title: Naïve hiPSCs on Vitronectin coating, rep. 1

description: 3'DGE mRNA-seq

data_processing:
Illumina novaSeq base call (BCL) files are converted in fastq file through bcl2fastq (version v2.20.0.422)
Sequence reads were trimmed using bbduk software (bbmap suite 37.31)
Alignment was performed with STAR 2.6.0a.
The expression levels of genes were determined with HTseq-counts 0.9.1.
Differential expression analysis was performed using edgeR
Genome_build: hg38_mm10
Supplementary_files_format_and_content: tab-delimited text files include raw counts for each Sample

growth_protocol: Seeded in microfluidics at 400 cells/mm2, on MEF feeder layer or Vitronectin coating. Both in RSET mediun under hypoxic conditions. Medium change was performed every 12 hours.

extract_protocol:
RNA was collected with RLT lysis buffer 72 h after seeding in microfluidics. RNA extraction from microfluidic channels was performed in triplicates from each condition, each replicate made by pulling together the lysates obtained from 3 channels.
NEGEDIA Digital mRNA-seq research grade sequencing service (Next Generation Diagnostics srl).

tag: culture substrate

value: cultured on Vitronectin coating (50 µg/ml)


title: HFF microfluidics day 1 rep. 1

status: Public on Nov 11 2021

type: SRA

city: Santander

first: Lucio

last: Di Filippo

state: Cantabria

address: PCTCAN - Cl. Albert Einstein, 22

country: Spain

institute: IBBTEC

description: 3'DGE mRNA-seq

library_source: transcriptomic

data_processing:
Illumina novaSeq base call (BCL) files are converted in fastq file through bcl2fastq (version v2.20.0.422)
Sequence reads were trimmed using bbduk software (bbmap suite 37.31)
Alignment was performed with STAR 2.6.0a.
The expression levels of genes were determined with HTseq-counts 0.9.1.
Differential expression analysis was performed using edgeR
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include raw counts for each Sample

molecule: total RNA

organism: Homo sapiens

source_name: fibroblasts (HFF-1, ATCC)

extract_protocol:
RNA was extracted with RNeasy Plus Micro Kit (Qiagen) following manufacturer instructions.
NEGEDIA Digital mRNA-seq research grade sequencing service (Next Generation Diagnostics srl).

tag: cell type

value: Fibroblast

tag: culture system

value: Microfluidics

tag: culture conditions

value: On Vitronectin (25 microg/ml) in High Glucose Dulbecco’s modified Eagle Medium (DMEM, ThermoFisher Scientific) supplemented with 10percent Fetal Bovine Serum (FBS, ThermoFisher Scientific)

tag: time point

value: Day 1 after seeding


title: Naïve hiPSCs on MEF feeder layer, rep. 2

description: 3'DGE mRNA-seq

source_name: Human naïve induced pluripotent stem cells (naïve hiPSCs, HPD06, from Nat Cell Biol. 2019 Feb;21(2):275-286)

value: cultured on a confluent layer of mitotically inactive MEFs (DR4, ATCC) in RSeT medium (Stemcell Technologies)


title: Naïve hiPSCs on Vitronectin coating, rep. 2

description: 3'DGE mRNA-seq


title: Naïve hiPSCs on MEF feeder layer, rep. 1

description: 3'DGE mRNA-seq


title: Naïve hiPSCs on Vitronectin coating, rep. 3

description: 3'DGE mRNA-seq


title: HFF well day 1 rep. 1

description: 3'DGE mRNA-seq

value: Glass coverslip in standard plate


title: HFF microfluidics day 4 rep. 1

description: 3'DGE mRNA-seq

value: Day 4 after seeding


title: Naïve hiPSCs on MEF feeder layer, rep. 3

description: 3'DGE mRNA-seq


title: HFF well day 7 rep. 2

description: 3'DGE mRNA-seq

value: Day 7 after seeding


title: KO_1_ATAC

status: Public on Oct 28 2021

city: Leiden

first: Lucia

last: Daxinger

address: Albinusdreef 2

country: Netherlands

institute: Leiden Univeristy Medica Center

library_source: genomic

data_processing:
Quality assessment of the raw sequencing reads was done using FastQC  v0.11.2. Adapters were removed by TrimGalore v0.4.5 using default parameters for paired-end Illumina reads, after which, quality filtering was performed by the same software. Reads smaller than 20bps and those with an error rate (TrimGalore option "-e") higher than 0.1 were discarded, after which a final quality assessment of the filtered reads was done with FastQC to identify possible biases left after filtering
The remaining reads were mapped to  the mouse reference genome (build mm10) using the Bowtie2 v2.3.5 using default parameters with the following exceptions: “–very-sensitive".
The peak calling was done with MACS2 2.1.4 with default parameters with the expceptions: -BAMPE --shift -100 --extsize 200
Genome_build: mm10
Supplementary_files_format_and_content: Peaks coordinates and differential peaks

