeq 500 following the manufacturer's protocols.

tag: passages

tag: strain

tag: restriction enzyme

value: anti-CTCF


title: ST3_2GLPH

city: Cambridge

first: Felix

last: Krueger

address: Granta Park

department: Bioinformatics

country: United Kingdom

institute: Altos Labs

description: glpNormalizedExpression.csv

data_processing:
The libraries were trimmed with Trim Galore v0.4.4 using default parameters. Trimmed data were mapped to the C. elegans WBCel235 genome assembly using HISAT2 v2.1.0 (Kim et al., 2015) guided by splice junctions taken from Ensembl v75. Mapped positions with MAPQ < 20 and all non-primary alignments were discarded.  Sequence processing was carried out by the Babraham Bioinformatics.
Paired-ended libraries were re-aligned as single-ended libraries. 100 bp libraries were hard-trimmed to 50 bp and re-aligned.
Quantitation and normalization were done using SeqMonk. Directional libraries were quantitated separately from non-directional libraries. Only exactly overlapping reads were assigned to a gene and transcript- isoforms were merged.
Libraries were normalized using the mean expression of genes whose expression levels were identified as consistent across all libraries. Table S19 lists the non-variable genes used for the normalization.
set15 RNAi datasets were quantitated using RNA-Seq quantitation option in SeqMonk
Genome_build: WBCel235
Supplementary_files_format_and_content: glp gene matrix - Matrix table (comma separated) with normalized read counts for every gene and every sample
Supplementary_files_format_and_content: set15 RNA table - Seqmonk Annotated Probe report (as comma-separated value file)

organism: Caenorhabditis elegans

source_name: whole-worm

growth_protocol: Worms were maintained at 16°C on NGM with OP50 E. coli. Synchronised experimental populations were prepared by washing gravid adults and eggs from plates and bleaching in a freshly prepared solution of 1% sodium hypochlorite and 1 M potassium hydroxide. Eggs were allowed to hatch overnight at room temperature in M9 solution (22 mM KH2PO4; 42 mM Na2HPO4; 86 mM NaCl; 1 mM MgSo4) to ensure all animals arrested at the L1 stage. For time series transcriptomics, glp-1(e2144)ts was crossed with an mlt-10p::GFP molting reporter  to identify the exact molting times and further aid synchronisation.

extract_protocol:
Samples of at least 1000 worms were washed 3X in M9 by settling then snap-frozen in Trizol and kept at -80C until library-prep. Samples were freeze-thawed 10 times to break worm cuticle and RNA was precipitated using chloroform-isopropanol. RNA was treated with 10U DNase I (Roche #04716728001) for 20 minutes at 37°C and purified on Qiagen RNeasy columns (QIAGEN 15596-026).
Libraries were prepared using combined protocols from SuperScript II Reverse Transcriptase (Invitrogen 18064-014), NEBNext mRNA Second Strand Synthesis Module (E6111), and NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB-E7645). Half reactions were used for all steps except the final PCR amplification. Briefly, Oligo d(T)25 beads (NEB-S1419S) were washed and resuspended in 2X RNA Binding Buffer (2 M LiCl , 80 mM Tris HCl (pH 7.5), 4 mM EDTA , 0.2% Triton X-100) in a 1:1 ratio and 500ng of total RNA was added. RNA was denatured by incubating at 65C for 5 minutes and mRNA was allowed to bind to beads. Beads were washed twice in Wash Buffer (150 mM LiCl , 20 mM Tris HCl (pH 7.5), 1.0 mM EDTA , 0.01% Triton X-100) and mRNA eluted in 10 mM Tris Buffer by incubating at 80C for 2 minutes. An equal volume of Binding Buffer was added, washed once more, and the mRNA was eluted into a First Strand Synthesis Reaction Buffer containing 4µl 5X First-Strand Buffer (Invitrogen), 1µl 50µM Random hexamers (Invitrogen N8080127), 0.5µl 10mM dNTP mix, and 1.5µl 0.1M DTT. 0.5µl RNaseOUT (Invitrogen 10777-019), 2.5µl 0.1µg/µl Actinomycin D (Sigma A1410), and 0.5µl SuperScript II Reverse Transcriptase were added and samples were incubated in a thermal cycler for 10 minutes at 25°C, 15 minutes at 42°C, and 15 minutes at 70°C. Second strand synthesis was performed immediately using the NEBNext mRNA Second Strand Synthesis Module. Libraries were then generated using the NEBNext Ultra II DNA Library Prep Kit.

value: heat stress by placing sealed 9 cm plates in a 34°C water bath for 30 minutes

value: 65 hours post hatch


title: Smooth muscle cell - D86_Proliferative

description: Proliferative.tsv


title: FGSC_CTCF_input


title: ST3_2GLPD

description: glpNormalizedExpression.csv

value: 5mM of  DTT/ Dithiothreitol(Sigma) for 1 hour


title: FGSC_CTCF_rep1


title: ST3_2GLPC

description: glpNormalizedExpression.csv

value: No treatment


title: Smooth muscle cell - D85_Quiescent

description: Quiescent.tsv


title: Smooth muscle cell - D90_Proliferative

description: Proliferative.tsv


title: siNipbl_FGSC_Rep1

data_processing:
For Hi-C pair-end raw data, we first trimmed the adaptor sequences and low-quality reads with BBmap (version 38.16). Then HiCPro (version 2.7) (Servant et al., 2015) was used to map, process and iteratively corrected normalization. Briefly, reads were independently aligned to the mouse reference genome (mm9) with the bowtie2 algorithm (Langmead and Salzberg, 2012). We discarded the uncut DNA reads, re-ligation reads, continuous reads and PCR artifacts. Unique mapped reads (MAPQ>10) were used to build the contact matrix.
Compartment analysis are used R package (HiTC) (Servant et al., 2012) pca.hic function to generate the PC1 eigenvectors using 400kb normalized matrices with following options: (normPerExpected=TRUE, npc=1)
TAD calling is done using Direction Index  method as previously described (Dixon et al., 2012)
Genome_build: mm9

growth_protocol: Six-week-old C57BL/6J female mice were intraperitoneally injected with 10 IU pregnant mare serum gonadotropin and then killed by cervical dislocation after 46-48h. Mouse MI oocytes were isolated by puncturing of ovaries with hypodermic needles.

extract_protocol:
HiC and library preparation was carried out using the in-situ method as described previously (Rao et. al., 2014)
DNA libraries were prepared for sequencing using standard Illumina protocols

value: Mbol


title: Smooth muscle cell - D85_Proliferative

description: Proliferative.tsv


title: siCTCF_FGSC_Rep2


title: siCTCF_FGSC_Rep1


title: Smooth muscle cell - D84_Proliferative

description: Proliferative.tsv


title: ST3_1GLPD

description: glpNormalizedExpression.csv

value: 41 hours post hatch


title: ST3_1GLPC

description: glpNormalizedExpression.csv


title: Smooth muscle cell - D83_Quiescent

description: Quiescent.tsv


title: Amniotic epithelial stem cells-1


title: Keratinocytes-1

value: adult


title: ST2_2GLPD

description: glpNormalizedExpression.csv


title: MI_Oocyte_Rep2

data_processing:
For Hi-C pair-end raw data, we first trimmed the adaptor sequences and low-quality reads with BBmap (version 38.16). Then HiCPro (version 2.7) (Servant et al., 2015) was used to map, process and iteratively corrected normalization. Briefly, reads were independently aligned to the mouse reference genome (mm9) with the bowtie2 algorithm (Langmead and Salzberg, 2012). We discarded the uncut DNA reads, re-ligation reads, continuous reads and PCR artifacts. Unique mapped reads (MAPQ>10) were used to build the contact matrix.
Compartment analysis are used R package (HiTC) (Servant et al., 2012) pca.hic function to generate the PC1 eigenvectors using 400kb normalized matrices with following options: (normPerExpected=TRUE, npc=1)
TAD calling is done using Direction Index  method as previously described (Dixon et al., 2012)
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited text files

source_name: metaphase I oocytes


title: ST2_2GLPP

description: glpNormalizedExpression.csv

value: 200mM of Paraquat (N, N′-dimethyl-4,4′-bipyridinium dichloride, Sigma) for 1 hour


title: MI_Oocyte_Rep1

source_name: metaphase II oocytes

value: metaphase II oocytes

tag: Sex

value: female


title: Smooth muscle cell - D82_Quiescent

description: Quiescent.tsv

value: ascending aorta


title: Smooth muscle cell - D86_Quiescent

description: Quiescent.tsv

value: Quiescent


title: Smooth muscle cell - D82_Proliferative

description: Proliferative.tsv

value: Proliferative


title: GV_Oocte_Rep2

source_name: GV stage oocytes

growth_protocol: GV stage oocytes were collected from the mouse ovary

value: GV stage oocytes


title: Smooth muscle cell - D81_Quiescent

description: Quiescent.tsv


title: ST2_2GLPH

description: glpNormalizedExpression.csv


title: Smooth muscle cell - D81_Proliferative

description: Proliferative.tsv


title: STO_RNA_Rep3

data_processing:
For RNA pair-end raw data, we first trimmed the adaptor sequences and low-quality reads with BBmap (version 38.16), then aligned to the mm9 reference genome using Hisat2 (version 4.8.2) (Pertea et al., 2016) with default parameters
Gene expression FPKM was calculated by Cufflinks (version 2.2.1) (Trapnell et al., 2012) using the RefSeq database from the UCSC genome browser. Sequencing depth was normalized.
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values for each Sample

source_name: SIM embryonic fibroblasts cells

extract_protocol:
Total RNA were extracted from 2-6 million cells using Trizol Reagent (Invitrogen). The RNA quality was assessed using Agilent Bioanalyzer 2100
RNA-Seq libraries were prepared using the KAPA Stranded mRNA-Seq kit following the manufacturer’s instructions


title: GV_Oocte_Rep1


title: ST2_2GLPC

description: glpNormalizedExpression.csv


title: ST2_1GLPP

description: glpNormalizedExpression.csv


title: ST2_1GLPH

description: glpNormalizedExpression.csv


title: Smooth muscle cell - D80_Quiescent

description: Quiescent.tsv


title: Smooth muscle cell - D84_Quiescent

description: Quiescent.tsv


title: ST3_1GLPH

description: glpNormalizedExpression.csv


title: ST2_1GLPD

description: glpNormalizedExpression.csv


title: ST2_1GLPC

description: glpNormalizedExpression.csv


title: Smooth muscle cell - D80_Proliferative

description: Proliferative.tsv


title: NSC_RNA_Rep2

source_name: Nerual stem cells


title: NSC_RNA_Rep1


title: STO_RNA_Rep2


title: STO_RNA_Rep1


title: ST1_2GLPP

description: glpNormalizedExpression.csv


title: Smooth muscle cell - D79_Quiescent

description: Quiescent.tsv


title: Smooth muscle cell - D83_Proliferative

description: Proliferative.tsv


title: ST1_2GLPH

description: glpNormalizedExpression.csv


title: STO_Rep1

growth_protocol: SSCs were cultured on mitomycin C (MMC)-treated mouse embryonic fibroblast (MEF) feeder cells with SSC culture medium.FGSCs were cultured on mitotically inactivated STO (SIM mouse embryo-derived thioguanine- and ouabain-resistant) cell feeders in minimum essential medium alpha (MEMa; Invitrogen) supplemented with 10% fetal bovine serum (FBS) (Life Technologies), 10 ng/mL mouse leukemia inhibitory factor (Santa Cruz Biotechnology), 20 ng/mL mouse epidermal growth factor (EGF) (PeproTech), 10 ng/mL basic fibroblast growth factor (bFGF) (PeproTech), 10 ng/mL mouse glial cell line-derived neurotrophic factor (GDNF) (PeproTech), 1mM non-essential amino acids (NEAA) (Life Technologies), 2 mM L-glutamine (Sigma), 30 mg/mL pyruvate (Amresco) and 50 mM -mercaptoethanol (Biotech).The primary NSCs was seeded onto poly-l-ornithine (Sigma-Aldrich) and laminin (Invitrogen) coated dishes, cultured as monocultures. Neural basal medium with 20ng/ml EGF (PeproTech), 20ng/ml bFGF(PeproTech), 20ng/ml Hepairn (Sigma-Aldrich) and 2% B27 (Invitrogen) was used as NSC proliferation medium. STOs were maintained in Dulbecco’s modified Eagle’s medium (DMEM) with high-glucose (Life Technologies), 10% FBS (Life Technologies), 1% non-essential amino acids (Life Technologies), 2mM glutamine (Sigma) and Penicillin (100U/ml, Sigma)/streptomycin (0.1mg/ml, Sigma).


