title: ADAB_RNA_THP1_WT_OLGO_01uM_NONE_NOsrm_24hr_S_3.1.1


title: ADAB_RNA_THP1_WT_OLGO_01uM_NONE_NOsrm_24hr_S_2.2.1

status: Public on Jul 30 2021

type: SRA

city: Bethesda

first: Kathleen

middle: Shaindel Metz

last: Reed

state: MD

address: 41 Medlars Dr, B507

department: Genetics and Molecular Biology

country: USA

institute: National Cancer Institute, NIH

library_source: transcriptomic

data_processing:
Libraries were sequenced as paired-end 75bp reads on an Illumina NextSeq 500, to an average depth of approximately 55-70 M reads per sample.
Low-quality reads and adapters were trimed using Trim Galore! (v 0.4.3; parameters: --paired)
Trimed reads were mapped to the hg19 transcriptome and quantified using Salmon (v 0.8.2; mapping mode, parameters: -l A)
Gene-level quantifications were summarized from each sample using tximport (v 1.2.0; default settings)
Differential analysis was conducted in R (v 3.5.1) with DESeq2 (v 1.22.2) using a design adjusting for replicate variability when calulating differences between groups (design: LRT, full=~ replicate + condition, reduced = ~ replicate, lfcShrink (apeglm), LFC threshold = 1, FDR-adjusted p-value threshold = 0.01)
Genome_build: hg19
Supplementary_files_format_and_content: ADAB_RNA_<CellType>_<Genotype>_<AbetaType>_<AbetaConc>_<OtherTreatments>_<Serum>_<Time>_S_quant.sf (Salmon output: transcript-level quantification, a tab-delimited file listing transcript name, length, effective length, TPM, and estimated number of reads mapped); ADAB_geneCounts.tsv (combined gene-level quantification listing ENSEMBL and HGNC gene identifiers, and raw counts from quant.sf "numReads" column for each sample); ADAB_Fig3_DESeqDesigns.xlsx (an excel file containing coldata objects and contrasts used in DESeq2 for each experiment, used to generate the bargraph in Figure 3).

molecule: total RNA

organism: Homo sapiens

source_name: THP-1 monocyte cell line

growth_protocol: Different cell types were grown under different conditions, as described in the "characteristics: growth conditions" in the SAMPLES section. iPSC-derived HPCs, iPSC-derived microglia, PBMCs and THP-1 cells were all differentiated prior to treatment. Other cell lines were cultured in the media listed.

extract_protocol:
RNA was extracted using a Qiagen RNeasy kit. RIN were checked with Tapestation RNA HS tape and confirmed to be in range of 8.5-10
Libraries were prepared using the KAPA RNA HyperPrep with RiboErase kit using 500 ng of isolated RNA as input.. Ribosomal RNA was removed using the NEBNext rRNA Depletion Kit.

treatment_protocol: Each sample was treated by substituting the growth media with fresh media containing the treatment, incubating for 24 or 4 hours, and then extracting RNA. For some treatments, this media contained 10% FBS, while others were serum-free. The amount of FBS in the treatment media is detailed in the "characteristics: serum in treatment" column in the SAMPLES section. Treatments included: PBS (control); a combination of 10 ng/mL LPS and 20 ng/mL IFN-gamma; oligmerized A-beta (oA[beta]) from two separate methods (A and B, from Tseng et al. 2017 and Abud 2017, respectively); and fibrilized A-beta (fAβ) from both methods. Fibrilized A-beta from Method A could be incubated for 5 or 7 days, and both forms are used. Details on length, concentration, and type of treatment are listed in the "characteristics: treatment" column of the SAMPLES section. Samples were collected from many different experiments across different days, as described in the "characteristics: experiment number" column. For each treatment, two replicates were conducted, as listed under the "characteristics: technical replicate" column.

tag: growth conditions

value: RPMI, 10% FBS, 1% pen/strep; differentiated to macrophages with 24hr of 25 uM PMA, then 72hr of rest

tag: treatment

value: 24hr 1 uM oA[beta] (Method B:Tseng et al. 2017)

tag: serum in treatment media

tag: experiment number

tag: technical replicate


title: ADAB_RNA_THP1_WT_NOAB_NONE_NONE_NOsrm_24hr_S_2.2.1

value: 24hr PBS


title: ADAB_RNA_THP1_WT_OLGO_05uM_NONE_NOsrm_24hr_S_2.2.1

value: 24hr 5 uM oA[beta] (Method B:Tseng et al. 2017)


title: ADAB_RNA_THP1_WT_OLGO_10uM_NONE_NOsrm_24hr_S_2.1.1

value: 24hr 10 uM oA[beta] (Method B:Tseng et al. 2017)


title: ADAB_RNA_THP1_WT_OLGO_01uM_NONE_NOsrm_24hr_S_2.1.1


title: ADAB_RNA_THP1_WT_NOAB_NONE_NONE_NOsrm_24hr_S_2.1.1

value: 4hr PBS


title: ADAB_RNA_THP1_WT_NOAB_NONE_NONE_NOsrm_04hr_S_1.2.1


title: ADAB_RNA_THP1_WT_NOAB_NONE_NONE_HIsrm_04hr_S_1.2.1

value: 10% FBS


title: ADAB_RNA_THP1_WT_NOAB_NONE_LPIF_NOsrm_24hr_S_3.2.1

value: 24hr 10 ng/mL LPS, 20 ng/mL IFN-gamma


title: ADAB_RNA_THP1_WT_OLGO_01uM_NONE_HIsrm_04hr_S_1.2.1

value: 4hr 1 uM oA[beta] (Method B:Tseng et al. 2017)


title: ADAB_RNA_THP1_WT_NOAB_NONE_NONE_NOsrm_04hr_S_1.1.1


title: ADAB_RNA_THP1_WT_OLGO_10uM_NONE_NOsrm_24hr_S_2.2.1


title: ADAB_RNA_THP1_WT_NOAB_NONE_NONE_HIsrm_04hr_S_1.1.1


title: ADAB_RNA_PBMC_WT_NOAB_NONE_NONE_NOsrm_24hr_S_1.2.1

source_name: Peripheral blood mononuclear cells (PBMCs)

value: DMEM, 10% FBS; differentiated to macrophages with 5d of 15 ng/mL rhGM-CSF


title: ADAB_RNA_PBMC_WT_OLGO_01uM_NONE_NOsrm_24hr_S_1.1.1


title: ADAB_RNA_U87a_WT_OLGO_01uM_NONE_NOsrm_24hr_S_1.2.1

source_name: U87 astrocyte cell line

value: EMEM, 10% FBS, 1% pen/strep


title: ADAB_RNA_PBMC_WT_NOAB_NONE_NONE_NOsrm_24hr_S_1.1.1


title: ADAB_RNA_U87a_WT_NOAB_NONE_NONE_NOsrm_24hr_S_1.1.1


title: ADAB_RNA_HMC3_WT_OLGO_01uM_NONE_NOsrm_24hr_S_1.2.1

source_name: HMC3 microglia cell line


title: ADAB_RNA_HMC3_WT_NOAB_NONE_NONE_NOsrm_24hr_S_1.2.1


title: ADAB_RNA_HMC3_WT_NOAB_NONE_NONE_NOsrm_24hr_S_1.1.1


title: ADAB_RNA_HMC3_WT_OLGO_01uM_NONE_NOsrm_24hr_S_1.1.1


title: ADAB_RNA_PBMC_WT_OLGO_01uM_NONE_NOsrm_24hr_S_1.2.1


title: ADAB_RNA_iHPC_FE_NOAB_NONE_NONE_NOsrm_NONE_S_1.2.1

source_name: iPSC-derived hematopoetic progenitor cells

value: Differentiated from iPSCs using STEMdiff Hematopoietic Kit; collected in medium B

value: No treatment


title: ADAB_RNA_iMGL_FE_NOAB_NONE_NONE_NOsrm_24hr_S_1.2.1

source_name: iPSC-derived microglia

value: Differentiated from iPSC-derived HPCs using STEMdiff microglia Differntiation/Maturation Kits; treated/collected in Microglia Matuation Media


title: ADAB_RNA_iMGL_FE_OLGO_01uM_NONE_NOsrm_24hr_S_1.2.1


title: ADAB_RNA_iMGL_FE_OLGO_01uM_NONE_NOsrm_24hr_S_1.1.1

value: Differentiated from iPSC-derived HPCs using STEMdiff microglia Differentiation/Maturation Kits; treated/collected in Microglia Maturation Media


title: ADAB_RNA_THP1_WT_OLGO_01uM_NONE_HIsrm_04hr_S_1.1.1


title: ADAB_RNA_iPSC_FE_NOAB_NONE_NONE_NOsrm_NONE_S_1.2.1

source_name: induced pluripotent stem cells (iPSC)

value: mTeSR1, 0.5 mM EDTA


title: mkkk18-ABA (04 hours) 3

status: Public on Jul 15 2021

city: Poznań

first: Agnieszka

last: Ludwików

address: Uniwersytetu Poznańskiego 6

department: Faculty of Biology

country: Poland

institute: Adam Mickiewicz University in Poznan

description: Examination of ABA treated samples of mkkk18-1

data_processing:
Adapter clipping: Adapters were clipped with fastx_clipper from FASTX Toolkit 0.0.14. Only reads at least 16 nt long and with clipped adapters were kept
Quality filtering: Quality filtering was done with fastq_quality_filter from FASTX Toolkit 0.0.14. The used parameters were: -q 20 -p 95
Reads collapsing: Reads collapsing was performed with fastx_collapser from FASTX Toolkit 0.0.14
Expression analysis: Calculation of mature miRNAs expression values were done using custom Python scripts. Here, FASTA files with collapsed reads as well as A. thaliana mature miRNAs from miRBase 22 were used. Expression for each miRNA is provided in reads per million (RPM) units.
Supplementary_files_format_and_content: TSV: The files contain the following fields: mature miRNA sequence, expression (RPM), miRNA names

organism: Arabidopsis thaliana

source_name: two weeks old seedlings

growth_protocol: Seeds of WT Arabidopsis thaliana, Columbia ecotype (Col-0), as well as abi1td, mapkkk17td, and mapkkk18td mutants were used in this study. After two days of stratification at 4°C, the plants were grown in Half Murashige and Skoog Basal Medium supplemented with sucrose.

extract_protocol:
For each condition (mock and ABA treated), three independent biological replicates were used and small RNA was extracted using Tri-reagent according to the manufacturer’s protocol (Direct-zol RNA Miniprep; ZYMO Research Corporation) and ABA application was confirmed by the amplification of ABA related marker mRNAs.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Seedlings were grown weeks for two weeks, then treated with ABA (±100 µM) for 4 hours.

tag: genotype

value: Salk Line Mutant

tag: ecotype

value: Columbia

tag: age

value: two weeks

value: ABA


title: ADAB_RNA_iMGL_FE_NOAB_NONE_NONE_NOsrm_24hr_S_1.1.1

value: 24hr PBS


title: ADAB_RNA_iPSC_FE_NOAB_NONE_NONE_NOsrm_NONE_S_1.1.1


title: mkkk18-ABA (04 hours) 2


title: mkkk18-ABA (04 hours) 1


title: ADAB_RNA_U87a_WT_OLGO_01uM_NONE_NOsrm_24hr_S_1.1.1

value: 24hr 1 uM oA[beta] (Method B:Tseng et al. 2017)


title: ADAB_RNA_THP1_WT_OLGO_05uM_NONE_NOsrm_24hr_S_2.1.1

value: RPMI, 10% FBS, 1% pen/strep; differentiated to macrophages with 24hr of 25 uM PMA, then 72hr of rest

value: 24hr 5 uM oA[beta] (Method B:Tseng et al. 2017)


title: mkkk18-Mock 1

description: Examination of mock samples of mkkk18-1

value: mock


title: mkkk17-ABA (04 hours) 3

description: Examination of both ABA treated samples of mkkk17-1


title: mkkk18-Mock 2

description: Examination of mock samples of mkkk18-1


title: ADAB_RNA_U87a_WT_NOAB_NONE_NONE_NOsrm_24hr_S_1.2.1


title: mkkk18-Mock 3

description: Examination of mock samples of mkkk18-1


title: mkkk17-Mock 2

description: Examination of mock samples of mkkk17-1


title: mkkk17-Mock 3

description: Examination of mock samples of mkkk17-1


title: mkkk17-ABA (04 hours) 2


title: ADAB_RNA_THP1_WT_NOAB_NONE_NONE_NOsrm_24hr_S_3.1.1


title: mkkk17-ABA (04 hours) 1


title: WT-ABA (04 hours) 3

description: Examination of ABA treated samples of wt col-0

value: Wild Type


title: abi1td-Mock 1

description: Examination of mock samples of abi1td


title: abi1td-ABA (04 hours) 1

description: Examination of ABA treated samples of abi1td


title: abi1td-Mock 2

description: Examination of mock samples of abi1td


title: abi1td-Mock 3

description: Examination of mock samples of abi1td


title: abi1td-ABA (04 hours) 2


title: WT-Mock 3

description: Examination of mock samples of wt col-0


title: 17.5L

city: Columbus

first: Amy

last: Hite

state: OH - Ohio

address: 1800 Cannon Drive 250 Lincoln Tower

department: Biomedical Informatics

institute: The Ohio State University

description:
SS17-5L
PHT_logCPMs_exprTable_v6.1.21.txt

data_processing:
Raw fastq was aligned to human reference genome GRCh38 with hisat2 v2.1.0.
Gene wise counts were generated with featureCounts from the subread package v1.5.1 for genes annotated by Ensembl GRCh38.92.
Counts from separate sequencing lanes for the same sample were summed.
Genes were filtered for at least 2 CPM in half the samples.
Genome_build: GRCh38
Supplementary_files_format_and_content: *logCPM_exprTable.txt files contain counts normalized as log2 CPM for genes with at least 2 counts per million reads.

source_name: Placenta

growth_protocol: Collected cells were plated at 10^6 cells/1.9 cm2 washed after 12 h to remove non-adherent cells, and cultured in Dulbecco’s modified Eagle’s medium containing F12 (DMEM/F12 Gibco), GlutaMAX, 10% heat-inactivated fetal bovine serum (HI-FBS, Atlanta Biologicals), 100 U/ml penicillin, and 100 mg/ml streptomycin (Invitrogen) at 37°C in 5% CO2 humidified cell culture incubator.