molecule: genomic DNA

organism: Mus musculus

source_name: mESC

growth_protocol: All mESC lines were cultured in serum conditions (Knockout DMEM (10829-018; Gibco), 10% FBS (DE14-801F; BioWhittaker), NEAA (11140; Gibco), L-Glutamine (25030-123; Gibco), Sodium Pyruvate (11360; Gibco), 2-Mercaptoethanol (31350; Gibco) and Leukemia Inhibitory Factor (ESG1107; Millipore)) plus MEK inhibitor PD0325901 (1 mM) and GSK3 inhibi- tor CHIR99021 (3 mM) (Axon Medchem) on 0.1% gelatin.

extract_protocol: ATAC-seq libraries were prepared as previously described (Buenrostro 2015). In brief, fifty thousand mouse embryonic stem cells were resuspended in 50 µL transposition mix (Nextera) and incubated for 30min at 37°C. Libraries were amplified by PCR with barcoded Nextera primers and sequenced on BGISEQ-500

treatment_protocol: No treatment

value: mESC

tag: strain

value: FVB/NJ

tag: genotype


title: Morc3_input_B

data_processing:
Sequencing adapters were remove with Trimmomatic (0.38) and read were mapped to the reference genome (mm10) using bowtie2 (2.3.4) with parameter "--very-sensitive-local"
Peaks were called using MACS2 (2.1.1) with the following parameters ( -g mm). Input dataset containing whole genomic DNA fragments were used as control.
Genome browser tracks (bigwig) were generated using Deeptools (3.1.2)  with parameters "--effectiveGenomeSize 2652783500  --binSize 10 --smoothLength 50 --normalizeUsing RPKM"
Genome_build: mm10
Supplementary_files_format_and_content: bigwig and peaks

extract_protocol:
Cells were cross linked with 1% formaldehyde M134-200ML; VWR) for 8 min at room temperature and glycine (125 mM; G8790-1KG; Sigma) was used to quench cross-linking for 5 min. Cells were washed twice with cold PBS and lysed in ChIP Buffer 1 (10mM Tris HCl (pH 8.0), 0,25% Triton X-100, 10mM EDTA, 0.5mM EGTA, Protease Inhibitor Cocktail (05056489001; Roche) and 1mM PMSF) for 15 minutes on a rotator at 4C. After centrifugation 5 minutes at 1,400g at 4C, cells were resuspended in ChIP Buffer 2 (10mM Tris-HCl (pH 8.0), 200mM NaCl, 10mM EDTA, 0.5mM EGTA, Protease Inhibitor Cocktail (05056489001; Roche) and 1mM PMSF). After centrifugation 5 minutes at 1,400g at 4C, cells were resuspended in ChIP Buffer 3 (10mM Tris-HCl (pH 8.0), 10mM EDTA, 0.5mM EGTA, 0,1% SDS, Protease Inhibitor Cocktail (05056489001; Roche) and 1mM PMSF and sonicated with Covaris S2 (Duty cycle: 10%, Intensity:5, Cycle/Burst:200 to obtain fragment between 200 and 600bp. Sheared chromatin was centrifuged at 12,000 g for 10 min at 4°C to discard the pellets. The supernatant was then diluted 10 times with ChIP dilution buffer (16.7mM Tris-HCl (pH8), 0.01% SDS, 1.1% TritonX-100, 1.2mM EDTA, 167mM NaCl) and incubated overnight with 5 g Morc3 antibody (Rockland; 100-401-N96S) or Rabbit IgG (Abcam ab37415). An input fraction for each sample was retained for downstream analysis. Samples were then incubated with Dynabeads Protein A (Invitrogen 10001D) for at least 4h rotating at 4C. After immunoprecipitation beads were washed with low-salt washing buffer (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl (pH 8.1), 150 mM NaCl), high-salt washing buffer (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl (pH 8.1), 500 mM NaCl), LiCl washing buffer (0.25 M LiCl, 1% NP40, 1% deoxycholate, 1 mM EDTA, 10 mM Tris-HCl (pH 8.1)) and TE buffer (10 mM Tris-HCl (pH 8.0), 1 mM EDTA). IP DNA and Input DNA samples were extracted with phenol-chloroform-isoamylalcohol (15593049; Fisher Scientific).
DNA from mESc was used for library preparation with the KAPA Hyper prep kit following manufacturer's instructions and libraries were sequenced on Illumina HiSeq 2000.

