title: NW4_S9

description: Paired-end strand-specific RNA-seq


title: DK1_S11

status: Public on Dec 02 2024

type: SRA

city: Marseille

first: Anne-Marie

last: François-Bellan

address: 27 Bd Jean Moulin

department: Facute de Medecine

country: France

institute: CNRS-AMU

description: Paired-end strand-specific RNA-seq

library_source: transcriptomic

data_processing:
HISAT2
FeatureCounts
Assembly: UCSC mm10
Supplementary files format and content: csv, counts

molecule: total RNA

organism: Mus musculus

source_name: Hypothalamus

extract_protocol:
Nucleospin RNA Macherey-Nagel
RNA library preparation with rRNA depletion.

tag: tissue

value: Hypothalamus

tag: time

value: night

tag: cell type

value: Hypothalamus cells

tag: genotype

value: magel2/necdin knokdown


title: mcm23Artt109D_H3K4me3_eSPAN

city: New York

first: Zhiguo

last: Zhang

state: NY

address: 1130 St. Nicholas Avenue

department: Pediatric and Genetics and Development

country: USA

institute: Columbia University

library_source: genomic

data_processing:
To improve mapping quality, raw sequencing reads were first processed with Trim Galore (v0.6.7) to remove low-quality reads and Illumina Prep Kit adaptors. The quality cutoff was set to 20, and the minimum required read length after trimming was 20 nt. Paired-end sequencing reads were mapped to yeast genome (sacCer3) using bowtie2 (V 2.2.4) with the following parameters: with --no-mixed --no-discordant --no-dovetail --no-contain --local --maxins 1000.
Sequence alignment map files, including uniquely mapped, PCR-duplicated, and multi-mapped reads, were transformed into BAM files using SAMtools (V 1.11).To obtain the accurate mapping reads, duplicate and multi-mapping reads were discarded and only paired-end reads with both ends aligning uniquely to the reference genome were used for further analysis.
Accurate early-firing region detection was achieved by using filtered paired-end reads of BrdU-IP-ssSeq signals to call broad peaks with MACS2 (V 2.2.5) for each replicate independently, applying a q-value cutoff of 0.001 and using the corresponding MNase-ssSeq Input samples as controls.
To calculate BrdU-IP-ssSeq and eSPAN strand bias, the filtered paired-end reads aligned to the Watson (W) and Crick (C) strands of the reference genome were partitioned using the bamtobed function of BEDTools (V 2.29.2) and custom Perl scripts. BrdU-IP-ssSeq and eSPAN bias was determined in 10bp bin from the segregated Watson and Crick reads using the formula Bias= (W-C)/(W + C) across the replicated regions. Bins with fewer than 10 sequencing reads were excluded. The eSPAN bias was furthermore normalized using the corresponding BrdU-IP-ssSeq strand bias.
Assembly: S. cerevisiae (UCSC sacCer3)
Supplementary files format and content: bigwig files were generated for plus strand, minus strand and both strands, scores represent the normalization reads density.

molecule: genomic DNA

organism: Saccharomyces cerevisiae

source_name: whole cell

growth_protocol: They were grown in rich medium (1% yeast extract, 2% peptone) supplemented with 2% glucose (YPD) at 30 °C. Exponentially growing cells were arrested at the G1 phase with 5 μg/ml alpha-factor (EZBiolab) for 3 hours in YPD medium at 25 °C when the OD600 reached 0.4-0.5. Prior to completion, cell morphology was monitored to ensure the G1 arrest (bar-shaped).

extract_protocol:
All ChIP and eSPAN assays were performed as described previously (Yu et al., 2014). To carry out ChIP for H3K4me3 and H3K56ac, chromatin was pelleted and washed twice with NP buffer (1.6 M sorbitol, 5 mM MgCl2, 50 mM NaCl, 2 mM CaCl2, 14 mM β-mercaptoethanol, 0.075% NP-40, 10 mM Tris-HCl (pH 7.4), 5 mM spermidine). The chromatin was then resuspended in the same buffer and digested with 4U MNase (9013-53-0, Worthington Biochemical) for 20 minutes at 37°C, resulting in primarily mono- and di-nucleosome fragments. The digestion was terminated by adding 5 μl of 0.5 M EDTA and 1/5 volume of 5x ChIP lysis buffer, followed by incubation on ice for at least 30 minutes. Following MNase digestion, the chromatin was cleared by centrifugation and then immunoprecipitated using specific antibodies (anti-H3K4me3 (ab8580, Abcam) and homemade anti-H3K56ac along with protein G Sepharose beads (17-0618-02, GE Healthcare). The beads were extensively washed, and DNA from both Input and ChIP samples was extracted via the Chelex-100 protocol and utilized for BrdU IP/eSPAN or purified using the MinElute PCR Purification Kit (28004, Qiagen) for ChIP. BrdU immunoprecipitation was performed using either input DNA for BrdU-IP-ssSeq, and H3K4me3 or H3K56ac ChIP DNAs for eSPAN. Briefly, input or ChIP DNA obtained from the Chelex-100 extraction was incubated at 100°C for 10 minutes and then immediately cooled on ice for 10 minutes. BrdU immunoprecipitation was conducted by diluting the DNA ten-fold with BrdU IP buffer (PBS, 0.0625% Triton X-100 (v/v), 6.7 μg/ml Escherichia coli tRNA, 0.17 μg/ml BrdU antibody (555627, BD Bioscience)) and rotating for 2 hours at 4°C. Protein G Sepharose beads were added and incubated for another hour at 4°C. After extensive washing, the DNA was extracted with 100 μl of 1x TE buffer containing 1% SDS at 65°C for 15 minutes and then eluted again with 50 μl of 1x TE buffer containing 1% SDS. The collected supernatants were subsequently purified using the MinElute PCR Purification Kit (Qiagen, 28004). Quantitative PCR was performed to analyze Input, BrdU-IP, ChIP, or eSPAN DNA using primers for the early replication origin ARS607 and the distant site ARS607+14kb.
Single-stranded DNA sequencing libraries were prepared using the Accel-NGS 1S Plus DNA Library Kit (10096, Swift Biosciences).

treatment_protocol: Arrested cells were collected by centrifugation, washed twice with cold H2O, and then released into fresh medium (YPD) at 25°C with 400 μg/ml BrdU (B5002, Sigma).

value: whole cell

tag: strain

tag: chip antibody

value: anti-H3K4me3 (ab8580, Abcam)

value: mcm2-3A mutant and Rtt109 KO

tag: treatment

value: MNase


title: TT-seq_dTAG-3h_PNUTS-DLD1_rep1

city: Shanghai

first: Aixia

last: Song

address: Dong'an Road

country: China

institute: Fudan University

data_processing:
The TT-seq raw reads were trimmed and then aligned to the hg19 or mm10 genome using STAR v2.7.5c with parameters “--outFilterMultimapNmax 1 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 -- outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.02 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 -outSAMtype BAM SortedByCoordinate”.
Duplicate and low-quality reads were removed, retaining only properly paired reads for downstream analyses.
The spike-in mm10 reads were quantified to generate the normalization factor. Strand-specific normalized bigwigs were generated with deepTools v3.5.0.
Assembly: hg19
Supplementary files format and content: bigWig
Library strategy: TT-seq

organism: Homo sapiens

growth_protocol: Human DLD-1 cells were grown in DMEM (Gibco) supplemented with 10% FBS (Yeasen) and 1 × Penicillin-Streptomycin (Thermo) at 37 °C, 5% CO2.

extract_protocol:
RNA was isolated with TRIzol. 100 μg RNA was fragmentated and  biotinylated. The biotinylated RNA  was immunoprecipitated and purified.
Libraries were prepared according to  ABclonal's instructions accompanying the ABclonal Stranded mRNA-seq Lib Prep Module for Illumina (ABclonal, RK20349). Libraries were sequenced on the Illumina NovaSeq 6000 following the manufacturer's protocols.

treatment_protocol: For TT-seq, cells were treated with dTAG 13 for 3,12 h,  the corresponding control cells were treated with vehicle only (DMSO) at the same vol/vol dilution. Cells were labeled by 4SU for 15min.  For DRB/TT-seq, cells were treated with dTAG 13 and DRB for 3h,  the corresponding control cells were treated with vehicle only (DMSO) at the same vol/vol dilution. Cells were labeled by 4SU for 10min.

tag: cell line

value: colorectal adenocarcinoma cell line

value: PNUTS-dTAG

value: treated with dTAG13 for 3 hours


title: MoAM, D14, Aged, 3

city: Vienna

first: Sylvia

last: Knapp

address: Währinger Gürtel 18-20

department: Department of Medicine I

country: Austria

institute: Medical University of Vienna

description: BSF_1396_H2GGMDRX3_1#S_63_41_S132809.bam

data_processing:
Convert BAM to FASTQ with picard SamToFastq (v2.25.5)
Pre-process with trimgalore (v0.6.6) --fastqc - length 15 and polyA --length 15 --aadapter A{20} -stringency 20 -e 0
Alignment to mm10 (GRCm39) with STAR (v2.7.9a) outFilterMismatchNoverLmax=0.1
Count matrix with Rsubread (v2.8.2) featureCounts countMultiMappingReads=FALSE GTF.featureType="gene"
Normalization with edgeR (3.36.0 calcNormFactors method="TMM" and cpm with normalized.lib.size=TRUE and log=FALSE
Assembly: mm10
Supplementary files format and content: tab-delimted text file includes raw counts
Supplementary files format and content: tab-delimted text file includes TMM normalized library size counts per million

source_name: Lung

extract_protocol:
RNA was isolated using the RNeasy Micro kit (Qiagen). Post isolation, RNA was precipitated with ice cold absolute ethanol, 3 M Sodium Acetate (NaOAc pH 5.2; ThermoFischer) and Linear Polyacrlamide (LPA; Sigma Aldrich) overnight and resuspended in 10 µl of 10 mM Tris buffer (pH 8.0; Invitrogen). RNA concentration was measured by fluorometric (Qubit) analysis
For Quant-seq, libraries were prepared using the QuantSeq 3’ mRNA-Seq Library Prep Kit (FWD) for Illumina (Lexogen) in combination with the PCR Add-on Kit for Illumina (Lexogen) and the UMI Second Strand Synthesis Module for QuantSeq FWD (Lexogen),

treatment_protocol: Mice were treated intratracheally with bleomycin (1U/Kg) . Cells (30,000-80,000) were sorted from the lungs into cold PBS 2% BSA, and the pellet resuspended in RLT Buffer (Qiagen).

value: Lung

value: MoAM

value: Lung fibrosis


title: NW3_S8

description: Paired-end strand-specific RNA-seq

value: WT


title: TT-seq_dTAG-1h_PNUTS-DLD1_rep2

value: treated with dTAG13 for 1 hours


title: AM, D7, Young, 1

description: BSF_1396_H2GGMDRX3_1#S_31_11_S132873.bam

value: AM


title: AM, D7, Aged, 1


title: TT-seq_dTAG-1h_PNUTS-DLD1_rep1


title: NW2_S7

description: Paired-end strand-specific RNA-seq

value: Hypothalamus


title: NW1_S6

description: Paired-end strand-specific RNA-seq

value: day


title: MoAM, D14, Aged, 2

description: BSF_1396_H2GGMDRX3_1#S_62_40_S132810.bam


title: WT_H3K4me3_eSPAN


title: MoAM, D14, Young, 3

description: BSF_1396_H2GGMDRX3_1#S_82_65_S132830.bam


title: TT-seq_DMSO_PNUTS-DLD1_rep1

value: treated with DMSO for 3 hours


title: TT-seq_DMSO_PNUTS-DLD1_rep2


title: mcm23Artt109Dchd1D_H3K4me3_eSPAN

value: mcm2-3A mutant, Rtt109 KO and Chd1 KO


title: TT-seq_dTAG-3h_PNUTS-DLD1_rep2


title: DW4_S5

description: Paired-end strand-specific RNA-seq

value: Hypothalamus cells


title: mcm23Achd1D_H3K4me3_ChIP

value: whole cell

value: anti-H3K4me3 (ab8580, Abcam)

value: mcm2-3A mutant and Chd1 KO


title: rtt109D_H3K4me3_eSPAN

value: Rtt109 KO

value: MNase


title: TT-seq_DMSO-3h_DRB-3h_release-20min_PNUTS-DLD1

value: colorectal adenocarcinoma cell line

value: PNUTS-dTAG

value: treated with DMSO&DRB for 3h


title: mcm23Artt109Dchd1D_H3K4me3_ChIP


title: MoAM, D14, Young, 2

description: BSF_1396_H2GGMDRX3_1#S_80_61_S132828.bam

value: Lung

value: MoAM

value: Lung fibrosis


title: MoAM, D7, Aged, 4

description: BSF_1396_H2GGMDRX3_1#S_69_47_S132815.bam


title: mcm23Aisw1D_H3K4me3_ChIP

value: mcm2-3A mutant and Isw1 KO


title: MoAM, D14, Young, 1

description: BSF_1396_H2GGMDRX3_1#S_78_67_S132826.bam


title: RNA-seq_dTAG-12h_PNUTS-DLD1_rep1

data_processing:
Raw reads were trimmed followed by mapping to the hg19 or mm10 genome using STAR v2.7.5c with the parameter ‘‘--outSAMtype BAM SortedByCoordinate --twopassMode Basic --outFilterMismatchNmax 3’’.
Low mapping quality reads and PCR duplicates were removed using SAMtools v1.9 96 and Picard v2.23.3 (https://broadinstitute.github.io/picard/). Calculation of the normalization factor was performed in the same way as described in ChIP-Rx.
Strand-specific normalized bigwigs were generated by deeptools v3.5.0.97 To identify differentially expressed genes, we collected the counts per gene by the featureCounts tool from the Rsubread R package v2.0.1.103 Differential expression analysis was then performed using DESeq2 R package v1.26.0.
Assembly: hg19
Supplementary files format and content: bigWig

extract_protocol:
RNA was isolated with TRIzol. 1 ug of total RNA was used for the construction of sequencing libraries.
Libraries were prepared according to  ABclonal's instructions accompanying the ABclonal Stranded mRNA-seq Lib Prep Module for Illumina (ABclonal, RK20349). Libraries were sequenced on the Illumina NovaSeq 6000 following the manufacturer's protocols.