extract_protocol:
Cells were lysed in TRIzol reagent (Invitrogen). PureLink RNA extraction kit with on-column DNase treatment (Invitrogen) was used to isolate RNA. Input RNA integrity number (RIN) were all > 7 and concentration was >100 ng/µl RNA, as determined with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA) and Qubit Fluorometer (Thermo Fisher).
RNA-seq libraries were generated with NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina (NEB #E7760L) and NEBNext® rRNA Depletion Kit with sample purification beads (NEB #E6350) with an input amount of 200 ng total RNA per sample. Libraries were pooled and sequenced on an Illumina NovaSeq SP flowcell in paired-end 150 bp format (Illumina, San Diego, CA) to a read yield between 70-80 million reads (equivalent to 35- 40 million clusters).

treatment_protocol: PHT and BeWo cells were infected, or not, in 6 well-cell culture plates with 4 x 10^6 WT Lm /well for 1h followed by 30 min gentamicin, and 3.5 h in gentamicin-free medium (5 h samples). Cells were pulsed with gentamicin for 30 min after 5 hours infection, and incubated in gentamicin free medium for another 5 hours (10 hours samples).

tag: trimester

value: term

tag: cell type

value: primary human cytotrophoblast (epithelial)

tag: batch

tag: listeria infection

value: Yes


title: abi1td-ABA (04 hours) 3


title: ADAB_RNA_iHPC_FE_NOAB_NONE_NONE_NOsrm_NONE_S_1.1.1

value: Differentiated from iPSCs using STEMdiff Hematopoietic Kit; collected in medium B

value: No treatment


title: WT-ABA (04 hours) 2


title: mkkk17-Mock 1

description: Examination of mock samples of mkkk17-1


title: 16.5L

description:
SS16-5L
PHT_logCPMs_exprTable_v6.1.21.txt


title: 15.5L

description:
SS15-5L
PHT_logCPMs_exprTable_v6.1.21.txt


title: WT-Mock 1

description: Examination of mock samples of wt col-0


title: WT-ABA (04 hours) 1


title: 17.5N

description:
SS17-5N
PHT_logCPMs_exprTable_v6.1.21.txt

value: No


title: WT-Mock 2

description: Examination of mock samples of wt col-0


title: 16.5N

description:
SS16-5N
PHT_logCPMs_exprTable_v6.1.21.txt


title: 15.5N

description:
SS15-5N
PHT_logCPMs_exprTable_v6.1.21.txt


title: set5_caco2_moi01_48hpi_RPF_rep2

status: Public on Jul 14 2021

city: Seoul

first: Daehyun

last: Baek

address: Rm 402, Bldg 504, School of Biological Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul

department: School of Biological Sciences

country: South Korea

institute: Seoul National University

data_processing:
1. Base-calling by RTA(Real Time Analaysis) software within HiSeq 2500 (mRNA-Seq) or HiSeq 2000 (sRNA-Seq)
2. Quality trimming by the highest scoring path algorithm (hsptrim-1.2.6)
3. Adapter trimming by cutadapt-1.2.1
4. Remove sequencing artifacts by fastx_artifacts_filter of fastx_toolkit
5. Remove ncRNA-derived reads by Bowtie2 alignment
6. Remove mycoplasma-derived reads by Bowtie2 alignment
7. Alignment of filtered reads to SARS-CoV-2 and host genome by STAR (mRNA-seq, RPF-seq, QTI-seq) or Bowtie2 (sRNA-seq)
8. Calculation of log2(expression fold changes) and differential expression for human genes by DESeq2
Genome_build: NC_045512.2 (SARS-CoV-2)
Genome_build: hg38 (GRCh38)
Genome_build: chlSab2
Supplementary_files_format_and_content: bigwig (coverage depth), tab-delimited text files, containing gene expression levels (average RPKM within replicates), log2(expression fold changes), and statistical significances calculated by DESeq2.

organism:
Homo sapiens
Severe acute respiratory syndrome coronavirus 2

source_name: Epithelial cell in human colorectal adenocarcinoma

growth_protocol: Calu-3 and Vero cells were cultured in DMEM with 10% FBS and 1% penicillin/streptomycin

extract_protocol:
For sRNA-seq, RNA was extracted using Trizol. For rest, cells were washed with PBS then lysed with lysis buffer (10 mM Tris-HCl (pH 7.4), 5 mM MgCl2, 100 mM KCl, 1% Triton X-100, 100 μg/ml CHX, 1 mM dithiothreitol, 0.2 U/μl RiboLock RNase inhibitor, and 1 × EDTA-free protease inhibitor cocktail). For RPF-seq and QTI-seq, lysates were treated with RNase I and ribosome protected fragments were isolated using illustra MicroSpin S-400 HR Columns (GE Healthcare).
All of the libraries (mRNA-seq, RPF-seq, QTI-seq, and sRNA-seq) were constructed following the Illumina Truseq small RNA library preparation protocol (TruSeq Small RNA Library Prep Guide, Part # 15004197 Rev. G)

treatment_protocol: Prior to lysis, Calu-3 and Vero cells were seeded in 100mm dishes, and were infected with SARS-CoV-2 (MOI = 10 or 0.1) for 1 hour then washed with PBS. At 0, 1, 2, 4, 12, 16, 24, 48 hpi (Calu-3) and 0, 24 hpi (Vero), both mock and infected dishes for RPF, QTI, and mRNA-seq were treated with either 100 μg/ml cycloheximide (CHX) or 2 µg/ml harringtonine (Harr) for 10 min.

tag: cell

value: infected, 48hpi

tag: concentration

value: MOI 0.1

tag: assay

value: RPF-seq

tag: biorep


title: set5_caco2_uninfected_QTI_rep2

value: uninfected

value: QTI-seq


title: set5_caco2_moi01_48hpi_RPF_rep1


title: set5_caco2_uninfected_QTI_rep1


title: set5_caco2_uninfected_RPF_rep2


title: set5_caco2_moi01_48hpi_QTI_rep2


title: set5_calu3_moi01_48hpi_QTI_rep1

source_name: Epithelial cell in human lung adenocarcinoma


title: set5_caco2_moi01_48hpi_QTI_rep1


title: set5_calu3_moi01_48hpi_QTI_rep2


title: set4_calu3_moi01_48hpi_RPF_rep1

status: Public on Jul 12 2021

description: RPF

tag: cell line

tag: rnase


title: set4_calu3_moi01_48hpi_RPF_rep2

description: RPF

tag: treatment


title: set5_calu3_moi01_48hpi_RPF_rep2


title: set5_calu3_moi01_48hpi_RPF_rep1


title: set3_calu3_moi10_24hpi_sRNA_rep2

description: sRNA

value: infected, 24hpi

value: MOI 10

value: small RNA-seq


title: set3_calu3_moi10_36hpi_QTI_rep2

description: QTI

value: infected, 36hpi


title: set3_calu3_moi10_24hpi_QTI_rep2

description: QTI


title: set3_calu3_moi10_16hpi_sRNA_rep2

description: sRNA

value: infected, 16hpi


title: set3_calu3_moi10_12hpi_sRNA_rep2

description: sRNA

value: infected, 12hpi


title: set3_calu3_moi10_16hpi_QTI_rep1

description: QTI


title: set3_calu3_moi10_24hpi_QTI_rep1

description: QTI


title: set3_calu3_moi10_12hpi_QTI_rep2

description: QTI


title: set3_calu3_moi10_36hpi_QTI_rep1

description: QTI


title: set3_calu3_moi10_36hpi_RPF_rep2

description: RPF


title: set3_calu3_moi10_16hpi_QTI_rep2

description: QTI


title: set3_calu3_moi10_12hpi_QTI_rep1

description: QTI


title: set3_calu3_moi10_24hpi_RPF_rep2

description: RPF


title: set5_caco2_uninfected_RPF_rep1


title: set3_calu3_moi10_16hpi_RPF_rep2

description: RPF


title: set3_calu3_moi10_36hpi_RPF_rep1

description: RPF


title: set3_calu3_moi10_36hpi_sRNA_rep2

description: sRNA


title: set3_calu3_moi10_12hpi_mRNA_rep4

value: mRNA-seq


title: set3_calu3_moi10_24hpi_mRNA_rep4


title: set3_calu3_moi10_12hpi_RPF_rep1

description: RPF


title: set3_calu3_moi10_16hpi_mRNA_rep4


title: set3_calu3_moi10_36hpi_mRNA_rep4


title: set3_calu3_moi10_12hpi_RPF_rep2

description: RPF


title: set3_calu3_moi10_16hpi_RPF_rep1

description: RPF


title: set3_calu3_moi10_36hpi_mRNA_rep3


title: set3_calu3_moi10_16hpi_mRNA_rep3


title: set3_calu3_moi10_24hpi_mRNA_rep3


title: set3_calu3_moi10_24hpi_mRNA_rep2


title: set3_calu3_moi10_36hpi_mRNA_rep2


title: set3_calu3_moi10_12hpi_mRNA_rep3


title: set3_calu3_moi10_16hpi_mRNA_rep2


title: set3_calu3_moi10_12hpi_mRNA_rep1


title: set3_calu3_moi10_36hpi_mRNA_rep1


title: set3_calu3_moi10_16hpi_mRNA_rep1


title: set2_calu3_moi10_4hpi_sRNA_rep2

value: infected, 4hpi


title: set3_calu3_moi10_12hpi_mRNA_rep2


title: set2_calu3_moi10_2hpi_sRNA_rep2

value: infected, 2hpi


title: set2_calu3_moi10_1hpi_sRNA_rep1

value: infected, 1hpi


title: set3_calu3_moi10_24hpi_RPF_rep1

description: RPF


title: set2_calu3_uninfected_sRNA_rep1

tag: concentration:


title: set2_calu3_moi10_0hpi_sRNA_rep1

value: infected, 0hpi


title: set2_calu3_moi10_4hpi_QTI_rep2


title: set2_calu3_moi10_2hpi_QTI_rep2


title: set2_calu3_moi10_0hpi_QTI_rep2


title: set2_calu3_moi10_1hpi_QTI_rep2


title: set2_calu3_uninfected_QTI_rep2


title: set2_calu3_moi10_4hpi_QTI_rep1


title: set2_calu3_uninfected_QTI_rep1


title: set3_calu3_moi10_24hpi_mRNA_rep1


title: set2_calu3_moi10_0hpi_QTI_rep1


title: set2_calu3_moi10_2hpi_sRNA_rep1


title: set2_calu3_moi10_4hpi_RPF_rep2


title: set2_calu3_moi10_1hpi_QTI_rep1


title: set2_calu3_moi10_4hpi_RPF_rep1


title: set2_calu3_uninfected_RPF_rep2


title: set2_calu3_moi10_1hpi_RPF_rep2


title: set2_calu3_moi10_2hpi_RPF_rep1


title: set2_calu3_moi10_1hpi_RPF_rep1


title: set2_calu3_moi10_0hpi_RPF_rep2


title: set2_calu3_moi10_0hpi_RPF_rep1


title: set2_calu3_moi10_2hpi_mRNA_rep4


title: set2_calu3_moi10_1hpi_mRNA_rep4


title: set2_calu3_uninfected_RPF_rep1


title: set2_calu3_moi10_4hpi_mRNA_rep3


title: set2_calu3_uninfected_mRNA_rep4


title: set2_calu3_moi10_0hpi_mRNA_rep4


title: set2_calu3_moi10_2hpi_mRNA_rep3


title: set2_calu3_moi10_2hpi_QTI_rep1


title: set2_calu3_moi10_0hpi_mRNA_rep3


title: set2_calu3_moi10_1hpi_mRNA_rep3


title: set2_calu3_moi10_2hpi_RPF_rep2


title: set2_calu3_uninfected_mRNA_rep3


title: set2_calu3_moi10_2hpi_mRNA_rep2


title: set2_calu3_moi10_4hpi_mRNA_rep2


title: set2_calu3_moi10_1hpi_mRNA_rep2


title: set2_calu3_uninfected_mRNA_rep2


title: set2_calu3_moi10_0hpi_mRNA_rep1


title: set2_calu3_moi10_1hpi_mRNA_rep1


title: set2_calu3_moi10_2hpi_mRNA_rep1


title: set1_calu3_uninfected_sRNA

growth_protocol: Calu-3 cells were cultured in DMEM with 10% FBS and 1% penicillin/streptomycin

treatment_protocol: Prior to lysis, cells were seeded in 100mm dishes, and treated cells were infected with SARS-CoV-2 (MOI = 0.1). At 48 hpi, both mock and treated dishes for RPF, QTI, and mRNA-seq were treated with either 100 μg/ml cycloheximide (CHX) or 2 µg/ml harringtonine (Harr) for 10 min.


title: set2_calu3_uninfected_mRNA_rep1


title: set2_calu3_moi10_4hpi_mRNA_rep1


title: set1_calu3_uninfected_QTI_rep3


title: set1_calu3_moi01_48hpi_QTI_rep2


title: set1_calu3_moi01_48hpi_sRNA


title: set2_calu3_moi10_4hpi_mRNA_rep4


title: set1_calu3_uninfected_QTI_rep2


title: set1_calu3_moi01_48hpi_QTI_rep1


title: set2_calu3_moi10_4hpi_sRNA_rep1


title: set1_calu3_uninfected_QTI_rep1


title: set1_calu3_moi01_48hpi_RPF_rep3


title: set1_calu3_moi01_48hpi_RPF_rep2


title: set2_calu3_moi10_0hpi_mRNA_rep2


title: set1_calu3_uninfected_RPF_rep3


title: set1_calu3_moi01_48hpi_mRNA_rep5


title: set1_calu3_moi01_48hpi_RPF_rep1


title: set1_calu3_uninfected_RPF_rep1


title: set1_calu3_moi01_48hpi_mRNA_rep4


title: set1_calu3_moi01_48hpi_QTI_rep3


title: set1_calu3_moi01_48hpi_mRNA_rep3


title: set1_calu3_uninfected_mRNA_rep6


title: set1_calu3_uninfected_mRNA_rep2


title: set1_calu3_moi01_48hpi_mRNA_rep1


title: set4_vero_moi01_24hpi_RPF_rep2

description: RPF

organism:
Chlorocebus aethiops
Severe acute respiratory syndrome coronavirus 2

source_name: Epithelial cell in green monkey kidney

value: Vero


title: set1_calu3_uninfected_mRNA_rep3


title: set1_calu3_uninfected_mRNA_rep5


title: set1_calu3_moi01_48hpi_mRNA_rep2

value: infected, 48hpi


title: set1_calu3_uninfected_mRNA_rep1


title: set4_vero_moi01_0hpi_RPF_rep2

description: RPF

value: MOI 0.1


title: set4_vero_moi01_24hpi_RPF_rep1

description: RPF

value: RPF-seq


title: RBE cells, DMSO 6H

status: Public on Jul 09 2021

city: Taoyuan

first: Chiao-Ping

last: Chen

address: No.259, Wenhua 1st Rd., Guishan Dist.