title: STO_Rep2


title: Smooth muscle cell - D78_Quiescent

description: Quiescent.tsv


title: Smooth muscle cell - D79_Proliferative

description: Proliferative.tsv


title: ST1_2GLPD

description: glpNormalizedExpression.csv


title: Smooth muscle cell - D78_Proliferative

description: Proliferative.tsv


title: NSC_Rep2

source_name: Nerual stem cell


title: Smooth muscle cell - D77_Quiescent

description: Quiescent.tsv


title: Smooth muscle cell - D77_Proliferative

description: Proliferative.tsv


title: NSC_Rep1


title: ST1_1GLPP

description: glpNormalizedExpression.csv


title: Smooth muscle cell - D76_Quiescent

description: Quiescent.tsv


title: ST1_1GLPD

description: glpNormalizedExpression.csv


title: ST1_1GLPH

description: glpNormalizedExpression.csv


title: SSC_Rep2

source_name: Spermatogonial stem cell

value: DBA/2 x CAG-EGFP


title: ST1_1GLPC

description: glpNormalizedExpression.csv


title: Smooth muscle cell - D76_Proliferative

description: Proliferative.tsv


title: Smooth muscle cell - D75_Quiescent

description: Quiescent.tsv


title: SSC_Rep1


title: Smooth muscle cell - D75_Proliferative

description: Proliferative.tsv


title: set15RNAi_GLP_d1

value: set-15 RNAi (GLP-GS)


title: FGSC_Rep1

source_name: Female germline stem cell

value: Ddx4-Cre; mT/mG


title: set15RNAi_GLPC_d1

value: No treatment (GLP-GS)


title: Smooth muscle cell - D73_Quiescent

description: Quiescent.tsv


title: Smooth muscle cell - D74_Quiescent

description: Quiescent.tsv


title: STO_H3K27ac_IP

data_processing:
For ChIP pair-end raw data, we first trimmed the adaptor sequences and low-quality reads with BBmap (version 38.16), then aligned to the mm9 reference genome using bowtie2 (version 2.3.4.1)(Langmead and Salzberg, 2012) with default parameters.
PCR duplicates were removed using Samtools (version 2.0.1) (Li et al., 2009) and generated normalized genome coverage tracks from uniquely mapping reads (MAPQ>10) using deepTools2 (version 3.1).
Genome_build: mm9
Supplementary_files_format_and_content: bigwig file

tag: antibody

value: anti-H3K27ac (ab4729, Abcam)


title: iPSC_Rep2

source_name: Induced pluripotent stem cell


title: Smooth muscle cell - D74_Proliferative

description: Proliferative.tsv


title: OEA084

description: glpNormalizedExpression.csv

value: 89 hours post hatch


title: STO_H3K27ac_Input


title: siNipbl_FGSC_Rep2


title: ST1_2GLPC

description: glpNormalizedExpression.csv

value: No treatment

value: 65 hours post hatch


title: Smooth muscle cell - D73_Proliferative

description: Proliferative.tsv


title: OEA134

description: glpNormalizedExpression.csv


title: Smooth muscle cell - D72_Quiescent

description: Quiescent.tsv


title: OEA069

description: glpNormalizedExpression.csv

value: 69 hours post hatch


title: STO_H3K27me3_Input


title: Smooth muscle cell - D72_Proliferative

description: Proliferative.tsv


title: OEA067

description: glpNormalizedExpression.csv


title: STO_H3K4me3_Input


title: FGSC_Rep2

value: Mbol


title: Smooth muscle cell - D71_Quiescent

description: Quiescent.tsv


title: Smooth muscle cell - D70_Quiescent

description: Quiescent.tsv


title: OEA064

description: glpNormalizedExpression.csv

value: 53 hours post hatch


title: Kdm1a-sg2

first: yujuan

last: jin

address: Yueyang Road 320#

institute: Shanghai Institutes for Biological Sciences, CAS

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perlscripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low-quality reads from raw data.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Bowtie v2.2.3 and paired-end clean reads were aligned to the reference genome using TopHat v2.0.12.
HTSeq v0.6.1 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Genome_build: mm10
Supplementary_files_format_and_content: RPKM, counts, sg1&sg2_vs_V2_diffgenes_RPKM_cutoff1.5

extract_protocol:
Total mRNA were extracted by Trizol reagent according to manufacturer's instructions.
Sequencing libraries were generated using NEBNext® Ultra™ RNA Libraryrep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

treatment_protocol: mouse SCLC cell line #3 was infected by Lenti-Crispr-V2, Lenti-Crispr-Kdm1a-sg1 or Lenti-Crispr-Kdm1a-sg2 virus respectively, and selected by puromycin for at least 1 week.

tag: cell line

value: small cell lung cancer (SCLC)

tag: genotype/variation

value: Kdm1a knock-out


title: iPSC_Rep1


title: Smooth muscle cell - D70_Proliferative

description: Proliferative.tsv

value: ascending aorta


title: Crispr-V2

value: control (Crispr-V2)


title: OEA076

description: glpNormalizedExpression.csv

value: 77 hours post hatch


title: Smooth muscle cell - D69_Quiescent

description: Quiescent.tsv

value: Quiescent


title: OEA061

description: glpNormalizedExpression.csv

value: 41 hours post hatch


title: Kdm1a-sg1


title: OEA065

description: glpNormalizedExpression.csv

value: 49 hours post hatch


title: OEA063

description: glpNormalizedExpression.csv

value: 101 hours post hatch


title: OEA058

description: glpNormalizedExpression.csv


title: Smooth muscle cell - D69_Proliferative

description: Proliferative.tsv

value: Proliferative


title: OEA071

description: glpNormalizedExpression.csv


title: Smooth muscle cell - D68_Quiescent

description: Quiescent.tsv


title: OEA057

description: glpNormalizedExpression.csv

value: 93 hours post hatch


title: norma3 rep2 line DN RFD 3.9 L

city: Boston

first: Ksenia

middle: S

last: Anufrieva

state: MA

address: 60 Fenwood Rd

institute: Brigham and Women's Hospital

description:
iPSCs from   Parkinson's disease patients  were differentiated into terminally differentiated neurons
norma3dn_2
TPM_DN.tsv

data_processing:
RNA-seq reads were trimmed for quality, paired reads were cropped using Trimmomatic (v. 0.35).
Trimmed RNAseq reads were quantified against Homo Sapiens GRCh38.13  genome annotation at the transcript level using Salmon (v.1.4). Results were aggregated to gene level using the R package tximport.
Differentially expressed genes were identified using the R package DESeq2.
Genome_build: GRCh38
Supplementary_files_format_and_content: TPM values for every gene and every sample

source_name: terminally differentiated neurons

growth_protocol: All cells were cultivated at 37°C under humidified atmosphere with 5% CO2. Neural progenitors were cultivated in DMEM/F12 containing 2% serum replacement (“Gibco”, USA), 1 mM non-essential amino acids (“Paneco”, Russian Federation), 2 mM L-glutamine (“ICN Biomedicals Inc”, USA), penicillin-streptomycin (50 U/ml; 50 µg/ml) (“Paneco”, Russian Federation), 1%  N2 supplement (“Life Technologies”, USA), 10 µM SB431542 (“Stemgent”, USA), and 80 ng recombinant Noggin (“Peprotech”, USA). Neurons were cultivated in DMEM/F12 containing 2% serum replacement (“Gibco”, USA), 1 mM non-essential aminoacids (“Paneco”, Russian Federation), 2 mM L-glutamine (“ICN Biomedicals Inc”, USA), penicillin-streptomycin (50 U/ml; 50 µg/ml) (“Paneco”, Russian Federation), 1% В27 supplement (“Life Technologies”, USA), 100 ng/ml recombinant Shh, 20 ng/ml recombinant FGF8, purmorphamine 2 µM all from (“Peprotech”, USA) for 10 days, and in DMEM/F12, containing 2% serum replacement (“Gibco”, USA), 1 mM non-essential aminoacids (“Paneco”, Russian Federation), 2 mM L-glutamine (“ICN Biomedicals Inc”, USA), penicillin-streptomycin (50 U/ml; 50 µg/ml) (“Paneco”, Russian Federation), 1% В27 supplement (“Life Technologies”, USA), 5 µM forskolin (“Stemgent”, USA),  20 ng/ml BDNF, 20 ng/ml GDNF, 200 µM ascorbic acid all from (“Peprotech”, USA) for 24 days.

extract_protocol:
Total RNA was isolated from neural progenitors using RNeasy Micro Kit (Qiagen, USA) followed by treatment with DNAse I (Qiagen, USA). The reaction was purifed with PureLink RNA Mini Kit (ThermoFisher, USA). RNA quality was checked by 2100 bioanalyzer (Agilent, USA). Enrichment of polyadenylated RNA and library preparation was performed with NEB Next Ultra II Directional RNA Library Prep (NEB, USA) according to the manufacturer’s protocol. Samples were sequenced on NextSeq 500 System (Illumina, USA) with NextSeq 500/550 High Output Kit v2.5 (75 Cycles).
Library preparation was performed with NEB Next Ultra II Directional RNA Library Prep (NEB, USA) according to the manufacturer’s protocol.

treatment_protocol: To obtain neural progenitors from iPSCs, the culture medium was replaced with a neuronal differentiation medium containing a cocktail of factors that stimulates differentiation in the neuronal direction. After 10-14 days of culturing, neural rosettes with specific “ridges” formed by iPSCs were mechanically transferred to a 24-well plate with extremely low adhesion, where neurospheres were formed. After 3-5 days, neurospheres were collected and treated with 0.05% trypsin. Thereafter, neurospheres were resuspended in DMEM with 10% FBS, then resuspended in growth medium for neural progenitors (DMEM/F12 containing 2% serum replacement (Gibco, USA), 1 mM non-essential amino acids (Paneco, Russian Federation), 2 mM L-glutamine (“ICN Biomedicals Inc”, USA), penicillin-streptomycin (50 U / ml; 50 µg / ml) (“Paneco”, Russian Federation), 1% N2 supplement (“Life Technologies” , USA), 10 μM SB431542 (Stemgent, USA), and 80 ng recombinant Noggin (Peprotech, USA), and transferred to Petri dishes coated with Matrigel. For differentiation into dopaminergic neurons, the neural progenitors were cultivated with DMEM/F12 containing 2% serum replacement (Gibco, USA), 1 mM non-essential aminoacids (Paneco, Russian Federation), 2 mM L-glutamine (ICN Biomedicals Inc ”, USA), penicillin-streptomycin (50 U / ml; 50 µg / ml) (“ Paneco ”, Russian Federation), 1% В27 supplement (“ Life Technologies ”, USA), 100 ng / ml recombinant Shh, 20 ng / ml recombinant FGF8, purmorphamine 2 µM all from (“Peprotech”, USA) for 10 days, and in DMEM / F12, containing 2% serum replacement (“Gibco”, USA), 1 mM non-essential aminoacids (“Paneco” , Russian Federation), 2 mM L-glutamine (“ICN Biomedicals Inc”, USA), penicillin-streptomycin (50 U / ml; 50 µg / ml) (“Paneco”, Russian Federation), 1% В27 supplement (“Life Technologies ”, USA), 5 µM forskolin (“ Stemgent ”, USA), 20 ng / ml BDNF, 20 ng / ml GDNF, 200 µM ascorbic acid all from (“ Peprotech ”, USA) for 24 days.