treatment_protocol: Cells were treated with dTAG 13 for 3,12 h,  the corresponding control cells were treated with vehicle only (DMSO) at the same vol/vol dilution

value: treated with dTAG13 for 12 hours


title: RNA-seq_DMSO-12h_PNUTS-DLD1_rep2

value: treated with DMSO for 12 hours


title: MoAM, D14, Aged, 1

description: BSF_1396_H2GGMDRX3_1#S_61_39_S132807.bam


title: mcm23A_H3K4me3_eSPAN

value: mcm2-3A mutant


title: DW4_S4

description: Paired-end strand-specific RNA-seq

value: Hypothalamus

value: day

value: WT


title: RNA-seq_dTAG-12h_PNUTS-DLD1_rep2


title: mcm23Artt109D_H3K4me3_ChIP

value: whole cell

value: anti-H3K4me3 (ab8580, Abcam)

value: mcm2-3A mutant and Rtt109 KO


title: rtt109D_H3K4me3_ChIP

value: Rtt109 KO

value: MNase


title: DW3_S3

description: Paired-end strand-specific RNA-seq

value: Hypothalamus cells


title: DW2_S2

description: Paired-end strand-specific RNA-seq


title: RNA-seq_DMSO-12h_PNUTS-DLD1_rep1

value: colorectal adenocarcinoma cell line

value: PNUTS-dTAG


title: mcm23A_H3K4me3_ChIP


title: RNA-seq_dTAG-3h_PNUTS-DLD1_rep2

value: treated with dTAG13 for 3 hours


title: DW1_S1

description: Paired-end strand-specific RNA-seq


title: RNA-seq_dTAG-3h_PNUTS-DLD1_rep1


title: MoAM, D7, Aged, 1

description: BSF_1396_H2GGMDRX3_1#S_64_42_S132812.bam

value: Lung

value: MoAM

value: Lung fibrosis


title: H6-Sept-23-Plate2-PEM_S186

city: Edmonton

first: Patrick

middle: E.

last: MacDonald

state: Alberta

address: 6-040 Li Ka Shing Centre

department: Pharmacology

country: Canada

institute: University of Alberta

library_source: transcriptomic single cell

data_processing:
Fastq files were trimmed using TrimGalore version 0.6.5 with auto-detection of adapter sequence
Aligned to the GRCh38 human genome, Ensembl release 104,and counted using STAR version 2.7.11a
Counts were decontaminatedusing celda (1.20.0) decontX in R (4.4.1)
Assembly: GRCh38, Ensembl release 104
Supplementary files format and content: Combined csv count table of all cells; raw counts with ENSG identifiers
Supplementary files format and content: Processed RData file containing a Seurat object with all cells, with gene symbols, decontaminated and normalized counts
Supplementary files format and content: Python h5ad file containing all cells, with gene symbols, decontaminated counts

source_name: islets

extract_protocol:
Isolated human islets were dispersed to single cells, and whole cell patch clamp electrophysiology was performed. Following, the cells were collected and sent for scRNA-seq (SmartSeq).
SmartSeq3

tag: donor

tag: plate

tag: cellid

value: islets

tag: time from_plating_(h)

tag: glucose mm

tag: experimental record

tag: age

tag: Sex

value: Male

tag: bmi

tag: cellsize f

tag: glycinecurrent(pa/pf)

tag: glycinecurrent+strychnine(pa/pf)

tag: glycinecurrentwashout(pa/pf)


title: WT_H3K4me3_ChIP

tag: tissue

tag: strain

tag: genotype


title: MoAM, D7, Young, 4

description: BSF_1396_H2GGMDRX3_1#S_86_66_S132834.bam

tag: cell type

tag: treatment


title: H4-Sept-23-Plate2-PEM_S184

tag: donor

tag: plate

value: female


title: mcm23Aisw1D_BrdU_S30_rep2

tag: chip antibody

value: anti-BrdU (555627, BD Bioscience)

value: mcm2-3A mutant and Isw1 KO


title: RNA-seq_DMSO-3h_PNUTS-DLD1_rep2

tag: cell line

value: treated with DMSO for 3 hours


title: H11-Sept-23-Plate2-PEM_S191

tag: cellid

tag: time from_plating_(h)

tag: glucose mm

tag: experimental record

value: male


title: MoAM, D7, Aged, 3

description: BSF_1396_H2GGMDRX3_1#S_68_46_S132816.bam


title: H10-Sept-23-Plate2-PEM_S190

value: ND

tag: age

tag: Sex

tag: bmi

tag: cellsize f


title: MoAM, D7, Young, 1

description: BSF_1396_H2GGMDRX3_1#S_83_69_S132829.bam

tag: tissue


title: G9-Sept-23-Plate2-PEM_S177

tag: glycinecurrent(pa/pf)

tag: glycinecurrent+strychnine(pa/pf)

tag: glycinecurrentwashout(pa/pf)


title: MDAMB468, 200nM selinexor, 24hr, 3

city: Minneapolis

first: R. Stephanie

last: Huang

state: MN

address: 308 Harvard St. SE

institute: University of Minnesota

data_processing:
FASTQ files were trimmed with Trimmomatic
Trimmed reads were aligned with HISAT2
Aligned reads were then sorted with SAMTools
featureCounts was used to obtain the cpm
Assembly: GRCh38
Supplementary files format and content: cleaned and aligned count reads; .txt file format

source_name: breast; mammary gland

growth_protocol: Cells were maintained in RPMI 1640 supplemented with 10% FBS at 37C and 5% CO2 atmosphere

extract_protocol:
RNA from cells was isolated and purified using Quick-RNA Miniprep Plus Kit (ZYMO Research)
Samples were sent to the Universitiy of Minnesota Genomic Center for processing

treatment_protocol: Cells were either treated with 200nM selinexor or DMSO control

value: breast; mammary gland

tag: cell type

value: epithelial cell

tag: time

value: 24hr post treatment

tag: treatment

value: 200nM selinexor


title: MoAM, D7, Young, 2

description: BSF_1396_H2GGMDRX3_1#S_84_73_S132832.bam

tag: genotype


title: isw1D_BrdU_S30_rep2

value: whole cell

tag: strain

tag: chip antibody

value: Isw1 KO

value: MNase


title: MDAMB468, 200nM selinexor, 24hr, 2

tag: cell line


title: G6-Sept-23-Plate2-PEM_S174

tag: donor

tag: plate

tag: cellid

tag: time from_plating_(h)

tag: glucose mm


title: MoAM, D7, Aged, 2

description: BSF_1396_H2GGMDRX3_1#S_67_45_S132813.bam

value: Lung

value: MoAM


title: RNA-seq_DMSO-3h_PNUTS-DLD1_rep1

value: colorectal adenocarcinoma cell line

value: PNUTS-dTAG


title: Monocytes, D7, Aged, 3

description: BSF_1396_H2GGMDRX3_1#S_89_64_S132835.bam

value: Monocytes

value: Lung fibrosis


title: mcm23Achd1D_BrdU_S30_rep2

value: anti-BrdU (555627, BD Bioscience)

value: mcm2-3A mutant and Chd1 KO


title: MDAMB468, 200nM selinexor, 24hr, 1


title: Monocytes, D7, Aged, 2

description: BSF_1396_H2GGMDRX3_1#S_88_78_S132836.bam


title: G4-Sept-23-Plate2-PEM_S172

value: islets

tag: experimental record

tag: age

tag: Sex

value: female

tag: bmi

tag: cellsize f


title: MDAMB468, DMSO control, 24hr, 3

tag: tissue

value: breast; mammary gland

tag: cell type

value: Vehicle


title: Monocytes, D7, Aged, 1

description: BSF_1396_H2GGMDRX3_1#S_87_76_S132833.bam

tag: treatment


title: MDAMB468, DMSO control, 24hr, 2

value: epithelial cell

tag: time

value: 24hr post treatment


title: chd1D_BrdU_S30_rep2

value: whole cell

tag: strain

tag: genotype

value: Chd1 KO


title: G2-Sept-23-Plate2-PEM_S170

value: ND

value: male

tag: glycinecurrent(pa/pf)

tag: glycinecurrent+strychnine(pa/pf)

tag: glycinecurrentwashout(pa/pf)


title: Monocytes, D7, Young, 2

description: BSF_1396_H2GGMDRX3_1#S_91_74_S132837.bam

value: Lung


title: chd1D_BrdU_S30_rep1

tag: chip antibody

value: MNase


title: MoAM, D7, Young, 3

description: BSF_1396_H2GGMDRX3_1#S_85_75_S132831.bam

value: MoAM


title: MDAMB468, DMSO control, 24hr,1

tag: cell line


title: Monocytes, D7, Young, 1

description: BSF_1396_H2GGMDRX3_1#S_90_72_S132838.bam

value: Monocytes


title: G10-Sept-23-Plate2-PEM_S178

tag: donor

tag: plate

tag: cellid

tag: time from_plating_(h)

tag: glucose mm


title: isw1D_BrdU_S30_rep1

value: Isw1 KO


title: mcm23Aisw1D_Input_S30_rep2

value: mcm2-3A mutant and Isw1 KO


title: MDAMB468, 200nM selinexor, 8hr, 3

value: 8hr post treatmnet

value: 200nM selinexor


title: mcm23Aisw1D_BrdU_S30_rep1

value: anti-BrdU (555627, BD Bioscience)


title: F9-Sept-23-Plate2-PEM_S165

value: islets

tag: experimental record

tag: age

tag: Sex

tag: bmi

tag: cellsize f


title: MDAMB468, 200nM selinexor, 8hr, 2

tag: tissue

value: breast; mammary gland

tag: cell type

tag: time

tag: treatment


title: MDAMB468, 200nM selinexor, 8hr, 1

value: epithelial cell


title: F5-Sept-23-Plate2-PEM_S161

value: female

tag: glycinecurrent(pa/pf)

tag: glycinecurrent+strychnine(pa/pf)

tag: glycinecurrentwashout(pa/pf)


title: mcm23Achd1D_BrdU_S30_rep1

value: whole cell

tag: strain

tag: chip antibody

tag: genotype

value: mcm2-3A mutant and Chd1 KO


title: isw1D_Input_S30_rep1


title: MDAMB468, DMSO control, 8hr, 3

tag: cell line

value: Vehicle


title: mcm23Achd1D_Input_S30_rep2


title: MDAMB468, DMSO control, 8hr, 2


title: F4-Sept-23-Plate2-PEM_S160

tag: donor

tag: plate

tag: cellid

tag: time from_plating_(h)

tag: glucose mm


title: mcm23Achd1D_Input_S30_rep1


title: G11-Sept-23-Plate2-PEM_S179

tag: experimental record

tag: age

tag: Sex

value: male

tag: bmi

tag: cellsize f


title: chd1D_Input_S30_rep2

tag: tissue

value: Chd1 KO

tag: treatment


title: MDAMB468, DMSO control, 8hr, 1

tag: cell type

tag: time


title: F11-Sept-23-Plate2-PEM_S167

tag: glycinecurrent(pa/pf)

tag: glycinecurrent+strychnine(pa/pf)

tag: glycinecurrentwashout(pa/pf)


title: HCC1806 cells, 200nM selinexor, 24hr, 3

tag: cell line

value: 24hr post treatment


title: F10-Sept-23-Plate2-PEM_S166

tag: donor

tag: plate

value: ND


title: E9-Sept-23-Plate2-PEM_S153

tag: cellid

tag: time from_plating_(h)


title: chd1D_Input_S30_rep1

tag: strain

tag: chip antibody

tag: genotype

value: MNase


title: HCC1806 cells, 200nM selinexor, 24hr, 2


title: mcm23Aisw1D_Input_S30_rep1


title: HCC1806 cells, 200nM selinexor, 24hr, 1


title: F6-Sept-23-Plate2-PEM_S162

tag: glucose mm

tag: experimental record

tag: age

tag: Sex

value: Male

tag: bmi


title: mcm23Artt109Dchd1D_BrdU_S30_rep2

tag: tissue

value: mcm2-3A mutant, Rtt109 KO and Chd1 KO

tag: treatment


title: isw1D_Input_S30_rep2

value: Isw1 KO


title: HCC1806 cells, DMSO control, 24hr, 3

tag: cell type

tag: time


title: HCC1806 cells, DMSO control, 24hr, 2

tag: cell line


title: mcm23Artt109Dchd1D_BrdU_S30_rep1


title: E6-Sept-23-Plate2-PEM_S150

tag: donor

tag: cellsize f

tag: glycinecurrent(pa/pf)

tag: glycinecurrent+strychnine(pa/pf)

tag: glycinecurrentwashout(pa/pf)


title: E8-Sept-23-Plate2-PEM_S152

tag: plate

tag: cellid

tag: time from_plating_(h)


title: mcm23Artt109Dchd1D_Input_S30_rep2

tag: strain

tag: chip antibody

tag: genotype


title: mcm23Artt109Dchd1D_Input_S30_rep1


title: F2-Sept-23-Plate2-PEM_S158

tag: glucose mm

tag: experimental record

tag: age

tag: Sex

tag: bmi


title: E4-Sept-23-Plate2-PEM_S148

tag: cell type


title: HCC1806 cells, DMSO control, 24hr, 1

tag: tissue

tag: cell line

tag: time

tag: treatment


title: HCC1806 cells, 200nM selinexor, 8hr, 3

value: 8hr post treatmnet

value: 200nM selinexor


title: mcm23Artt109D_BrdU_S30_rep2

value: anti-BrdU (555627, BD Bioscience)

value: mcm2-3A mutant and Rtt109 KO


title: E11-Sept-23-Plate2-PEM_S155

tag: donor

value: islets

tag: cellsize f

tag: glycinecurrent(pa/pf)

tag: glycinecurrent+strychnine(pa/pf)

tag: glycinecurrentwashout(pa/pf)


title: mcm23Artt109D_BrdU_S30_rep1

tag: strain

tag: chip antibody


title: rtt109D_BrdU_S30_rep1

tag: genotype

value: Rtt109 KO


title: rtt109D_BrdU_S30_rep2

value: whole cell


title: HCC1806 cells, 200nM selinexor, 8hr, 1

value: breast; mammary gland

value: epithelial cell


title: HCC1806 cells, DMSO control, 8hr, 3

value: Vehicle


title: E10-Sept-23-Plate2-PEM_S154

tag: plate

tag: cellid

tag: time from_plating_(h)

tag: glucose mm

tag: experimental record

value: male


title: mcm23Artt109D_Input_S30_rep2

tag: tissue


title: HCC1806 cells, DMSO control, 8hr, 2

tag: cell line

tag: cell type


title: E1-Sept-23-Plate2-PEM_S145

tag: age

tag: Sex

value: female

tag: bmi


title: HCC1806 cells, DMSO control, 8hr, 1

tag: time

tag: treatment


title: rtt109D_Input_S30_rep2


title: D8-Sept-23-Plate2-PEM_S140

tag: donor

value: ND

tag: cellsize f

tag: glycinecurrent(pa/pf)

tag: glycinecurrent+strychnine(pa/pf)

tag: glycinecurrentwashout(pa/pf)


title: D9-Sept-23-Plate2-PEM_S141

tag: plate

tag: cellid


title: mcm23Artt109D_Input_S30_rep1

tag: strain

tag: chip antibody

tag: genotype

value: MNase


title: CAL120 cells, 200nM selinexor, 24hr, 3

tag: tissue

tag: cell line

value: epithelial-like and fibroblast-like

value: 24hr post treatment


title: D7-Sept-23-Plate2-PEM_S139

tag: cell type

tag: time from_plating_(h)