country: Taiwan

institute: Chang Gung University

data_processing:
Illumina Casava1.8.2 software used for basecalling.
The raw output file of each individual library was > 3GB. The sequence of each read was trimmed based on the quality score (Q30), and read lengths less than 45 bp were discarded prior to further analysis.
The differentially expressed genes were selected for more than 2-fold changes and p-values for differences in ex-pression of less than 0.05.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include fold change (log2) and p-values for each sample
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Cell lysate

growth_protocol: RBE and SK-Hep-1 were authenticated and cultured in RPMI medium 1640 (Gibco) and DMEM (Gibco) containing 10% FBS, respectively.

extract_protocol:
Total RNA 200ng from each cell line sample was prepared for sequencing using Illumina TruSeq Stranded mRNA Sample Preparation Kit.
Fifteen-cycle-PCR was performed, and the libraries were quantified using the LC480 qPCR system (Roche). Then, all libraries were pooled into a new 1.5 ml tube as a 10 nM pooled DNA library. The final pool was used for sequencing (illumina NextSeq sequencer, 2×150bp).

treatment_protocol: HDM201 and/or GSK2830371 were initially dissolved in DMSO and used to dose cells at a final concentration of 0.5% DMSO for 6 or 24 hours.

value: RBE

value: cholangiocarcinoma cell

value: DMSO

tag: time

value: 6 hours


title: set4_vero_moi01_0hpi_RPF_rep1

description: RPF


title: set1_calu3_uninfected_RPF_rep2

value: uninfected


title: set1_calu3_moi01_48hpi_mRNA_rep6


title: RBG31066_XN3392_protein

city: Cambridge

first: Bertie

last: Gottgens

address: Jeffrey Cheah Biomedical Centre

country: United Kingdom

institute: University of Cambridge

description:
protein
preQC_mRNAraw_FL-FBM-CB.csv
postQC_mRNAraw_FL-FBM-CB.csv
preQC_ADTraw_FL-FBM-CB.csv
overlap_ADTonmRNAraw_FL-FBM-CB.csv

data_processing:
Library strategy: CITE-Seq
Mapped to hg38 with either cellranger (mRNA samples) or CITE-Seq count (protein samples).
Souporcell run on mRNA samples.
Genome_build: hg38 (GRCh38)
Supplementary_files_format_and_content: Count matrices in .csv format.

extract_protocol:
Samples were extracted and MNCs isolated using ficoll. A detailed protocol of cell processing, CD34+ enrichment, TotalSeq-A staining and FACs sorting can be found in Simultaneous analysis of single-cell transcriptomes and cell surface protein expression of human haematopoietic and stem cells using the 10x Genomics platform.
Sequencing libraries were prepared following 10x Genomics manufacturer's protocol and Biolegend TotalSeq™-A Antibodies and Cell Hashing with 10x Single Cell 3' Reagent Kit v3 or v3.1 Protocol.
10x Single Cell 3′ Kit v3.1 + surface protein (TotalSeq-A).

tag: tissue

value: Cord blood

tag: development stage

value: newborn


title: RBG33508_F90_F103_F107_protein

value: Fetal liver

value: stage 3


title: RBG33507_F90_F103_F107_mRNA

description:
mRNA
preQC_mRNAraw_FL-FBM-CB.csv
postQC_mRNAraw_FL-FBM-CB.csv
preQC_ADTraw_FL-FBM-CB.csv
overlap_ADTonmRNAraw_FL-FBM-CB.csv

data_processing:
Mapped to hg38 with either cellranger (mRNA samples) or CITE-Seq count (protein samples).
Souporcell run on mRNA samples.
Genome_build: hg38 (GRCh38)
Supplementary_files_format_and_content: Count matrices in .csv format.


title: RBG33503_F96_protein

value: Fetal bone marrow


title: RBG33507_F90_F103_F107_protein


title: RBG33500_F109_F94_F96_protein


title: RBG33503_F96_mRNA


title: RBG33496_F107_CIMA-90_CIMA-100_mRNA

value: Bone marrow


title: RBG33500_F109_F94_F96_mRNA


title: RBG33493_F90_F103_F107_protein

description:
protein
preQC_ADTraw_FBM-MNCs.csv
postQC_ADT_raw_FBM-MNCs.csv
overlap_ADTonmRNA_raw_FBM-MNCs.csv
preQC_mRNAraw_FBM-MNCs.csv
postQC_mRNAraw_FBM-MNCs.csv

source_name: MNCs

value: MNCs


title: Denatured_SP-D_2

status: Public on Jul 08 2021

city: Boston

first: Matthew

middle: K

last: Waldor

state: MA

address: 181 Longwood Avenue

department: Microbiology

institute: Harvard Medical School

description: Denatured protein

data_processing:
Reads were trimmed using Trim Galore with automatic adapter sequence detection.
Trimmed reads were mapped to the V. cholerae reference genome and annotation using RNA STAR.
Feature Counts was used to build a count matrix from mapped reads using the Ensembl annotation as a guide.
Genome_build: V. cholerae KW3 genome (NZ_CP006947.1, NZ_CP006948.1).
Supplementary_files_format_and_content: FeatureCounts.txt: Tab-delimited text file
Supplementary_files_format_and_content: SPD_Denatured_FinalAnalysisDESeq2.csv: Comma-separated txt file

organism: Vibrio cholerae H1

source_name: in vitro culture (AKI medium)

growth_protocol: in vitro culture in AKI medium.

extract_protocol:
Total RNA were harvested and preserved using Trizol reagent. Total RNA was extracted using the RNeasy mini kit (Qiagen).
Migs center.

treatment_protocol: SP-D and denatured SP-D.

tag: culture type

value: in vitro

tag: condition

value: Denatured SP-D


title: RBG33494_CIMA-60_CIMA-58_F103_mRNA


title: RBG33494_CIMA-60_CIMA-58_F103_protein


title: RBG33508_F90_F103_F107_mRNA


title: Denatured_SP-D_3

description: Denatured protein


title: RBG33496_F107_CIMA-90_CIMA-100_protein


title: RBG31066_XN3392_mRNA


title: RBG33493_F90_F103_F107_mRNA

description:
mRNA
preQC_ADTraw_FBM-MNCs.csv
postQC_ADT_raw_FBM-MNCs.csv
overlap_ADTonmRNA_raw_FBM-MNCs.csv
preQC_mRNAraw_FBM-MNCs.csv
postQC_mRNAraw_FBM-MNCs.csv


title: SP-D_2

description: Functional protein

value: SP-D


title: SP-D_3

description: Functional protein


title: RRBS_WT_5dpf_Livers_3

status: Public on Jul 07 2021

city: Abu Dhabi

first: Kirsten

last: Sadler Edepli

state: Abu Dhabi

department: Biology

country: United Arab Emirates

institute: New York University Abu Dhabi

library_source: genomic

data_processing:
Illumina Casava1.8 software used for basecalling.
The raw reads were quality assessed using FastQC  v0.11.5, then quality trimmed using Trimmomatic. were “trimmomatic_adapter.fa:2:30:10 TRAILING:3 LEADING:3 SLIDINGWINDOW:4:15 MINLEN:36”
For ATACseq, reads that passed quality control were aligned to reference genome GRCz10 using bwa-mem. In RRBS, Qualified reads were aligned to the genome reference GRCz10 by Bismark-0.22.3 with default parameters ,  while calling CpG methylation
In ATAC-seq, the resulting BAM alignments were then processed through PICARD tools to clean, sort and deduplicate
For ATACseq peaks calling,  MACs2 was adopted with -f BAMPE, q-vaule 0.05
In RRBS,  Bismark_methylation_extractor extracted CpG methylation as .bed files from aligned files
Genome_build: GRCz10
Supplementary_files_format_and_content: bed files provides called peaks from concatenated bam files and methylation of each called CpG site

molecule: genomic DNA

organism: Danio rerio

source_name: 5 dpf Livers

growth_protocol: Zebrafish larvae were kept in 10 cm petri dish at a density of 60 larvae/plate (30ml) in a 10:14 light/dark cycle.

extract_protocol:
10 or 20 wildtype 5 dpf (120 hpf) zebrafish embryo livers were dissected, pooled per library preparation. For RRBS, Genomic DNA was extracted from 40 dissected livers by using a DNA extraction buffer (10mM Tris-HCl pH9, 10mM EDTA, 200mM NaCl, 0.5% DSD, 200µg/ml proteinase K) as previously described (Chernyavskaya et al., 2017). DNA was resuspended in water and quantified by Qubit dsDNA High Sensitivity kit.
ATAC-seq: Protocol as described in Buenrostro et al (2015): doi:10.1002/0471142727.mb2129s109, using illumina barcoded primers for sequencing. In RRBS, DNA quantitiy and quality was assesed by Qbit. 50-150ng of DNA was used for library prep. Libraries were prepared according to Garrett-Bakelman et al., 2015 with some modifications. To avoid loss of gDNA, after MspI digestion, end

treatment_protocol: Zebrafish larvae were anethetized in tricane and collected at 120 hpf for liver dissection.

tag: age

value: 120 hpf


title: 7-Pre-xRT

status: Public on Jul 06 2021

city: Charlestown

first: David

middle: T

last: Ting

department: Cancer Center

institute: Massachusetts General Hospital

data_processing:
Reads aligned to HG38
Deduplicated BAM files used with HTSeq-Count to create count tables
Data was analyzed with DESeq2 for differential expresison analysis
Genome_build: GRCH38
Supplementary_files_format_and_content: Raw and normalized read counts in Text format

source_name: metastatic tumor

growth_protocol: biopsies were taken from out of field metastatic tumor sites

extract_protocol:
RNA extraction from fresh frozen samples was done using the  AllPrep DNA/RNA kit fron Qiagen
The Smarter Stranded Total RNA-Seq kit v2 (634413, Illumina) was used with 10 ng RNA input, according to the manufacturer instructions to generate libraries.
Dual-indexed pooled libraries were sequenced on the Illumina NextSeq 500 platform using a 150 cycles kit with paired end read mode.

treatment_protocol: samples were snap frozen in liquid nitrogen

value: metastatic tumor

tag: cancer type

value: MSS CRC

tag: time point

value: Pre-xRT

tag: sequencning run


title: SP-D_1

description: Functional protein


title: 19-1250_714R2: iEF + EF (714) Replicate 2

status: Public on Jun 15 2021

first: Megann

middle: A.

last: Boone

state: OH

address: 700 Children's Drive, WA5011

department: Center for Childhood Cancer

institute: Nationwide Children's Hospital

description: RNA-sequencing was performed on A673 cells with endogenous EWS/FLI knocked-down and EWS/FLI cDNA (EF(714)) was expressed.

data_processing:
FASTQC and Multiqc were used for raw sequence quality control.
Trim_galore was used to trim low-quality and overrepresented sequences.
Two-pass STAR appraoch (STAR version 2.5.2b) was used to align sequences to hg19 human reference genome.
RSeQC was used to evaluate post-mapping sequence quality.
DESeq2 was used to identify different analysis of genes.
Genome_build: hg19
Supplementary_files_format_and_content: fastq files include raw reads of each samples; bigwig files are aligned, trimmed, normalized reads combined for each samples from separate replicates.

source_name: A673 cells

growth_protocol: Ewing sarcoma cells (A673) were seeded at 50-70% confluency and left to adhere overnight.

extract_protocol:
Total RNA was extracted using the RNeasy kit (Qiagen) and gDNA Eliminator columns (Qiagen) were used to remove residual genomic DNA.  3 ug of total RNA was used for library prep.
TruSeq Stranded mRNA Kit

treatment_protocol: Endogenous EWS/FLI protein was knocked down in A673 cells using an shRNA targeting the 3'-UTR of the native transcript (iEF); iLuc (a shRNA targeting the firefly luciferase gene) was used as a control for knockdown. cDNA constructs were expressed: empty vector control (Empty Vector), EWS/FLI (EF), or two mutant EWS/FLI constructs (EF DBD and EF DBD+). Antiobiotic selection was used to select for cells expressing these constructs and cells were collected after 8 days.  Whole cell total RNA was extracted using a Qiagen RNeasy Extraction kit and genomic DNA was removed uisng Qiagen gDNA Eliminator columns.

tag: disease state of cells

value: Ewing sarcoma


title: 19-1245_714R1: iEF + EF (714) Replicate 1


title: 19-1249_197R2: iEF + Empty vector (197) Replicate 2

description: RNA-sequencing was performed on A673 cells with endogenous EWS/FLI knocked-down.


title: set1_calu3_uninfected_mRNA_rep4

value: mRNA-seq


title: 19-1244_197R1: iEF + Empty vector (197) Replicate 1


title: 19-1248_iLucR2: iLuc + Empty vector (iLuc) Replicate 2

description: RNA-sequencing was performed on A673 cells containing the endogenous EWS/FLI protein.


title: 19-1243_iLucR1: iLuc + Empty vector (iLuc) Replicate 1


title: MRC5_VA UV_24 h Cytoplasm

status: Public on Jun 08 2021

city: Guangzhou

first: Yuming

last: Wang

state: Guangdong

address: Room 512, Anatomy Building

department: School of Basic Medical Science

country: China

institute: Guangzhou medical university

data_processing:
Raw data of fastq format were firstly processed through in-house perl scripts to obtain clean reads by removing reads containing adapter, poly-N and low quality reads.
Paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
FeatureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with FPKM for every transcript in all samples.