value: neurons presumably dopaminergic

tag: genotype

value: normal

tag: subject status

value: Parkinson's disease patient


title: norma3 rep3 line DN RFD 3.9 L

description:
iPSCs from   Parkinson's disease patients  were differentiated into terminally differentiated neurons
norma3dn_3
TPM_DN.tsv


title: OEA055

description: glpNormalizedExpression.csv

value: No treatment

value: 73 hours post hatch


title: STO_H3K27me3_IP

value: anti-H3K27me3 (07-449, Milipore)


title: OEA054

description: glpNormalizedExpression.csv


title: STO_H3K4me3_IP

value: anti-H3K4me3 (ab8580, Abcam)


title: norma3 rep1 line DN RFD 3.9 L

description:
iPSCs from   Parkinson's disease patients  were differentiated into terminally differentiated neurons
norma3dn_1
TPM_DN.tsv


title: Smooth muscle cell - D68_Proliferative

description: Proliferative.tsv


title: Smooth muscle cell - D67_Quiescent

description: Quiescent.tsv


title: Smooth muscle cell - D67_Proliferative

description: Proliferative.tsv


title: Smooth muscle cell - D71_Proliferative

description: Proliferative.tsv


title: norma1 rep3 line NP RG2L

description:
iPSCs from  healthy donors  were differentiated into uncommitted neural progenitors
norma1np_3
TPM_NP.tsv

source_name: neural progenitors

value: neural progenitors

value: healthy donor


title: OEA053

description: glpNormalizedExpression.csv

value: 45 hours post hatch


title: OEA052

description: glpNormalizedExpression.csv


title: OEA051

description: glpNormalizedExpression.csv

value: 97 hours post hatch


title: Smooth muscle cell - D66_Quiescent

description: Quiescent.tsv

value: ascending aorta

value: Quiescent


title: Smooth muscle cell - D63_Quiescent

description: Quiescent.tsv


title: OEA049

description: glpNormalizedExpression.csv

value: 77 hours post hatch


title: Smooth muscle cell - D64_Quiescent

description: Quiescent.tsv


title: OEA048

description: glpNormalizedExpression.csv


title: Smooth muscle cell - D66_Proliferative

description: Proliferative.tsv


title: Smooth muscle cell - D65_Proliferative

description: Proliferative.tsv


title: OEA050

description: glpNormalizedExpression.csv


title: OEA047

description: glpNormalizedExpression.csv

value: 89 hours post hatch


title: OEA043

description: glpNormalizedExpression.csv


title: Smooth muscle cell - D61_Quiescent

description: Quiescent.tsv


title: OEA045

description: glpNormalizedExpression.csv

value: 69 hours post hatch


title: Smooth muscle cell - D62_Proliferative

description: Proliferative.tsv

value: Proliferative


title: OEA042

description: glpNormalizedExpression.csv


title: Smooth muscle cell - D63_Proliferative

description: Proliferative.tsv


title: OEA044

description: glpNormalizedExpression.csv

value: 49 hours post hatch


title: OEA041

description: glpNormalizedExpression.csv


title: Smooth muscle cell - D60_Quiescent

description: Quiescent.tsv


title: OEA040

description: glpNormalizedExpression.csv

value: 41 hours post hatch


title: Smooth muscle cell - D59_Quiescent

description: Quiescent.tsv


title: OEA039

description: glpNormalizedExpression.csv

value: 65 hours post hatch


title: OEA038

description: glpNormalizedExpression.csv

value: No treatment


title: Smooth muscle cell - D59_Proliferative

description: Proliferative.tsv


title: Smooth muscle cell - D60_Proliferative

description: Proliferative.tsv


title: Smooth muscle cell - D62_Quiescent

description: Quiescent.tsv


title: Smooth muscle cell - D58_Quiescent

description: Quiescent.tsv


title: NoN12

description: glpNormalizedExpression.csv

value: 10mg/ml Nystatin was not added to the plate.


title: NoN18

description: glpNormalizedExpression.csv


title: Smooth muscle cell - D58_Proliferative

description: Proliferative.tsv


title: NoN09

description: glpNormalizedExpression.csv


title: NoN04

description: glpNormalizedExpression.csv


title: Smooth muscle cell - D57_Quiescent

description: Quiescent.tsv


title: NoN06

description: glpNormalizedExpression.csv


title: HMRC037

description: glpNormalizedExpression.csv

value: 161 hours post hatch


title: Smooth muscle cell - D56_Quiescent

description: Quiescent.tsv


title: Smooth muscle cell - D56_Proliferative

description: Proliferative.tsv


title: Smooth muscle cell - D57_Proliferative

description: Proliferative.tsv


title: HMRC036

description: glpNormalizedExpression.csv

value: 137 hours post hatch


title: Smooth muscle cell - D55_Quiescent

description: Quiescent.tsv


title: Smooth muscle cell - D55_Proliferative

description: Proliferative.tsv


title: Smooth muscle cell - D54_Quiescent

description: Quiescent.tsv


title: Smooth muscle cell - D61_Proliferative

description: Proliferative.tsv


title: Smooth muscle cell - D54_Proliferative

description: Proliferative.tsv


title: HMRC032

description: glpNormalizedExpression.csv

value: 209 hours post hatch


title: HMRC030

description: glpNormalizedExpression.csv


title: HMRC031

description: glpNormalizedExpression.csv

value: 185 hours post hatch


title: HMRC028

description: glpNormalizedExpression.csv

value: 233 hours post hatch


title: HMRC027

description: glpNormalizedExpression.csv


title: Smooth muscle cell - D53_Proliferative

description: Proliferative.tsv


title: Smooth muscle cell - D52_Proliferative

description: Proliferative.tsv


title: HMRC026

description: glpNormalizedExpression.csv


title: Smooth muscle cell - D53_Quiescent

description: Quiescent.tsv


title: Smooth muscle cell - D51_Quiescent

description: Quiescent.tsv


title: HMRC025

description: glpNormalizedExpression.csv


title: EXOSC3-mAID_6h_EPAP_rep1

city: Aarhus C

first: Torben

middle: Heick

last: Jensen

address: C. F. Møller Alle 3

country: Denmark

institute: Aarhus University

data_processing:
3'end seq reads were trimmed using the bbduk.sh script from BBMAP and homopolymeric A-stretches removed from reads.
The data was mapped using STAR against a compound index composed of hg38 merged with ERCC spike-ins.
5' ends of uniquely mapped reads were used for downstream analysis.
Genome_build: hg38
Supplementary_files_format_and_content: bigWig files were generated from bam files using a custom script. The score represents normalized counts per base.

source_name: tissue culture cells

growth_protocol: Cells were maintained in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% fetal bovine serum (FBS) and 1% penicillin/streptomycin (P/S) at 37°C and 5% CO2.

extract_protocol:
RNA was isolated by TRIzol (Ambion) and treated with TURBO DNase (Ambion) according to the manufacturer’s instructions. Six in vitro transcribed spike-in RNAs were added, with  spike-in sequences being  identical to ERCC spike-ins. ERCC-00092, ERCC-00136 and ERCC-00043 were transcribed in the presence of 4sU, whereas ERCC-00170, ERCC-00002 and ERCC-00145 were transcribed without 4sU and serve as negative control in the 4sU purification step.
Extracted RNA was subjected to 4sU purification followed by 3'end in vitro polyadenylation (E.coli poly(A) polymerase, EPAP) of half of each sample. In vitro polyadenylated samples (EPAP) were rRNA depleted. QuantSeq REV sequencing library preparation and  pA+ RNA 3'end sequencing (multiplexing of 10 - 12 libraries, NextSeq SR75 High Output run) was performed by Lexogen GmbH at the Vienna Biocenter Core Facilities.
RNA 3'end seq, single-end

treatment_protocol: For AID-mediated protein depletion, 750 µM Indole-3-acetic acid sodium salt (IAA, Sigma-Aldrich) was added to the culture medium for the indicated time periods (0h, 2h, 6h). 10 min before harvesting, 4-thiouridine (4sU) was added to the growth medium for metabolic labelling of newly synthesized RNA.

value: HeLa, incl. OsTIR1 expression

value: homoygous C-terminal mAID tagging of EXOSC3

value: 6h IAA (750µM), 10 min 4sU

tag: pap treatment

value: EPAP

tag: fraction

value: newly synthesized RNA, (rRNA depleted)


title: Smooth muscle cell - D50_Proliferative

description: Proliferative.tsv

tag: tissue

value: ascending aorta


title: EXOSC3-mAID_2h_EPAP_rep1

value: 2h IAA (750µM), 10 min 4sU


title: EXOSC3-mAID_0h_EPAP_rep2

value: no IAA, 10 min 4sU


title: HMRC021

description: glpNormalizedExpression.csv

value: 117 hours post hatch


title: HMRC022

description: glpNormalizedExpression.csv

value: 49 hours post hatch


title: Smooth muscle cell - D49_Proliferative

description: Proliferative.tsv

value: Proliferative


title: Smooth muscle cell - D49_Quiescent

description: Quiescent.tsv

value: Quiescent


title: HMRC018

description: glpNormalizedExpression.csv

value: No treatment


title: EXOSC3-mAID_0h_EPAP_rep1


title: HMRC035

description: glpNormalizedExpression.csv

value: 257 hours post hatch


title: HMRC017

description: glpNormalizedExpression.csv

value: 45 hours post hatch


title: Smooth muscle cell - D48_Proliferative

description: Proliferative.tsv


title: ZFC3H1-mAID_6h_EPAP_rep1

value: homoygous C-terminal mAID tagging of ZFC3H1


title: ZFC3H1-mAID_6h_EPAP_rep2


title: HMRC016

description: glpNormalizedExpression.csv

value: 209 hours post hatch


title: HMRC015

description: glpNormalizedExpression.csv

value: 185 hours post hatch


title: Smooth muscle cell - D47_Proliferative

description: Proliferative.tsv


title: Smooth muscle cell - D47_Quiescent

description: Quiescent.tsv


title: EXOSC3-mAID_6h_EPAP_rep2

value: HeLa, incl. OsTIR1 expression

value: homoygous C-terminal mAID tagging of EXOSC3


title: HMRC014

description: glpNormalizedExpression.csv


title: HMRC012

description: glpNormalizedExpression.csv

value: 97 hours post hatch


title: ZFC3H1-mAID_0h_EPAP_rep2

value: EPAP

value: newly synthesized RNA, (rRNA depleted)


title: ZFC3H1-mAID_2h_EPAP_rep1

value: 2h IAA (750µM), 10 min 4sU


title: Smooth muscle cell - D48_Quiescent

description: Quiescent.tsv

value: ascending aorta


title: Smooth muscle cell - D46_Quiescent

description: Quiescent.tsv


title: EXOSC3-mAID_2h_EPAP_rep2


title: Smooth muscle cell - D50_Quiescent

description: Quiescent.tsv


title: HMRC023

description: glpNormalizedExpression.csv

value: 69 hours post hatch


title: ZFC3H1-mAID_0h_EPAP_rep1

value: no IAA, 10 min 4sU


title: HMRC011

description: glpNormalizedExpression.csv


title: HMRC010

description: glpNormalizedExpression.csv

value: 137 hours post hatch


title: Smooth muscle cell - D45_Quiescent

description: Quiescent.tsv

value: Quiescent


title: ZCCHC8-mAID_6h_EPAP_rep2

value: homoygous C-terminal mAID tagging of ZCCHC8

value: 6h IAA (750µM), 10 min 4sU


title: HMRC009

description: glpNormalizedExpression.csv

value: No treatment

value: 161 hours post hatch


title: Smooth muscle cell - D45_Proliferative

description: Proliferative.tsv

value: Proliferative


title: Smooth muscle cell - D46_Proliferative

description: Proliferative.tsv


title: ZCCHC8-mAID_6h_EPAP_rep1


title: Smooth muscle cell - D44_Quiescent

description: Quiescent.tsv


title: ZCCHC8-mAID_2h_EPAP_rep1


title: ZCCHC8-mAID_2h_EPAP_rep2


title: Smooth muscle cell - D44_Proliferative

description: Proliferative.tsv


title: HMRC008

description: glpNormalizedExpression.csv

value: 185 hours post hatch


title: HMRC007

description: glpNormalizedExpression.csv


title: ZCCHC8-mAID_0h_EPAP_rep2

value: HeLa, incl. OsTIR1 expression


title: HMRC006

description: glpNormalizedExpression.csv

value: 257 hours post hatch


title: ZFC3H1-mAID_2h_EPAP_rep2

value: homoygous C-terminal mAID tagging of ZFC3H1


title: ZCCHC8-mAID_0h_EPAP_rep1

value: EPAP


title: HMRC004

description: glpNormalizedExpression.csv

value: 117 hours post hatch


title: OsTIR1_6h_EPAP_rep1

value: no mAID tag

value: newly synthesized RNA, (rRNA depleted)