tag: antibody

value: None (input)


title: Morc3_input_D


title: Morc3_input_C


title: Morc3_input_A


title: Morc3_ChIP_D


title: Morc3_ChIP_A


title: KO_2_ATAC


title: WT_1_ATAC

value: WT


title: HFF well day 4 rep. 1

description: 3'DGE mRNA-seq


title: WT_2_ATAC


title: HFF microfluidics day 4 rep. 3

description: 3'DGE mRNA-seq


title: HFF well day 1 rep. 2

description: 3'DGE mRNA-seq


title: Morc3_ChIP_B


title: H3K9me3_input

data_processing:
Quality assessment of the raw sequencing reads was done using FastQC  v0.11.2. Adapters were removed by TrimGalore v0.4.5 using default parameters for paired-end Illumina reads, after which, quality filtering was performed by the same software. Reads smaller than 20bps and those with an error rate (TrimGalore option "-e") higher than 0.1 were discarded, after which a final quality assessment of the filtered reads was done with FastQC to identify possible biases left after filtering
The remaining reads were mapped to  the mouse reference genome (build mm10) using the Bowtie2 v2.3.5 using default parameters with the following exceptions: “–very-sensitive".
The peak calling was done with SICER2
Genome_build: mm10
Supplementary_files_format_and_content: bigwig and peaks

growth_protocol: All mESC lines were cultured in serum conditions (Knockout DMEM (10829-018; Gibco), 10% FBS (DE14-801F; BioWhittaker), NEAA (11140; Gibco), L-Glutamine (25030-123; Gibco), Sodium Pyruvate (11360; Gibco), 2-Mercaptoethanol (31350; Gibco) and Leukemia Inhibitory Factor (ESG1107; Millipore)) plus MEK inhibitor PD0325901 (1 mM) and GSK3 inhibitor CHIR99021 (3 mM) (Axon Medchem) on 0.1% gelatin.

extract_protocol:
Cells were cross linked with 1% formaldehyde (M134-200ML; VWR) for 8 min at room temperature and glycine (125 mM; G8790-1KG; Sigma) was used to quench cross-linking for 5 min. Cells were washed twice with cold PBS and lysed in NP Buffer (150 mM NaCl, 50 mM Tris–HCl (pH 7.5), 5 mM EDTA, 0.5% NP-40, 1% Triton X-100, Protease Inhibitor Cocktail (05056489001; Roche)). Nuclei were sheared by sonication (Covaris). For each H3K9me3 ChIP-seq experiment, 25 µg of sample chromatin was mixed with 50 ng spike-in Drosophila chromatin (53083; Active Motif). Mixture of experimental chromatin and spike-in chromatin was then incubated with a mix containing 4 µg of H3K9me3 antibody (abcam ab8898) and 2 µg of spike-in antibody (104597; Active Motif) at 4°C overnight. The next day, Protein A Sepharose beads (175280-01; GE Health Care) were first blocked with 1mg/ml BSA (10484; Affymetrix) and then added to each chromatin-antibody mix and incubated at 4°C for at least 3 h. After immunoprecipitation, beads were washed with low-salt washing buffer (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris–HCl (pH 8.1), 150 mM NaCl), high-salt washing buffer (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris–HCl (pH 8.1), 500 mM NaCl), LiCl washing buffer (0.25 M LiCl, 1% NP40, 1% deoxycholate, 1 mM EDTA, 10 mM Tris–HCl (pH 8.1)) and TE buffer (10 mM Tris–HCl (pH 8.0), 1 mM EDTA). DNA was extracted using phenol-chloroform-isoamylol (15593-049; Life Technologies)
About 20ng of DNA from mESCcells was used for library preparation with the KAPA Hyper Kit following manufacturer's instructions and sequenced at Macrogen on HiseqX

value: not provided

tag: chip antibody

value: none (input)


title: KO_2_MommeD

data_processing:
The adaptors of RNA-seq samples were removed by the tool trim_galore using default parameters for paired-end Illumina reads, after, a quality filtering was driven by the same software and the results were supervised using FastQC
The remained reads were mapped to mm10 mouse genome using STAR aligner with the following parameters –outputMultimapperOrder random –twopassMode Basic.
the duplicated reads were marked by Piccard tools and then, the quantification versus GENCODE MV16 was driven by htseq-count v0.91
Genome_build: mm10
Supplementary_files_format_and_content: RNA_seq_counts_genes_MommeD.txt
Supplementary_files_format_and_content: RNA_seq_counts_TE_MommeD.csv

extract_protocol:
Total RNA was isolated with QIAzol (5346994; Qiagen) followed by isopropanol precipitation protocol.
Libraries were sequenced with 100bp paired-end (PE) on BGI