growth_protocol: MRC5_VA cells were routinely maintained in DMEM supplemented with 10% FBS at 37°C in a 5% CO2 water-saturated environment.

extract_protocol:
Total RNA for each cellular fraction was isolated by Trizol reagent. NEBNext® Ultra™ RNA Library Prep Kit (Cat#E7530L) was used with 1 μg of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Cells were treated with 10 J/m2 UV-C light and recovered for the indicated time in the study.

tag: cell type

value: normal lung tissue-derived fibroblast cells

value: treated with 10 J/m2 UV-C irradiation and recovered for 24 hours


title: MRC5_VA UV_24 h Chromatin


title: MRC5_VA UV_3 h Chromatin

value: treated with 10 J/m2 UV-C irradiation and recovered for 3 hours


title: MRC5_VA UV_3 h Cytoplasm


title: Denatured_SP-D_1

description: Denatured protein


title: Control4

status: Public on Jun 04 2021

city: South San Francisco

first: Xin

last: Luo

state: CA

address: 750 Gateway Blvd

department: Research and Development

institute: Amgen Inc

data_processing:
cell ranger (V3.1.0) mkref package was used to create a “pre-mRNA” reference with pre-built GRCh38 reference package and cell ranger count pipeline was used to align the fastq reads and generated QC matrix and count matrix.
The Count matrix was further analyzed with Seurat R package for batch effect correction by canonical correlation analysis, filtering, normalization, variable features identification and dimensional reduction by Principal Component Analysis (PCA). The top 30 PCAs were used in graph-based clustering based on Louvain, and cluster specific marker genes were identified with FindAllMarkers function in Seurat, cell types were determined by cross-referencing with well-established cell type markers in literature
Genome_build: GRCh38
Supplementary_files_format_and_content: cell.counts.*.txt contain the raw UMI count matrix of all samples with genes in rows and cells in columns, cell.metadata.*.csv contains metainformation of all samples with cells in rows and labels in columns. For each sample, the cell ranger output filtered matrix files including barcodes.tsv, features.tsv and matrix.mtx were included as processed data files as well.

molecule: polyA RNA

source_name: Left Ventricle

extract_protocol:
Five 10 µm curls cut from OCT embedded human cardiac tissue were homogenized using a 2 ml Dounce homogenizer with 1 ml chilled lysis buffer (10mM Tris-HCl (pH 7.4), 10 mM NaCl, 3 mM MgCl2, 0.1% NP-40 and 0.2 U/ml RNase inhibitor). After filtering through a 40 µm cell trainer, nuclei were centrifuged at 700 x g for 5 min at 4oC. The nuclei were subsequently washed with 500 ml and then resuspended in 300 ml of Nuclei Wash/Resuspension Buffer (1x PBS with 2% BSA and 0.2 U/ml RNase inhibitor). 1 ml DRAQ5 (5 mM solution, Thermo Cat #62251) was added, and DRAQ5+ nuclei were sorted (70 mm nozzle on a BD Aria) into 50 ml Nuclei Wash Buffer (3 X 0.2 U/ml RNase inhibitor). Sorted nuclei were directly added to a reverse transcription master mix diluted with water to manufacturer’s specifications
Libraries were prepared using the 10X Chromium Single Cell 3' v3 Gene Expression Kit.

tag: gender

value: Male

value: Heart

tag: tissue region

value: Left Ventricle

tag: race

value: White or Caucasion

tag: disease status

value: NF


title: MRC5_VA UV_30 min Chromatin

tag: cell line

tag: treatment

value: treated with 10 J/m2 UV-C irradiation and recovered for 30 minutes


title: MRC5_VA no UV Chromatin

value: untreated


title: 20-Pre-xRT


title: MRC5_VA UV_30 min Cytoplasm


title: Control2

value: Female

value: Asian


title: Control3

value: Hispanic or Latino


title: MRC5_VA no UV Cytoplasm


title: HF

value: White or Caucasian

value: Heart Failure (HF)


title: mouse_scar_3

status: Public on May 31 2021

city: Vienna

first: Vera

last: Vorstandlechner

address: Waehringer Guertel 18-20

country: Austria

institute: Medical University of Vienna

data_processing:
Raw sequencing data were demultiplexed, aligned to a reference genome (GrCh38/mm10) and counted using Cell Ranger (version 3.0.2; 10x Genomics).
Genome_build: GrCh38/mm10
Supplementary_files_format_and_content: mtx (count matrix in sparse matrix format), barcodes.tsv (barcode ids), features.tsv: (gene ids)

organism: Mus musculus

source_name: scar 8 weeks

extract_protocol:
Four mm biopsies were taken from human skin, human scar, and from mouse scar tissue, and enzymatically digested with MACS Miltenyi Whole Skin Dissociation Kit (Miltenyi Biotec, Bergisch-Gladbach, Germany) for 2.5h according to the manufacturer´s protocol. After processing on a GentleMACS OctoDissociator (Miltenyi), cell suspensions were passed through a 70 µm and a 40 µm filter and stained with DAPI nuclear dye. Cells were sorted on a MoFlo Astrios high speed cell sorting device (Beckman-Coulter, Brea, CA, USA), and only DAPI-negative cells, representing viable cells, were used for single cell RNAseq. Immediately after sorting, viable cells were loaded on a 10X-chromium instrument (Single cell gene expression 3‘v2/3, 10X Genomics, Pleasanton, CA, USA) to generate GEMs. GEM-generation, library preparation, RNA-sequencing, demultiplexing and counting were done by the Biomedical Sequencing Core Facility of the Center for Molecular Medicine (CeMM, Vienna, Austria). Sequencing was performed on an Illumina HiSeq 3000/4000 (Illumina, San Diego, CA, USA) with 3 samples per lane, 2x75bp, and paired-end sequencing.
Single-cell libraries were generated using the Chromium Controller and Single Cell 3− Library & Gel Bead Kit versions 2 and 3 (10x Genomics) according to the manufacturer’s protocol.

value: dermal scar cells

tag: strain

value: Balb/c

tag: molecule

value: total mRNA

tag: chemistry

value: Single Cell 3' v3


title: Control1

tag: tissue


title: clr4D_RNA-seq_rep3

city: Planegg

first: Sigurd

middle: J

last: Braun

address: Großhaderner Str. 9

department: BMC

country: Germany

institute: LMU

description: RNA sequencing of clr4∆ cells

data_processing:
Raw read were de-multiplexed. Adapter-trimmed reads were aligned to the S. pombe reference genome (ASM294v2.27) and a custom GTF file using STAR (v2.7.3a) and processed using RSEM (v1.3.3).
Differential expression was analysed using the DESeq2 (v1.22.2) and tximport (v1.10.1) R libraries.
Bedgraph coverage files were generated using genomecov (bedtools v2.29.1).
Genome_build: ASM294v2.27
Supplementary_files_format_and_content: Bedgraph files of coverag

organism: Schizosaccharomyces pombe

source_name: logarithmically growing clr4∆ cells

growth_protocol: Standard conditions were used to produce logarithmically growing cultures in rich media (YES).

extract_protocol:
RNA was extracted using TRIzol
Library was constructed using NEBNext Ultra Directional RNA Library Prep Kit for Illumina (NEB#E7420), according to manufacturer's recommendation.

tag: batch

value: g


title: clr4D_RNA-seq_rep1

description: RNA sequencing of clr4∆ cells

value: f


title: wt_RNA-seq_rep13

description: RNA sequencing of WT cells

source_name: logarithmically growing WT cells

value: WT


title: man1D_RNA-seq_rep3

description: RNA sequencing of man1∆ cells

source_name: logarithmically growing man1∆ cells


title: man1D_RNA-seq_rep2

description: RNA sequencing of man1∆ cells


title: clr4D_RNA-seq_rep2

description: RNA sequencing of clr4∆ cells


title: wt_RNA-seq_rep12

description: RNA sequencing of WT cells


title: wt_RNA-seq_rep11

description: RNA sequencing of WT cells


title: air1D_RNA-seq_rep2

description: RNA sequencing of air1∆ cells

source_name: logarithmically growing air1∆ cells

value: e


title: air1D_RNA-seq_rep1

description: RNA sequencing of air1∆ cells


title: lem2D_RNA-seq_rep6

description: RNA sequencing of lem2∆ cells

source_name: logarithmically growing lem2∆ cells


title: wt_RNA-seq_rep9

description: RNA sequencing of WT cells

value: d


title: lem2D_RNA-seq_rep4

description: RNA sequencing of lem2∆ cells


title: mouse_scar_1

source_name: scar 6 weeks


title: mouse_scar_4


title: rrp6D_RNA-seq_rep2

description: RNA sequencing of rrp6∆ cells

source_name: logarithmically growing rrp6∆ cells

value: c


title: lem2D_RNA-seq_rep3

description: RNA sequencing of lem2∆ cells


title: mouse_scar_2


title: wt_RNA-seq_rep8

description: RNA sequencing of WT cells


title: wt_RNA-seq_rep7

description: RNA sequencing of WT cells


title: lem2D_RNA-seq_rep2

description: RNA sequencing of lem2∆ cells


title: rrp6D_RNA-seq_rep1

description: RNA sequencing of rrp6∆ cells


title: wt_RNA-seq_rep6

description: RNA sequencing of WT cells


title: man1D_RNA-seq_rep1

description: RNA sequencing of man1∆ cells


title: ccr4D_RNA-seq_rep1

description: RNA sequencing of ccr4∆ cells

source_name: logarithmically growing ccr4∆ cells

value: b


title: ccr4D_RNA-seq_rep2

description: RNA sequencing of ccr4∆ cells


title: lem2D_RNA-seq_rep1

description: RNA sequencing of lem2∆ cells


title: lem2D_RNA-seq_rep5

description: RNA sequencing of lem2∆ cells


title: red1D_RNA-seq_rep2

description: RNA sequencing of red1∆ cells

source_name: logarithmically growing red1∆ cells

value: a


title: wt_RNA-seq_rep4

description: RNA sequencing of WT cells


title: wt_RNA-seq_rep2

description: RNA sequencing of WT cells


title: erh1D_RNA-seq_rep2

description: RNA sequencing of erh1∆ cells

source_name: logarithmically growing erh1∆ cells


title: wt_RNA-seq_rep10

description: RNA sequencing of WT cells


title: wt_RNA-seq_rep3

description: RNA sequencing of WT cells


title: wt_RNA-seq_rep1

description: RNA sequencing of WT cells


title: human_scar_2

source_name: scar

tag: diagnosis

value: hypertrophic scar


title: human_scar_3


title: red1D_RNA-seq_rep1

description: RNA sequencing of red1∆ cells


title: human_scar_1


title: human_skin_3

source_name: skin

value: skin cells

value: healthy control

value: Single Cell 3' v2


title: wt_RNA-seq_rep5

description: RNA sequencing of WT cells


title: human_skin_2


title: FAW-25_1

status: Public on May 26 2021

city: Gimcheon

first: Mohammad

last: Vatanparast

address: 167, Yongjeon-ro

department: Plant quarantine technology center

institute: Animal and Plant Quarantine Agency

data_processing:
HiSeq 4000 System (Illumina, San Diego, USA) used for basecalling.
Quality-filtered and adapter-trimmed using Trimmomatic v0.38. FastQC v0.11.7 was used to check data quality before and after trimming. de novo transcriptome assembly was performed using Trinity version trinity rnaseq r20140717, bowtie 1.1.2. Trinity groups transcripts into clusters based on shared sequence content. For assembled genes, longest contigs of the assembled contigs are filtered and clustered into the non-redundant transcripts using CD-HIT version 4.6. ORF prediction for unigenes was performed using TransDecoder version 3.0.1. For the differentially expressed gene analysis, the abundances of unigenes across samples were estimated into read count as an expression measure by RSEM algorithm (RSEM version v1.2.29, bowtie 1.1.2.
Unigenes were searched against Kyoto Encyclopedia of Genes and Genomes (KEGG) v20190104 (http://www.genome.jp/kegg/ko.html), NCBI Nucleotide (NT) v20180116 (https://www.ncbi.nlm.nih.gov/nucleotide/), Pfam v20160316 (https://pfam.xfam.org/), Gene ontology (GO) v20180319 (http://www.geneontology.org/),  NCBI non-redundant Protein (NR) v20180503 (https://www.ncbi.nlm.nih.gov/protein/), UniProt v20180116 (http://www.uniprot.org/), and EggNOG (http://eggnogdb.embl.de/) using BLASTN of NCBI BLAST and BLASTX of DIAMOND version 0.9.21 (https://github.com/bbuchfink/diamond) with an E-value default cutoff of E-value 10-5.
Quality check was done for all samples, so that if more than one read count value was 0, it was not included in the analysis. In order to reduce systematic bias, estimates the size factors from the count data and applies Relative Log Expression (RLE) normalization with DESeq2 R library. Using each sample has normalized value, the high expression similarities were grouped together by Hierarchical Clustering Analysis and graphically shown in a 2D plot to show the variability of the total data using Multidimensional Scaling Analysis. Significant unigene results were analyzed as up and down-regulated count by log2FC ≥ 2 and ≤ -2, distribution of expression level between two groups was plotted as volcano plot (https://huygens.science.uva.nl/VolcaNoseR) and simple bar plots. Heat maps were generated using the online tool Heatmapper (http://www.heatmapper.ca/expression/). The KEGG analysis were done to identify the enrichment pathways and heat maps of shared unigenes at both treatment groups (T4 and T40) in comparison with T25 were plotted. In these cases, to get more effective DEGs, the DEGs were limited to log2FC ≥ 5 and ≤ -5, with a P-value<0.01.
The ten genes in response to low (T4) and high temperature (T40) were chosen for validation using RT-qPCR. To do that, FAW larvae were incubated at 4, and 40 °C in separated groups including 10 larvae, for 16 h. RNA extraction and cDNA synthesis were performed according ‘RNA extraction and RT-qPCR’ section. Specific primers were designed using Primer Quest tool (www.idtdna.com) (Table S8). Expression level of EF1α as reference gene was used to normalize target gene expression levels under different treatments. PCR products were assessed by melting curve analysis. Quantitative analysis was performed using comparative CT (2−ΔΔCT) method. Finally, the data compared according ratio of fold change (FC) and ratio of mRNA expression level for all selected genes.
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Spodoptera frugiperda

source_name: Spodoptera frugiperda

growth_protocol: The larvae of Spodoptera frugiperda (F0 generation) were obtained from Frotier Agriculture Sciences (Newark, DE, USA). They were raised until pupation under laboratory-controlled conditions (26°C, 70% RH, and a photoperiod of 14 h:10 h [L:D]). The larvae were fed an artificial diet (Newark, DE, USA) during their development. The diet was changed every day for larvae. These larvae were grown in plastic containers with aerated lids measuring 40 x 20 x 15 cm. From the third instar onwards, larvae were reared separately to prevent cannibalism. This was carried out in Petri dishes (8.5 cm diameter). Pupae were sexed and kept with the larvae in the same place. Pupae were monitored on a regular basis before moths appeared.