title: Smooth muscle cell - D43_Proliferative

description: Proliferative.tsv

value: ascending aorta


title: Smooth muscle cell - D43_Quiescent

description: Quiescent.tsv


title: Smooth muscle cell - D42_Proliferative

description: Proliferative.tsv


title: HMRC001

description: glpNormalizedExpression.csv

value: 97 hours post hatch


title: OsTIR1_0h_EPAP_rep1

value: no IAA, 10 min 4sU


title: Smooth muscle cell - D41_Quiescent

description: Quiescent.tsv

value: Quiescent


title: DAO33

description: glpNormalizedExpression.csv

value: 1mM Δ7-Dafachronic acid (3-oxo-cholest-4-en-26-oic acid/Cayman #14101)

value: 45 hours post hatch


title: EXOSC3-mAID_6h_noPAP_rep2

value: homoygous C-terminal mAID tagging of EXOSC3

value: 6h IAA (750µM), 10 min 4sU

value: noPAP

value: newly synthesized RNA


title: DAO30

description: glpNormalizedExpression.csv


title: Smooth muscle cell - D41_Proliferative

description: Proliferative.tsv

value: Proliferative


title: EXOSC3-mAID_6h_noPAP_rep1

value: HeLa, incl. OsTIR1 expression


title: Smooth muscle cell - D40_Quiescent

description: Quiescent.tsv


title: DAO27

description: glpNormalizedExpression.csv

value: 93 hours post hatch


title: EXOSC3-mAID_2h_noPAP_rep2

value: 2h IAA (750µM), 10 min 4sU


title: DAO24

description: glpNormalizedExpression.csv

value: 69 hours post hatch


title: EXOSC3-mAID_2h_noPAP_rep1


title: Smooth muscle cell - D39_Quiescent

description: Quiescent.tsv


title: Smooth muscle cell - D39_Proliferative

description: Proliferative.tsv


title: EXOSC3-mAID_0h_noPAP_rep2


title: Smooth muscle cell - D40_Proliferative

description: Proliferative.tsv


title: DAO18

description: glpNormalizedExpression.csv


title: Smooth muscle cell - D38_Quiescent

description: Quiescent.tsv


title: DAO21

description: glpNormalizedExpression.csv

value: 117 hours post hatch


title: EXOSC3-mAID_0h_noPAP_rep1


title: HMRC005

description: glpNormalizedExpression.csv

value: No treatment


title: Smooth muscle cell - D42_Quiescent

description: Quiescent.tsv

value: ascending aorta


title: Smooth muscle cell - D38_Proliferative

description: Proliferative.tsv


title: DAO12

description: glpNormalizedExpression.csv


title: DAO15

description: glpNormalizedExpression.csv


title: Smooth muscle cell - D37_Quiescent

description: Quiescent.tsv


title: DAO10

description: glpNormalizedExpression.csv


title: OsTIR1_2h_EPAP_rep1

value: no mAID tag

value: EPAP

value: newly synthesized RNA, (rRNA depleted)


title: ZFC3H1-mAID_2h_noPAP_rep2

value: homoygous C-terminal mAID tagging of ZFC3H1


title: ZFC3H1-mAID_6h_noPAP_rep1


title: Smooth muscle cell - D37_Proliferative

description: Proliferative.tsv


title: DAO07

description: glpNormalizedExpression.csv

value: 1mM Δ7-Dafachronic acid (3-oxo-cholest-4-en-26-oic acid/Cayman #14101)


title: ZFC3H1-mAID_2h_noPAP_rep1


title: DAO04

description: glpNormalizedExpression.csv


title: ZFC3H1-mAID_0h_noPAP_rep2

value: no IAA, 10 min 4sU


title: DAO01

description: glpNormalizedExpression.csv

value: 45 hours post hatch


title: Smooth muscle cell - D36_Proliferative

description: Proliferative.tsv


title: Smooth muscle cell - D35_Quiescent

description: Quiescent.tsv

value: Quiescent


title: Smooth muscle cell - D35_Proliferative

description: Proliferative.tsv


title: AAO45

description: glpNormalizedExpression.csv

value: 50uM of Arachidonic acid (C20:4n6, Cayman)


title: AAO48

description: glpNormalizedExpression.csv


title: AAO43

description: glpNormalizedExpression.csv


title: Smooth muscle cell - D34_Quiescent

description: Quiescent.tsv


title: AAO41

description: glpNormalizedExpression.csv


title: ZFC3H1-mAID_6h_noPAP_rep2

value: 6h IAA (750µM), 10 min 4sU

value: noPAP

value: newly synthesized RNA


title: Smooth muscle cell - D33_Proliferative

description: Proliferative.tsv

value: Proliferative


title: Smooth muscle cell - D32_Quiescent

description: Quiescent.tsv


title: Smooth muscle cell - D34_Proliferative

description: Proliferative.tsv


title: AAO38

description: glpNormalizedExpression.csv

value: 93 hours post hatch


title: ZFC3H1-mAID_0h_noPAP_rep1

value: HeLa, incl. OsTIR1 expression


title: ZCCHC8-mAID_2h_noPAP_rep1

value: homoygous C-terminal mAID tagging of ZCCHC8

value: 2h IAA (750µM), 10 min 4sU


title: ZCCHC8-mAID_6h_noPAP_rep1


title: ZCCHC8-mAID_6h_noPAP_rep2


title: Smooth muscle cell - D32_Proliferative

description: Proliferative.tsv

value: ascending aorta


title: AAO32

description: glpNormalizedExpression.csv


title: AAO35

description: glpNormalizedExpression.csv

value: No treatment


title: ZCCHC8-mAID_0h_noPAP_rep2


title: OsTIR1_6h_noPAP_rep1

value: no mAID tag


title: ZCCHC8-mAID_2h_noPAP_rep2


title: ZCCHC8-mAID_0h_noPAP_rep1


title: Smooth muscle cell - D31_Quiescent

description: Quiescent.tsv


title: Smooth muscle cell - D31_Proliferative

description: Proliferative.tsv


title: Smooth muscle cell - D36_Quiescent

description: Quiescent.tsv


title: OsTIR1_2h_noPAP_rep1


title: OsTIR1_0h_noPAP_rep1


title: AAO26

description: glpNormalizedExpression.csv

value: 69 hours post hatch


title: Smooth muscle cell - D30_Quiescent

description: Quiescent.tsv


title: Focused screen, upper bin, 80k cells

city: Heidelberg

first: Benedikt

last: Rauscher

address: Meyerhofstr. 1

country: Germany

institute: EMBL

data_processing:
gRNA abundance was quantified using mageck count (Mageck v 0.5.9.4)
Genome_build: hg38
Supplementary_files_format_and_content: .txt file containing raw gRNA counts were generated using mageck count (Mageck v 0.5.9.4).

source_name: HeLa cells

growth_protocol: HeLa cell lines (HeLa Kyoto , HeLa with organelle markers, HeLa Tet::Cas9 RelA-mNeonGreen) were maintained in DMEM (Thermo, 41965039) supplemented with 10% FBS and penicillin–streptomycin (P/S) (Thermo).

extract_protocol:
Genomic DNA was prepared from sorted lower and upper bins and input samples containing 80,000 to 2 Mio cells per sample. Monarch genomic DNA purification kit (New England Biolabs) was used for gDNA preparations while including the RNase treatment. CROP/gRNA loci were amplified from gDNA using a nested PCR strategy with outer primers and barcoded inner primers containing Illumina adapters.
Libraries were pooled and sequenced using an Illumina NextSeq 500 in high output mode with 8 reads to read out the i7 barcode, and 67 reads on Read1 to read through the stagger sequence and identify the gRNA. CRISPR guide RNA library sequencing

treatment_protocol: 5 Mio cells HeLa Tet::Cas9 RelA-mNeonGreen were plated out per 15 cm plate 24 hours before transduction to reach 40-50% confluency at the time point of transduction. 12 plates were transduced with 5 µl 40x concentrated virus in the presence of polybrene per genome-wide sublibrary. For the NFkB focused library, 6 plates were transduced. 24 hours after transduction, cells were collected and plated out in the same number of plates in the presence of Puromycin (concentrations as above for individual gRNAs). Dead cells were collected 24 h after addition of Puromycin, with maximum cell death occurring until 48 hours after addition of Puromycin. 4 days after transduction, medium was changed again and cells were cultivated further in the presence of Puromycin and Doxycycline, followed by 7 days without Doxycycline. Cells were split four times during these 2 weeks of cultivation, while 3 Mio cells were plated out per 15 cm plate and the number of plates were adjusted to keep at least 1000x coverage of each sublibrary. On the day of analysis, cells were treated with TNFa and collected as described above. Cells for each sublibrary were prepared in several batches of 2-3 plates, in order not to exceed 2 hours of storage on ice during recording.

value: cervical cancer

value: HeLa

tag: library

value: Focused screen, upper bin, 80k cells


title: Smooth muscle cell - D30_Proliferative

description: Proliferative.tsv

source_name: Smooth Muscle Cell


title: AAO20

description: glpNormalizedExpression.csv

value: 45 hours post hatch


title: Focused screen, upper bin, 480k cells

value: Focused screen, upper bin, 480k cells


title: Smooth muscle cell - D29_Quiescent

description: Quiescent.tsv

value: Quiescent


title: AAO16

description: glpNormalizedExpression.csv

value: 50uM of Arachidonic acid (C20:4n6, Cayman)

value: 117 hours post hatch


title: Smooth muscle cell - D29_Proliferative

description: Proliferative.tsv

value: Proliferative


title: AAO13

description: glpNormalizedExpression.csv

value: 93 hours post hatch


title: AAO10

description: glpNormalizedExpression.csv


title: Focused screen, upper bin, 320k cells

value: Focused screen, upper bin, 320k cells


title: Focused screen, upper bin, 160k cells

value: Focused screen, upper bin, 160k cells


title: AAO07

description: glpNormalizedExpression.csv


title: AAO05

description: glpNormalizedExpression.csv


title: Smooth muscle cell - D28_Proliferative

description: Proliferative.tsv


title: Smooth muscle cell - D27_Quiescent

description: Quiescent.tsv


title: Smooth muscle cell - D27_Proliferative

description: Proliferative.tsv


title: AAO29

description: glpNormalizedExpression.csv


title: AAO02

description: glpNormalizedExpression.csv


title: Focused screen, lower bin, 480k cells

value: Focused screen, lower bin, 480k cells


title: Focused screen, lower bin, 400k cells

value: Focused screen, lower bin, 400k cells


title: Smooth muscle cell - D26_Proliferative

description: Proliferative.tsv

value: ascending aorta


title: Focused screen, lower bin, 320k cells

value: Focused screen, lower bin, 320k cells


title: AAO23

description: glpNormalizedExpression.csv

value: No treatment


title: Focused screen, lower bin, 160k cells

value: cervical cancer

value: Focused screen, lower bin, 160k cells


title: Smooth muscle cell - D25_Quiescent

description: Quiescent.tsv


title: Smooth muscle cell - D25_Proliferative

description: Proliferative.tsv


title: Focused screen, unsorted, 80k cells

value: HeLa

value: Focused screen, unsorted, 80k cells


title: Focused screen, upper bin, 400k cells

value: Focused screen, upper bin, 400k cells


title: Focused screen, unsorted, 480k cells

value: Focused screen, unsorted, 480k cells


title: Smooth muscle cell - D24_Proliferative

description: Proliferative.tsv


title: Smooth muscle cell - D28_Quiescent

description: Quiescent.tsv

value: Quiescent


title: dfi1_null_vehicle_3

first: Carol

last: Kumamoto

state: Massachusetts

address: 150 Harrison Ave., Tufts University, Department of Molecular Biology and Microbiology, Jaharis 429

department: Molecular Biology and Microbiology

institute: Tufts University

description:
MMINUS_vs_MPLUS.pariwise.gene_exp.diff
BMINUS_vs_MMINUS.pariwise.gene_exp.diff

data_processing:
Raw read files in compressed fastq format were generated using Casava v1.8.0
Raw read files were mapped to reference genome using HISAT v2.1.0
Mapped reads were used as input for pair-wise differential expression analysis using Cuffdiff (Cufflinks v2.2.1)
Genome_build: NC_032089.1 Candida albicans SC5314
Supplementary_files_format_and_content: Differential expression analysis output from cuffdiff ("gene_exp.diff")

organism: Candida albicans

source_name: yeast cells

growth_protocol: Cells from fresh streaks were grown for 8 hours in CM-U at 30C. Cultures were diluted 1:1000 into fresh CM-U and grown overnight.