title: KO_1_MommeD


title: WT_2_MommeD


title: WT_1_MommeD


title: KO_3_MommeD


title: KO_1_CRISPR

data_processing:
The adaptors of RNA-seq samples were removed by the tool trim_galore using default parameters for paired-end Illumina reads, after, a quality filtering was driven by the same software and the results were supervised using FastQC
The remained reads were mapped to mm10 mouse genome using STAR aligner with the following parameters –outputMultimapperOrder random –twopassMode Basic.
the duplicated reads were marked by Piccard tools and then, the quantification versus GENCODE MV16 was driven by htseq-count v0.91
Genome_build: mm10
Supplementary_files_format_and_content: excel tables

extract_protocol:
Total RNA was isolated with QIAzol (5346994; Qiagen) followed by isopropanol precipitation protocol.
Libraries were sequenced on NoveSeq 6000  (100bp PE)


title: H3K9me3_KO1_MommeD


title: KO_2_CRISPR


title: H3K9me3_WT2_MommeD


title: H3K9me3_WT1_MommeD


title: WT_3_MommeD


title: Morc3_ChIP_C


title: KO_3_CRISPR


title: WT_3_CRISPR


title: WT_1_CRISPR


title: WT_2_CRISPR


title: Total RNAseq of cell sample c14

status: Public on Sep 13 2021

city: Winnipeg

first: James

middle: Ronald

last: Davie

state: Manitoba

address: 745 Bannatyne Avenue, RM 333A

department: Biochemistry and Medical Genetics

country: Canada

institute: University of Manitoba

data_processing:
The reads from the NextSeq 500 were mapped using LifeScope Genomic Analysis Software v2.5.1 (Life Technologies).
2-mismatch setting and a minimum mapping quality score of 8 was allowed. More than 88% of reads were mapped.
The RPKM values were obtained using HOMER. Raw read counts were obtained from the sequencing platforms separately.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: processed_data.csv: Comma-separated text file

source_name: human fibroblast cell /CCD-1070Sk

extract_protocol:
Total RNA was isolated from untreated and treated CCD-1070Sk using RNeasy Mini Kit (QIAGEN) according to manufacturer’s instructions.
Total RNA was quantified by the Qubit 2.0 Fluorometer (Life Technologies) and run on the Bioanalyzer 2100 (Agilent) to analyze the RNA integrity. RNA (1-5μg) with RIN 7-10 was used for ribosomal RNA depletion using the Ribo-Zero kit (Illumina) according to the manufacturer’s instructions. Strand specific library construction and sequencing on the 5500 × l SOLiD™ System. For sequencing on the Illumina sequencers, library preparation was done using the NEBNext Ultra Directional RNA Library Prep Kit for Illumina (New England Biolabs). The libraries were sequenced at Genome Quebec, Montreal, Quebec and sequenced on the Illumina HiSeq4000 (PE100) and at the Illumina Epigenetics Platform, University of Lethbridge, Lethbridge, Alberta on the NextSeq 500 system.

treatment_protocol: After serum starvation, the cells were treated with EGF (30 ng/ml, cat no. PHG0311, Invitrogen, MD, USA (now Life Technologies)) or TPA (100 nM, Sigma, Saint Louis Missouri, USA) respectively, for indicated time periods. For MSK inhibition studies, serum starved cells were pre-treated with 10 µM H89 (Calbiochem, Cat No. 371962-1M, EMD Millipore Corp., Billerica, MA, USA) for 30 min followed by treatment with EGF (30ng/ml) or TPA (100 nM) for indicated time periods. Alternatively, serum-starved cells were incubated with 10 µM H89 or 100 nM Rp-CAMPS (END Millipore Sigma) 30 min before addition of EGF or TPA plus the inhibitor for 60 min.

tag: cell line

value: fibroblast

tag: condition

value: serum starved

tag: treatment

value: H89 + TPA treated

tag: time

value: 1 hr


title: Total RNAseq of cell sample c2

value: EGF treated


title: Total RNAseq of cell sample c8

value: EGF + H89 treated


title: Total RNAseq of cell sample c5

value: No treatment

value: 0 hr


title: Total RNAseq of cell sample c17

value: H89 treated


title: Total RNAseq of cell sample c16

value: TPA treated


title: Total RNAseq of cell sample c13


title: Total RNAseq of cell sample c7


title: Total RNAseq of cell sample c1


title: Total RNAseq of cell sample c18

value: TPA + H89 treated


title: Total RNAseq of cell sample c6


title: H3K9me3_KO2_MommeD

value: mESC


title: Total RNAseq of cell sample c15


title: Total RNAseq of cell sample c12

value: H89 + EGF treated


title: Total RNAseq of cell sample c9


title: Total RNAseq of cell sample c10


title: Total RNAseq of cell sample c11


title: SCG_MBMMet2_KO2

status: Public on Aug 29 2021

city: Boston

first: Shenglin

last: Mei

state: MA

address: 10 Shattuck Street

country: USA

institute: Harvard medical school (DMBI)

description: cell.annotation.csv on Series record

data_processing:
FASTQ files were processed with the CellRanger software (10x Genomics, Inc., version 2.0). Mouse genome mm10 was used as the reference genome (10x Genomics, Inc.) to generate the matrix files containing cell barcodes and transcript counts. Quality control metrics were used to select cells with total UMI more than 600.
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: count matrix in csv

source_name: bone marrow

growth_protocol: CCR6 KO mouse models were developed by Deltagen, Inc and ordered from The Jackson Laboratory and (B6.129P2-Ccr6tm1Dgen/J, #005793) and compared to age and gender match control mice C57BL6/J mice (#000664). All mice were maintained in pathogen-free conditions and all procedures were approved by the institutional Animal Care and Use Committee of Massachusetts General Hospital.