tag: glucose mm

tag: experimental record

tag: age


title: rtt109D_Input_S30_rep1

tag: treatment


title: E5-Sept-23-Plate2-PEM_S149

tag: donor

tag: Sex

tag: bmi

tag: cellsize f


title: CAL120 cells, 200nM selinexor, 24hr, 2

tag: time


title: mcm23A_BrdU_S30_rep2

value: mcm2-3A mutant


title: CAL120 cells, 200nM selinexor, 24hr, 1


title: E2-Sept-23-Plate2-PEM_S146

tag: plate

tag: cellid

tag: glycinecurrent(pa/pf)

tag: glycinecurrent+strychnine(pa/pf)

tag: glycinecurrentwashout(pa/pf)


title: D5-Sept-23-Plate2-PEM_S137


title: D6-Sept-23-Plate2-PEM_S138

value: Male


title: CAL120 cells, DMSO control, 24hr, 3

tag: tissue

tag: cell line


title: mcm23A_BrdU_S30_rep1

tag: strain

tag: chip antibody

tag: genotype


title: WT_BrdU_S30_rep2

value: WT


title: CAL120 cells, DMSO control, 24hr, 1

tag: cell type


title: D2-Sept-23-Plate2-PEM_S134

tag: time from_plating_(h)

tag: glucose mm

tag: experimental record

tag: age


title: WT_BrdU_S30_rep1

value: anti-BrdU (555627, BD Bioscience)

tag: treatment


title: HCC1806 cells, 200nM selinexor, 8hr, 2

tag: time

value: 8hr post treatmnet

value: 200nM selinexor


title: D1-Sept-23-Plate2-PEM_S133

tag: donor

tag: plate

value: islets

tag: Sex

tag: bmi

tag: cellsize f


title: mcm23A_Input_S30_rep2

tag: tissue

value: whole cell


title: CAL120 cells, 200nM selinexor, 8hr, 1

value: breast; mammary gland

tag: cell line


title: CAL120 cells, 200nM selinexor, 8hr, 3


title: D11-Sept-23-Plate2-PEM_S143

tag: cellid

tag: glycinecurrent(pa/pf)

tag: glycinecurrent+strychnine(pa/pf)

tag: glycinecurrentwashout(pa/pf)


title: D4-Sept-23-Plate2-PEM_S136

tag: cell type

tag: time from_plating_(h)


title: C9-Sept-23-Plate2-PEM_S129

tag: glucose mm

tag: experimental record


title: CAL120 cells, DMSO control, 8hr, 3

tag: treatment


title: testis_CAST_5_49221

city: Bar Harbor

first: Laura

last: Reinholdt

state: ME

address: 600 Main Street

institute: The Jackson Laboratory

data_processing:
FastQC (version 0.11.33) was used to assess the demultiplexed reads prior to alignment. Since the CAST/EiJ, Mus musculus castaneous sub-species genome is significantly diverged from the mouse reference genome (C57BL/6J, Mus musculus domesticus), reads were aligned using EMASE, Expectation-Maximization (EM) algorithm for Allele Specific Expression (ASE). This algorithm accounts for strain-specific genetic variation by aligning to transcriptomes adjusted for known genetic variation, and estimates transcript abundances by allele and by gene (PMID: 29444201). See https://github.com/TheJacksonLaboratory/cs-nf-pipelines/wiki/EMASE-Pipeline-ReadMe for code
Assembly: GRCm38
Supplementary files format and content: Processed files are  Individual sample ‘read count per transcript’ (**_pe_ec_emase-zero_m2.counts)

molecule: polyA RNA

source_name: testis

extract_protocol:
Tissues were homogenized in TRIzol Reagent (ThermoFisher) using a Pellet Pestle Motor (Kimbal) and RNA was isolated using the miRNeasy Mini kit (Qiagen), according to manufacturers’ protocols, including the optional DNase digest step. RNA concentration and quality were assessed using the Nanodrop 2000 spectrophotometer (Thermo Scientific) and the RNA 6000 Nano Assay (Agilent Technologies). All samples had RIN values above 9
Stranded libraries were constructed using the KAPA mRNA HyperPrep Kit (Roche Sequencing and Life Science), according to the manufacturer’s protocol.  Briefly, the protocol entails isolation of polyA containing mRNA using oligo-dT magnetic beads, RNA fragmentation, first and second strand cDNA synthesis, ligation of Illumina-specific adapters containing a unique barcode sequence for each library, and PCR amplification. The quality and concentration of the libraries were assessed using the D5000 ScreenTape (Agilent Technologies) and KAPA Library Quantification Kit (Roche Sequencing and Life Science), respectively, according to the manufacturers’ instructions.
Libraries were sequenced 100 bp paired-end on an Illumina HiSeq 4000 using HiSeq 3000/4000 SBS Kit reagents.

value: testis

tag: genotype

value: CAST


title: mcm23A_Input_S30_rep1

tag: strain

tag: chip antibody


title: C8-Sept-23-Plate2-PEM_S128

tag: donor

tag: plate

tag: age

tag: Sex


title: CAL120 cells, 200nM selinexor, 8hr, 2

tag: tissue

tag: cell line

tag: time


title: CAL120 cells, DMSO control, 8hr, 1

value: Vehicle


title: CAL120 cells, DMSO control, 24hr, 2


title: D12-Sept-23-Plate2-PEM_S144

tag: cellid

tag: bmi

tag: cellsize f

tag: glycinecurrent(pa/pf)

tag: glycinecurrent+strychnine(pa/pf)


title: testis_CAST_4_49219


title: D10-Sept-23-Plate2-PEM_S142

tag: cell type

tag: time from_plating_(h)

tag: glucose mm

tag: experimental record

value: male

tag: glycinecurrentwashout(pa/pf)


title: WT_Input_S30_rep1

tag: strain

tag: chip antibody

tag: genotype

tag: treatment


title: tesits_CAST_4_49218

source_name: tesits

tag: tissue

value: tesits


title: WT_Input_S30_rep2

value: MNase


title: CAL120 cells, DMSO control, 8hr, 2

tag: cell line

value: epithelial-like and fibroblast-like


title: BT549 cells, 200nM selinexor, 24hr, 2

value: epithelial cell

tag: time

value: 24hr post treatment


title: testis_CAST_5_49220


title: BT549 cells, 200nM selinexor, 24hr, 1


title: C7-Sept-23-Plate2-PEM_S127

tag: donor

tag: plate

tag: cellid

value: ND

tag: age

tag: Sex


title: BT549 cells, 200nM selinexor, 24hr, 3

tag: cell type


title: C6-Sept-23-Plate2-PEM_S126

tag: time from_plating_(h)

value: Male

tag: bmi

tag: cellsize f

tag: glycinecurrent(pa/pf)

tag: glycinecurrent+strychnine(pa/pf)


title: C3-Sept-23-Plate2-PEM_S123

tag: glucose mm

tag: experimental record

tag: glycinecurrentwashout(pa/pf)


title: ovary_CAST_5_49217

source_name: ovary

tag: tissue

value: ovary

tag: genotype


title: BT549 cells, DMSO control, 24hr, 2

tag: cell line

tag: time

tag: treatment


title: C2-Sept-23-Plate2-PEM_S122

tag: donor

tag: plate

tag: cellid


title: BT549 cells, 200nM selinexor, 8hr, 3

tag: cell type

value: 8hr post treatmnet


title: C4-Sept-23-Plate2-PEM_S124

tag: time from_plating_(h)

tag: age

tag: Sex

value: female


title: C11-Sept-23-Plate2-PEM_S131

value: islets

tag: bmi

tag: cellsize f

tag: glycinecurrent(pa/pf)


title: ovary_CAST_5_49216


title: BT549 cells, DMSO control, 24hr, 3


title: BT549 cells, DMSO control, 24hr,1


title: testis_CAST_2_49212


title: C10-Sept-23-Plate2-PEM_S130

tag: glucose mm

tag: experimental record

tag: glycinecurrent+strychnine(pa/pf)


title: testis_CAST_2_49213

tag: tissue

tag: genotype


title: testis_CAST_3_49214


title: C1-Sept-23-Plate2-PEM_S121

tag: glycinecurrentwashout(pa/pf)


title: BT549 cells, 200nM selinexor, 8hr, 2

tag: cell line

tag: time

tag: treatment

value: 200nM selinexor


title: C12-Sept-23-Plate2-PEM_S132

tag: donor

tag: plate

tag: cellid


title: testis_CAST_1_49211


title: C5-Sept-23-Plate2-PEM_S125

tag: cell type

tag: time from_plating_(h)

tag: age


title: BT549 cells, 200nM selinexor, 8hr, 1

value: breast; mammary gland


title: BT549 cells, DMSO control, 8hr, 3


title: B9-Sept-23-Plate2-PEM_S117

tag: Sex

tag: bmi

tag: cellsize f


title: testis_CAST_1_49210

value: testis


title: B8-Sept-23-Plate2-PEM_S116

tag: glucose mm

tag: experimental record

tag: glycinecurrent(pa/pf)


title: ovary_CAST_4_49209

tag: tissue

tag: genotype

value: CAST


title: BT549 cells, DMSO control, 8hr, 1

tag: cell line

value: Vehicle


title: ovary_CAST_4_49208


title: B7-Sept-23-Plate2-PEM_S115

value: male

tag: glycinecurrent+strychnine(pa/pf)

tag: glycinecurrentwashout(pa/pf)


title: testis_CAST_3_49215


title: BT549 cells, DMSO control, 8hr, 2

tag: time

tag: treatment


title: 0090_AMD-A2E_5umol_L_3d_QD-Blue light_1min

city: Biberach

first: Petr

last: Taus

address: Birkendorfer Straße 65

country: Germany

institute: Boehringer Ingelheim

data_processing:
Sequencing reads from the RNAseq experiment were processed with a pipeline built upon the ENCODE’ “Long RNA-seq” pipeline: filtered reads were mapped against the Homo sapiens (human) genome hg38/GRCh38 (primary assembly, excluding alternate contigs) using the STAR aligner (STAR version 2.5.2b) allowing for soft clipping of adapter sequences. For quantification of transcript levels, the Ensembl version 86 annotation files were used, corresponding to GENCODE 25. Annotated samples were quantified using RSEM(RSEM version 1.3.0) and featureCount(featureCount version 1.5.1). Quality controls were implemented using FastQC(FastQC version 0.11.5), picardmetrics (picardmetrics version 0.2.4), and dupRadar(dupRadar version 1.0.0) at the respective steps.
Assembly: Homo sapiens (human) genome hg38/GRCh38 (primary assembly, excluding alternate contigs)
Supplementary files format and content: csv file includes raw counts for each sample

source_name: iPSC-RPE

extract_protocol:
Total RNA was extracted using phenol chloroform-based extraction and subsequently isolated with the MagMAX-96 Total RNA Isolation Kit (Thermo Fisher Scientific, AM1830), with DNase digestion prior to final elution (Qiagen, 79254).
The library was constructed with 250ng of total RNA using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina #E7760, the NEBNext Poly(A) mRNA Magnetic Isolation Module #E7490 upstream and the NEBNext 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 SPRIselect Beads.

value: iPSC-RPE


title: ovary_CAST_3_49207


title: B5-Sept-23-Plate2-PEM_S113

tag: donor

tag: plate

tag: cellid


title: 0089_AMD-A2E_5umol_L_3d_QD-No light

tag: cell type


title: 0088_AMD-DMSO_1%_3d_QD-Blue light_1min


title: B6-Sept-23-Plate2-PEM_S114

tag: time from_plating_(h)

tag: age

tag: Sex


title: ovary_CAST_2_49205


title: 0087_AMD-DMSO_1%_3d_QD-No light


title: ovary_CAST_3_49206


title: B4-Sept-23-Plate2-PEM_S112

tag: glucose mm

tag: bmi

tag: cellsize f


title: B3-Sept-23-Plate2-PEM_S111

tag: experimental record

tag: glycinecurrent(pa/pf)


title: ovary_CAST_2_49204

tag: tissue

tag: genotype


title: 0086_AMD-None_3d-No light


title: B2-Sept-23-Plate2-PEM_S110

tag: glycinecurrent+strychnine(pa/pf)

tag: glycinecurrentwashout(pa/pf)