extract_protocol:
After 30 min of treatment, cells were harvested, washed, and frozen in RNAlater. RNA was harvested from frozen cells using the Qiagen RNeasy kit.
Total RNA was used as input to prepare RNASeq library using Illumina TruSeq RNA library preparation kit

treatment_protocol: When cultures reached approximately OD600=1, they were treated with either 4uM A23187 or an equal voume of 100% ethanol vehicle. Treatment proceeded for 30 minutes before collection.

value: BWP17, dfi1[delta]::FRT/dfi1[delta]::FRT, ura3[delta]::imm434/URA3, his1[delta]/HIS1+, arg4[delta]/ARG4+

value: 100% Ethanol vehicle


title: dfi1_null_vehicle_2


title: dfi1_null_treatment_1

description:
MMINUS_vs_MPLUS.pariwise.gene_exp.diff
BPLUS_vs_MPLUS.pariwise.gene_exp.diff


title: dfi1_null_treatment_3


title: dfi1_null_treatment_2


title: Focused screen, unsorted, 400k cells

value: Focused screen, unsorted, 400k cells


title: Focused screen, lower bin, 80k cells

value: Focused screen, lower bin, 80k cells


title: Focused screen, unsorted, 320k cells

value: Focused screen, unsorted, 320k cells


title: Smooth muscle cell - D23_Quiescent

description: Quiescent.tsv


title: Smooth muscle cell - D23_Proliferative

description: Proliferative.tsv

value: Proliferative


title: dfi1_null_vehicle_1


title: Smooth muscle cell - D22_Quiescent

description: Quiescent.tsv


title: Smooth muscle cell - D26_Quiescent

description: Quiescent.tsv


title: WT_treatment_2

description:
BMINUS_vs_BPLUS.pariwise.gene_exp.diff
BPLUS_vs_MPLUS.pariwise.gene_exp.diff

value: BWP17, ura3[delta]::imm434/URA3, his1[delta]/HIS1+, arg4[delta]/ARG4+


title: Smooth muscle cell - D22_Proliferative

description: Proliferative.tsv

value: ascending aorta


title: Genome-wide screen, upper sorted bin, sub-library 6


title: Genome-wide screen, upper sorted bin, sub-library 5


title: WT_treatment_1


title: Focused screen, unsorted, 160k cells

value: Focused screen, unsorted, 160k cells


title: WT_vehicle_3

description:
BMINUS_vs_BPLUS.pariwise.gene_exp.diff
BMINUS_vs_MMINUS.pariwise.gene_exp.diff


title: Smooth muscle cell - D21_Proliferative

description: Proliferative.tsv


title: Smooth muscle cell - D20_Quiescent

description: Quiescent.tsv


title: WT_vehicle_2


title: Genome-wide screen, upper sorted bin, sub-library 4


title: Genome-wide screen, upper sorted bin, sub-library 3


title: Smooth muscle cell - D20_Proliferative

description: Proliferative.tsv


title: WT_vehicle_1


title: Smooth muscle cell - D19_Quiescent

description: Quiescent.tsv


title: Genome-wide screen, upper sorted bin, sub-library 2


title: Nextflex_miRXplore_Rep06

organism: synthetic construct

source_name: miRXplore Universal Reference

value: miRXplore Universal Reference

tag: protocol

value: NEXTFLEX

tag: disease

value: No

value: Operator 1


title: Genome-wide screen, lower sorted bin, sub-library 6

value: cervical cancer

value: HeLa


title: Nextflex_miRXplore_Rep05

tag: operator


title: Nextflex_miRXplore_Rep04


title: Genome-wide screen, lower sorted bin, sub-library 5


title: WT_treatment_3

tag: treatment


title: Nextflex_miRXplore_Rep03


title: Smooth muscle cell - D18_Quiescent

description: Quiescent.tsv


title: Smooth muscle cell - D18_Proliferative

description: Proliferative.tsv


title: Nextflex_miRXplore_Rep02


title: Smooth muscle cell - D17_Proliferative

description: Proliferative.tsv


title: Genome-wide screen, lower sorted bin, sub-library 3


title: Smooth muscle cell - D17_Quiescent

description: Quiescent.tsv


title: CleanTag_miRXplore_Rep06

value: CleanTag


title: CleanTag_miRXplore_Rep05


title: Smooth muscle cell - D16_Proliferative

description: Proliferative.tsv


title: Genome-wide screen, unsorted, sub-library 6


title: Nextflex_miRXplore_Rep01


title: CleanTag_miRXplore_Rep04


title: Smooth muscle cell - D15_Quiescent

description: Quiescent.tsv

value: Quiescent


title: Genome-wide screen, lower sorted bin, sub-library 1


title: Smooth muscle cell - D15_Proliferative

description: Proliferative.tsv


title: CleanTag_miRXplore_Rep03


title: Genome-wide screen, unsorted, sub-library 5


title: Genome-wide screen, upper sorted bin, sub-library 1


title: Smooth muscle cell - D14_Quiescent

description: Quiescent.tsv


title: Genome-wide screen, unsorted, sub-library 2


title: Genome-wide screen, lower sorted bin, sub-library 4


title: CleanTag_miRXplore_Rep01


title: Smooth muscle cell - D13_Quiescent

description: Quiescent.tsv


title: Genome-wide screen, unsorted, sub-library 3


title: CleanTag_miRXplore_Rep02


title: Smooth muscle cell - D19_Proliferative

description: Proliferative.tsv


title: Smooth muscle cell - D14_Proliferative

description: Proliferative.tsv


title: Genome-wide screen, lower sorted bin, sub-library 2


title: RealSeq_miRXplore_Rep06

value: RealSeq


title: Genome-wide screen, unsorted, sub-library 1


title: Plasmid library, genome-wide, sub-library 6


title: Smooth muscle cell - D12_Quiescent

description: Quiescent.tsv


title: RealSeq_miRXplore_Rep05


title: Smooth muscle cell - D13_Proliferative

description: Proliferative.tsv


title: RealSeq_miRXplore_Rep04


title: Plasmid library, genome-wide, sub-library 5


title: Plasmid library, genome-wide, sub-library 4


title: Plasmid library, genome-wide, sub-library 3


title: RealSeq_miRXplore_Rep02


title: Smooth muscle cell - D11_Quiescent

description: Quiescent.tsv


title: Genome-wide screen, unsorted, sub-library 4


title: Smooth muscle cell - D11_Proliferative

description: Proliferative.tsv


title: Plasmid library, genome-wide, sub-library 2


title: Smooth muscle cell - D10_Quiescent

description: Quiescent.tsv


title: RealSeq_miRXplore_Rep01


title: Qiaseq_miRXplore_Rep06

value: Qiaseq


title: Smooth muscle cell - D10_Proliferative

description: Proliferative.tsv


title: Plasmid library, genome-wide, sub-library 1


title: Smooth muscle cell - D9_Proliferative

description: Proliferative.tsv


title: Qiaseq_miRXplore_Rep03


title: Qiaseq_miRXplore_Rep05


title: YTHDC2_CLIP_WT_2

city: New York

first: Yuhki

last: Saito

state: NY

address: 1230 York avenue

institute: The Rockefeller University

data_processing:
We followed standard/BruU-CLIP data analysis pipeline using CTK (https://zhanglab.c2b2.columbia.edu/index.php/Standard/BrdU-CLIP_data_analysis_using_CTK). The deposited fastq files are raw data before collapsing PCR duplicates.
removal of 3'adaptor (GTGTCAGTCACTTCCAGCGG)
collapsing of exact sequences
stripping of random barcodes
alignment with BWA (mm10)
collapsing of PCR duplicates (unique CLIP tags)
Peak calling by using unique CLIP tags
Genome_build: mm10
Supplementary_files_format_and_content: Bedgraph files generated from YTHDC2 unique CLIP tags for genome browser

source_name: Testes

extract_protocol:
Tissues were UV-irradiated and subjected to YTHDC2 CLIP with anti-YTHDC2 antibodies (ab220160 from Abcam and 27779-1-AP from Proteintech) . Detailed desription in accompanying paper.
Partial RNase A digestion, linker ligation, reverse transcription, criculation and PCR amplificiation

value: Testes

tag: age

value: 24 weeks


title: Qiaseq_miRXplore_Rep02


title: Qiaseq_miRXplore_Rep01


title: Smooth muscle cell - D9_Quiescent

description: Quiescent.tsv


title: YTHDC2_CLIP_WT_1

tag: strain

value: 20 weeks


title: Smooth muscle cell - D8_Quiescent

description: Quiescent.tsv


title: Smooth muscle cell - D8_Proliferative

description: Proliferative.tsv

value: Proliferative


title: Smooth muscle cell - D12_Proliferative

description: Proliferative.tsv


title: RealSeq_miRXplore_Rep03


title: Smooth muscle cell - D7_Quiescent

description: Quiescent.tsv


title: YTHDC2_CLIP_WLA_homo_2


title: Smooth muscle cell - D7_Proliferative

description: Proliferative.tsv


title: YTHDC2_CLIP_WLA_homo_1


title: Smooth muscle cell - D6_Quiescent

description: Quiescent.tsv


title: MKO_SCNT_E19p5_placenta_RNA_rep1

first: Wenhao

last: Zhang

address: Warren Alpert Bldg, Rm 160, 200 Longwood Ave

department: Genetics

institute: Harvard Medical School

data_processing:
Adaptors were firstly trimmed by Trim Galore with parameters --illumina --paired. Adaptor trimmed reads were mapped to mm9 using TopHat (v2.1.1) with parameter -p 2 -g 1 --no-coverage-search. Then, expression values represented by Fragments per Kilobase per Million (FPKM) of the protein-coding genes were calculated by Cufflinks (v2.2.1) based on annotations from RefSeq database.
Supplementary_files_format_and_content: Tab-delimited text files for RNA seq including FPKM values for each gene

source_name: Spongiotrophoblast of placenta

extract_protocol: Spongiotrophoblast from placenta was dissected and lysed with TRIzol reagent (Ambion, Cat. 15596026). RNA was extracted by isopropanol precipitation. 10 µg RNA was DNase I (Fermentas, Cat. EN0521) treated at 37°C for 1 hour. RNA with polyA tails were captured and purified using DynabeadsTM mRNA Purification Kit (ThermoFisher Scientific, 61006). Purified RNA was fragmented with RNA Frag. Buffer (NEB, Cat. E6186A) at 95°C for 5 min. Reaction was then stopped and RNA was purified. First stand cDNA was synthesized with a commercial kit using both oligo dT and random primers (Invitrogen, Cat. 18080-051). Second strand cDNA was synthesized with second strand synthesis buffer (Invitrogen, Cat. 10812014) containing MgCl2, DTT, dNTP, dUTP, RNase H (Fermentas, Cat. EN0202), E. coli DNA ligase (NEB, Cat. M0205S) and DNA polymerase I (NEB, Cat. M0209S). DNA was purified after 2-hour incubation on thermomixer at 16°C. Synthesized cDNA was subjected to library preparation using NEBNext UltraTM II DNA library Prep Kit for Illumina (NEB, E7103) according to manufacturer’s instructions.