extract_protocol:
sCells were cultured maintained in DMEM (Corning, 15-013-CV) complemented with 10% FBS (GIBCO by Life Technologies, A31605-01) and 1% Penicillin-Streptomycin (GIBCO by Life Technologies, 15140-122).
Dissociation of tissues into single cells: All samples were collected in Media 199 supplemented with 2% (v/v) FBS. Single cell suspensions of the tumors were obtained by cutting the tumor in to small pieces (1mm3) followed by enzymatic dissociation for 45 minutes at 37°C with shaking at 120 rpm using Collagenase I, Collagenase II, Collagenase III, Collagenase IV (all at a concentration of 1 mg/ml) and Dispase (2mg/ml) in the presence of RNase inhibitors (RNasin (Promega) and RNase OUT (Invitrogen)). Erythrocytes were subsequently removed by ACK Lysing buffer (Quality Biological) and cells resuspended in Media 199 supplemented with 2% (v/v) FBS for further analysis.

treatment_protocol: The RM1-BoM1 cell line was obtained from the Power laboratory41 (REF 41) and was established from the parental prostate cancer mouse models RM1 (RAS and c-Myc oncogenes were overexpressed in normal epithelial prostate cell and injected in syngeneic mice to form tumors41 (REF 41). We enriched RM1-BoM1 cells negative for GFP negative and transduced with Tdtomato (LeGO-T2, Addgene #27342) and luciferase (pENTR221-Firefly, Addgene, #79495). We injected 2.105 RM1-BoM1 cells into the left ventricle of C57Bl/6 mice and monitored bone metastases development by sequential bioluminescence imaging, bone metastatic cells were harvested and selected for the Luciferase and Tdtomato expression. We used the mouse as a bioreactor and repeated a second round of injection and isolation of bone metastases cells in order to establish the RM1-BoM3 bone metastatic cells. The RM1-BoM3 1.104 to 2.104 RM1-BoM3 cells were inoculated through intracardiac injection into mice and bone metastases were monitored by Bioluminescence imaging.

tag: tissue

value: bone marrow

value: CCR6 KO

tag: phenotype

value: bone metastasis


title: WT_Bl6_mouse_Naive-2

status: Public on Aug 30 2021

value: Naïve Mice

value: WT


title: SCG_MBMMet1_WT1

description: cell.annotation.csv on Series record


title: SCG_MBMMet1_WT2

description: cell.annotation.csv on Series record


title: HBEC2 siY/T-rep3

status: Public on Aug 19 2021

city: BOSTON

first: Boting

last: Ning

state: Massachusetts

address: 72 E Concord St

institute: BOSTON UNIVERSITY

description: Gene expression data from human bronchial epithelial cells treated with YAP/TAZ siRNA.

data_processing:
FASTQ files were generated and demultiplexed using the Illumina BaseSpace platform.
FASTQ files were aligned to the human genome (hg19) using STAR v2.5.3a in a two-pass manner.
Quality control was performed using FastQC v0.11.3 and RSeQC v2.6.4 and summarized using MultiQC v0.9.
Transcript and gene level counts were generated using RSEM v1.3.0 and Ensembl annotation (build 92).
Genome_build: hg19
Supplementary_files_format_and_content: raw counts

source_name: Human Bronchial Epithelial Cells

growth_protocol: Human bronchial epithelial cells were cultured in PneumaCult-Ex Plus.

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit (Qiagen).
Libraries were prepared using the Illumina® TruSeq® RNA Sample Preparation Kit v2 according to the manufacturer's protocol.

treatment_protocol: Cells were transfected either with one of three control siRNAs (Control siRNA 1: Qiagen siRNA control #1027310; Control siRNA 2: Dharmacon ON-TARGETplus Non-targeting siRNA #1 [D-001810-0]; Control siRNA 3: Dharmacon ON-TARGETplus Non-targeting siRNA #2 [D-001810-0]) or with YAP/TAZ targeting siRNA (UGUGGAUGAGAUGGAUACA)

value: Human Bronchial Epithelial Cells

tag: sirna

value: YAP/TAZ siRNA


title: WT_Bl6_mouse_Naive-1


title: SCG_MBMMet1_KO1

description: cell.annotation.csv on Series record


title: HBEC2 siY/T-rep2


title: HBEC2 siY/T-rep1


title: HBEC2 Control3-rep3

description: Gene expression data from human bronchial epithelial treated with control siRNA.