title: ovary_CAST_1_49203


title: 0085_AMD-A2E_5umol_L_3d_QD-Blue light_1min


title: ovary_B6Cast_5_49201


title: 0084_AMD-A2E_5umol_L_3d_QD-No light


title: B11-Sept-23-Plate2-PEM_S119


title: ovary_CAST_1_49202


title: B12-Sept-23-Plate2-PEM_S120

value: collection failed


title: ovary_B6Cast_5_49200


title: B10-Sept-23-Plate2-PEM_S118


title: 0081_AMD-None_3d-No light


title: B1-Sept-23-Plate2-PEM_S109


title: 0082_AMD-DMSO_1%_3d_QD-No light


title: A9-Sept-23-Plate2-PEM_S105


title: testis_B6Cast_5_49196


title: ovary_B6Cast_4_49199


title: 0079_AMD-A2E_5umol_L_3d_QD-No light


title: 0078_AMD-DMSO_1%_3d_QD-Blue light_1min


title: A6-Sept-23-Plate2-PEM_S102


title: 0077_AMD-DMSO_1%_3d_QD-No light


title: testis_B6Cast_4_49195


title: A8-Sept-23-Plate2-PEM_S104


title: A4-Sept-23-Plate2-PEM_S100


title: 0076_AMD-None_3d-No light


title: A5-Sept-23-Plate2-PEM_S101


title: testis_B6Cast_4_49194


title: A3-Sept-23-Plate2-PEM_S99


title: 0080_AMD-A2E_5umol_L_3d_QD-Blue light_1min


title: A2-Sept-23-Plate2-PEM_S98


title: 0075_Healthy-A2E_5umol_L_3d_QD-Blue light_1min


title: 0074_Healthy-A2E_5umol_L_3d_QD-No light


title: 0083_AMD-DMSO_1%_3d_QD-Blue light_1min


title: testis_B6Cast_2_49190


title: ovary_B6Cast_4_49198


title: testis_B6Cast_2_49191


title: testis_B6Cast_5_49197


title: A12-Sept-23-Plate2-PEM_S108


title: 0072_Healthy-DMSO_1%_3d_QD-No light


title: testis_B6Cast_1_49189


title: 0073_Healthy-DMSO_1%_3d_QD-Blue light_1min


title: A11-Sept-23-Plate2-PEM_S107


title: A7-Sept-23-Plate2-PEM_S103


title: testis_B6Cast_1_49188


title: testis_B6Cast_3_49193


title: 0071_Healthy-None_3d-No light


title: testis_B6Cast_3_49192


title: A10-Sept-23-Plate2-PEM_S106


title: ovary_B6Cast_3_49187


title: A1-Sept-23-Plate2-PEM_S97


title: 0070_Healthy-A2E_5umol_L_3d_QD-Blue light_1min


title: ovary_B6Cast_3_49186


title: ovary_B6Cast_2_49185


title: 0069_Healthy-A2E_5umol_L_3d_QD-No light


title: H8-Sept-23-Plate1-PEM_S92


title: 0068_Healthy-DMSO_1%_3d_QD-Blue light_1min


title: H6-Sept-23-Plate1-PEM_S90


title: H7-Sept-23-Plate1-PEM_S91


title: 0066_Healthy-None_3d-No light


title: ovary_B6Cast_1_49182


title: H5-Sept-23-Plate1-PEM_S89


title: ovary_B6Cast_2_49184


title: 0067_Healthy-DMSO_1%_3d_QD-No light


title: ovary_B6Cast_1_49183


title: 0065_Healthy-A2E_5umol_L_3d_QD-Blue light_1min


title: H2-Sept-23-Plate1-PEM_S86


title: 0064_Healthy-A2E_5umol_L_3d_QD-No light


title: ovary_B6_5_49180


title: 0063_Healthy-DMSO_1%_3d_QD-Blue light_1min


title: H11-Sept-23-Plate1-PEM_S95


title: ovary_B6_4_49179


title: H4-Sept-23-Plate1-PEM_S88

value: Female


title: H10-Sept-23-Plate1-PEM_S94


title: 0061_Healthy-None_3d-No light


title: 0062_Healthy-DMSO_1%_3d_QD-No light


title: H1-Sept-23-Plate1-PEM_S85


title: testis_B6_5_49177


title: ovary_B6_4_49178


title: 0060_AMD-A2E_5umol_L_3d_QD-Blue light_1min


title: G8-Sept-23-Plate1-PEM_S80


title: testis_B6_5_49176


title: G7-Sept-23-Plate1-PEM_S79


title: 0058_AMD-DMSO_1%_3d_QD-Blue light_1min


title: testis_B6_4_49174


title: G6-Sept-23-Plate1-PEM_S78


title: G5-Sept-23-Plate1-PEM_S77


title: G4-Sept-23-Plate1-PEM_S76


title: testis_B6_3_49173


title: 0056_AMD-None_3d-No light


title: testis_B6_3_49172


title: 0057_AMD-DMSO_1%_3d_QD-No light


title: testis_B6_4_49175


title: ovary_B6_5_49181


title: 0054_AMD-A2E_5umol_L_3d_QD-No light


title: testis_B6_2_49170


title: testis_B6_2_49171


title: 0055_AMD-A2E_5umol_L_3d_QD-Blue light_1min


title: 0053_AMD-DMSO_1%_3d_QD-Blue light_1min


title: G2-Sept-23-Plate1-PEM_S74


title: G10-Sept-23-Plate1-PEM_S82


title: CAP Macrophages Air 30 days bio rep5

city: Louisville

first: Eric

middle: Christian

last: Rouchka

state: Kentucky

address: 522 East Gray Street

department: Biochemistry and Molecular Genetics

institute: University of Louisville

data_processing:
Raw sequences were checked for quality values using fastQC v0.10.1.  Quality trimming was not deemed necessary.
The sequences were directly aligned to the Mus musculus reference genome assembly (mm10) using Star version 2.6.
Read counts for gene regions were obtained with HTSeq v.0.10.0 using Ensembl annotations (GRCm38.93).
Assembly: mm10/GRCm38.93
Supplementary files format and content: tab-delimited file includes raw counts for each sample

source_name: spleen macrophages

extract_protocol:
Tissue was disrupted and total RNA isolated using Qiagen Rneasy kit according to manufacturer's instructions.
NEBNext Ultra II RNA Library Prep Kit for Illumina was used for library prep

treatment_protocol: Mice were exposed to filtered air or PM2.5 for 30 days and spleens were collected.  In the second experiment, mice were exposed to filtered air following air or PM2.5 for 30 days and macrophages were isolated from spleen.

value: spleen macrophages

tag: strain

value: Wild Type C57BL/6J

tag: treatment

value: CAP exposure

tag: time

value: 30 days


title: 0052_AMD-DMSO_1%_3d_QD-No light


title: testis_B6_1_49169


title: CAP Macrophages Air 30 days bio rep4


title: 0059_AMD-A2E_5umol_L_3d_QD-No light


title: 0051_AMD-None_3d-No light


title: F9-Sept-23-Plate1-PEM_S69

tag: donor

tag: plate

tag: cellid

value: ND


title: ovary_B6_3_49167

value: ovary


title: G1-Sept-23-Plate1-PEM_S73

tag: cell type

tag: time from_plating_(h)

tag: age

value: female


title: CAP Macrophages Air 30 days bio rep1

value: Air exposure


title: 0049_AMD-A2E_5umol_L_3d_QD-No light


title: F7-Sept-23-Plate1-PEM_S67

value: islets

tag: glucose mm

tag: Sex

tag: bmi


title: CAP Macrophages Air 30 days bio rep2


title: ovary_B6_2_49165


title: F6-Sept-23-Plate1-PEM_S66

tag: experimental record

tag: cellsize f

tag: glycinecurrent(pa/pf)


title: ovary_B6_3_49166

tag: tissue

tag: genotype


title: 0048_AMD-DMSO_1%_3d_QD-Blue light_1min


title: G11-Sept-23-Plate1-PEM_S83

tag: glycinecurrent+strychnine(pa/pf)

tag: glycinecurrentwashout(pa/pf)


title: ovary_B6_2_49164


title: F5-Sept-23-Plate1-PEM_S65


title: Spleen Macrophages Air 30days bio rep5

tag: strain

tag: treatment

tag: time


title: Spleen Macrophages Air 30days bio rep4


title: 0046_AMD-None_3d-No light


title: ovary_B6_1_49163


title: testis_B6_1_49168


title: CAP Macrophages Air 30 days bio rep3


title: F4-Sept-23-Plate1-PEM_S64

tag: donor

tag: plate

tag: cellid


title: ovary_B6_1_49162


title: Spleen Macrophages Air 30days bio rep3


title: Spleen Macrophages Air 30days bio rep2


title: 0050_AMD-A2E_5umol_L_3d_QD-Blue light_1min

tag: cell type


title: 0044_Healthy-A2E_5umol_L_3d_QD-No light


title: F8-Sept-23-Plate1-PEM_S68

tag: time from_plating_(h)

tag: glucose mm

tag: age


title: Spleen Macrophages Air 30days bio rep1


title: F11-Sept-23-Plate1-PEM_S71

tag: experimental record

tag: Sex

tag: bmi


title: 0045_Healthy-A2E_5umol_L_3d_QD-Blue light_1min


title: KOLF2-HAND1KO-BSA-DAY6-R3

city: Farmington

first: Paul

last: Robson

state: CT

address: 10 Discovery Dr

institute: The Jackson Laboratory For Genomic Medicine

description: HAND1_KO_Bulk_salmon.merged.gene_tpm_length_scaled.tsv

data_processing:
Reads were aligned to the GRCh38 reference genome downloaded from NCBI (Ensembl Release 93, https://www.ncbi.nlm.nih.gov/assembly/GCF_000001405.27) by the pipeline called nf-core/rnaseq (v3.0) with default parameters. Briefly, FASTQ files were processed by FastQC for quality control and adapter sequences were trimmed  by Trim Galore, ribosomal RNA were removed by SortMeRNA. After pre-processing of raw FASTQ data, the alignment and quantification were done by STAR and Salmon separately. Gene expression matrix scaled by both library size and gene length (salmon.merged.gene_tpm_length_scaled.tsv) from Salmon were used as input for DESeq2 package to perform differential gene analysis.
Assembly: GRCh38

extract_protocol:
Wild type hiPSC cell KOLF2.C1 were seeded in 6-well plate at 50k cells per well and then differentiated in different conditions (BS, BSA, BSA-83). Differentiated cells were harvested at day 6 for total RNA extraction using NucleoSpin® RNA Plus (Takara, #740984.250) according to the instructions.  For time course bulk RNA sequencing.  WT and HAND1-/- KOLF2.C1 were seeded in 6-well plate as 50k cells per well and then cultured in StemFlex media or differentiated at different time points to ensure collection of differentiated cells at the same day.
RNA-seq libraries were prepared with KAPA Stranded Total RNA-Seq kit (Roche) according to manufacturer’s instruction. The samples were normalized to 300ngs input and spiked in with ERCC. First, ribosomal RNA was depleted using RiboErase followed by DNase treatment. Purified RNA was then fragmented at 85°C for 6 mins, targeting fragments range 250-300bp. Fragmented RNA is reverse transcribed with an incubation of 25°C for 10mins, 42°C for 15mins and an inactivation step at 70°C for 15mins. This was followed by second strand synthesis at 16°C, 60mins. Double stranded cDNA fragments were purified using Ampure XP beads (Beckman). The dscDNA were then A-tailed, and ligated with illumina unique adaptors (illumina). Adaptor-ligated DNA was purified using Ampure XP beads. This is followed by 10 cycles of PCR amplification. The final library was cleaned up using AMpure XP beads. Quantification of libraries were performed using real-time qPCR (Thermo Fisher). Sequencing was performed on Illumina NovaSeq platform generating paired end reads of 2X150bp.

tag: cell line

value: Differentiated cells

value: BSA


title: KOLF2-HAND1KO-BSA-DAY6-R2

tag: genotype


title: CAP Air 30 days bio rep4

source_name: spleen

tag: tissue

value: spleen


title: KOLF2-HAND1KO-BSA-DAY6-R1


title: 0047_AMD-DMSO_1%_3d_QD-No light


title: KOLF2-HAND1KO-BSA-DAY4-R3


title: 0041_Healthy-None_3d-No light


title: F10-Sept-23-Plate1-PEM_S70

tag: cellsize f

tag: glycinecurrent(pa/pf)

tag: glycinecurrent+strychnine(pa/pf)

tag: glycinecurrentwashout(pa/pf)


title: F1-Sept-23-Plate1-PEM_S61

tag: donor


title: E9-Sept-23-Plate1-PEM_S57

tag: plate


title: CAP Air 30 days bio rep3

tag: strain

tag: treatment

tag: time


title: KOLF2-HAND1KO-BSA-DAY4-R2

tag: cell type


title: CAP Air 30 days bio rep2


title: E8-Sept-23-Plate1-PEM_S56

tag: cellid

tag: time from_plating_(h)

tag: glucose mm

tag: age


title: CAP Air 30 days bio rep1


title: 0040_Healthy-A2E_5umol_L_3d_QD-Blue light_1min


title: KOLF2-HAND1KO-BSA-DAY4-R1

tag: cell line


title: F2-Sept-23-Plate1-PEM_S62

tag: experimental record

tag: Sex

tag: bmi


title: 0039_Healthy-A2E_5umol_L_3d_QD-No light


title: Spleen Air 30days bio rep4

tag: tissue


title: 0038_Healthy-DMSO_1%_3d_QD-Blue light_1min


title: Spleen Air 30days bio rep3


title: KOLF2-HAND1KO-BSA-DAY3-R2

tag: genotype


title: KOLF2-HAND1KO-BSA-DAY3-R3


title: E6-Sept-23-Plate1-PEM_S54

tag: cellsize f

tag: glycinecurrent(pa/pf)

tag: glycinecurrent+strychnine(pa/pf)

tag: glycinecurrentwashout(pa/pf)


title: E5-Sept-23-Plate1-PEM_S53

tag: donor

tag: plate


title: 0037_Healthy-DMSO_1%_3d_QD-No light

tag: cell type


title: 0043_Healthy-DMSO_1%_3d_QD-Blue light_1min


title: Spleen Air 30days bio rep2

tag: strain

tag: treatment

tag: time


title: 0036_Healthy-None_3d-No light


title: KOLF2-HAND1KO-BSA-DAY3-R1


title: E4-Sept-23-Plate1-PEM_S52

tag: cellid

tag: time from_plating_(h)

tag: glucose mm

tag: age


title: Spleen Air 30days bio rep1


title: 0035_Healthy-A2E_5umol_L_3d_QD-Blue light_1min


title: E3-Sept-23-Plate1-PEM_S51

tag: experimental record

tag: Sex

tag: bmi


title: KOLF2-HAND1KO-BSA-DAY2-R2

tag: cell line

tag: genotype


title: KOLF2-HAND1KO-BSA-DAY2-R3


title: 0034_Healthy-A2E_5umol_L_3d_QD-No light


title: E2-Sept-23-Plate1-PEM_S50

tag: cellsize f

tag: glycinecurrent(pa/pf)

tag: glycinecurrent+strychnine(pa/pf)


city: 广州市

first: Jiahao

state: 广东省

address: 海珠区昌岗东路250号

institute: 广州医科大学附属第二医院

data_processing:
CLC Genomics Workbench w 11.0.1
Sequence reads were trimmed for adaptor sequencelow-qualty sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrcM3/mm10 using CLC genonic benchwork (parameters-mismath cost 2 inserton cost 3 deleton cost 3 length fracton: 0.8 similarity fraction:0.8)
Read count extraction and normalization were performed using CLC genomic benchwork

source_name: LA4 cells

growth_protocol: The LA4 cell line was purchased from the, and was maintained in Ham’s F-12K medium (Invitrogen, Thermo Fisher Scientific, Waltham, Mass) supplemented with 10% fetal bovine serum (Invitrogen), and 100 units/mL penicillin plus 100 μg/mL streptomycin (Invitrogen) at 37°C with 5% CO2.

extract_protocol:
RNA was extracted using the PureLink RNA Mini Kit (Thermo Fisher Scientific)
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols

treatment_protocol: Cells were grouped as the control group (LA4 cells and lymphocytes without any time of co-culture) and the LA4 +C group (LA4 cells were co‐cultured with 10 times lymphocytes for different time).

value: LA4 cells

value: Lung epithelial cells

value: WT


title: E7-Sept-23-Plate1-PEM_S55

tag: donor

tag: plate

value: male

tag: glycinecurrentwashout(pa/pf)


title: 0033_Healthy-DMSO_1%_3d_QD-Blue light_1min

tag: cell type

value: iPSC-RPE


title: LA4 cells and lymphocytes without any time of co-culture

institute: 广州医科大学附属第二医院

tag: treatment


title: 0032_Healthy-DMSO_1%_3d_QD-No light


title: CTR2_Heart_3

first: Kangni

last: Jia

state: Shanghai

address: 227 Chongqing South Road, Huangpu District, Shanghai, China

institute: Shanghai Jiaotong University

data_processing:
The libraries were sequenced on an illumina Novaseq 6000 platform and 150 bp paired-end reads were generated. The clean reads were mapped to the mouse genome (GRCm38) using HISAT2. Differential expression analysis was performed using the DESeq (2012) R package.
Assembly: GRCm38
Supplementary files format and content: csv file includes raw Counts for each sample

source_name: left ventricle

extract_protocol:
For RNA extraction, total RNA was extracted using the Trizol extraction method.
Libraries were constructed using TruSeq Stranded mRNA LT Sample Prep Kit (Illumina, San Diego, CA, USA) according to the manufacturer’s instructions.