value: Spongiotrophoblast of placenta

value: Slc38a4 maternal knockout SCNT


title: MKO_SCNT_E19p5_placenta_RNA_rep2


title: MKO_SCNT_E14p5_placenta_RNA_rep2


title: Smooth muscle cell - D6_Proliferative

description: Proliferative.tsv

value: ascending aorta


title: Qiaseq_miRXplore_Rep04

value: miRXplore Universal Reference


title: YTHDC2_CLIP_WT_3


title: MKO_SCNT_E14p5_placenta_RNA_rep1


title: Smooth muscle cell - D5_Proliferative

description: Proliferative.tsv


title: WT_SCNT_E19p5_placenta_RNA_rep2

value: wild type SCNT


title: YTHDC2_CLIP_WLA_homo_3


title: Smooth muscle cell - D4_Quiescent

description: Quiescent.tsv


title: Smooth muscle cell - D16_Quiescent

description: Quiescent.tsv


title: WT_SCNT_E19p5_placenta_RNA_rep1


title: C4_S8

city: Montpellier

first: Frederic

last: Michon

address: 80, rue Augustin Fliche

department: Institute for Neurosciences of Montpellier

country: France

institute: Inserm

data_processing:
bcl2fastq2 Conversion Software was used to convert BCL files to FASTQ file format and demultiplex samples.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using Trimmomatic. Parameters used: :2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36
Trimmed reads were mapped to zebrafish GRCz11 genome using STAR aligner (2.6.0c) with parameters  --runThreadN 20 --chimSegmentMin 12 --chimJunctionOverhangMin 12 --chimSegmentReadGapMax 3 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --alignSJstitchMismatchNmax 5 -1 5 5 --outFilterType BySJout --outFilterMismatchNmax 999 --outSAMattributes NH HI NM MD AS nM jM jI XS --outSAMtype BAM SortedByCoordinate --outSAMmapqUnique 60 --quantMode GeneCounts --twopassMode Basic
Counts per gene were calculated using featureCounts software using Ensembl release 97 zebrafish gtf-files. Parameters used: -s 2 -T 20 -t exon -g gene_id
Differential expression analysis used the DESeq2 software in R environment. Procedures included: Normalization of count values between samples using a geometric mean, estimation of sample-wise factors to correct for library size variability (for example), estimation of dispersion (i.e. variance, scatter) of gene-wise values between conditions, negative binomial linear model and Wald test to produce p-values, removal of low-expression outliers (using Cook's distance) results to optimize for p-value adjustment and finally, multiple testing adjustment of p-values with Benjamini-Hochberg procedure.
Genome_build: zebrafish GRCz11 (GCA_000002035.4)
Supplementary_files_format_and_content: Raw count matrix of sequencing reads (featureCounts meta-feature level) as .xlsx

organism: Danio rerio

source_name: Cornea

extract_protocol: Illumina protocols

value: Wild type (AB background)

value: Cornea

value: 183 days old

value: No treatment


title: T4_S6

value: Abrasion


title: T3_S5

value: 148 days old


title: T2_S2

value: 145 days old


title: Smooth muscle cell - D4_Proliferative

description: Proliferative.tsv


title: T1_S1

description: Excluded from analysis, based on PCA

value: 180 days old


title: Smooth muscle cell - D3_Proliferative

description: Proliferative.tsv


title: WT_SCNT_E14p5_placenta_RNA_rep1


title: WT_SCNT_E14p5_placenta_RNA_rep2


title: IVF_E19p5_placenta_RNA_rep2

value: in vitro fertilized (IVF)


title: C3_S7


title: Smooth muscle cell - D3_Quiescent

description: Quiescent.tsv

value: Quiescent


title: C1_S3


title: C2_S4


title: Smooth muscle cell - D2_Quiescent

description: Quiescent.tsv


title: Smooth muscle cell - D2_Proliferative

description: Proliferative.tsv


title: Healthy Donor 2

city: Singapore

first: Christine

last: Cheung

state: Singapore

address: 59 Nanyang Drive

country: Singapore

institute: Lee Kong Chian School of Medicine

data_processing:
Raw sequencing data was also processed by NovogeneAIT Genomics (Singapore) using CellRanger (10x Genomics) with reads mapped to the human genome assembly (GRCh38).
Genome_build: GRCh38
Supplementary_files_format_and_content: Filtered feature-barcode matrices containing detected cellular barcodes
Supplementary_files_format_and_content: Feature.tsv and barcode.tsv files containing corresponding row and column indices for respenctive data matrix

source_name: Endothelial cells

growth_protocol: BOECs were generated as per described by Ormiston, M. L. et al. (2015) with modifications. Briefly, peripheral blood samples (5 – 9 mL) was diluted 1:1 with phosphate-buffered saline (PBS) and separated to obtain buffy coat by density gradient centrifugation over Ficoll® Paque (GE Healthcare). The buffy coat, which was enriched with peripheral blood mononuclear cells (PBMCs), was carefully collected, washed with PBS, resuspended in heparin-free, EGM-2 medium (Lonza) supplemented with 16% defined foetal bovine serum (FBS; Hyclone) and counted. Plasma was also collected and stored at -80°C. Then, the PBMCs were seeded into collagen I-coated well(s) accordingly so that the cell density was ≥1.5 × 106 cells/cm2. Medium was changed every two to three days. Outgrowth colonies should appear between seven to 14 days post-seeding. The cells were expanded to passage 3 before any applications were performed on them, including phenotyping and functional evaluation, in order to opt out unwanted leukocytes. After passage 3, BOECs were cultured on collagen-I-coated tissue culture dishes in heparin-free, EGM-2 with 10% heat-inactivated FBS with media change every 2 – 3 days. BOECs from passages 4 to 8 were used in experiments.

extract_protocol:
BOECs from 2 PCV and 2 normal lines were seeded and subjected to orbital flow as described in Orbital Flow Setup. After 24h of orbital flow, the BOECs were trypsinized, resuspended in heparin-free, EGM-2 medium (10% heat-inactivated FBS) and counted using Trypan blue and an automated cell counter (Countess II, Thermo Fisher Scientific) and resuspended appropriately for loading onto 10X Genomics Chromium Controller chip by facility personnel at Single-cell Omics Centre (SCOC), Genome Institute Singapore (GIS).
Each BOEC cell line was prepared as a separate scRNA-seq library using Chromium Single Cell 3’ v3 Reagent Kit (10X Genomics) by SCOC GIS and the final ready-to-sequence libraries were handed over with quantification and quality assessment reports from Bioanalyzer Agilent 2100 using the High Sensitivity DNA chip (Agilent Genomics). Individual libraries were pooled equimolarly and sent for sequencing by NovogeneAIT Genomics (Singapore).

treatment_protocol: BOECs were trypsinized and counted with 0.4% Trypan Blue (Gibco, Thermo Fisher Scientific) staining on an automated cell counter (Countess II, Thermo Fisher Scientific) before diluting and seeding onto rat-tail collagen Type1 (Corning)-coated 12-well plates to give 120,000 viable cells per well. Seeded wells were incubated for 48h in a 5% CO2, 37°C, humidified incubator before overlying media was replaced with 800ml of fresh heparin-free, EGM-2 medium (10% heat-inactivated FBS) to give a liquid height of ~2mm per well. Plates were then replaced onto an orbital shaker (orbital radius of 0.1cm) in a 5% CO2, 37°C, humidified incubator and rotated at 210rpm for 24h.

value: Healthy Donor

tag: cell type

value: Blood outgrowth endothelial cells

value: Orbital shear setup 24h


title: IVF_E19p5_placenta_RNA_rep1

value: Spongiotrophoblast of placenta


title: Smooth muscle cell - D1_Proliferative

description: Proliferative.tsv

value: ascending aorta

value: Proliferative


title: Healthy Donor 1


title: IVF_E14p5_placenta_RNA_rep2


title: Spatial_transcriptomics_5 weeks (CS15) human embryo_8

city: Los Angeles

first: Feiyang

last: Ma

state: CA

address: 610, Charles Young Dr East, TLSB 3000C

department: Molecular Biology Institute

institute: UCLA

description: 5 weeks (CS15) human embryo

data_processing:
Library strategy: Spatial transcriptomics
Libraries were sequenced on an Illumina Nova-Seq (Illumina, San Diego, CA) as 150bp paired end reads and were converted from bcl files to fastq files using bcl2fastq.
After sequencing, the reads were aligned to the human genome (hg38), and the expression matrix was extracted using the spaceranger pipeline.
Loupe files from the spaceranger pipeline were used to make the plots.
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene in every spot
Supplementary_files_format_and_content: png file contains H&E staining image

molecule: polyA RNA

source_name: Transverse section of a human embryo (5 weeks, CS15). Dorsal aorta, between vitelline vessels and umbilical cord. Umbillical vessels.

extract_protocol:
CS15d embryo in toto was frozen in OCT medium and stored at −80°C until sectioning.
Optimization of tissue permeabilization was performed on 10-μm-thick sections using Visium Spatial Tissue Optimization Reagents Kit (10X Genomics, Pleasanton, CA, USA), which established an optimal permeabilization time of 30 minutes. Samples were mounted onto a Gene Expression slide (10X Genomics), fixed in ice-cold methanol, stained with hematoxylin and eosin, and scanned with Aperio scanner (Leica Biosystems, Germany). Tissue permeabilization was performed to release the poly-A mRNA for capture by the poly(dT) primers precoated on the slide, which include an Illumina TruSeq Read, spatial barcode, and unique molecular identifier (UMI). Visium Spatial Gene Expression Reagent Kit (10X Genomics) was used for reverse transcription to produce spatially barcoded full-length cDNA and for second strand synthesis followed by denaturation to allow a transfer of the cDNA from the slide into a tube for amplification and library construction. Visium Spatial Single Cell 3’ Gene Expression libraries consisting of Illumina paired-end sequences flanked with P5/P7 were constructed after enzymatic fragmentation, size selection, end repair, A-tailing, adaptor ligation, and PCR. Dual Index Kit TT Set A (10X Genomics) was used to add unique i7 and i5 sample indexes and generate TruSeq Read 1 for sequencing the spatial barcode and UMI and TruSeq Read 2 for sequencing the cDNA insert, respectively. Sequencing was performed on Illumina NovaSeq 6000.

tag: time


title: PCV Patient 2

value: PCV Patient


title: IVF_E14p5_placenta_RNA_rep1


title: IVF_E9p5_placenta_RNA


title: PCV Patient 1


title: Spatial_transcriptomics_5 weeks (CS15) human embryo_7

description: 5 weeks (CS15) human embryo


title: shFSCN1 1

city: Wuhan

first: Dong

last: Chen

state: Hubei

address: 388 GaoXin 2nd Road, East Lake Hi-Tech Development Zone

department: Center for Genome Analysis

institute: ABLife, Inc.

data_processing:
Illumina bcl2fastq software used for basecalling.
3' adapter (end1:AGATCGGAAGAGC;end2:AGATCGGAAGAGC) and low quality bases trimmed using FASTX-Toolkit (Version 0.0.13). the short reads less than 16nt were also dropped.
Reads were mapped using tophat2 --read-edit-dist 4 -N 4 --b2-N 1 -a 8 -m 0 -g 20 -p 16 --no-discordant. Uniq mapped reads were remained. while several mapped reads have the same start position and end position, only one is considered.
edgeR was used to the DEG analysis with FC>2  Pvalue <= 0.01 Qvalue <= 0.05
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include gene FPKM values for each sample

source_name: HeLa cell

growth_protocol: HeLa cells were cultured under standard conditions with Dulbecco’s modified Eagle’s medium (DMEM) with 10% fetal bovine serum (FBS), 100 µg/mL streptomycin, and 100 U/mL penicillin.

extract_protocol:
The RNA was treated with RQ1 DNase (Promega, Madison, WI, USA) to remove DNA. The quality and quantity of the purified RNA were assessed by measuring the absorbance at 260 nm/280 nm (A260/A280) using Smartspec Plus (BioRad, USA). The integrity of each RNA sample was further verified by 1.5% agarose gel electrophoresis.electrophoresis.
A total 1μg RNA for each sample was used for RNA-seq library preparation. PolyA mRNAs were purified and concentrated with oligo(dT)-conjugated magnetic beads (Invitrogen, Carlsbad, CA, USA) before directional RNA-seq library preparation. The frag¬mented RNA wereend repaired and 5' adaptor ligation. Then, reverse transcription was performed with RT primer harboring 3' adaptor sequence and randomized hexamer. The cDNAs were purified, amplified, and stored at -80°C until they were used for sequencing.