extract_protocol:
RNAs samples were extracted from whole body of Sposoptera frugiperda larvae using Trizol reagent (Invitrogen, Carlsbad, CA, USA). After RNA extraction, it was resuspended in nuclease-free water and quantified using a spectrophotometer (NanoDrop, Thermo Scientific, Wilmington, DE, USA). cDNA was then synthesized from RNA (1 μg) using RT PreMix (Intron Biotechnology, Seoul, Korea) containing oligo dT primer according to the manufacturer's instruction.
Illumina sequencing was performed on Macrogen to achieve short-read RNA sequences (Seoul, South Korea). The TruSeQ Stranded MRNA LT Sample Prep Kit (Illumina, San Diego, USA) has been used to build each library with a 1 μg total RNA of the whole group of 5 individuals Spodoptera frugiperda larvae per treatment and with the 101 bp pair end reading HiSeq 400 System (Illumina, San Diego, USA), it was sequenced.

treatment_protocol: To perform transcriptomic analysis fourth instar larvae were incubated at 4 and 40°C for 16 hours as temperature treatment groups to conduct transcriptomic analysis. The control group consisted of larvae incubated at 25°C. A total of 30 larvae were considered for each temperature. The larvae from each group were immediately frozen in liquid nitrogen and preserved at -80°C for subsequent experiments after the temperature procedure.

value: The fall armyworm

value: Whole body

tag: age

value: Fourth instar larvae

tag: genotype

value: Wild type

value: No


title: FAW-40_1


title: FAW-4_1


title: erh1D_RNA-seq_rep1

description: RNA sequencing of erh1∆ cells


title: human_skin_1

value: total mRNA


title: A673: WT1

status: Public on May 14 2021

city: New York

first: Caleb

last: Lareau

state: New York

address: 417 E 68th St, Zuckerman - ZRC 1132

institute: Memorial Sloan Kettering

data_processing:
Sequencing reads were aligned and paired, filtered for long-range contacts, and removed of duplicates using the HiC-Pro pipeline (PMID: 26619908).
Loop calling was performed with hichipper (PMID: 29489746) for each sample in a single experimental analysis set
Differential loop inference was performed using diffloop (PMID: 29028898)
Genome_build: hg19
Supplementary_files_format_and_content: High confidence loop calls and differential loop calls for the samples combined; individual per-sample loop calls

extract_protocol:
Cells were fixed with formaldehyde and then the genome was digested with restriction enzyme. Proximity ligation was carried out, followed by sonication and immunoprecipitation with an antibody directed towards SMC1.
Library was prepared by Tn5 transposition per nextera instructions

treatment_protocol: Stag2Null samples were derived from single-cell clones that were modified by Crispr/Cas9

value: Ewing Sarcoma


title: A673: STAG2KO2


title: A673: WT2

value: WT


title: A673: STAG2KO1


title: hiPSC_MM_2

status: Public on May 05 2021

city: Biberach

first: Bernd

last: Weigle

address: Birkendorfer Str. 65

department: Cancer Immunology & Immune Modulation

institute: Boehringer Ingelheim Pharma GmbH&Co KG

description: tpm.txt

data_processing:
Demultiplexing was performed using bcl2fastq v2.20.0.422 from Illumina 356 (https://emea.support.illumina.com/downloads/bcl2fastq-conversion-software-v2-20.html ). Sequencing reads from the RNA-seq experiment were processed with a pipeline building upon the implementation of the ENCODE “Long RNA-seq” pipeline, also described in (Schlager et al., 2020): filtered reads were mapped against the Homo sapiens (human) genome hg38/GRCh38 (primary 360 assembly, excluding alternate contigs) using the STAR (v2.5.2b) aligner (Dobin et al., 2013) allowing for soft clipping of adapter sequences. For quantification, we used transcript annotation files from Ensembl version 86, which corresponds to GENCODE 25. Gene expression levels were quantified with the above annotations, using RSEM (v1.3.0) (Li and Dewey, 2011) and featureCounts (v1.5.1) (Liao, Smyth and Shi, 2014). Quality controls were implemented using FastQC (v0.11.5) (Andrews, 2015) [Available online at: http://www.bioinformatics.babraham.ac.uk/projects/fastqc/ ], picardmetrics (v0.2.4) [ Slowikowski K. (2016): Available online at: https://github.com/slowkow/picardmetrics ] and dupRadar (v1.0.0) (Sayols, Scherzinger and Klein, 2016) at the respective steps.
Genome_build: hg38 (GRCh38)
Supplementary_files_format_and_content: tpm.txt contains expression levels (tpm) in tab-separated format.

source_name: hiPSC

extract_protocol:
One million cells were collected, centrifuged, washed in PBS, and lysed in RLT buffer (79216, Qiagen) before storage at -80C. RNA was later extracted using the Qiagen RNeasy Mini Kit (74104, Qiagen, USA) according to manufacturer’s specifications. An on-column DNA digestion (DNASE10-1SET, Sigma) was performed and the final elution volume was 30 uL. Total RNA was quantitatively and qualitatively assessed using the fluorescence-based Broad Range Quant-iT RNA Assay Kit (Q33140, ThermoFisher) and the Standard Sensitivity RNA Analysis DNF-471 Kit (DNF-471-0500, Agilent) on a 48-channel Fragment Analyzer (Agilent), respectively. Concentrations averaged at 25ng/μL while RIN ranged from 8.2 to 10, with a median of 9.9.
Thirty-three human macrophage- and monocyte-derived RNA samples were normalized on the MicroLab STAR automated liquid platform (Hamilton). Total RNA input of 200ng was used for library construction with the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina #E7760, together with the NEBNext Poly(A) mRNA Magnetic Isolation Module #E7490 upstream and the NEXNext Multiplex Oligos for Illumina #E7600 downstream (all New England Biolabs). The only deviation from the manufacturer’s protocol was the use of Ampure XP beads (Beckman Coulter) for double-stranded cDNA purification, instead of the recommended SPRIselect Beads. mRNA sequencing libraries were quantified by the High Sensitivity dsDNA Quanti-iT Assay Kit (ThermoFisher) on a Synergy HTX (BioTek). Library molarity averaged at 16nM. Final library size distribution was also assessed (smear analysis of ~410bp average and adapter dimer presence <0.5%) by the High Sensitivity Small Fragment DNF-477 Kit on a 48-channel Fragment Analyzer (Agilent). 32 out of 33 sequencing libraries passed quality check and were then normalized on the MicroLab STAR (Hamilton), pooled and spiked in with PhiX Control v3 (Illumina). The library pool was subsequently clustered with the HiSeq 3000/4000 SR Cluster Kit on a cBot; and sequenced on a HiSeq 4000 Sequencing System (Illumina) with dual index, single read at 85 bp length (Read parameters: Rd1: 86, Rd2: 8, Rd3: 8), reaching an average depth of 24 million Pass-Filter reads per sample (14.6% CV).

value: hiPSC-derived macrophages (M-CSF)


title: hiPSC_GM_5

description: tpm.txt

value: hiPSC-derived macrophages (GM-CSF)


title: hiPSC_MM_1

description: tpm.txt


title: hiPSC_MM_3

description: tpm.txt


title: hiPSC_GM_3

description: tpm.txt


title: hiPSC_GM_2

description: tpm.txt


title: hiPSC_Mono_2

description: tpm.txt

value: hiPSC-derived monocytes


title: hiPSC_GM_1

description: tpm.txt


title: Donor_MM_6

description: tpm.txt

source_name: PBMC

value: PBMC-derived macrophages (M-CSF)


title: hiPSC_Mono_1

description: tpm.txt


title: Donor_MM_2

description: tpm.txt


title: Donor_MM_5

description: tpm.txt


title: hiPSC_Mono_3

description: tpm.txt


title: Donor_MM_3

description: tpm.txt


title: Donor_MM_1

description: tpm.txt


title: Donor_GM_5

description: tpm.txt

value: PBMC-derived macrophages (GM-CSF)


title: Donor_GM_3

description: tpm.txt


title: Donor_GM_2

description: tpm.txt


title: Donor_GM_6

description: tpm.txt


title: Donor_Mono_6

description: tpm.txt

value: PBMC monocytes


title: Donor_GM_1

description: tpm.txt


title: Donor_Mono_4

description: tpm.txt


title: hiPSC_GM_4

description: tpm.txt


title: Donor_MM_4

description: tpm.txt


title: Donor_GM_4

description: tpm.txt


title: hiPSC_MM_4

description: tpm.txt


title: hiPSC_Mono_4

description: tpm.txt


title: Donor_Mono_3

description: tpm.txt


title: Donor_Mono_1

description: tpm.txt


title: HEK_HiC_NUP_IDR_FS_A9_2.2

status: Public on Apr 19 2021

city: Chapel Hill

first: Douglas

middle: H

last: Phanstiel

state: NC

address: 104 Manning Dr (Thurston Bowles Building), Rm 4019

institute: University of North Carolina at Chapel Hill

description:
PJA27_2_USPD16100712-6_HL7GYDSXX_L3
processed data file:
HEK_HiC_NUP_IDR_FS_A9_megaMap_inter_30.hic.gz
HEK_HICCUPS_NUP_IDR_FS_A9_15_postprocessed_pixels_10000.bedpe
NUP98-HOXA9 fusion with a phenylalanine to serine (F to S) mutant intrinsically disordered region (NUP_IDR_FS/A9) retrovirally transduced into the HEK293FT cell line to produce stable NUP_IDR_FS/A9 cell lines.

data_processing:
In situ Hi-C datasets were processed using the Juicer Hi-C pipeline with default parameters as described in Durand et al(Durand et al., 2016). MboI was used as the restriction enzyme, and reads were aligned to the hg19 human reference genome with bwa (version 0.7.17).
A Hi-C mega map was constructed by combining all replicates for each condition (i.e. NUP_IDR_WT/A9 or NUP_IDR_FS/A9).
Loops were detected using HiCCUPS from the Juicer tools software (version 1.11.09) as described in Rao et al.(Rao et al., 2014) via the following command: “hiccups -m 2048 -c 2 -r 5000,10000,25000 -k KR -f 0.1,0.1,0.1 -p 4,2,1 -i 8,6,4 -t 0.2,1.5,1.5,1.75 -d 30000,30000,60000”.
Genome_build: hg19
Supplementary_files_format_and_content: hic and bedpe files

source_name: NUP_IDR_FS/A9 expressing HEK293FT cell line

growth_protocol: HEK293FT cells were obtained from ATCC and maintained using recommended culture conditions.

extract_protocol: In situ Hi-C was performed exactly as described by Rao et al(Rao et al., 2014). Five million of cells were crosslinked in 1% of formaldehyde for ten minutes with stirring and quenched by adding 2.5M glycine to a final concentration of 0.2M for 5 min with rocking. Cells were pelleted by spinning at 300g for 5 min at 4°C. The pellet was washed with cold PBS and spun again prior to freezing in liquid nitrogen. Cells were lysed with 10mM Tris-HCl pH8.0, 10mM NaCl, 0.2% Igepal CA630 and protease inhibitors (Sigma, P8340) for 15 min on ice. Cells were pelleted and washed once more using the same buffer. Pellets were resuspended in 50μl of 0.5% SDS and incubates for 7 min at 62°C. Next, reactions were quenched with 145μl of water and 25μl of 10% Triton X-100 (Sigma, 93443) at 37°C for 15 min. Chromatin was digested overnight with 25μl of 10X NEBuffer2 and 100U of MboI at 37°C with rotation. Reactions were incubated at 62°C for 20 min to inactivate MboI and then cooled to room temperature. Fragment overhangs were repaired by adding 37.5 μl of 0.4mM biotin-14-dATP, 1.5 μl of 10mM dCTP, 1.5 μl of 10mM dGTP, 1.5 μl of 10mM dTTP, and 8 μl of 5U/ul DNA Polymerase I, Large (Klenow) Fragment and incubating at 37°C for 1.5 hr. Ligation was performed by adding 667 μl of water, 120 μl of 10X NEB T4 DNA ligase buffer, 100 μl of 10% Triton X-100, 12 μl of 10 mg/ml BSA, and 1 μl of 2000 U/ul T4 DNA Ligase and incubating at room temperature for 4 hr with slow rotation. Samples were pelleted at 2500g and resuspended in 432 μl water, 18 μl 20 mg/ml proteinase K, 50 μl 10% SDS, 46 μl 5M NaCl and incubated for 30 min at 55°C. The temperature was raised to 68°C and incubated overnight. Samples were cooled to room temperature. 874 μl of pure ethanol and 55 μl of 3M sodium acetate pH 5.2 were added to each tube which were subsequently incubated for 15 min at −80°C. Tubes were spun at max speed at 2°C for 15 min and washed twice with 70% ethanol. The resulting pellet was resuspended in 130 μl of 10mM Tric-HCl, pH8 and incubated at 37°C for 15 min. DNA was sheared using an LE220 Covaris Focused-ultrasonicator to a fragment size of 300-500 bp. Sheared DNA was size selected using AMPure XP beads. 110 μl of beads were added to each reaction and incubated for 5 min. Using a magnetic stand supernatant was removed and added to a fresh tube. 30μl of fresh AMPure XP beads were added and incubated for 5 min. Beads were separated on a magnet and washed twice with 700 μl of 70% ethanol without mixing. Beads were left to dry and then sample was eluted using 300 μl of 10 mM Tris-HCl, pH 8. 150 of 10 mg/ml Dynabeads MyOne Streptavidin T1 beads were washed resuspended in 300 μl of 10 mM Tris HCl, pH 7.5. This solution was added to the samples and incubated for 15 min at room temperature. Beads were washed twice with 600μl Tween Washing Buffer (TWB; 250 μl Tris-HCl, pH 7.5, 50 μl 0.5 M EDTA, 10 mL 5M NaCl, 25 μl Tween 20, and 39.675 mL water) at 55°C for 2 min with shaking. Sheared ends were repaired by adding 88 μl 1X NEB T4 DNA ligase buffer with 1mM ATP, 2 μl of 25 mM dNTP mix, 5 μl of 10U/μl NEB T4 PNK, 4ul of 3U/μl NEB T4 DNA polymerase I, 1μl of 5U/μl NEB DNA polymerase I, Large (Klenow) Fragment and incubating at room temperature for 30 min. Beads were washed two more times with TWB for 2 min at 55°C with shaking. Beads were washed once with 100 μl 1X NEBuffer 2 and resuspended in 90 μl of 1X NEBuffer 2, 5 μl of 10 mM dATP, 5μl of 5U/μl NEB Klenow exo minus, and incubated at 37°C for 30 min. Beads were washed two more times with TWB for 2 min at 55°C with shaking. Beads were washed once in 50 μl 1X Quick Ligation reaction buffer and resuspended in 50 μl 1X Quick Ligation reaction buffer. 2 μl of NEB DNA Quick ligase and 3 μl of an illumina indexed adaptor were added and the solution was incubated for 15 min at room temperature. Beads were reclaimed using the magnet and washed two more times with TWB for 2 min at 55°C with shaking. Beads were washed once in 100 μl 10 mM Tris-HCl, pH 8 and resuspended in 50 μl 10 mM Tris-HCl, pH8. Hi-C libraries were amplified for 7-12 cycles in 5 μl PCR primer cocktail, 20 μl of Enhanced PCR mix, and 25 μl of DNA on beads. The PCR settings included 3 min of 95°C followed by 7-12 cycles of 20 s at 98°C, 15 s at 60°C, and 30 s at 72°C. Samples were then held at 72°C for 5 min before lowering to 4°C until samples were collected. Amplified samples were brought to 250 μl with 10 mM Tris-HCl, pH 8. Samples were separated on a magnet and supernatant was transferred to a new tube. 175 μl of AMPure XP beads were added to each sample and incubated for 5 min. Beads were separated on a magnet and washed once with 700 μl of 70% ethanol. Supernatant was discarded. 100 μl of 10 mM Tris-HCl and 70 μl of fresh AMPure XP beads were added and the solution was incubated for 5 min at room temperature. Beads were separated with a magnet and washed twice with 700 μl 70% ethanol. Beads were left to dry until cracking started to be observed and eluted in 25 μl of Tris HCl, pH 8.0.