tag: tissue

value: left ventricle

value: Male

value: intraperitoneally administered tamoxifen (20 mg/kg/day) for five consecutive days


title: E10-Sept-23-Plate1-PEM_S58

tag: cellid

tag: time from_plating_(h)


title: KOLF2-HAND1KO-BSA-DAY2-R1

tag: time


title: CTR2_Heart_2


title: E1-Sept-23-Plate1-PEM_S49

tag: glucose mm

tag: experimental record

tag: age

value: Female


title: CTR2_Heart_1

tag: Sex


title: KOLF2-BSA-DAY6-R1

tag: cell line

tag: genotype


title: 0030_AMD-A2E_5umol_L_3d_QD-Blue light_1min


title: D9-Sept-23-Plate1-PEM_S45

value: ND

tag: bmi

tag: cellsize f

tag: glycinecurrent(pa/pf)


title: iCKO_Heart_3

value: Ddx5flox/flox Myh6MerCreMer


title: D8-Sept-23-Plate1-PEM_S44

tag: donor

tag: plate

tag: glycinecurrent+strychnine(pa/pf)


title: iCKO_Heart_2

tag: treatment


title: KOLF2-BSA-DAY4-R2

tag: cell type


title: 0028_AMD-DMSO_1%_3d_QD-Blue light_1min


title: KOLF2-BSA-DAY6-R3


title: 0027_AMD-DMSO_1%_3d_QD-No light


title: KOLF2-BSA-DAY6-R2


title: iCKO_Heart_1

tag: tissue


title: E11-Sept-23-Plate1-PEM_S59

tag: cellid

tag: time from_plating_(h)

value: female

tag: glycinecurrentwashout(pa/pf)


title: D6-Sept-23-Plate1-PEM_S42

tag: glucose mm

tag: experimental record


title: CTR1_Heart_8w_3

tag: Sex


title: CTR1_Heart_8w_2


title: 0031_Healthy-None_3d-No light


title: KOLF2-BSA-DAY3-R3

tag: cell line

tag: time


title: 0025_AMD-A2E_5umol_L_3d_QD-Blue light_1min


title: 0026_AMD-None_3d-No light


title: D4-Sept-23-Plate1-PEM_S40

tag: age

tag: bmi


title: 0024_AMD-A2E_5umol_L_3d_QD-No light


title: KOLF2-BSA-DAY3-R2

tag: genotype


title: 0029_AMD-A2E_5umol_L_3d_QD-No light


title: CTR1_Heart_8w_1


title: D3-Sept-23-Plate1-PEM_S39

tag: donor

tag: cellsize f

tag: glycinecurrent(pa/pf)


title: KOLF2-BSA-DAY3-R1

tag: treatment


title: KOLF2-BSA-DAY4-R3

tag: cell type


title: mCKO_Heart_8w_3

tag: tissue

value: DDX5fl/fl MYH6Cre+


title: KOLF2-BSA-DAY2-R3


title: 0023_AMD-DMSO_1%_3d_QD-Blue light_1min


title: KOLF2-BSA-DAY4-R1


title: KOLF2-BSA-DAY2-R2


title: D12-Sept-23-Plate1-PEM_S48

tag: plate

tag: cellid

value: islets

tag: glycinecurrent+strychnine(pa/pf)


title: D2-Sept-23-Plate1-PEM_S38

tag: time from_plating_(h)

tag: glucose mm

tag: glycinecurrentwashout(pa/pf)


title: D5-Sept-23-Plate1-PEM_S41

tag: experimental record

tag: Sex


title: mCKO_Heart_8w_1


title: 0022_AMD-DMSO_1%_3d_QD-No light


title: KOLF2-BSA-DAY2-R1

tag: cell line

value: Differentiated cells

tag: time


title: 0021_AMD-None_3d-No light


title: LPS_BMDCs, Pde5 knockout, replicate 2

city: Hangzhou

first: Ting

last: Zhou

state: Zhejiang

address: No. 600 Dunyu Road, Xihu District

department: Immunology and Microbiology

institute: Westlake University

data_processing:
Illumina Casava2.19 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using fastp v0.12.4.
The clean sequenced reads were mapped to mm10 whole genome using hisat2 v2.2.1.
HISAT2 alignments were used to generate genomic features using featureCounts v2.0.1.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include readcount values for each sample

source_name: Bone marrow

extract_protocol:
Retinas were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Bone marrow

tag: tumor stage

value: 9 days

value: immune cells

tag: genotype

value: Pde5 knockout


title: BS-DAY6-R3

value: WT

value: BS


title: 0020_AMD-A2E_5umol_L_3d_QD-Blue light_1min

value: iPSC-RPE


title: D10-Sept-23-Plate1-PEM_S46

tag: donor

tag: age

tag: bmi

tag: cellsize f


title: D1-Sept-23-Plate1-PEM_S37

tag: cell type

tag: glycinecurrent(pa/pf)


title: BS-DAY6-R2

tag: treatment


title: LPS_BMDCs, control, replicate 2

tag: tissue


title: LPS_BMDCs, Pde5 knockout, replicate 1


title: 0019_AMD-A2E_5umol_L_3d_QD-No light


title: mCKO_Heart_8w_2

value: left ventricle


title: 0018_AMD-DMSO_1%_3d_QD-Blue light_1min


title: BS-DAY6-R1


title: BMDCs, Pde5 knockout, replicate 2

value: Pde5  knockout


title: 0017_AMD-DMSO_1%_3d_QD-No light


title: D11-Sept-23-Plate1-PEM_S47

tag: plate

tag: cellid

tag: time from_plating_(h)

tag: glycinecurrent+strychnine(pa/pf)


title: 0016_AMD-None_3d-No light


title: BSA-DAY6-R3

value: BSA


title: BMDCs, Pde5 knockout, replicate 1


title: 0015_Healthy-A2E_5umol_L_3d_QD-Blue light_1min


title: C7-Sept-23-Plate1-PEM_S31

tag: glucose mm

tag: experimental record

tag: Sex

value: male

tag: glycinecurrentwashout(pa/pf)


title: BMDCs, control, replicate 2

tag: tumor stage

tag: time

tag: genotype


title: BSA-DAY6-R2

tag: cell line


title: C6-Sept-23-Plate1-PEM_S30

tag: donor

value: ND

tag: age

tag: bmi

tag: cellsize f


title: C5-Sept-23-Plate1-PEM_S29

tag: cell type

tag: glycinecurrent(pa/pf)


title: BSA-DAY6-R1

tag: treatment


title: BSA-83-DAY6-R3


title: 0014_Healthy-A2E_5umol_L_3d_QD-No light


title: BMDCs, control, replicate 1

tag: tissue


title: C4-Sept-23-Plate1-PEM_S28

tag: plate

tag: cellid

tag: time from_plating_(h)

value: Female

tag: glycinecurrent+strychnine(pa/pf)


title: BSA-83-DAY6-R2


title: C8-Sept-23-Plate1-PEM_S32

tag: glucose mm

tag: experimental record

tag: Sex

tag: glycinecurrentwashout(pa/pf)


title: Tumoral DCs, late_stage, replicate 1

source_name: Tumor

value: Tumor

tag: tumor stage

value: late

tag: time

value: 14 days

tag: genotype


title: C9-Sept-23-Plate1-PEM_S33

tag: donor

value: islets

tag: age

value: female

tag: bmi


title: LPS_BMDCs, control, replicate 1

value: Bone marrow

value: 9 days

tag: cell type


title: 0013_Healthy-DMSO_1%_3d_QD-Blue light_1min


title: BSA-83-DAY6-R1

tag: cell line

value: Differentiated cells

tag: treatment


title: Tumoral DCs, late_stage, replicate 2

tag: tissue

value: immune cells

value: WT


title: C3-Sept-23-Plate1-PEM_S27

tag: plate

tag: cellid

tag: cellsize f

tag: glycinecurrent(pa/pf)


title: C2-Sept-23-Plate1-PEM_S26

tag: time from_plating_(h)

tag: glucose mm

tag: experimental record

tag: glycinecurrent+strychnine(pa/pf)


title: 0012_Healthy-DMSO_1%_3d_QD-No light

value: iPSC-RPE


title: C11-Sept-23-Plate1-PEM_S35

tag: Sex

tag: glycinecurrentwashout(pa/pf)


title: 0010_Healthy-A2E_5umol_L_3d_QD-Blue light_1min


title: NRCM_DDX5_RIP2

data_processing:
The libraries were sequenced on an HiSeq X Ten platform.
The clean reads were mapped to the Rattus norvegicus genome (rn6) using Tophat(v2.0.13) .
Assembly: rn6
Supplementary files format and content: bw file for each RIP-seq sample

organism: Rattus norvegicus

source_name: primary neonatal rat cardiomyocytes

extract_protocol:
The RNA immunoprecipitation assay was performed using the Magna RIP Kit (No.17-701, Millipore, MA, USA) following manufacturer’s instructions.
Using Qubit and Agilent2200 to detect antibody-specific enriched RNA fragments.Libraries were constructed using TruSeq Stranded mRNA LT Sample Prep Kit (Illumina, San Diego, CA, USA) according to the manufacturer’s instructions.

value: Male

value: primary neonatal rat cardiomyocytes

value: cardiomyocytes

tag: genotype


title: NRCM_input2


title: NRCM_input3


title: cell hashing data of immune cell samples from WT & IL33 KO BM12 heart grafts

city: Pittsburgh

first: Khodor

middle: I

last: Abou-Daya

state: PA

address: 200 Lothrop Street

department: Surgery

institute: Starzl Transplantation Institute

description: Hashtag-derived Oligonucleotide (HTO)

data_processing:
CellRanger count to get cell ranger output of barcode, feature, and matrix files.
Files were imported into Partek flow version 10.0.23.0425, the dataset was then filtered to remove potential doublets and low-quality and dead cells using the following criteria: only cells with gene expression counts between 1,500 and 15,000, detected expressed genes between 400 and 4,000, and mitochondrial counts less than 20% were included in downstream analyses. The expression matrix was then normalized to the binary logarithm of counts per million (CPM) plus one, log2(CPM+1).
Assembly: mm10
Supplementary files format and content: single cell gene expression count matrix of quality controlled and normalized data, Bm12WT&IL33KO_heartTx_mRNA.txt
Supplementary files format and content: HTO single cell annotation and immune cell type classification, Bm12WT&IL33KO_heartTx_HTO.txt

source_name: heart graft

extract_protocol:
Mice were euthanized and immediately perfused with PBS containing 0.5% heparin via the left ventricle. Heart tissue was minced by scissors and then placed in 10ml RPMI digestion buffer (10% FBS, 12.5mg collagenase IV (Thermo Fisher; 17104019) and DNAse I (Sigma Aldrich; DN25-1G)) and further homogenized using Miltenyi GentleMacs C tubes and Miltenyi tissue dissociator. The tissue homogenate was incubated in a shaker at 250 rpm and 37°C for 45 minutes. After digestion, homogenate was passed through a 70 μm strainers, centrifuged, and immune cells were then separated by a density gradient using Lympholyte-M (Cedarlane; CL5031) according to the manufacturer’s protocol. Interphase cells were isolated, washed with RPMI, and then further purified using Miltenyi Biotec Debris removal solution (130-109-398) per manufacturer’s instructions.
The hashing protocol described by Stoekius et al in 2017 was used to generate a hastagoligo (HTO) library and a 3' gene expression library
cell hashing and 3' gene expression

value: heart graft

value: BM12 WT and IL33 KO

value: transplant to B6 mouse


title: Tumoral DCs, early_stage, replicate 2

value: Tumor

tag: tumor stage

value: early

tag: time

value: 7 days


title: C12-Sept-23-Plate1-PEM_S36

tag: donor

tag: cell type

value: islets

value: ND

tag: age

tag: bmi


title: NRCM_DDX5_RIP3

tag: cell line

tag: treatment


title: 0009_Healthy-A2E_5umol_L_3d_QD-No light


title: C10-Sept-23-Plate1-PEM_S34

tag: plate

tag: cellid

value: female

tag: cellsize f


title: 0007_Healthy-DMSO_1%_3d_QD-No light


title: 0042_Healthy-DMSO_1%_3d_QD-No light


title: Tumoral DCs, early_stage, replicate 1

tag: tissue


title: 0008_Healthy-DMSO_1%_3d_QD-Blue light_1min


title: Heart,  Hypoxia_TAC_6

city: Braunschweig

first: Robert

last: Geffers

address: Inhoffenstr. 7

department: Dep. Molecular Bacteriology

institute: HCI - Helmholtz Centre for Infection Research

data_processing:
RTA 3.4.4, bcl2fastq 2.20.0.422 (Illumina)
Trimmed reads (adapter trimming tool: ngs-bits: SeqPurge, v2021_09 ) were aligned to the murine reference genome version GRCm39 using the open source short-read aligner STAR (v2.7.3a).
Feature counts were determined using the “featureCounts” tool of “subread” (v2.0.0).
Transcript annotation was performed using the “rc_annotate” pipeline of “megSAP” (v0.2-777-g581100f2).
Assembly: GRCm39
Supplementary files format and content: Tab-delimited text files include raw counts for each sample.

source_name: Heart

extract_protocol:
NucleoSpin RNA kit (Macherey-Nagel, Düren, Germany)
The RNA sequencing library was generated from 100 ng of total RNA using the NEBNext® Single Cell/Low Input RNA Library Prep Kit (New England BioLabs, Frankfurt, Germany).

treatment_protocol: C57/Bl6J mice were subjected to transverse aortic constriction (TAC) using suture around a blunt 25-G needle placed between the innominate artery and the left common carotid artery. Mice were sacrificed on the third day. The apex of the heart was used for RNA extraction.