value: Control siRNA 3


title: HBEC2 Control3-rep2


title: HBEC1 Control3-rep3


title: HBEC2 Control1-rep1

value: Control siRNA 1


title: HBEC2 Control2-rep3

value: Control siRNA 2


title: HBEC1 siY/T-rep1


title: HBEC2 Control1-rep3


title: HBEC1 siY/T-rep2


title: HBEC1 siY/T-rep3


title: HBEC2 Control1-rep2


title: HBEC2 Control2-rep1


title: HBEC2 Control2-rep2


title: HBEC2 Control3-rep1


title: HBEC1 Control2-rep3


title: HBEC1 Control3-rep1


title: HBEC1 Control2-rep2


title: HBEC1 Control2-rep1


title: HBEC1 Control1-rep2


title: HBEC1 Control1-rep1


title: HBEC1 Control1-rep3


title: subj07_blood_CD8_D28_uninf

status: Public on Jul 01 2021

city: Berlin

first: January

last: Weiner

address: Charitéplatz 1

department: CUBI

country: Germany

institute: Berlin Institute of Health, Charité Medical University of Berlin

data_processing:
Sequence reads were trimmed for adaptor sequence and mapped to hg38 human genome using STAR v2.5.3a
Read counts were calculated using htseq-count.
Expression analysis performed with R package edgeR v3.12.1
Transcripts with counts of zero variance were filtered out; for the remaining scaling normalization was performed. In filtration process, transcripts with entrezID were selected.
Genome_build: GRCh38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample.

source_name: blood

extract_protocol:
Cells sorted into RLT buffer and RNA extracted with Qiagen micro RNA kit.
cDNA generation and amplification with SMartSeq v4 kit. Sequence libraries prepared with Nextera XT kit.

treatment_protocol: CD4+ and CD8+ T cells isolated from blood and bronchoalveolar lavage by flowcytometric sorting

tag: cd type

tag: time [days]