treatment_protocol: Retrovirus or lentivirus was packaged and produced in 293 cells, and the stable cell lines were generated by viral infection followed by drug selection as performed before (Cai et al., 2013; Lu et al., 2016; Xu et al., 2015).

tag: cell line background

tag: genotype/variation

value: expressing NUP_IDR_FS/A9

tag: nha9 idr type

value: F to S mutant

tag: biological replicate

tag: technical replicate


title: HEK_HiC_NUP_IDR_WT_A9_2.1

description:
PJA30_1_USPD16100712-12_HL7GYDSXX_L3
processed data file:
HEK_HiC_NUP_IDR_WT_A9_megaMap_inter_30.hic.gz
HEK_HICCUPS_NUP_IDR_WT_A9_15_postprocessed_pixels_10000.bedpe
NUP98-HOXA9 fusion with a wild type intrinsically disordered region (NUP_IDR_WT/A9) retrovirally transduced into the HEK293FT cell line to produce stable NUP_IDR_WT/A9 cell lines.

source_name: NUP_IDR_WT/A9 expressing HEK293FT cell line

value: expressing NUP_IDR_WT/A9

value: Wildtype


title: Bap1flfl_H2AK119ub1_ChIPseq_UNT_rep1

status: Public on May 03 2021

city: Oxford

first: Nadezda

middle: A

last: Fursova

address: South Parks Rd

department: Department of Biochemistry

institute: University of Oxford

description:
BAP1ff_UNT_Rep1_H2AK119ub1_ChIPseq_S1
processed data file:
mESC_BAP1ff_UNT_H2AK119ub1_mm10.UniqMapped_sorted_rmdup_downsampled_MERGED.MACS2.bw

data_processing:
For cChIP-seq, Bowtie 2 was used to align paired-end reads to the concatenated mouse and spike-in genome sequences (mm10+dm6 for native cChIP-seq for histone modifications; mm10+hg19 for cross-linked cChIP-seq for Polycomb factors and Pol II) with the “--no-mixed” and “--no-discordant” options. Non-uniquely mapping reads were discarded, and PCR duplicates were removed with Sambamba.
For visualization of cChIP-seq, the data were internally calibrated using dm6 or hg19 spike-in as described previously (Fursova et al. 2019). Briefly, uniquely aligned mm10 reads were randomly subsampled based on the total number of spike-in (dm6 or hg19) reads in each sample. To account for variations in the spike-in cell mixing, we used the ratio of spike-in/mouse total read counts in the corresponding Input samples to correct the subsampling factors. After normalisation, read coverages across genomic regions of interest (RING1B peaks for H2AK119ub1, H3K27me3, RING1B and SUZ12 cChIP-seq, TSS ± 2.5 kb for H3K27ac, H3K4me3 and H3K4me1 cChIP-seq, or gene bodies for total Pol II, Ser5P- and Ser2P-Pol II cChIP-seq) were compared for individual biological replicates using multiBamSummary and plotCorrelation from deepTools. For each experimental condition, biological replicates correlated well (Pearson correlation coefficient > 0.9) and were merged for downstream analysis.
For comparative box plot analysis, genomic regions of interest were annotated with read counts from merged spike-in normalised replicates using multiBamSummary from deeptools ( “--outRawCounts”).
Genome_build: mm10; dm6; hg19
Supplementary_files_format_and_content: bigWig files showing the genome coverage for merged spike-in normalised biological replicates were generated using the pileup function from MACS2.
Supplementary_files_format_and_content: bed files containing genomic intervals that were defined as active promoters, active enhancers and intergenic active enhancers based on the high enrichment of ATAC-seq and H3K27ac cChIP-seq signal in untreated Bap1fl/fl cells and the overlap with a comprehensive set of gene annotations. H3K27ac-positive ATAC peaks overlapping with transcription start site (TSS) +/- 1 kb regions were considered to be active promoters, while H3K27ac-positive ATAC peaks located further than 1 kb away from TSS of genes were considered to be active enhancers. Active enhancers that didn't overlap with any gene bodies from our comprehensive set of gene annotations (intergenic active enhancers) were used for all the downstream analysis.
Supplementary_files_format_and_content: bed files containing coordinates for the mm10 genome segmentation using a 13-state ChromHMM model: *segments.bed is a BED4 file (chr, start, end, state name) used for read annotation and *dense.bed is a BED file used for visualisation in the UCSC Genome browser in the dense format (all genome annotations are shown on a single line with different states represented by different colors).

organism:
Drosophila melanogaster
Mus musculus

source_name: mESCs with Drosophila spike-in, untreated control, H2AK119ub1 ChIP-seq

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

extract_protocol:
For RING1B and SUZ12 cChIP-seq, 5×107 mouse ESCs (untreated and OHT-treated) were crosslinked in 10 ml 1x PBS with 2 mM DSG (Thermo Scientific) for 45 minutes at 25°C, and then with 1% formaldehyde (methanol-free, Thermo Scientific) for a further 15 minutes. Crosslinking was stopped by quenching with 125 mM glycine. Crosslinked ESCs were mixed with 2×106 human HEK293T cells, which have been similarly double-crosslinked, and incubated in lysis buffer (50 mM HEPES pH 7.9, 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% NP40, 0.25% Triton-X100, 1x PIC (Roche)) for 10 minutes at 4˚C. Released nuclei were washed (10 mM Tris-HCl pH 8, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 1x PIC (Roche)) for 5 minutes at 4˚C. Chromatin was then resuspended in 1 ml of sonication buffer (10 mM Tris-HCl pH 8, 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% Na deoxycholate, 0.5% N-lauroylsarcosine, 1x PIC (Roche)) and sonicated for 30 minutes using the BioRuptor Pico (Diagenode), shearing genomic DNA to an average size of 0.5 kb. Following sonication, TritonX-100 was added to a final concentration of 1%, followed by centrifugation at 20,000 g for 10 min at 4°C to collect the clear supernatant fraction. For cChIP-seq for Pol II and its phosphorylated forms, 5×107 ESCs (untreated and OHT-treated) were crosslinked in 10 ml 1x PBS with 1% formaldehyde (methanol-free, Thermo Scientific) for 10 min at 25°C and then quenched by addition of 125 mM glycine. Cross-linked ESCs were mixed with 2×106 human HEK293T cells, which have been similarly single-crosslinked, and then incubated in FA-lysis buffer (50 mM HEPES pH 7.9, 150 mM NaCl, 2 mM EDTA, 0.5 mM EGTA, 0.5% NP40, 0.1% sodium deoxycholate, 0.1% SDS, 10 mM NaF, 1 mM AEBSF, 1×PIC) for 10 min at 4˚C. Chromatin was sonicated for 30 min using the BioRuptor Pico (Diagenode), followed by centrifugation at 20,000 g for 10 min at 4°C to collect the clear supernatant fraction.  For RING1B and SUZ12 ChIP, sonicated chromatin was diluted 10-fold with ChIP dilution buffer (1% Triton-X100, 1 mM EDTA, 20 mM Tris-HCl pH 8, 150 mM NaCl, 1xPIC). For Pol II ChIP, 300 ug of chromatin per one IP was diluted in FA-lysis buffer up to a final volume of 1 ml. Diluted chromatin was pre-cleared for 1 hr using Protein A agarose beads (Repligen) that were pre-blocked with 1 mg/ml BSA and 1 mg/ml yeast tRNA. For each ChIP reaction, 1 ml of diluted and pre-cleared chromatin was incubated overnight with the appropriate antibody, anti-RING1B (CST, D22F2, 3 ul), anti-SUZ12 (CST, D39F6, 3 ul), anti-Rpb1-NTD (CST, D8L4Y, 15 μl) as a measure of total Pol II levels, anti-Rpb1-CTD-Ser5P (CST, D9N5I, 12.5 μl) and anti-Rpb1-CTD-Ser2P (CST, E1Z3G, 12.5 μl) as a measure of Pol II phosphorylation levels. To capture antibody-bound chromatin, ChIP reactions were incubated with pre-blocked protein A agarose beads (Repligen) for 2 hr (RING1B and SUZ12) or 3 hr (Pol II) at 4°C. For RING1B and SUZ12, ChIP washes were performed as described previously (Farcas et al. 2012). For Pol II, washes were performed with FA-Lysis buffer, FA-Lysis buffer containing 500 mM NaCl, DOC buffer (250 mM LiCl, 0.5% NP-40, 0.5% sodium deoxycholate, 2 mM EDTA, 10 mM Tris-HCl pH 8), followed by two washes with TE buffer (pH 8). ChIP DNA was eluted in elution buffer (1% SDS, 0.1 M NaHCO3) and cross-linking was reversed overnight at 65oC with 200 mM NaCl and 2 ul RNase A (Sigma). Matched input samples (10% of original ChIP reaction) were treated identically. The following day, ChIP samples and inputs were incubated with Proteinase K (Sigma) for at least 1.5 hr at 56°C and purified using ChIP DNA Clean and Concentrator Kit (Zymo Research).  For native cChIP-seq for H2AK119ub1, H3K27me3, H3K27ac, H3K4me3, and H3K4me1, 5×107 mouse ESCs (untreated and OHT-treated) were mixed with 2×107 Drosophila SG4 cells in 1x PBS. Mixed cells were pelleted and nuclei were released by resuspending in ice-cold lysis buffer (10 mM Tris-HCl pH 8, 10 mM NaCl, 3 mM MgCl2, 0.1% NP40, 5 mM sodium butyrate, and 5 mM N-ethylmaleimide). Nuclei were then washed and resuspended in 1 ml of MNase digestion buffer (10 mM Tris-HCl pH 8.0, 10 mM NaCl, 3 mM MgCl2, 0.1% NP40, 0.25 M sucrose, 3 mM CaCl2, 10 mM sodium butyrate, 10 mM N-ethylmaleimide, and 1x PIC (Roche)). Each sample was incubated with 200 units of MNase (Fermentas) at 37°C for 5 min, followed by the addition of 4 mM EDTA to halt MNase digestion. Following centrifugation at 1500 g for 5 min at 4°C, the supernatant (S1) was retained. The remaining pellet was incubated with 300 µl of nucleosome release buffer (10 mM Tris-HCl pH 7.5, 10 mM NaCl, 0.2 mM EDTA, 10 mM sodium butyrate, 10 mM N-ethylmaleimide, and 1x PIC (Roche)) at 4°C for 1 hr, passed five times through a 27G needle using a 1 ml syringe, and spun at 1500 g for 5 min at 4°C. The second supernatant (S2) was collected and combined with the corresponding S1 sample from above. Digestion to mostly mono-nucleosomes was confirmed by agarose gel electrophoresis of purified S1/S2 DNA.  For ChIP, S1/S2 nucleosomes were diluted 10-fold in Native ChIP incubation buffer (70 mM NaCl, 10 mM Tris pH 7.5, 2 mM MgCl2, 2 mM EDTA, 0.1% TritonX-100, 10 mM sodium butyrate (for H3K27ac and H3K4me3 ChIPs), 10 mM N-ethylmaleimide, and 1xPIC (Roche)). Each ChIP reaction, 1 ml of diluted nucleosomes was incubated overnight at 4oC with the appropriate antibody, anti-H2AK119ub1 (CST, D27C4, 5 ul), anti-H3K27me3 (in-house, 5 ul), anti-H3K27ac (CST, D5E4, 3 μl), anti-H3K4me3 (in-house, 4 ul) or anti-H3K4me1 (CST, D1A9, 5 ul). Antibody-bound nucleosomes were captured for 1 hr at 4°C using protein A agarose (Repligen) beads, pre-blocked in Native ChIP incubation buffer supplemented with 1 mg/ml BSA and 1 mg/ml yeast tRNA, and collected by centrifugation. Immunoprecipitated material was washed four times with Native ChIP wash buffer (20 mM Tris pH 7.5, 2 mM EDTA, 125 mM NaCl, 0.1% Triton-X100) and once with TE buffer (pH 8). ChIP DNA was eluted using 100 ul of elution buffer (1% SDS, 0.1 M NaHCO3) for 30 min at room temperature, and then purified using ChIP DNA Clean and Concentrator Kit (Zymo Research). For each ChIP sample, DNA from a matched input control (corresponding to 10% of original ChIP reaction) was purified in the same way.
cChIP-seq libraries for both ChIP and Input samples were prepared using NEBNext Ultra II DNA Library Prep Kit for Illumina, following manufacturer’s guidelines. Samples were indexed using NEBNext Multiplex Oligos. The average size and concentration of all libraries were analysed using the 2100 Bioanalyzer High Sensitivity DNA Kit (Agilent) followed by qPCR quantification using SensiMix SYBR (Bioline, UK) and KAPA Illumina DNA standards (Roche). Libraries were sequenced as 40 bp paired-end reads in biological triplicate or quadruplicate on Illumina NextSeq 500 platform.