value: Heart

value: Hypoxia

value: TAC surgery


title: NRCM_DDX5_RIP1

value: WT


title: NRCM_input1


title: single cell gene expression of immune cells from WT & IL33 KO BM12 heart grafts

description: PolyA RNA

value: immune cells


title: 0006_Healthy-None_3d-No light

value: iPSC-RPE


title: 0011_Healthy-None_3d-No light


title: C1-Sept-23-Plate1-PEM_S25

tag: time from_plating_(h)

tag: glucose mm

tag: experimental record

value: Female

tag: glycinecurrent(pa/pf)


title: 0005_Healthy-A2E_5umol_L_3d_QD-Blue light_1min


title: NRCM_input

value: primary neonatal rat cardiomyocytes

value: cardiomyocytes

tag: Sex

value: Male

tag: genotype


title: B8-Sept-23-Plate1-PEM_S20

value: male

tag: glycinecurrent+strychnine(pa/pf)

tag: glycinecurrentwashout(pa/pf)


title: Heart,  Hypoxia_TAC_5


title: B9-Sept-23-Plate1-PEM_S21

tag: donor

tag: cell type


title: Heart,  Hypoxia_TAC_4


title: 0003_Healthy-DMSO_1%_3d_QD-Blue light_1min


title: Heart,  Hypoxia_TAC_3


title: 0004_Healthy-A2E_5umol_L_3d_QD-No light


title: mcm23Aisw1D_H3K56ac_eSPAN_rep2

source_name: whole cell

value: whole cell

tag: strain

tag: chip antibody

value: anti-H3K56ac (Zhang Lab)

value: mcm2-3A mutant and Isw1 KO

value: MNase


title: B6-Sept-23-Plate1-PEM_S18

value: islets

value: ND

tag: age

tag: bmi


title: Heart,  Hypoxia_TAC_2

value: Heart

tag: cell line

tag: treatment


title: B7-Sept-23-Plate1-PEM_S19

tag: plate

tag: cellid

tag: cellsize f


title: NRCM_DDX5_RIP


title: 0002_Healthy-DMSO_1%_3d_QD-No light


title: Heart,  Hypoxia_TAC_1

tag: tissue

value: Hypoxia


title: mcm23Achd1D_H3K56ac_eSPAN_rep2

value: mcm2-3A mutant and Chd1 KO


title: B4-Sept-23-Plate1-PEM_S16

tag: time from_plating_(h)

tag: glucose mm

tag: experimental record

tag: glycinecurrent(pa/pf)


title: Heart,  Hypoxia_Sham_6

tag: genotype

value: WT

value: Sham surgery


title: B5-Sept-23-Plate1-PEM_S17

tag: donor

tag: Sex

tag: glycinecurrent+strychnine(pa/pf)

tag: glycinecurrentwashout(pa/pf)


title: isw1D_H3K56ac_eSPAN_rep2

tag: strain

tag: chip antibody

value: Isw1 KO


title: chd1D_H3K56ac_eSPAN_rep2

value: Chd1 KO


title: 8_2_FTS_3_S44, SH-SY5Y cells, 8:2 FTS

city: Buffalo

first: Charikleia

last: Karageorgiou

address: 109 Cooke Hall, Mary Talbert Way

department: Department of Biological Sciences

institute: University at Buffalo

data_processing:
Mutltiple tools (FastQC, MultiQC, hisat2, samtools, featureCounts, DESeq2)
Sequence reads were assessed with FastQC and MultiQC
RNA-seq reads were mapped to the human transcriptome reference (hg38) from Ensemble using hisat2
RNA-seq reads were quantified using featureCounts
The differential expression analysis was carried out using DESeq2
Please note that two of the sequenced 21 samples (6 treatments and 1 control, with three replicates for each) did not pass the FastQC and MultiQC, and have been eliminated from the downstream analysis. Thus, the normalised_expression.txt contains total 19 data columns.
Assembly: hg38
Supplementary files format and content: raw counts, Deseq2 normalized values for each Sample

growth_protocol: SH-SY5Y cells were cultured based on their guidelines. Cells were grown in 10 cm plates and allowed to reach a confluency of 85% after approximately 5-6 days. After reaching 85% confluency cells were sub-cultured to new 10 cm plates at a 1:10 ratio. PBS was used to rinse cells before sub culturing and trypsin was used to uplift cells from plate. Cellular media was replaced every 3-4 days as needed

extract_protocol:
RNA was extracted using TriZol using Invitrogen protocols
RNA libraries for RNA-seq were prepared using the Illumina RiboZero Total Stranded RNA library prep kit following manufacturer's protocols.

treatment_protocol: After the 11-day differentiation SH-SY5Y cells in 10 cm plates were exposed to 30 µM PFAS. PFAS treatments included PFOA, PFOS, PFDA, PFDS, 8:2 FTOH, and 8:2 FTS. Final treatment solutions included 1% MeOH. Treatments lasted 24 hours and were done in triplicate.

tag: cell line

tag: cell type

value: neuroblastoma cells differentiated to neuronal-like cells

value: 8:2 FTS


title: B3-Sept-23-Plate1-PEM_S15

tag: plate

tag: age

value: female

tag: bmi


title: Heart,  Hypoxia_Sham_5

tag: tissue

tag: treatment


title: 8_2_FTS_2_S43, SH-SY5Y cells, 8:2 FTS


title: B2-Sept-23-Plate1-PEM_S14

tag: cellid

tag: time from_plating_(h)

tag: glucose mm

value: male

tag: cellsize f


title: mcm23A_H3K56ac_eSPAN_rep2

data_processing:
To improve mapping quality, raw sequencing reads were first processed with Trim Galore (v0.6.7) to remove low-quality reads and Illumina Prep Kit adaptors. The quality cutoff was set to 20, and the minimum required read length after trimming was 20 nt. Paired-end sequencing reads were mapped to yeast genome (sacCer3) using bowtie2 (V 2.2.4) with the following parameters: with --no-mixed --no-discordant --no-dovetail --no-contain --local --maxins 1000.
Sequence alignment map files, including uniquely mapped, PCR-duplicated, and multi-mapped reads, were transformed into BAM files using SAMtools (V 1.11).To obtain the accurate mapping reads, duplicate and multi-mapping reads were discarded and only paired-end reads with both ends aligning uniquely to the reference genome were used for further analysis.
Accurate early-firing region detection was achieved by using filtered paired-end reads of BrdU-IP-ssSeq signals to call broad peaks with MACS2 (V 2.2.5) for each replicate independently, applying a q-value cutoff of 0.001 and using the corresponding MNase-ssSeq Input samples as controls.
To calculate BrdU-IP-ssSeq and eSPAN strand bias, the filtered paired-end reads aligned to the Watson (W) and Crick (C) strands of the reference genome were partitioned using the bamtobed function of BEDTools (V 2.29.2) and custom Perl scripts. BrdU-IP-ssSeq and eSPAN bias was determined in 10bp bin from the segregated Watson and Crick reads using the formula Bias= (W-C)/(W + C) across the replicated regions. Bins with fewer than 10 sequencing reads were excluded. The eSPAN bias was furthermore normalized using the corresponding BrdU-IP-ssSeq strand bias.
Assembly: S. cerevisiae (UCSC sacCer3)
Supplementary files format and content: bigwig files were generated for plus strand, minus strand and both strands, scores represent the normalization reads density.

extract_protocol:
All ChIP and eSPAN assays were performed as described previously (Yu et al., 2014). To carry out ChIP for H3K4me3 and H3K56ac, chromatin was pelleted and washed twice with NP buffer (1.6 M sorbitol, 5 mM MgCl2, 50 mM NaCl, 2 mM CaCl2, 14 mM β-mercaptoethanol, 0.075% NP-40, 10 mM Tris-HCl (pH 7.4), 5 mM spermidine). The chromatin was then resuspended in the same buffer and digested with 4U MNase (9013-53-0, Worthington Biochemical) for 20 minutes at 37°C, resulting in primarily mono- and di-nucleosome fragments. The digestion was terminated by adding 5 μl of 0.5 M EDTA and 1/5 volume of 5x ChIP lysis buffer, followed by incubation on ice for at least 30 minutes. Following MNase digestion, the chromatin was cleared by centrifugation and then immunoprecipitated using specific antibodies (anti-H3K4me3 (ab8580, Abcam) and homemade anti-H3K56ac along with protein G Sepharose beads (17-0618-02, GE Healthcare). The beads were extensively washed, and DNA from both Input and ChIP samples was extracted via the Chelex-100 protocol and utilized for BrdU IP/eSPAN or purified using the MinElute PCR Purification Kit (28004, Qiagen) for ChIP. BrdU immunoprecipitation was performed using either input DNA for BrdU-IP-ssSeq, and H3K4me3 or H3K56ac ChIP DNAs for eSPAN. Briefly, input or ChIP DNA obtained from the Chelex-100 extraction was incubated at 100°C for 10 minutes and then immediately cooled on ice for 10 minutes. BrdU immunoprecipitation was conducted by diluting the DNA ten-fold with BrdU IP buffer (PBS, 0.0625% Triton X-100 (v/v), 6.7 μg/ml Escherichia coli tRNA, 0.17 μg/ml BrdU antibody (555627, BD Bioscience)) and rotating for 2 hours at 4°C. Protein G Sepharose beads were added and incubated for another hour at 4°C. After extensive washing, the DNA was extracted with 100 μl of 1x TE buffer containing 1% SDS at 65°C for 15 minutes and then eluted again with 50 μl of 1x TE buffer containing 1% SDS. The collected supernatants were subsequently purified using the MinElute PCR Purification Kit (Qiagen, 28004). Quantitative PCR was performed to analyze Input, BrdU-IP, ChIP, or eSPAN DNA using primers for the early replication origin ARS607 and the distant site ARS607+14kb.
Single-stranded DNA sequencing libraries were prepared using the Accel-NGS 1S Plus DNA Library Kit (10096, Swift Biosciences).

value: whole cell

tag: genotype

value: mcm2-3A mutant


title: WT_H3K56ac_eSPAN_rep2

value: anti-H3K56ac (Zhang Lab)


title: Heart,  Hypoxia_Sham_4


title: 8_2_FTS_1_S42, SH-SY5Y cells, 8:2 FTS


title: B12-Sept-23-Plate1-PEM_S24

tag: donor

tag: experimental record

tag: Sex

tag: glycinecurrent(pa/pf)


title: Heart,  Hypoxia_Sham_3


title: mcm23Aisw1D_H3K56ac_ChIP_rep2

tag: strain

tag: chip antibody

value: mcm2-3A mutant and Isw1 KO

value: MNase


title: 8_2_FTOH_3_S47, SH-SY5Y cells, 8:2 FTOH

tag: cell line

tag: cell type

value: 8:2 FTOH


title: 0001_Healthy-None_3d-No light

value: iPSC-RPE


title: Heart,  Hypoxia_Sham_2

value: Heart

value: Hypoxia


title: B1-Sept-23-Plate1-PEM_S13

tag: plate

value: islets

tag: age

value: Female

tag: glycinecurrent+strychnine(pa/pf)

tag: glycinecurrentwashout(pa/pf)


title: B10-Sept-23-Plate1-PEM_S22

tag: cellid

value: ND

tag: bmi


title: 8_2_FTOH_2_S46, SH-SY5Y cells, 8:2 FTOH

value: WT

tag: treatment


title: Heart,  Hypoxia_Sham_1

tag: tissue

value: Sham surgery


title: mcm23Achd1D_H3K56ac_ChIP_rep2

tag: genotype

value: mcm2-3A mutant and Chd1 KO


title: A9-Sept-23-Plate1-PEM_S9

tag: donor

tag: time from_plating_(h)

tag: glucose mm

value: female

tag: cellsize f


title: Heart,  Normoxia_TAC_6

value: Normoxia

value: TAC surgery


title: PFOS_3_S32, SH-SY5Y cells, PFOS

value: neuroblastoma cells differentiated to neuronal-like cells

value: PFOS


title: A8-Sept-23-Plate1-PEM_S8

tag: experimental record

tag: Sex

value: male

tag: glycinecurrent(pa/pf)


title: chd1D_H3K56ac_ChIP_rep2

value: whole cell

tag: strain

tag: chip antibody

value: anti-H3K56ac (Zhang Lab)

value: Chd1 KO

value: MNase


title: Heart,  Normoxia_TAC_5

value: Heart

tag: cell line


title: PFOS_2_S31, SH-SY5Y cells, PFOS

tag: cell type


title: Heart,  Normoxia_TAC_4


title: mcm23A_H3K56ac_ChIP_rep2

value: mcm2-3A mutant


title: A7-Sept-23-Plate1-PEM_S7

tag: plate

value: islets

tag: age

tag: glycinecurrent+strychnine(pa/pf)

tag: glycinecurrentwashout(pa/pf)


title: PFOS_1_S30, SH-SY5Y cells, PFOS

tag: treatment


title: D7-Sept-23-Plate1-PEM_S43

tag: cellid

value: ND

tag: bmi


title: A6-Sept-23-Plate1-PEM_S6

tag: donor

tag: time from_plating_(h)


title: WT_H3K56ac_ChIP_rep2

tag: tissue

tag: genotype

value: WT


title: isw1D_H3K56ac_ChIP_rep2

value: Isw1 KO


title: PFOA_3_S35, SH-SY5Y cells, PFOA

value: PFOA


title: 8_2_FTOH_1_S45, SH-SY5Y cells, 8:2 FTOH

value: 8:2 FTOH


title: PFOA_2_S34, SH-SY5Y cells, PFOA


title: mcm23Achd1D_H3K56ac_eSPAN_rep1

value: mcm2-3A mutant and Chd1 KO


title: A4-Sept-23-Plate1-PEM_S4

tag: glucose mm

tag: experimental record

tag: Sex

value: Female

tag: cellsize f


title: isw1D_H3K56ac_eSPAN_rep1

tag: strain

tag: chip antibody


title: A3-Sept-23-Plate1-PEM_S3

tag: plate

tag: cell type

value: female

tag: glycinecurrent(pa/pf)


title: PFOA_1_S33, SH-SY5Y cells, PFOA

tag: cell line

value: neuroblastoma cells differentiated to neuronal-like cells


title: Heart,  Normoxia_TAC_1

value: Normoxia

tag: treatment

value: TAC surgery


title: PFDS_3_S41, SH-SY5Y cells, PFDS

value: PFDS


title: Heart,  Normoxia_Sham_6

value: Sham surgery


title: Heart,  Normoxia_TAC_3


title: Heart,  Normoxia_Sham_5


title: A5-Sept-23-Plate1-PEM_S5

tag: cellid

tag: age

value: male

tag: glycinecurrent+strychnine(pa/pf)

tag: glycinecurrentwashout(pa/pf)


title: WT_H3K56ac_eSPAN_rep1

tag: tissue

value: whole cell

value: anti-H3K56ac (Zhang Lab)

value: MNase


title: mcm23Aisw1D_H3K56ac_eSPAN_rep1

tag: genotype

value: mcm2-3A mutant and Isw1 KO


title: A12-Sept-23-Plate1-PEM_S12

tag: donor

value: islets

tag: time from_plating_(h)