tag: infection status

value: uninfected

tag: patient

tag: age

tag: Sex

value: M


title: subj07_blood_CD4_D00_uninf


title: subj07_blood_CD4_D07_uninf


title: subj07_BAL_CD8_D07_uninf

source_name: BAL


title: subj07_blood_CD8_D07_uninf


title: subj07_BAL_CD8_D00_uninf


title: subj07_BAL_CD4_D00_uninf


title: subj07_BAL_CD4_D07_uninf


title: subj06_blood_CD8_D28_uninf


title: HBEC1 Control3-rep2

tag: cell type


title: subj06_blood_CD4_D28_uninf


title: subj06_blood_CD8_D00_uninf


title: subj06_blood_CD4_D07_uninf


title: subj06_BAL_CD8_D00_uninf


title: subj06_blood_CD8_D07_uninf


title: subj06_BAL_CD8_D28_uninf


title: subj06_BAL_CD4_D00_uninf


title: subj05_blood_CD8_D07_uninf


title: subj05_blood_CD8_D28_uninf


title: subj06_BAL_CD8_D07_uninf


title: subj07_blood_CD4_D28_uninf


title: subj07_blood_CD8_D00_uninf


title: subj06_BAL_CD4_D07_uninf


title: subj06_BAL_CD4_D28_uninf


title: subj05_blood_CD4_D07_uninf


title: subj05_blood_CD4_D00_uninf


title: subj05_blood_CD8_D00_uninf


title: subj05_blood_CD4_D28_uninf


title: subj05_BAL_CD8_D07_uninf


title: subj05_BAL_CD4_D28_uninf


title: subj05_BAL_CD8_D00_uninf


title: subj04_blood_CD8_D07_uninf


title: subj05_BAL_CD4_D00_uninf


title: subj05_BAL_CD4_D07_uninf


title: subj04_blood_CD8_D00_uninf


title: subj04_blood_CD4_D07_uninf


title: subj04_blood_CD4_D00_uninf


title: subj06_blood_CD4_D00_uninf


title: subj04_BAL_CD8_D07_uninf


title: subj04_BAL_CD4_D07_uninf


title: subj04_BAL_CD8_D00_uninf


title: subj04_BAL_CD4_D00_uninf


title: subj05_BAL_CD8_D28_uninf


title: subj03_blood_CD8_D00_uninf


title: subj03_blood_CD8_D28_uninf


title: subj02_blood_CD8_D00_uninf

value: F


title: subj03_blood_CD8_D07_uninf


title: subj03_BAL_CD4_D28_uninf


title: subj03_BAL_CD8_D07_uninf


title: subj03_BAL_CD8_D28_uninf


title: subj02_blood_CD8_D07_uninf


title: subj02_blood_CD4_D07_uninf


title: subj03_blood_CD4_D28_uninf


title: subj03_BAL_CD4_D00_uninf


title: subj03_blood_CD4_D07_uninf


title: subj03_BAL_CD8_D00_uninf


title: subj03_BAL_CD4_D07_uninf


title: subj02_blood_CD4_D28_uninf


title: subj02_BAL_CD8_D00_uninf


title: subj02_BAL_CD8_D07_uninf


title: subj02_BAL_CD8_D28_uninf


title: subj02_blood_CD4_D00_uninf


title: subj03_blood_CD4_D00_uninf


title: subj02_BAL_CD4_D07_uninf


title: subj02_BAL_CD4_D00_uninf


title: subj02_BAL_CD4_D28_uninf


title: subj01_blood_CD8_D07_uninf


title: subj01_blood_CD8_D28_uninf


title: subj02_blood_CD8_D28_uninf


title: subj01_BAL_CD8_D28_uninf


title: subj01_blood_CD4_D07_uninf


title: subj01_blood_CD8_D00_uninf


title: subj01_BAL_CD8_D07_uninf


title: subj01_blood_CD4_D00_uninf


title: subj01_BAL_CD8_D00_uninf


title: subj01_BAL_CD4_D07_uninf


title: subj01_BAL_CD4_D28_uninf


title: subj01_blood_CD4_D28_uninf


title: subj05_blood_CD8_D28_inf

value: infected


title: subj04_blood_CD8_D28_inf


title: subj05_BAL_CD4_D28_inf


title: subj05_blood_CD8_D00_inf


title: subj05_blood_CD4_D28_inf


title: subj05_blood_CD8_D07_inf


title: subj05_BAL_CD4_D00_inf


title: subj05_BAL_CD8_D00_inf


title: subj05_BAL_CD8_D28_inf


title: subj01_BAL_CD4_D00_uninf


title: subj04_blood_CD8_D00_inf


title: subj05_blood_CD4_D07_inf


title: subj04_blood_CD8_D07_inf


title: subj05_BAL_CD8_D07_inf


title: subj04_blood_CD4_D28_inf


title: subj04_blood_CD4_D00_inf


title: subj04_blood_CD4_D07_inf


title: subj04_BAL_CD8_D28_inf


title: subj04_BAL_CD8_D07_inf


title: subj04_BAL_CD4_D00_inf


title: subj03_blood_CD8_D00_inf


title: subj03_blood_CD4_D28_inf


title: subj05_blood_CD4_D00_inf


title: subj04_BAL_CD4_D28_inf


title: subj04_BAL_CD4_D07_inf


title: subj04_BAL_CD8_D00_inf


title: subj03_blood_CD8_D07_inf


title: subj03_BAL_CD8_D07_inf


title: subj03_blood_CD4_D07_inf


title: subj03_blood_CD4_D00_inf


title: subj03_BAL_CD4_D00_inf


title: subj02_blood_CD8_D00_inf


title: subj02_blood_CD8_D28_inf


title: subj02_blood_CD4_D07_inf


title: subj02_BAL_CD8_D28_inf


title: subj03_BAL_CD8_D00_inf


title: subj02_blood_CD4_D28_inf


title: subj02_BAL_CD8_D00_inf


title: subj02_blood_CD4_D00_inf


title: subj02_BAL_CD8_D07_inf


title: subj02_BAL_CD4_D28_inf


title: subj02_BAL_CD4_D07_inf


title: subj01_blood_CD8_D28_inf


title: subj01_blood_CD8_D07_inf


title: subj01_blood_CD8_D00_inf


title: subj03_blood_CD8_D28_inf


title: subj01_blood_CD4_D28_inf


title: subj01_BAL_CD8_D28_inf


title: subj01_BAL_CD4_D28_inf


title: subj01_BAL_CD8_D00_inf


title: subj03_BAL_CD4_D07_inf


title: subj01_blood_CD4_D00_inf


title: subj01_BAL_CD4_D00_inf


title: subj01_BAL_CD4_D07_inf


title: subj01_BAL_CD8_D07_inf


title: subj01_blood_CD4_D07_inf


title: subj02_blood_CD8_D07_inf


title: Uninjured RNAseq rep1

status: Public on Apr 14 2021

city: Madison

first: jianhong

last: ou

state: WI

address: 330 N Orchard Street

institute: Morgridge institute for research

data_processing:
Sequenced reads were trimmed for adaptor sequence TrimGalore (v.0.6.4), then mapped to danRer10 whole genome using STAR (v2.6.1d) with default setting
Read counts for each gene provied in the reference s3://ngi-igenomes/igenomes//Danio_rerio/UCSC/danRer10/Annotation/Genes/genes.gtf were prepared by subread::featureCounts (v1.6.4)
Genome_build: danRer10
Supplementary_files_format_and_content: text file with raw reads counts by featureCounts v1.6.4

organism: Danio rerio

source_name: adult heart ventricles

growth_protocol: Adult zebrafish were raised using standard practice.