treatment_protocol: To induce conditional removal of BAP1, Bap1fl/fl mESCs were treated with 800 nM 4-hydroxytamoxifen (OHT) for 96 hr.

tag: cell type

value: mouse embryonic stem cells (mESCs)

value: Bap1fl/fl; Rosa26::ERT2-Cre

tag: clone

tag: replicate

tag: treatment agent

tag: treatment time point

value: 0 hr

tag: spike-in reference organism

value: Drosophila melanogaster

tag: spike-in cell line

tag: ChIP

tag: antibody

value: Cell Signaling Technology(#D27C4 )


title: Bap1flfl_uH2A.NInput_UNT_rep1

description:
BAP1ff_UNT_Rep1_NativeInput_S7
processed data file:
mESC_BAP1ff_UNT_uH2A.NInput_mm10.UniqMapped_sorted_rmdup_downsampled_MERGED.MACS2.bw

source_name: mESCs with Drosophila spike-in, untreated control, gDNA-seq

tag: cell line

tag: strain


title: HEK_HiC_NUP_IDR_FS_A9_1.1

description:
PJA27_1_USPD16093532-5_HGV2VDSXX_L2
processed data file:
HEK_HiC_NUP_IDR_FS_A9_megaMap_inter_30.hic.gz
HEK_HICCUPS_NUP_IDR_FS_A9_15_postprocessed_pixels_10000.bedpe
NUP98-HOXA9 fusion with a phenylalanine to serine (F to S) mutant intrinsically disordered region (NUP_IDR_FS/A9) retrovirally transduced into the HEK293FT cell line to produce stable NUP_IDR_FS/A9 cell lines.


title: Donor_Mono_2

description: tpm.txt


title: HEK_HiC_NUP_IDR_WT_A9_2.2

description:
PJA30_3_USPD16100712-AK13279_HL7GYDSXX_L3
processed data file:
HEK_HiC_NUP_IDR_WT_A9_megaMap_inter_30.hic.gz
HEK_HICCUPS_NUP_IDR_WT_A9_15_postprocessed_pixels_10000.bedpe
NUP98-HOXA9 fusion with a wild type intrinsically disordered region (NUP_IDR_WT/A9) retrovirally transduced into the HEK293FT cell line to produce stable NUP_IDR_WT/A9 cell lines.


title: HEK_HiC_NUP_IDR_FS_A9_1.2

description:
PJA27_2_USPD16093532-6_HGV2VDSXX_L2
processed data file:
HEK_HiC_NUP_IDR_FS_A9_megaMap_inter_30.hic.gz
HEK_HICCUPS_NUP_IDR_FS_A9_15_postprocessed_pixels_10000.bedpe
NUP98-HOXA9 fusion with a phenylalanine to serine (F to S) mutant intrinsically disordered region (NUP_IDR_FS/A9) retrovirally transduced into the HEK293FT cell line to produce stable NUP_IDR_FS/A9 cell lines.


title: atac_hft_w24_p6_r2

status: Public on Mar 31 2021

city: Stanford

first: Alex

middle: E

last: Trevino

state: California

address: 279 Campus Drive West

department: Genetics

institute: Enable Medicine

description:
atac_counts.tsv.gz
atac_consensus_peaks.bed.gz
atac_gene_activities.tsv.gz
atac_chromVAR_TF_activities.tsv.gz
atac_cell_metadata.txt
atac_sample_qc.txt
peak_gene_links.tsv.gz

data_processing:
Raw sequencing data were converted to fastq format using cellranger atac mkfastq (10x Genomics, v.3.1.0). scRNA-seq reads were aligned to the GRCh38 (hg38) reference genome and quantified using cellranger count (10x Genomics, v.3.1.0). ‘Velocyto’ (v.0.17.17) [La Manno et al. 2018] was used to obtain splicing-specific count data for downstream RNA velocity analysis.
Genome_build: hg38

source_name: Cerebral cortex

extract_protocol:
Samples were dissociated in papain and resuspended in ice-cold PBS + 0.02% BSA. For ATAC-seq, resuspension buffer (RSB) and lysis buffer (ALB) were prepared ice-cold. RSB: 10 mM Tris pH 7.4, 10 mM NaCl, 3 mM MgCl2. ALB: RSB + 0.1 % Tween-20 + 0.1% NP-40. Dissociated cells were counted and 100,000 cells were incubated for 5 minutes on ice in 100 uL ALB. ALB was diluted by adding 900 uL RSB, then samples were centrifuged at 500 x g for 5 minutes at 0 C. Nuclei were resuspended in 1X Nuclei Dilution Buffer (10X), checked for complete lysis, and counted. 4,000 cells per channel were loaded onto the Chromium 10X controller for ATAC, and 10,000 cells were loaded for RNA.
Libraries were constructed using the 10X Genomics 3' RNA v3 kits or the ATAC-seq kits

tag: age

tag: extraction

value: dissociation, nuclear isolation


title: atac_hft_w24_p6_r3


title: atac_hft_w24_p6_r4


title: atac_hft_w24_p6_r1


title: HEK_HiC_NUP_IDR_WT_A9_1.1

description:
PJA30_1_USPD16093532-12_HGV2VDSXX_L2
processed data file:
HEK_HiC_NUP_IDR_WT_A9_megaMap_inter_30.hic.gz
HEK_HICCUPS_NUP_IDR_WT_A9_15_postprocessed_pixels_10000.bedpe
NUP98-HOXA9 fusion with a wild type intrinsically disordered region (NUP_IDR_WT/A9) retrovirally transduced into the HEK293FT cell line to produce stable NUP_IDR_WT/A9 cell lines.

tag: cell line background

tag: genotype/variation


title: Donor_Mono_5

description: tpm.txt


title: atac_hft_w21_p5_r1


title: atac_hft_w21_p5_r4


title: HEK_HiC_NUP_IDR_WT_A9_1.2

description:
PJA30_2_USPD16093532-19_HGV2VDSXX_L2
processed data file:
HEK_HiC_NUP_IDR_WT_A9_megaMap_inter_30.hic.gz
HEK_HICCUPS_NUP_IDR_WT_A9_15_postprocessed_pixels_10000.bedpe
NUP98-HOXA9 fusion with a wild type intrinsically disordered region (NUP_IDR_WT/A9) retrovirally transduced into the HEK293FT cell line to produce stable NUP_IDR_WT/A9 cell lines.

tag: nha9 idr type

tag: biological replicate


title: atac_hft_w20_p3_r1


title: atac_hft_w16_p7_r3


title: atac_hft_w21_p5_r2


title: atac_hft_w16_p7_r1


title: atac_hft_w21_p5_r3


title: atac_hft_w16_p7_r2


title: HEK_HiC_NUP_IDR_FS_A9_2.1

description:
PJA27_1_USPD16100712-5_HL7GYDSXX_L3
processed data file:
HEK_HiC_NUP_IDR_FS_A9_megaMap_inter_30.hic.gz
HEK_HICCUPS_NUP_IDR_FS_A9_15_postprocessed_pixels_10000.bedpe
NUP98-HOXA9 fusion with a phenylalanine to serine (F to S) mutant intrinsically disordered region (NUP_IDR_FS/A9) retrovirally transduced into the HEK293FT cell line to produce stable NUP_IDR_FS/A9 cell lines.

tag: technical replicate


title: rna_hft_w24_p6_r2

description:
rna_counts.tsv.gz
rna_spliced_counts.tsv.gz
rna_unspliced_counts.tsv.gz
rna_ambiguous_counts.tsv.gz
rna_cell_metadata.txt
rna_sample_qc.txt

value: dissociation, whole cell


title: rna_hft_w21_p5_r1


title: rna_hft_w20_p3_r1


title: rna_hft_w21_p5_r2


title: Young4 [bulk_ATACseq_human]

status: Public on Mar 22 2021

city: Melbourne

first: Enzo

last: Porrello

state: Victoria

address: c/o Royal Children’s Hospital

department: Cell Biology

country: Australia

institute: Murdoch Children's Research Institute

description:
Pcm1(+) nuclei extracted from heart muscle.
Transposed DNA
atac_hum_tss_pe_mapk30_q30.mx.all_unfiltered.csv
atac_hum_tss_pe_mapk30_q30.mx.hum.fix_filt.csv
humanATAC_peaks_cov2_rmBL.bed.saf.pe.q30.mx.all.fix_filt.csv
humanATAC_peaks_cov2_rmBL.bed.saf.pe.q30.mx.all_unfiltered.csv
humanATAC_peaks_cov2_rmBL.bed.saf.pe.q30.mx.hum.fix_filt.csv

data_processing:
Trimming using the Skewer (version 0.2.2).
Aligned to the human genome (GRCh38.96/hg38) using Burrows-Wheeler Aligner (BWA, version 0.7.17).
Duplicated reads were removed using Samtools (Samtools, version1.8). Reads of mapping quality (Q≤30) were removed using Samtools. Peak calling was performed using MACS (version 1.4.2-1). Peaks that were detected in at least 2 samples were used to curate a peak set.
Mapped reads were counted to 1kb ± transcription start site with featureCounts (v1.5.0). Individual sample’s peaks counted to the curated peak sets using FeatureCounts (v1.5.0).
Genes or peaks with less than an average of 10 reads per sample across the experiment were filtered.
Genome_build: GRCh38.96/hg38
Supplementary_files_format_and_content: Raw counts or filtered counts of sequencing reads.

source_name: human left ventricle heart muscle

extract_protocol:
DNA transposition was performed from sorted Pcm1(+) nuclei as previously described (Buenrostro JD, Wu B, Chang HY, and Greenleaf WJ. ATAC-seq: A Method for Assaying Chromatin Accessibility Genome-Wide. Curr Protoc Mol Biol. 2015;109:21 9 1-9.).
Library was prepared as previously described (Buenrostro JD, Wu B, Chang HY, and Greenleaf WJ. ATAC-seq: A Method for Assaying Chromatin Accessibility Genome-Wide. Curr Protoc Mol Biol. 2015;109:21 9 1-9.).

tag: tissue

value: up to 1g of left ventricular heart muscle

tag: diagnosis

value: healthy non-cardiovascular disease

tag: developmental stage

value: young

tag: Sex

value: Male


title: rna_hft_w16_p7_r2


title: rna_hft_w20_p3_r2


title: Young1 [bulk_ATACseq_human]


title: atac_hft_w20_p3_r2


title: hiPSCCM7 [bulk_ATACseq_human]

description:
Pcm1(+) nuclei extracted
Transposed DNA
atac_hum_tss_pe_mapk30_q30.mx.all_unfiltered.csv
humanATAC_peaks_cov2_rmBL.bed.saf.pe.q30.mx.all.fix_filt.csv
humanATAC_peaks_cov2_rmBL.bed.saf.pe.q30.mx.all_unfiltered.csv

source_name: 2D in vitro cultured human induced pluripotent stem cell derived cardiomyocytes

growth_protocol: Culture protocol: Stem cells were cultured on matrigel coated T75 flask on mTeSR1 until 70-90% confluent and passaged to 6 well plates. Cells were then differentiated using cardiomyocyte differentiation cocktails and cultured for 4 weeks before harvesting for PCM1 sorting.

tag: cell type

value: Female


title: hiPSCCM6 [bulk_ATACseq_human]

value: induced pluripotent stem cell derived cardiomyocytes


title: rna_hft_w24_p6_r1


title: hiPSCCM4 [bulk_ATACseq_human]


title: hiPSCCM5 [bulk_ATACseq_human]


title: hiPSCCM2 [bulk_ATACseq_human]


title: hiPSCCM3 [bulk_ATACseq_human]


title: Adult7 [bulk_ATACseq_human]

description:
Pcm1(+) nuclei extracted from heart muscle.
Transposed DNA
atac_hum_tss_pe_mapk30_q30.mx.all_unfiltered.csv
atac_hum_tss_pe_mapk30_q30.mx.hum.fix_filt.csv
humanATAC_peaks_cov2_rmBL.bed.saf.pe.q30.mx.all.fix_filt.csv
humanATAC_peaks_cov2_rmBL.bed.saf.pe.q30.mx.all_unfiltered.csv
humanATAC_peaks_cov2_rmBL.bed.saf.pe.q30.mx.hum.fix_filt.csv
humanATAC_peaks_cov2_rmBL.bed.saf.pe.q30.mx.MvsF.fix_filt.csv

value: adult


title: Fetal3 [bulk_ATACseq_human]


title: rna_hft_w16_p7_r1


title: Adult5 [bulk_ATACseq_human]


title: Adult6 [bulk_ATACseq_human]


title: Fetal1 [bulk_ATACseq_human]


title: hiPSCCM1 [bulk_ATACseq_human]


title: Adult9 [bulk_ATACseq_human]


title: Fetal2 [bulk_ATACseq_human]


title: Adult13 [bulk_ATACseq_human]


title: Adult4 [bulk_ATACseq_human]


title: Adult8 [bulk_ATACseq_human]


title: Adult12 [bulk_ATACseq_human]


title: Adult3 [bulk_ATACseq_human]


title: Adult11 [bulk_ATACseq_human]


title: Adult2 [bulk_ATACseq_human]


title: Young2 [bulk_ATACseq_human]


title: Adult10 [bulk_ATACseq_human]


title: Young4 [bulk_RNAseq_human]

description:
Pcm1(+) nuclei extracted from left ventricular muscle.
rRNA depleted RNA
hrna_dev_mf_fulllen_se_strrev_q30.mx.all.fix_filt.csv
hrna_dev_mf_fulllen_se_strrev_q30.mx.all_unfiltered.csv

data_processing:
Trimming using the Skewer (version 0.2.2).
Aligned to the human genome (GRCh38.96/hg38) using STAR (version 2.5.3a).
Reads aligning to Ensembl-annotated whole genes on the correct strand with a strict mapping quality (Q≥30) were counted with featureCounts (v1.5.0).
Genes with less than an average of 10 reads per sample across the experiment were filtered.
Genome_build: GRCh38.96/hg38
Supplementary_files_format_and_content: Raw counts or filtered counts of sequencing reads.