tag: glucose mm

value: ND

tag: bmi


title: PFDS_2_S40, SH-SY5Y cells, PFDS

value: WT


title: Heart,  Normoxia_TAC_2

value: Heart


title: Heart,  Normoxia_Sham_3


title: A11-Sept-23-Plate1-PEM_S11

tag: experimental record

tag: Sex

tag: cellsize f


title: mcm23A_H3K56ac_eSPAN_rep1

tag: strain

tag: chip antibody

value: mcm2-3A mutant


title: mcm23Aisw1D_H3K56ac_ChIP_rep1


title: PFDS_1_S39, SH-SY5Y cells, PFDS

tag: cell line

tag: cell type


title: Heart,  Normoxia_Sham_4

tag: treatment


title: A10-Sept-23-Plate1-PEM_S10

tag: plate

tag: cellid

tag: age

tag: glycinecurrent(pa/pf)


title: PFDA_2_S37, SH-SY5Y cells, PFDA

tag: genotype

value: PFDA


title: Heart,  Normoxia_Sham_2

tag: tissue


title: A2-Sept-23-Plate1-PEM_S2

tag: donor

tag: time from_plating_(h)

tag: glycinecurrent+strychnine(pa/pf)

tag: glycinecurrentwashout(pa/pf)


title: chd1D_H3K56ac_ChIP_rep1

value: Chd1 KO


title: PFDA_3_S38, SH-SY5Y cells, PFDA

value: neuroblastoma cells differentiated to neuronal-like cells


title: Heart,  Normoxia_Sham_1

value: Normoxia


title: A1-Sept-23-Plate1-PEM_S1

tag: glucose mm

tag: experimental record

tag: Sex

value: female

tag: bmi


title: PFDA_1_S36, SH-SY5Y cells, PFDA

tag: cell line


title: mcm23Achd1D_H3K56ac_ChIP_rep1

tag: strain

tag: chip antibody

value: mcm2-3A mutant and Chd1 KO


title: H7-April-2023-Plate4-PEM_S349

tag: plate

tag: cell type

tag: cellsize f


title: Control_3_S29, SH-SY5Y cells, Control

tag: treatment

value: Control


title: Control_2_S28, SH-SY5Y cells, Control

tag: genotype


title: ST_PRV_UL13null_rep3

first: Samie

last: Jaffrey

state: New York

address: 1300 York Ave

institute: Weill Cornell Medicine

data_processing:
*library strategy: CROWN-seq
To obtain reads for individual libraries from the pooled sequencing results, we performed two steps processing by Cutadap3. First, we removed the low-quality reads by parameters: cutadapt -a ANNNNNNNNNNNNAGATCGGAAGAGCACACGTC -A NNTAAGATCGGAAGAGCGTCGTG --max-n 0 -m 32 -q 20 -e 0.25. Second, we extract different libraries by pattern recognition: cutadapt -g [sample #1]=GCGA -g [sample #2]=GTGC -g [sample #3]=ATCA -g [sample #4]=GGAC. The extracted reads were stored in different FASTQ files for further analysis.
To analyze individual libraries, we first remove the AT adapter sequences at the beginning of read1. Then the UMI sequences in both read1 and read2 were extracted by UMI-tools4 (umitools extract --bc-pattern2 NNNNNNNNN -p NN).
To map the reads to reference genome, we first in silico A-to-G and T-to-C converted reference genome of pig (Ensembl Sscrofa11.1 r110) and PRV (GCA_000843825.1). We then built HISAT2 indexes on these converted reference genome. The reads were mapped to the converted reference genome by the CROWN-seq alignment pipeline (https://github.com/jhfoxliu/CROWN-Seq). Notably, only unique alignments were used in analyses.
After alignment, we removed PCR duplications by UMI-tools. We then calculated the coverages of the 5’ end mapped to reference genome, which represents the positions of transcription-start nucleotides.
For A-started transcripts, m6Am level was calculated as the number of A (m6Am) reads versus the sum of A reads and G (Am) reads. To annotate snRNA genes, we used snRNA annotations in Ensembl Sscrofa11.1 r110.
Assembly: Ensembl Sscrofa11.1 r110; GCA_000843825.1
Supplementary files format and content: CSV, base counts for transcription-start nucleotides
Supplementary files format and content: TXT, base counts for transcription-start nucleotides

organism:
Sus scrofa
Suid alphaherpesvirus 1

source_name: ST

growth_protocol: Swine testicle (ST) cells were cultured in MEM (Gibco) supplemented with 10 % fetal calf serum (FCS), 1 mM sodium pyruvate, 105 U/l penicillin, 100 mg/l streptomycin and 50 mg/l gentamycin. HEK293T cells were cultured in DMEM (Gibco) supplemented with 10 % FCS, 105 U/l penicillin, 100 mg/l streptomycin and 50 mg/l gentamycin. Both cell lines were obtained from the American Type Culture Collection (ATCC) and were tested to be free of mycoplasma contamination via de LookOut Mycoplasma PCR detection kit (Sigma-Aldrich). Wild-type NIA3 PRV strain and an isogenic UL13null mutant (M137) were previously described and were kindly donated by the ID-DLO (The Netherlands) (De Wind et al., 1992; de Wind et al., 1990).

extract_protocol:
RNA isolations were performed using the RNeasy minikit (Qiagen) according to the manufacturer’s procedure. Purified RNA was treated with RNase-free DNase I (New England Biolabs) at 37°C for 10 min to remove contaminating DNA. To stop DNase I activity, EDTA (Invitrogen) was added at a final concentration of 5 mM and samples were incubated at 75°C for 10 min.
CROWN-seq is performed as previously described with some modifications. ~30 μg total RNA input was used for the CROWN-seq libraries. The RNA input was converted by sodium nitrite as described in the GLORI protocol1. After conversion, the m7G capped 5’ end RNA fragments were isolated based on a modified ReCappable-seq workflow2. In brief, the converted m7G capped RNAs were firstly recapped by 3´-Desthiobiotin-GTP. Then the recapped RNA fragments were enriched on streptavidin beads. Different from the original ReCappable-seq protocol, we performed on-beads 3’ adapter ligation, where a barcoded 3’ DNA adapter (/rApp/ANNNNNNNNXXXXAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAAAAAAAAAAAAAAACCCCCCCCCCAAAAAAAAAAAAAAA/3AmMO/, X=barcode) was ligated to the enriched RNA fragments. We used four different barcodes to label different samples. After adapter ligation, 2-4 samples in different barcodes were pooled. This pooling strategy can increase the yield of library. The pooled RNA fragments were then treated by 5´ Deadenylase (NEB #M0331S) and RecJf (NEB #M0264S), which can remove the exceeded 3’ adapter. After a second round streptavidin enrichment, the RNA fragments were eluted into water. To ligate 5’ adapter, we used RppH (NEB #M0356S) to release the 3´-Desthiobiotin caps, which results in monophosphate 5’ ends readily for ligation. We then ligated a 5’ adapter (rCrCrUrArCrArCrGrArCrGrCrUrCrUrUrCrCrGrArUrCrUrArUrNrN) which contain unique molecular identifier (UMI) to the RNA fragments. After adapter ligation, reverse transcription primer (GACGTGTGCTCTTCCGATCT) was annealed to the 3’ adapter (75°C 5 min, 37 °C 15 min, then 25 °C 15 min). Reverse transcription was performed with SuperScript III (Thermo Fisher #18080093). After reverse transcription, cDNA was amplified with Phusion PCR master mix (NEB #M0531S) and NEBNext multiplex oligos (NEB #E7780S). Amplified libraries were size selected by SPRIselect beads (Beckman #B23317). Size selected libraries were then sequenced by NovaSeqX in PE100 mode.

treatment_protocol: Confluent cells were infected at an MOI of 10 and lysed at 16 hpi unless otherwise mentioned.

value: ST

value: PRV UL13 null


title: mcm23A_H3K56ac_ChIP_rep1

tag: tissue

value: whole cell

value: anti-H3K56ac (Zhang Lab)


title: H5-April-2023-Plate4-PEM_S347

source_name: islets

tag: donor

tag: cellid

tag: age

tag: glycinecurrent(pa/pf)


title: ST_PRV_UL13null_rep1


title: ST_PRV_UL13null_rep2


title: chd1D_H3K56ac_eSPAN_rep1

value: MNase


title: WT_H3K56ac_ChIP_rep1


title: H4-April-2023-Plate4-PEM_S346

value: islets

tag: time from_plating_(h)

tag: glucose mm

value: male

tag: glycinecurrent+strychnine(pa/pf)

tag: glycinecurrentwashout(pa/pf)


title: H6-April-2023-Plate4-PEM_S348

tag: experimental record

value: ND

tag: Sex

tag: bmi


title: ST_PRV_WT_rep3

tag: cell line

value: PRV wild-type


title: Control_1_S27, SH-SY5Y cells, Control

tag: cell type

value: WT


title: EPIC10RNA_Healthy_Control

city: Cincinnati

first: Matthew

last: Weirauch

state: Ohio

address: 3333 Burnet Avenue

department: Center for Autoimmune Genomics and Etiology (CAGE)

institute: Cincinnati Children's Hospital Medical Center

data_processing:
RNA sequencing data was processed using the nf-core/rnaseq pipeline (version 3.8.1)
The quality of sequences were assessed using FASTQC (verson 0.11.9) and the low quality bases and adapter sequences were then trimmed and filtered using Cutadapt (version 3.4). Ribosomal RNA sequences were subsequently removed from the aligned data using SortMeRNA (version 4.3.4
The resulting alignments were sorted and indexed using SAMtools (verson 1.15.1)
the quality of the RNA sequencing data, several tools were employed, including RseqQC (version 3.0.1), Qualimap (version 2.2.2-dev), dupRadar (version 1.18.0), and Preseq (version 3.1.1).
differential gene expression analysis was performed using DESeq2 (version 1.30.1)

source_name: Saliva

extract_protocol:
Total RNA was extracted using Qiagen RNeasy purification procedure and mRNA was purified using oligo(dT)-attached magnetic beads.
First, the mRNA molecules were fragmented and converted into cDNA through reverse transcription using random hexamer primers. Following this, the cDNA fragments were processed by end-repair, adenylation, and adapter ligation, and then amplified through PCR to enrich the cDNA fragments. After purification, the library's quality was assessed using the Agilent Technologies 2100 bioanalyzer. Finally, the double-stranded PCR products were denatured, circularized using a splint oligo sequence, and amplified with phi29 DNA polymerase to generate DNA nanoballs (DNBs), each containing more than 300 copies of a single molecule, forming the final library.

tag: race

value: Black

value: Female

tag: condition

value: Healthy

value: Saliva


title: isw1D_H3K4me3_eSPAN

first: Zhiguo

address: 1130 St. Nicholas Avenue

tag: strain

tag: chip antibody

value: anti-H3K4me3 (ab8580, Abcam)

tag: genotype

value: Isw1 KO

tag: treatment


title: G7-April-2023-Plate4-PEM_S339

tag: donor

tag: plate

tag: cellid

tag: age

value: female

tag: cellsize f


title: EPIC09RNA_Healthy_Control

tag: tissue


title: ST_PRV_WT_rep2

value: ST


title: ST_PRV_WT_rep1


title: G6-April-2023-Plate4-PEM_S338

tag: time from_plating_(h)

tag: glucose mm

tag: experimental record

tag: glycinecurrent(pa/pf)

tag: glycinecurrent+strychnine(pa/pf)

tag: glycinecurrentwashout(pa/pf)


title: G5-April-2023-Plate4-PEM_S337

tag: cell type

tag: Sex

tag: bmi


title: SupT1 infected, Nanopore, 24hpi, rep2

city: Würzburg

first: Neva

last: Caliskan

address: Josef-Schneider-Str. 2/D15

institute: Helmholtz Institute for RNA-based Infection Research (HIRI)

description:
Library name: Nanopore_24h_2
Nanopore_24h_2
Nanopore_seq_HCMV_splice_isoforms.xlsx
HIV1_NL43-corrected_w_TSO.fa
HIVNL43_all_iso.bed
HIVNL43_all_iso.gtf

data_processing:
DMS-Seq: Reads were trimmed using cutadapt v 1.18 and aligned to the reference sequence using bowtie2. Further analysis was carried out using the rf-count and rf-norm modules of RNA Framework package v2.7.2.
Nanopore: Acquired Nanopore data was base called in “sup” mode with Guppy version 6.5.7 and filtered for minimal qscore of 10. Isoforms were identified with Isoquant version 3.3.0 using a GTF file containing all previously reported isoforms (HIVNL43_all_iso.gtf). Only uniquely identified isoforms were counted. To identify those isoforms that may express the novel peptides, the nucleotide sequence of all reported isoforms was searched for the iORFs or/and first AUG and in silico translated using Biopython 1.79 in a custom python script.
Assembly: GCF_000001405.36, AF324493
Supplementary files format and content: DMS-Seq: The mutationMap files are in RC (RNA Count) format according to the RNA framework standard (https://rnaframework-docs.readthedocs.io/en/latest/rf-count/).
Supplementary files format and content: Nanopore: The enclosed excel file contains a list of all potential HIV transcripts isoforms with Nanopore read-counts supporting each isoform. Furthermore, information on the two identified iORFs are indicated for each isoform. The enclosed fasta file, bed file and gtf file were used for the transcript isoform deconvolution.