treatment_protocol: To knockdown FSCN1, shRNA against human FSCN1 transfection of HeLa cells was performed using lipofectAMINE 2000 (Invitrogen, Carlsbad, CA, USA) according to the manufacturer's protocol. Transfected cells were harvested after 48 h for analysis.

value: HeLa cell

value: transfected with FSCN1 shRNA


title: YTHDC2_CLIP_KO_2

value: Testes

value: 8.5 weeks


title: Spatial_transcriptomics_5 weeks (CS15) human embryo_6

description: 5 weeks (CS15) human embryo

source_name: Transverse section of a human embryo (5 weeks, CS15). Dorsal aorta, between vitelline vessels and umbilical cord.


title: Spatial_transcriptomics_5 weeks (CS15) human embryo_5

description: 5 weeks (CS15) human embryo


title: WT_SCNT_E9p5_placenta_RNA

value: wild type SCNT


title: Spatial_transcriptomics_5 weeks (CS15) human embryo_2

description: 5 weeks (CS15) human embryo

source_name: Transverse section of a human embryo (5 weeks, CS15). Dorsal aorta, mid/lower liver


title: STZ_hl2

city: Beijing

first: Rongrong

last: Hua

state: China

address: Beijing

department: Department of Radiology

institute: the Third Medical Centre, Chinese People’s Liberation Army General Hospital

data_processing:
Illumina Casava 1.8 software used for base-calling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: Sscrofa11.1
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

organism: Sus scrofa

source_name: Blood serum

extract_protocol:
RNA was extracted according to the previous description (Hua et al., 2018), whose integrity was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA). A total amount of 1 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system. Then, the clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina Novaseq platform and 150 bp paired-end reads were generated.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: Ba-Ma mini pigs

value: Peripheral blood


title: shFSCN1 2


title: YTHDC2_CLIP_Adult_4


title: STZ_hl5


title: Spatial_transcriptomics_5 weeks (CS15) human embryo_1

description: 5 weeks (CS15) human embryo

source_name: Transverse section of a human embryo (5 weeks, CS15). Dorsal aorta, upper/mid liver


title: STZ_hl1


title: shCtrl 1

value: transfected with empty vector


title: shCtrl 2


title: STZ_hc1


title: YTHDC2_CLIP_Adult_2


title: Infection with CBDV rep 2

city: Chicago

first: Dongbo

last: Yang

state: IL

address: 929 E 57th St

institute: University of Chicago

description: CBDV+virus rep 2

data_processing:
The libraries were sequenced by a Novaseq 6000 in two runs to generate paired-end 100bp reads. For each sample, the raw FASTQ files from two flow cells were combined before downstream processing.
RNA-seq data were analyzed using a local Galaxy  20.05 instance. Quality and adapter trimming were performed on the raw sequencing reads using Trim Galore! 0.6.3.
The reads were mapped to both the human genome (UCSC hg19 with GENCODE annotation) and the SARS-COV-2 genome (NCBI Assembly ASM985889v3 with Emsembl annotation) using RNA STAR  2.7.5b.
The resulting mapped reads from each sample were counted by featureCounts  1.6.4 for per gene read counts.
The raw counts were analyzed for differential expression between experimental conditions using DESeq2  1.22.1 .
Genome_build: Human (hg19), SRAS-COV-2 (NCBI Assembly ASM985889v3)
Supplementary_files_format_and_content: Tab delimited text file containing a matrix table with raw gene counts for every gene and every sample

source_name: A549 cells with ACE2 overexpression

growth_protocol: A549-ACE2 cells were maintained in 2% FBS DMEM media in 5% CO2.

extract_protocol:
Total RNA extraction by the NucleoSpin 96 RNA kit (Takarabio, 740709)
RNA libraries were prepared for sequencing by the University of Chicago Genomics Facility following standard protocols.

treatment_protocol: Two hours before infection, cannabidiol or vehicle was added to the cells. Cannabidiol (Cayman Chemical, 90080) was dissolved in a 10mM stock solution with DMSO (Sigma-Aldrich, D2650-100mL). Final concentration of CBD was 10uM in cells. Then, the cells were mock treated or infected with SARS-COV-2 (USA-WA1/2020) at MOI 3.0. Infection was performed by removing the media with drug, adding viral media and incubating for 1.5 hours. Then the virus media was removed and replaced with fresh 2% FBS DMEM media with drug. For the CBDV experiment, identical conditions and procedures were used.

value: A549 cells with ACE2 overexpression

tag: infection

value: SARS-CoV-2 MOI 3

value: Cannabidivarin 10uM


title: Infection with CBDV rep 1

description: CBDV+virus rep 1

tag: cell line


title: STZ_hc3


title: Spatial_transcriptomics_5 weeks (CS15) human embryo_4

description: 5 weeks (CS15) human embryo

source_name: Transverse section of a human embryo (5 weeks, CS15). Dorsal aorta and vitelline artery juncture. Umbillical vessels.


title: STZ_hl3


title: Infection with vehicle rep 3

description: Veh+virus rep 3

value: DMSO


title: YTHDC2_CLIP_KO_1


title: YTHDC2_CLIP_Adult_3


title: STZ_hc2


title: Infection with vehicle rep 2

description: Veh+virus rep 2


title: YTHDC2_CLIP_Adult_1


title: Infection with CBDV rep 3

description: CBDV+virus rep 3


title: YTHDC2_CLIP_8dpp_3


title: STZ_hl4


title: Infection with vehicle rep 1

description: Veh+virus rep 1


title: YTHDC2_CLIP_8dpp_2


title: hl_STZ2


title: hl_STZ1


title: Mock with CBDV rep 3

description: CBDV-virus rep 3

value: Mock


title: YTHDC2_CLIP_8dpp_1


title: hl_STZ3


title: Mock with CBDV rep 2

description: CBDV-virus rep 2


title: hl_STZ4


title: YTHDC2_CLIP_10dpp_2


title: hc_STZ4


title: hc_STZ2


title: Mock with vehicle rep 3

description: Veh-virus rep 3


title: YTHDC2_CLIP_10dpp_1


title: Mock with vehicle rep 1

description: Veh-virus rep 1


title: Control4

value: Control


title: Control3


title: RenCa, 3D rep2

city: Warsaw

first: Klaudia

last: Brodaczewska

address: Szaserow 128

country: Poland

institute: Military Institute of Medicine

data_processing:
Single-end reads were aligned to Ensembl GRCm38 mouse genome with STAR (v2.7)
Counts were obtained using featureCounts v1.6.3
Genome_build: mmu38
Supplementary_files_format_and_content: tab-delimited text file include table with raw gene counts for every gene and every sample

source_name: renal cell cancer

growth_protocol: Two-dimensional cultures were maintained under standard culture conditions (5% CO2, 21% pO2). RenCa - 6600 cells/cm2, B16F10 3300 cells/cm2, were seeded and cultivated for 5 days. For obtaining spheroids 500 cells were resuspended in 20 µL medium supplemented with 0.25% methylcellulose (vol/vol in medium), (R&D Systems, USA) and seeded as a single hanging drop, on the cover of culture plate. Drops were kept in standard culture conditions (5% CO2, 21% pO2) for 72h. After that time the drops were individually transferred to a 96-well plate. The plates were previously covered with 1% agarose dissolved in double distilled water (w/vol, VWR, Belgium). Cells aggregates expanded for another four days period.

extract_protocol:
total RNA was isolated using RNeasy Mini Kit (Qiagen, Hilden, Germany), according to the manufacturer’s instructions with subsequent DNA cleanup with TURBO DNA-free Kit (Thermo Fisher Scientific, USA). Concentration of obtained RNA was measured with RNA BR Assay Kit (Thermo Fisher Scientific, USA), while its quality and integrity- with Qubit RNA IQ Assay Kit (Thermo Fisher Scientific, USA). Samples with IQ > 8,5 only were used for sequencing.
cDNA libraries were obtained from mRNA, by purifying 1µg of total RNA with NEBNext® Poly(A) mRNA Magnetic Isolation Module (New England Biolabs), using Ultra RNA Library Prep Kit for Illumina (New England Biolabs) and NEBNext Multiplex Oligos for Ilumina (New England Biolabs), per producers protocols. Libraries were purified with NEBNext Sample purification Beads (New England Biolabs) and their quality was confirmed by High Sensitivity DNA Kit (Agilent, USA) and Bioanalyzer (Agilent, USA).

value: RenCa

value: renal cell cancer cell

tag: growth protocol

value: spheroid culture


title: RenCa, 2D rep2

value: monolayer culture


title: Control2


title: RenCa, 2D rep1


title: A549_Veh_mock-3

description: Mock with vehicle rep 3


title: A549_Veh_mock-2

description: Mock with vehicle rep 2


title: A549_Veh_mock-1

description: Mock with vehicle rep 1


title: Control1


title: A549_CBD_mock-3

description: Mock with CBD rep 3

value: Cannabidiol 10uM


title: Col-0_light

first: Xin-Jian

last: He

address: No. 7, zhongguancun life science park road, changping district

institute: National Institute of Biological Sciences

data_processing:
Zebracall software used for basecalling.
After removing adapter and filtering low-quality reads, the clean reads were aligned to the Arabidopsis genome (TAIR10) using HISAT2 with the default parameters.
The reads mapped on the exon were counted using featureCounts.
The differentially expressed genes were identified with log2(fold change) >1 or <-1 and p-value<0.01 using edgeR.
Genome_build: TAIR10
Supplementary_files_format_and_content: Tab-delimited text file include normalized reads or reads count for each sample.

organism: Arabidopsis thaliana

source_name: seedlings

growth_protocol: Arabidopsis seedlings were grown on MS (Murashige and Skoog) medium plates at 23°C with a 16-h light/8-h dark photoperiod.

extract_protocol:
Total RNA was extracted with TRI Reagent (Sigma, T9424) from 2-week-old seedlings and was then used for reverse transcription or RNA deep sequencing.
Sequencing libraries were built for RNA-seq (the single-ended 50-bp and paired-end 150-bp strategy).

treatment_protocol: MS plates with seedlings were wrapped in foil for dark treatment.

value: seedlings

tag: genotype

value: wild type

value: light


title: A549_CBD_mock-2

description: Mock with CBD rep 2


title: Col-0_dark

value: dark


title: Mock with CBDV rep 1

description: CBDV-virus rep 1


title: YTHDC2_CLIP_10dpp_3

value: Testes


title: FSC-A Low HSC 1

first: Yeojin

last: Lee

address: 650 WEST 168TH STREET, BB 1108

institute: Columbia University Medical Center

data_processing:
The RNA-seq pipeline from Basepair (www.basepairtech.com) was used for the analysis. Expression count was analyzed by STAR and differential expression by DESeq2 (P < 0.05 and fold-change > 2).
Genome_build: mm10
Supplementary_files_format_and_content: Text files include normalized expression count values for each sample

source_name: FSC-A Low HSCs from WT P0 livers

extract_protocol:
P0 liver cells were stained for Lineage- Sca1+ cKit+ CD150+ CD48- HSCs. 100-200 HSCs were FACS sorted into 0.2% Triton X-100 and then proceeded to library preparation.
RNA libraries were prepared for sequencing using the Smart-seq2 method.