extract_protocol:
RNA extraction was performed from sorted Pcm1(+) nuclei. Nuclei were lysed in TRIzol® Reagent (15596018, Invitrogen) and then processed with Direct-zol™ RNA Microprep kit (Zymo/ Integrated Science, R2060).
Ribosomal RNA was depleted from total RNA using NEBNext rRNA Depletion Kit (Human/Mouse/Rat) (E6310, New England Biolabs) followed by library generation using NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (E7760, New England Biolabs) to select library fragment sizes of 200-400bp.

value: Young


title: Young1 [bulk_RNAseq_human]


title: Young2 [bulk_RNAseq_human]


title: Adult1 [bulk_ATACseq_human]


title: Young3 [bulk_RNAseq_human]


title: Fetal6 [bulk_RNAseq_human]

description:
Pcm1(+) nuclei extracted from left ventricular muscle.
rRNA depleted RNA
hrna_dev_mf_fulllen_se_strrev_q30.mx.all.fix_filt.csv
hrna_dev_mf_fulllen_se_strrev_q30.mx.all_unfiltered.csv
hrna_dev_mf_fulllen_se_strrev_q30.mx.all.MvsF.fix_filt.csv

value: Fetal


title: Fetal4 [bulk_RNAseq_human]


title: Fetal1 [bulk_RNAseq_human]


title: Fetal3 [bulk_RNAseq_human]


title: Fetal5 [bulk_RNAseq_human]


title: Fetal2 [bulk_RNAseq_human]


title: Adult6 [bulk_RNAseq_human]

value: Adult


title: Adult5 [bulk_RNAseq_human]


title: Adult8 [bulk_RNAseq_human]


title: Adult3 [bulk_RNAseq_human]


title: Adult4 [bulk_RNAseq_human]


title: Adult9 [bulk_RNAseq_human]


title: Adult11 [bulk_RNAseq_human]


title: AAV-PR-M-2 [bulk_RNAseq_AAV_PGR]

description:
Pcm1(+) nuclei extracted from ventricular muscle.
rRNA depleted RNA
mrna_fulllen_pe_strrev_q30.mx.AAV_PR.unfiltered.txt
mrna_fulllen_pe_strrev_q30.mx.AAV_PR.fix_filt.txt

data_processing:
Trimming using the Skewer (version 0.2.2).
Aligned to the mouse genome (GRCm38.96/mm10) using STAR (version 2.5.3a).
Reads aligning to Ensembl-annotated whole genes on the correct strand with a strict mapping quality (Q≥30) were counted with featureCounts (v1.5.0).
Genes with less than an average of 10 reads per sample across the experiment were filtered.
Genome_build: GRCm38.96/mm10
Supplementary_files_format_and_content: Raw counts or filtered counts of sequencing reads.

source_name: mouse ventricular muscle

treatment_protocol: At post-natal day 1 (P1), male and female C57BL/6J mice received a single intraperitoneal injection of AAV serotype 6 vectors lacking insert (AAV_Con) or human PR (AAV_PGR) and tissues were collected at post-natal day 56.

tag: strain/background

value: 3-6 whole ventricular muscle

tag: vector

value: Postnatal day 56


title: Adult1 [bulk_RNAseq_human]


title: AAV-PR-F-1 [bulk_RNAseq_AAV_PGR]


title: Adult10 [bulk_RNAseq_human]


title: AAV-PR-M-3 [bulk_RNAseq_AAV_PGR]


title: AAV-MCS-M-3 [bulk_RNAseq_AAV_PGR]


title: AAV-MCS-M-1 [bulk_RNAseq_AAV_PGR]


title: AAV-PR-F-2 [bulk_RNAseq_AAV_PGR]


title: AAV-MCS-F-4 [bulk_RNAseq_AAV_PGR]


title: AAV-MCS-F-2 [bulk_RNAseq_AAV_PGR]


title: Young3 [bulk_ATACseq_human]


title: Adult2 [bulk_RNAseq_human]


title: PR-WT-M-2 [bulk_RNAseq_PrKO]

description:
Pcm1(+) nuclei extracted from ventricular muscle.
rRNA depleted RNA
mrna_fulllen_pe_strrev_q30.mx.PRKO.all.fix_filt.txt
mrna_fulllen_pe_strrev_q30.mx.PRKO.unfiltered.txt

tag: genotype


title: AAV-MCS-F-3 [bulk_RNAseq_AAV_PGR]


title: PR-WT-M-1 [bulk_RNAseq_PrKO]


title: AAV-PR-F-4 [bulk_RNAseq_AAV_PGR]


title: PR-WT-F-3 [bulk_RNAseq_PrKO]


title: AAV-MCS-F-1 [bulk_RNAseq_AAV_PGR]


title: AAV-PR-M-1 [bulk_RNAseq_AAV_PGR]


title: PR-WT-M-4 [bulk_RNAseq_PrKO]


title: PR-WT-F-1 [bulk_RNAseq_PrKO]


title: PR-WT-F-2 [bulk_RNAseq_PrKO]


title: PR-WT-M-3 [bulk_RNAseq_PrKO]


title: PR-KO-M-3 [bulk_RNAseq_PrKO]


title: PR-KO-F-3 [bulk_RNAseq_PrKO]


title: AAV-MCS-M-2 [bulk_RNAseq_AAV_PGR]


title: PR-KO-M-4 [bulk_RNAseq_PrKO]


title: PR-KO-M-2 [bulk_RNAseq_PrKO]


title: PR-KO-F-4 [bulk_RNAseq_PrKO]


title: PR-KO-M-1 [bulk_RNAseq_PrKO]


title: PR-KO-F-1 [bulk_RNAseq_PrKO]


title: Adult7 [bulk_RNAseq_human]


title: PR-KO-F-2 [bulk_RNAseq_PrKO]


title: Fetal3 [snRNAseq_human]

description:
Nuclei extracted from left ventricular muscle.
10x Chromium single nuclei RNA-seq.

data_processing:
Sequenced read were processed, aligned to human genome (GRCh38.96/hg38), counted and filtered using Cell Ranger (v3.0.2).
Genome_build: GRCh38.96/hg38
Supplementary_files_format_and_content: *_processed.tar: Tar files include barcodes.tsv, features.tsv, matrix.mtx. Filtered counts of sequencing reads.

extract_protocol:
Sorted cardiac nuclei were directed processed according to Chromium Next GEM Single Cell 3’ GEM, Library & Gel Bead Kit v3.1 protocol (PN-1000121).
Libraries were made according to Chromium Next GEM Single Cell 3’ GEM, Library & Gel Bead Kit v3.1 protocol (PN-1000121).

value: ~100mg of left ventricular heart muscle


title: Young1 [snRNAseq_human]


title: Young3 [snRNAseq_human]


title: Fetal1 [snRNAseq_human]


title: Fetal2 [snRNAseq_human]


title: Adult3 [snRNAseq_human]


title: Input

status: Public on Mar 15 2021

city: Madrid

first: Enrique

last: Carrillo de Santa Pau

address: C/ Melchor Fernández Almagro, 3

department: Cancer Cell Biology Programme

country: Spain

institute: Spanish National Cancer Research Centre (CNIO)

description: Input DNA

data_processing:
Image analysis, per-cycle basecalling and quality score assignment was performed with Illumina Real Time Analysis software. Conversion of BCL files to FASTQ format was performed with the bcl2fastq Software (Illumina).
ChIP-seq reads were aligned to the hg19 genome assembly using RubioSeq version 3.8.1 with parameters by default (https://www.sciencedirect.com/science/article/pii/S0169260716307386?via%3Dihub)
libraries were normalized to the lowest number of reads
peaks were called using RubioSeq version 3.8.1 with parameters by default (https://www.sciencedirect.com/science/article/pii/S0169260716307386?via%3Dihub)
Genome_build: hg19
Supplementary_files_format_and_content: txt files: original output from MACS software for peaks; bw: BigWig for visualization in UCSC genome browser; txt *mod* files: MACS output removing paths

growth_protocol: RT112 bladder cancer cells (from F. Radvanyi, Institut Curie, Paris, France) were grown in Dulbecco’s Modified Eagle’s Medium (DMEM) supplemented with 10% heat-inactivated FBS (Fetal Bovine Serum) and 1 mM sodium pyruvate.

extract_protocol:
Cells were cross-linked with 1% formaldehyde added to the media for 15 minutes at RT. After quenching with 0.125M Glycine, fixed cells were washed twice with PBS, pelleted and lysed in lysis buffer (1%SDS, 10mM EDTA, 50mM Tris-HCl pH8.1) at 2x107 cells/ml. Sonication was performed with a Covaris system (shearing time 20 min, 20% duty cycle, intensity 6, 200 cycles per burst and 30s per cycle) in a minimum volume of 2ml.
1 to 5ng of DNA per sample were used as provided by the user. Samples were processed through subsequent enzymatic treatments of end-repair, dA-tailing, and ligation to adapters with "NEBNext Ultra II DNA Library Prep Kit for Illumina" from New England BioLabs (catalog # E7645). Adapter-ligated libraries were completed by limited-cycle PCR and extracted with a [single] double-sided SPRI size selection. Resulting average fragment size is 370 bp from which 120 bp correspond to adaptor sequences. Libraries were applied to an Illumina flow cell for cluster generation and sequenced on an Illumina instrument (see below) by following manufacturer's protocols.

treatment_protocol: Cells were harvested after 48h in serum-free medium.

tag: tissue origin

value: bladder carcinoma

value: Cancer cell line

tag: cell line

value: female

tag: chip antibody


title: Adult2 [snRNAseq_human]


title: SMC1

description: SMC1 replicate 1

value: Rabbit polyclonal serum against SMC1 was obtained by using as immunogen a synthetic peptide (CDLTKYPDANPNPNEQ)


title: Adult1 [snRNAseq_human]


title: SMC1a

description: SMC1 replicate 2


title: SA1a

description: SA1 replicate 2

value: Rabbit polyclonal serum against SA1 was obtained by using as immunogen a synthetic peptide (CEDDSGFGMPMF)


title: SA2

description: SA2 replicate 1

value: Rabbit polyclonal serum against SA2 was obtained by using as immunogen a synthetic peptide (CDPASIMDESVLGVSMF)


title: COV9: COVID sample 9

status: Public on Mar 09 2021

city: Pavia

first: Maria

last: Garofalo

address: Via Mondino 2

country: Italy

institute: IRCCS Mondino Foundation

data_processing:
FastQ files were generated via llumina bcl2fastq2 Version 2.17.1.14
Gene and transcript intensities were computed using STAR/RSEM software using Gencode Release m24 (GRCm38) as a reference, using the “-strandness forward” option. Differential expression analysis for mRNA and lncRNA was performed using R package DESeq2
Genome_build: HG19

source_name: Frontal cortex

growth_protocol: Autoptic human brain samples were collected. Slices of anterior frontal lobe were fresh cut into about 10 mm thickness and frozen at -80°C.

extract_protocol:
Samples were homogenized and total RNA was isolated by Trizol® reagent (Life Science Technologies, Italy) following the manufacturer’s specifications. RNAs were quantified using a Nanodrop ND-100 Spectrophotometer (Nanodrop Technologies, Wilmington, USA) and a 2100 Bioanalyzer (Agilent RNA 6000 Nano Kit, Waldbronn, Germany); RNAs with a 260:280 ratio of ≥1.5 and an RNA integrity number of ≥8 were subjected to deep sequencing.
Sequencing libraries were prepared by the Lexogen CORALL Total RNA-Seq Library Prep Kit using 500-ng total RNA (Lexogen). Qualities of sequencing libraries were assessed with 4200 TapeStation with the DNA1000 reagent kit. RNA processing has been carried out using Illumina NextSeq 500 Sequencing.

tag: disease

tag: dementia status

value: Dementia

value: Frontal cortex


title: COV8: COVID sample 8


title: SA2a

description: SA2 replicate 2


title: SA1

description: SA1 replicate 1

data_processing:
Image analysis, per-cycle basecalling and quality score assignment was performed with Illumina Real Time Analysis software. Conversion of BCL files to FASTQ format was performed with the bcl2fastq Software (Illumina).
ChIP-seq reads were aligned to the hg19 genome assembly using RubioSeq version 3.8.1 with parameters by default (https://www.sciencedirect.com/science/article/pii/S0169260716307386?via%3Dihub)
libraries were normalized to the lowest number of reads
peaks were called using RubioSeq version 3.8.1 with parameters by default (https://www.sciencedirect.com/science/article/pii/S0169260716307386?via%3Dihub)
Genome_build: hg19
Supplementary_files_format_and_content: txt files: original output from MACS software for peaks; bw: BigWig for visualization in UCSC genome browser; txt *mod*files MACS output removing paths


title: COV1: COVID sample 1


title: COV5: COVID sample 5


title: Young2 [snRNAseq_human]

value: healthy non-cardiovascular disease

value: Female


title: COV7: COVID sample 7

value: No Dementia


title: COV3: COVID sample 3


title: BB247: CTRL sample 247

value: Control


title: BB271: CTRL sample 271


title: BB138: CTRL sample 138


title: BB236: CTRL sample 236


title: BB47: CTRL sample 47


title: BB118: CTRL sample 118


title: BB120: CTRL sample 120


title: COV4: COVID sample 4


title: hiPSC_Mono_5

description: tpm.txt

value: hiPSC-derived monocytes


title: COV10: COVID sample 10