molecule: cytoplasmic RNA

organism:
Homo sapiens
Human immunodeficiency virus 1

extract_protocol:
Nanopore: To analyze the HIV transcriptome in infected SupT1 cells at 8, 16 and 24 hpi 30 μg of Trizol extracted RNA was treated with 3 μL of Turbo DNase in 150 μL total volume for 30 min at 37 °C. RNA was purified with Macherey-Nagel PCR Clean-up kit using NTC buffer according to manufacturer’s instructions.
DMS-Seq: For in vivo DMS modification of HIV-1 gRNA, 40 mL of SupT1 cells were infected with VSV pseudotyped HIV-1 (ΔEnv). 24 h post infection, 5 mL of cells were probed with 85 mM of dimethyl sulfate (DMS) for 6 min at 37°C, placed immediately on ice and the reaction was quenched by addition of 100 mM of β-mercaptoethanol. Cells were pelleted by centrifugation for 5 min at 400 g, 4°C and washed with PBS. The cell pellet was directly resuspended in 1 mL of TRI reagent (Sigma-Aldrich) and total RNA was extracted according to the manufacturer’s instructions. Ten μg of total cellular RNA were treated with 4 U of TURBO DNase (ThermoFisher Scientific) for 30 min at 37°C. The RNA was purified using NucleoSpin Gel and PCR Clean- Up (Macherey-Nagel, NTC buffer), according to the manufacturer´s instructions.
Nanopore: 1 ug of RNA was reverse transcribed with SuperScript IV (Invitrogen) using primer GTACAGGCAAAAAGCAGCTGCT according to manufacturer’s instructions in a 10 μL reaction. The cDNA was purified with Macharey-Nagel PCR Clean-up kit using NTC buffer and eluted in 20 μL H2O. RNA was digested in a 10 μL reaction containing 3 μL cDNA product with 0.5 μL RNase A (NEB) and 0.5 μL RNase T1 (NEB) and incubation at 37 °C for 30 min, followed by column purification as described above. Next, PCR amplification of 20 μL of the RNase-digested, purified cDNA in a 100 μL reaction with Primestar GXL (Takara) using primers GGTCTCTCTGGTTAGACCAGATCTGAG and GTACAGGCAAAAAGCAGCTGCT was performed with 12 cycles of denaturation at 98 °C for 10 sec, annealing at 55 °C for 15 sec and extension at 68 °C for 2 min. PCR products were purified with a 1:1 ratio of Mag-Bind TotalPure NGS beads (Omega Bio-Tek) according to the manufacturer’s recommendations and eluted in 14 μL H2O. Next, 80 ng PCR product in 5 μ was end repaired by addition of 0.7 μL NEBNext End Repair buffer (NEB) and 0.3 μL NEBNext End Repair Enzyme Mix (NEB), mixed thoroughly by pipetting and incubated for 5 min at 25 °C followed by 5 min at 65 °C. Nanopore native ligation barcoding barcodes (ONT SQK-NBD114.96) were ligated by transfer of 3.5 μL of end-repaired product into a new well, followed by addition of 1.5 μL of barcode and 5 μL of Blunt/TA ligation master mix (NEB). After incubation at 25 °C for 20 min, 1 μL of EDTA (SQK802 NBD114.96) was added, samples were pooled and purified with 0.4 volumes of Ampure XP beads (SQK-NBD114.96). Barcoded DNA was eluted in 31 μL of H2O. To ligate the motor protein 30 μL of the barcoded DNA was mixed with 10 μ of 5x Quick Ligation Buffer (NEB), 5 μL of NA and 5 μL of high concentration T4 DNA ligase (NEB) was added. After incubation for 20 min at 25 °C, 0.4 volumes of Ampure XP beads (SQK-NBD114.96) were added, beads were washed twice with 125 μL Short Fragment Buffer (SFB, SQK-NBD114.96) and eluted in 14 μL of Elution Buffer (EB, SQK-NBD114.96). DNA concentration was quantified with AccuClear Ultra High Sensitivity dsDNA Quantitation Solution (Biotium) and 10 fmol was prepared for sequencing on a R10.4.1 Flongle flow cell (FLO-FLG114) by addition of 15 μL sequencing buffer (SB) and 10 μL loading beads (LIB). Data was acquired on a MinION Mk1b with MinKNOW version 23.04.3.
DMS-Seq: Reverse transcription was performed on 1 μg of purified RNA mixed with 0.5 mM dNTPs, 0.25 μM of RT primer (5´- CTT GTC TAT CGG CTC CTG CTT C - 3´) in a final volume of 12 μL. The RNA was denatured at 65°C for 5 min and placed on ice. The reverse transcription reaction was performed by addition of 1 mM of MnCl2, 1x MarathonRT buffer (Tris-HCl 50 mM, pH 8.3; KCl 200 mM; Glycerol 20%), 0.2 μL RNasin (Promega) and 40 U of MarathonRT 93 in 25 μL final volume. The reactions were incubated for 8 h at 42°C. Newly synthesized cDNAs were diluted 8 times and PCR amplified: 10 μL of diluted cDNA were mixed with 0.2 mM dNTPs, 0.25 μM of both Forward (5´ - TCG TCG GCA GCG TCA GAT GTG TAT AAG AGA CAG CTA CCA TAA TGA TAC AGA AAG GC - 3´) and Reverse (5´ - GTC TCG TGG GCT CGG AGA TGT GTA TAA GAG ACA GGT CTC TTC CCC AAA CCT GAA G - 3´) primers, 10 μL of Q5 Buffer 5x, and 1 U Q5 polymerase (NEB) in 50 μL final volume. The initial denaturation was performed at 98 °C for 2 min, followed by 25 cycles of 10 sec at 98°C, 20 sec at 55°C and 30 sec 721 at 72°C before a final extension at 72°C for 5 min. Amplicon quality was controlled on an agarose gel 1%. DNA amplicons were purified by solid-phase reversible immobilization (SPRI) using Mag-Bind TotalPure NGS beads (Omega Biotek) following the manufacturer´s instruction, with a DNA to beads ratio of 1:0.8. Nextera indexes were added by PCR, 80 ng of purified DNA were mixed with 1x Q5 Buffer, 0.2 mM dNTPs, 0.02 U of Q5 polymerase and 2.5 μL of Nextera Index (Illumina) in a 14 μL reaction. The initial denaturation was performed at 98 °C for 2 min, followed by 5 cycles of 30 sec at 98°C, 30 sec at 62°C and 1 min at 72°C before a final extension at 72°C for 5 min. Quality of libraries was assessed by agarose gel electrophoresis. Equal amounts of each sample were pooled together followed by a final SPRI purification (DNA to beads ratio of 1:0.8). Paired-end PE150 sequencing was carried out on an Illumina Novaseq instrument (Novogene).

tag: cell line

value: T-cell


title: EPIC08RNA_Healthy_Control

tag: race

tag: condition


title: EPIC07RNA_Healthy_Control


title: chd1D_H3K4me3_ChIP

last: Zhang

institute: Columbia University

value: whole cell

tag: strain

tag: chip antibody

tag: genotype

value: Chd1 KO

tag: treatment


title: isw1D_H3K4me3_ChIP

tag: tissue

value: MNase


title: G4-April-2023-Plate4-PEM_S336

data_processing:
Fastq files were trimmed using TrimGalore version 0.6.5 with auto-detection of adapter sequence
Aligned to the GRCh38 human genome, Ensembl release 104,and counted using STAR version 2.7.11a
Counts were decontaminatedusing celda (1.20.0) decontX in R (4.4.1)
Assembly: GRCh38, Ensembl release 104
Supplementary files format and content: Combined csv count table of all cells; raw counts with ENSG identifiers
Supplementary files format and content: Processed RData file containing a Seurat object with all cells, with gene symbols, decontaminated and normalized counts
Supplementary files format and content: Python h5ad file containing all cells, with gene symbols, decontaminated counts

extract_protocol:
Isolated human islets were dispersed to single cells, and whole cell patch clamp electrophysiology was performed. Following, the cells were collected and sent for scRNA-seq (SmartSeq).
SmartSeq3

tag: donor

tag: plate

tag: cellid

value: islets

tag: time from_plating_(h)

tag: age

tag: cellsize f


title: SupT1 infected, Nanopore, 24hpi, rep1

description:
Library name: Nanopore_24h_1
Nanopore_24h_1
Nanopore_seq_HCMV_splice_isoforms.xlsx
HIV1_NL43-corrected_w_TSO.fa
HIVNL43_all_iso.bed
HIVNL43_all_iso.gtf

tag: cell type


title: EPIC05RNA_Healthy_Control

tag: Sex


title: F6-April-2023-Plate4-PEM_S328

tag: glucose mm

tag: experimental record

value: male

tag: bmi

tag: glycinecurrent(pa/pf)

tag: glycinecurrent+strychnine(pa/pf)

tag: glycinecurrentwashout(pa/pf)


title: SupT1 infected, Nanopore, 16hpi, rep1

description:
Library name: Nanopore_16h_1
Nanopore_16h_1
Nanopore_seq_HCMV_splice_isoforms.xlsx
HIV1_NL43-corrected_w_TSO.fa
HIVNL43_all_iso.bed
HIVNL43_all_iso.gtf

tag: cell line


title: F7-April-2023-Plate4-PEM_S329

value: ND


title: EPIC06RNA_Healthy_Control

tag: race

tag: condition


title: EPIC04RNA_Healthy_Control

tag: tissue


title: F5-April-2023-Plate4-PEM_S327

tag: donor

tag: plate


title: EPIC03RNA_Healthy_Control


title: SupT1 infected, Nanopore, 8hpi, rep2

description:
Library name: Nanopore_8h_2
Nanopore_8h_2
Nanopore_seq_HCMV_splice_isoforms.xlsx
HIV1_NL43-corrected_w_TSO.fa
HIVNL43_all_iso.bed
HIVNL43_all_iso.gtf


title: chd1D_H3K4me3_eSPAN

tag: strain

tag: chip antibody

tag: genotype

tag: treatment


title: F4-April-2023-Plate4-PEM_S326

tag: cellid

tag: cell type

tag: time from_plating_(h)

tag: age

tag: Sex

tag: cellsize f


title: EPIC02RNA_Healthy_Control


title: PHILO, hemp, IgG, set2, rep3

city: Piscataway

first: Mark

last: Zander

address: 190 Frelinghuysen Rd

institute: Rutgers State University of New Jersey

data_processing:
ChIP-seq reads were aligned to the TAIR10 (Arabidopsis thaliana), SLM_r2.0.pmol (Solanum lycopersicum), cs10 (Cannabis sativa) using Bowtie2 (version 2.4.1).
To generate ChIP-seq coverage plots, bamCoverage (binSize 5) from deepTools (version 3.5.2) was used.
Histone marks domains were identified with epic2 (version 0.0.52) using default parameters and IgG samples as controls.
Assembly: TAIR10 (Arabidopsis thaliana), SLM_r2.0.pmol (Solanum lycopersicum), cs10 (Cannabis sativa)
Supplementary files format and content: bigwig, domain.csv

organism: Cannabis sativa

source_name: two-week-old whole seedling

growth_protocol: Ten-day-old Col-0 Arabidopsis seedlings, two-week-old Micro-Tom tomato (Solanum lycopsericum) seedlings, and two-week-old Otto II Boax hemp (Cannabis sativa)seedlings grown under a 16 h light/8 h dark cycle were used for PHILO ChIP-seq analysis.

extract_protocol:
Tissues were crosslinked with 1% formaldehyde solution for 2 x 10 min. After quenching, samples were shock-frozen, ground and chromatin was subsequently extracted. Chromatin was sonicated with a Diagenode Bioruptor.
Libraries were prepared as follows. End repair (5 μl of End Repair Reaction Buffer + 2.5 μl of End Repair Enzyme Mix from the NEBNext End Repair Module (New England Biolabs)), A-tailing (2.5 µl NEBnext dA-Tailing Reaction Buffer + 1.5 µl Klenow Fragment (3'5' exo-) (New England Biolabs)), adapter ligation(1 µl TruSeq DNA Unique Dual Indexes (UDIs) v2 (Illumina), 2.5 µl T4 DNA Ligase Reaction Buffer + 1.25 µl T4 DNA Ligase (New England Biolabs)), and PCR enrichment (12.5 µl NEBNext High-Fidelity 2X PCR Master Mix (New England Biolabs).

treatment_protocol: no treatment

value: IgG (#015-000-003, Jackson ImmunoResearch)

value: Otto II Boax


title: E6-April-2023-Plate4-PEM_S318

first: Patrick

address: 6-040 Li Ka Shing Centre

tag: glucose mm

tag: experimental record

tag: bmi

tag: glycinecurrent(pa/pf)

tag: glycinecurrent+strychnine(pa/pf)

tag: glycinecurrentwashout(pa/pf)


title: EPIA09RNA_Patient_OSA

tag: race

value: Black

tag: condition

value: OSA

tag: tissue


title: PHILO, hemp, IgG, set2, rep2

tag: chip antibody

tag: genotype


title: EPIA08RNA_Patient_OSA

value: Female


title: PHILO, hemp, IgG, set2, rep1

tag: treatment


title: PHILO, hemp, H3K4me3, set2, rep3

value: anti-H3K4me3 (#04-475, Millipore Sigma)


title: isw1D_H3K56ac_ChIP_rep1

city: New York

tag: strain

value: anti-H3K56ac (Zhang Lab)


title: EPIA07RNA_Patient_OSA

value: Saliva


title: E4-April-2023-Plate4-PEM_S316

tag: donor

tag: plate

tag: cellid

tag: cell type

tag: time from_plating_(h)


title: SupT1 infected, Nanopore, 16hpi, rep2

description:
Library name: Nanopore_16h_2
Nanopore_16h_2
Nanopore_seq_HCMV_splice_isoforms.xlsx
HIV1_NL43-corrected_w_TSO.fa
HIVNL43_all_iso.bed
HIVNL43_all_iso.gtf

tag: cell line


title: PHILO, hemp, H3K4me3, set2, rep2


title: D6-April-2023-Plate4-PEM_S308

tag: glucose mm

tag: experimental record

tag: age

tag: Sex

value: female

tag: bmi

tag: cellsize f


title: E5-April-2023-Plate4-PEM_S317

tag: glycinecurrent(pa/pf)

tag: glycinecurrent+strychnine(pa/pf)

tag: glycinecurrentwashout(pa/pf)


title: EPIA05RNA_Patient_OSA

tag: race

tag: condition

tag: tissue


title: PHILO, hemp, H3K4me3, set2, rep1

tag: chip antibody

tag: genotype

tag: treatment


title: D5-April-2023-Plate4-PEM_S307

tag: donor

tag: plate

tag: cellid

tag: cell type

tag: time from_plating_(h)


title: EPIA04RNA_Patient_OSA

tag: Sex


title: EPIA06RNA_Patient_OSA


title: Carotid Artery Ligation - Nrf3 Knockout rep 2

city: shanghai

first: shasha

last: sun

address: No. 1665 Kangjiang Road

institute: Xinhua Hospital affiliated to Shanghai Jiaotong University School of Medicine

data_processing:
The clean reads were obtained after removal of reads containing adapter, ploy-N and at low quality from raw data. HISAT2 was used to align the clean reads to the mouse reference genome mm9 with default pa- rameters. HTSeq was subsequently employed to convert aligned short reads into read counts for each gene model.
Differential expression was assessed by DEseq/DESeq2/edgeR/DEGseq using read counts as input. The Benjamini–Hochberg multiple test correction method was enabled. Differentially expressed genes were chosen according to the criteria of fold change > 2 and adjusted p-value < 0.05.
All the differentially expressed genes were used for heat map analysis and KEGG ontology enrichment analyses. For KEGG enrichment anal- ysis, a P-value < 0.05 was used as the threshold to determine significant enrichment of the gene sets.
Assembly: mm9
Supplementary files format and content: gene_exp.xlsx

source_name: Carotid Artery

extract_protocol:
Total mRNA was extracted using the Trizol Reagent (Thermo, 15596026).
Total RNA was isolated from cells/tissues using the Magzol Reagent (Magen, China)according to the man- ufacturer’s protocol, The quantity and integrity of RNA yield was assessed by using the K5500(BeijingKaiao, China) and the Agilent 2200 TapeStation (Agilent Technologies, USA) separately.

value: Carotid Artery


title: D7-April-2023-Plate4-PEM_S309

last: MacDonald

institute: University of Alberta

tag: glucose mm

tag: experimental record

tag: age

tag: bmi