value: liver

value: HSC

value: wild-type


title: FSC-A Low HSC 3


title: FSC-A Low HSC 2


title: RenCa, 3D rep1


title: A549_CBD_mock-1

description: Mock with CBD rep 1

value: A549 cells with ACE2 overexpression


title: hc_STZ3

value: Ba-Ma mini pigs

value: Peripheral blood


title: FSC-A High HSC 4

source_name: FSC-A High HSCs from WT P0 livers


title: dcp5-1  T15 poly rep3

city: Shenzhen

first: Bosheng

last: Li

state: Guangdong

address: SUStech Huiyuan #1 406

department: MCDB

institute: SUSTC (current, may different with previous institution )

description: polysomal mRNA

data_processing:
Bowtie for alignment, v2, default parameter
Cufflink for expression profiling, V2.1.0, default parameter
Genome_build: TAIR10
Supplementary_files_format_and_content: wzy_raw_data.xlsx

source_name: seedling

growth_protocol: Sueface sterilized seeds were imbibed in water at 4 °C for 3 days and germinated on 1x MS agar at standard condition (16h ligth/8h dark, 22 °C) for 5 days

extract_protocol:
Polysomal RNA were extracted from the mixed polysome fractions that were separated in a 10% to 50% sucrose gradient. Total RNA were extracted from each input lysate.
stander Illumina mRNA-seq protocol

treatment_protocol: Seedlings were rested in 1 x MS liquid medium for 30 min and subjected to 1 x MS liquid  medium supplie with 150 mM NaCl for 0 or 15 min

tag: ecotype

value: 15 min with 150 mM NaCl


title: FSC-A High HSC 3


title: A549_Veh_infect-3

description: Infection with vehicle rep 3

value: SARS-CoV-2 MOI 3

value: DMSO


title: A549_Veh_infect-2

description: Infection with vehicle rep 2


title: hc_STZ1


title: dcp5-1  T15 poly rep1

description: polysomal mRNA


title: FSC-A High HSC 2


title: A549_Veh_infect-1

description: Infection with vehicle rep 1


title: dcp5-1 T15 input rep3

description: Total RNA


title: FSC-A High HSC 1


title: A549_CBD_infect-3

description: Infection with CBD rep 3


title: dcp5-1 T15 input rep2

description: Total RNA


title: A549_CBD_infect-2

description: Infection with CBD rep 2


title: dcp5-1 T15 input rep1

description: Total RNA


title: Tpo Tsc1KO HSC 4 (Tsc1)

source_name: HSCs from Vav1-cre; Tsc1fl/fl; TpoKO P0 livers

value: Vav1-cre; Tsc1fl/fl; TpoKO


title: A549_CBD_infect-1

description: Infection with CBD rep 1


title: Tpo Tsc1KO HSC 2 (Tsc1)


title: yolk sac 4.5 week

data_processing:
Sequencing was performed on Illumina NovaSeq 6000.
The raw reads were mapped to human reference genome (refdata-cellranger-GRCh38-1.2.0) using cellranger count.
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with raw gene counts for each cell

source_name: yolk sac

extract_protocol:
For single cell RNA-sequencing, dissociated cells were stained with the following antibodies: human-CD45-APC-H7 cl.2D1 (BioLegend 368516; 1:100), CD34-BV605 cl. 581 , CD34-BV605 cl. 581 , CD90-APC cl. 5E10 (BD 562556; 1:100), CD38-PE-Cy7 cl. HIT2 (BD 560677; 1:100), CD43-FITC cl.1G10 (BD 555475; 1:20), CD235a-PE cl. 3H9. CD34+ and/or CD31+ cells were sorted into PBS 0.04% BSA using a BD FACS Aria cell sorter. Placenta, second trimester liver and cord blood were magnetically enriched for CD34+ cells using human CD34 MicroBead Kit UltraPure (Miltenyi) and following manufacturer instructions.
For the generation of single-cell gel beads in emulsion, cells were loaded on a Chromium single cell instrument (10x Genomics) with an estimated targeted cell recovery of ~5,000 cells as per manufacturer’s protocol. In brief, single-cell suspension of cells in 0.4% BSA-PBS were added to each channel on the 10X chip. Cells were partitioned with Gel Beads into emulsion in the Chromium instrument where cell lysis and barcoded reverse transcription of RNA occurred following amplification. Single-cell RNAseq libraries were prepared by using the Chromium single cell 3’ library and gel bead kit v2 (10X Genomics).


title: dcp5-1 T0 poly rep2

description: polysomal mRNA

value: 0 min with 150 mM NaCl


title: Tpo Tsc1KO HSC 3 (Tsc1)


title: dcp5-1 T0 poly rep3

description: polysomal mRNA


title: dcp5-1 T0 poly rep1

description: polysomal mRNA


title: placenta 4.5 week

source_name: placenta


title: dcp5-1 T0 input rep3

description: Total RNA


title: dcp5-1  T15 poly rep2

description: polysomal mRNA


title: vitelline artery 4.5 week

source_name: vitelline artery


title: liver 8 week

source_name: liver


title: TpoKO HSC 1 (Tsc1)

source_name: HSCs from TpoKO P0 livers

value: Tpo-/-


title: TpoKO HSC 2 (Tsc1)


title: liver 6 week


title: dcp5-1 T0 input rep1

description: Total RNA


title: Control HSC 3 (Tsc1)

source_name: HSCs from control P0 livers

value: control (Tpo wild-type)


title: Control HSC 2 (Tsc1)


title: Col-0 T15 poly rep3

description: polysomal mRNA

value: wildtype


title: liver 4.5 week


title: liver 5.5 week


title: Col-0 T15 poly rep2

description: polysomal mRNA


title: Control HSC 1 (Tsc1)


title: liver 15 week


title: TpoKO HSC 5


title: Col-0 T15 poly rep1

description: polysomal mRNA


title: Tpo Tsc1KO HSC 1 (Tsc1)


title: liver 11 week


title: Col-0 T15 input rep3

description: Total RNA


title: heart 4.5 week

source_name: heart


title: TpoKO HSC 4


title: TpoKO HSC 3 (Tsc1)


title: TpoKO HSC 3


title: head 4.5 week

source_name: head


title: dcp5-1 T0 input rep2

description: Total RNA


title: Col-0 T15 input rep2

description: Total RNA


title: TpoKO HSC 2


title: Col-0 T0 poly rep3

description: polysomal mRNA


title: Col-0 T15 input rep1

description: Total RNA


title: Col-0 T0 poly rep2

description: polysomal mRNA


title: cord blood 40 week

source_name: cord blood


title: cord 4.5 week

source_name: cord


title: WT HSC 4

source_name: HSCs from WT P0 livers


title: TpoKO HSC 1


title: Mock with vehicle rep 2

description: Veh-virus rep 2

source_name: A549 cells with ACE2 overexpression

value: Mock


title: aorta-gonad-mesonephros 6 week

source_name: aorta-gonad-mesonephros


title: Col-0 T0 poly rep1

description: polysomal mRNA


title: WT HSC 3


title: aorta-gonad-mesonephros 5.5 week


title: Col-0 T0 input rep3

description: Total RNA


title: WT HSC 2


title: aorta-gonad-mesonephros 5 week


title: Col-0 T0 input rep2

description: Total RNA


title: aorta-gonad-mesonephros 4.5 week


title: Col-0 T0 input rep1

description: Total RNA


title: WT HSC 1


title: Hypoxia_Acriflavine_HUVEC_3 [Hyp_ACF_3]

status: Public on Jan 19 2022

city: bad nauheim

first: Stefan

last: Günther

address: ludwigtr. 43

institute: MPI for heart and lung research

description: E21_3141_Lib_Leisegang_ML1529-2_Probe_15

data_processing:
The resulting raw reads were assessed for quality, adapter content and duplication rates with FastQC.
Trimmomatic version 0.39 was employed to trim reads after a quality drop below a mean of Q20 in a window of 10 nucleotides. Only reads between 30 and 150 nucleotides were cleared for further analyses.
Trimmed and filtered reads were aligned versus the Ensembl human genome version hg38 (ensemble release 104) using STAR 2.7.9a with the parameter “--outFilterMismatchNoverLmax 0.1” to increase the maximum ratio of mismatches to mapped length to 10%.
The number of reads aligning to genes was counted with featureCounts 2.0.2 tool from the Subread package. Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded.
The Ensemble annotation was enriched with UniProt data based on Ensembl gene identifiers.
Genome_build: hg38
Supplementary_files_format_and_content: library size normalized counts

growth_protocol: Culturing of pooled human umbilical vein endothelial cells (HUVEC) purchased from PromoCell (C-12203, Lot No. 405Z013, 408Z014, 416Z042, Heidelberg, Germany) was performed at 37°C with 5% CO2. Dishes were coated with gelatin (Sigma-Aldrich, G1890-500G) prior to culturing. Endothelial growth medium (EGM) was prepared by supplementing endothelial basal medium (EBM) with human recombinant epidermal growth factor (EGF), EndoCGS-Heparin (PeloBiotech, Germany), 8% fetal calf serum (FCS) (S0113, Biochrom, Germany), penicillin (50 U/ml) and streptomycin (50 µg/ml) (15140-122, Gibco/ Lifetechnologies, USA). Biological replicates comprised at least three different batches from passage 3. For hypoxia treatment, cells were incubated for 16h in a SciTive Workstation (Baker Ruskinn, Leeds, UK) at 1% O2 and 5% CO2.

extract_protocol:
Total RNA Isolation was performed using the RNA Mini Kit (Bio&Sell).
1µg of total RNA was used as input for SMARTer Stranded Total RNA Sample Prep Kit - HI Mammalian (Takara) using manufactures protocols.

treatment_protocol: Hypoxia was performed for 16h (1% O2) with  DMSO or Acriflavine (10µM) treatment.

value: 16h (1% O2) with Acriflavine (10µM)


title: Hypoxia_DMSO_HUVEC_3 [Hyp-DMSO_3]

description: E21_3141_Lib_Leisegang_ML1529-2_Probe_11

value: human umbilical vein endothelial cells (HUVEC)

value: 16h (1% O2) with DMSO


title: Hypoxia_Acriflavine_HUVEC_1 [Hyp_ACF_1]

description: E21_3141_Lib_Leisegang_ML1529-2_Probe_13


title: Hypoxia_DMSO_HUVEC_1 [Hyp-DMSO_1]


title: 94CFARAging

city: Cleveland

first: Mark

last: Cameron

state: OH

address: 10900 Euclid Ave

department: Population and Quantitative Health Sciences

institute: Case Western Reserve University

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using skewer v0.2.2, then mapped to GRCh38 whole genome using Hisat2 v2.0.5
Read summarization was performed by the program featureCounts v1.5.0-p2 as part of the SubRead package.
Counts Per Million (CPM) values were generated through the edgeR Library v3.16.5 in R
Genome_build: GRCh38
Supplementary_files_format_and_content: Matrices in CSV format containing raw as well as normalized Log2(n+3) CPM summarized reads

source_name: Donor: 9002 Status: HIVPositive Age: Young Timepoint: T1 Response: Responder

growth_protocol: in vivo

extract_protocol:
RNA was extracted from 1 million PBMC using RNeasy Plus Mini Kit from QIAGEN
RNA libraries were prepared for sequencing using the Illumina TruSeq Stranded Total RNA - Globin kit.

tag: hiv status

value: HIVPositive

tag: donor id

value: Young

tag: timepoint

tag: response

value: Responder

value: PBMC


title: Hypoxia_DMSO_HUVEC_2 [Hyp-DMSO_2]

description: E21_3141_Lib_Leisegang_ML1529-2_Probe_10


title: 92CFARAging

source_name: Donor: 1158 Status: HIVNegative Age: Young Timepoint: T0 Response: Responder

value: HIVNegative

tag: tissue


title: 89CFARAging

source_name: Donor: 1166 Status: HIVNegative Age: Young Timepoint: T1 Response: NonResponder

value: NonResponder


title: 9CFARAging

source_name: Donor: 2302 Status: HIVPositive Age: OLD Timepoint: T0 Response: NonResponder

value: OLD


title: 86CFARAging

source_name: Donor: 751 Status: HIVNegative Age: Young Timepoint: T1 Response: NonResponder


title: 91CFARAging

source_name: Donor: 1100 Status: HIVPositive Age: Young Timepoint: T1 Response: NonResponder


title: 79CFARAging

source_name: Donor: 1179 Status: HIVNegative Age: Young Timepoint: T0 Response: Responder


title: 81CFARAging

source_name: Donor: 1304 Status: HIVPositive Age: OLD Timepoint: T1 Response: Responder