extract_protocol:
toRNA was extracted using Trizol and standard purification measures
Libraries were constrcuted using the Illumina Tru-Seq mRNA cloning kit

treatment_protocol: Fish were incubated overnight in 5uM tamoxifen (18 hrs).

tag: creer

value: negative

tag: developmental stage

value: Adult


title: Uninjured RNAseq rep2


title: subj02_BAL_CD4_D00_inf


title: S10599: ETA sheet-2

status: Public on Apr 13 2021

city: Yokohama-shi

first: Jafar

last: Sharif

state: Kanagawa-ken

address: 1-7-22 Suehiuro-cho, Tsurumi-ku

department: IMS

country: Japan

institute: RIKEN

data_processing:
Transcripts Per Kilobase Million (TPM) values were calculated with Salmon.
Raw reads were mapped to the mouse (mm9) genome using Bowtie2.
Genome_build: mm9
Supplementary_files_format_and_content: TPMs for each sample

source_name: Ear skin

extract_protocol:
Mouse ear was dissected and separate the dorsal and ventral side of skin. Ear was incubated with dispase solution or exofoliative toxin A solution at 37 °C. Epidermal sheet and ETA sheet were removed and subjected to isolation of total RNA. Total RNA was prepared using the RNeasy mini kit (QIAGEN). ど
RNA-seq library was prepared by the NEB Next Ultra Directional RNA Library Prep Kit for Illumina (New England Biolabs, Ipswich, MA, USA). Libraries were quantified using the KAPA Library Quantification Kit (Illumina GA). Samples were multiplexed, adjusted to 2 nM, and sequenced on an Illumina HiSeq 2000 instrument. Reads were generated via 25 bp paired-end sequencing.

tag: strain

value: Ear

value: 8 week old

tag: gender

value: female


title: GNPs control rep 2

status: Public on Apr 16 2021

city: Kanazawa

first: Atsuki

last: Kawamura

state: Ishikawa

address: 13-1 Takaramachi

department: Department of Histology and Cell Biology

institute: Graduate School of Medical Sciences, Kanazawa University

data_processing:
Trimming of adapter sequences was performed with Trimmomatic (version 0.39).
RNA-seq: The total amount of each transcript was calculated with the use of a series of programs including HISAT2 (version 2.1.0), featureCounts (version 2.0.0) and DESeq2 (version 1.26.0). RNA-seq reads were mapped against the mouse (mm10) genome.
ChIP-seq: The pair-end reads were mapped to mm10 genome with bowtie (version 2.2.3), and duplicated reads were removed with samtools (version 1.9). Markedly enriched regions of the genome were identified with the MACS2 peak caller (version 2.1.0, with the option “-p 1e-5 --gsize mm --nomodel --extsize 160”). Peak annotation was identified with the ChIPseeker (1.22.1), and heatmap and density profiles were created using ngsplot (2.47).
Genome_build: mm10
Supplementary_files_format_and_content: bigwig files were generated using MACS2; text file includes DESeq2 results

source_name: Granule neuron progenitors

extract_protocol: GNPs were isolated from the cerebellum of mice at P7 by Percoll density gradient centrifugation. RNA was harvested using Trizol reagent.  NEBNext Ultra Directional RNA Library Prep Kit for Illumina (New England Biolabs) was used with 1 µg of total RNA for the construction of sequencing libraries. ChIP was subjected with antibodies to CHD8 or normal IgG. Purified DNA was used to prepare a library with the use of SMARTer ThruPLEX DNA-Seq kit and SMARTer DNA unique dual index kit.

value: Cerebellum

value: Postnatal day 7

tag: genotype


title: S10596: Epidermal sheet-1


title: GNPs control rep 1


title: Human primary fibroblasts, E.g. stimulated, rep2

status: Public on Feb 21 2021

description:
Human primary fibroblasts, E.g. stimulated
S11

data_processing:
Reads were aligned to the Genome Reference Consortium Human Build 38 patch release 7 (GRCh38.p7) genome using the STAR aligner v. 2.7.5a
Quality control (QC) of the reads was inspected using the multiqc reporting tool  summarizing on a number of approaches, including fastqc (available online at: http://www.bioinformatics.babraham.ac.uk/projects/fastqc), dupradar , qualimap  and RNA-SeqC . Raw counts were extracted using the STAR program.
Genome_build: GRCh38.p7
Supplementary_files_format_and_content: count_matrix.xlsx

growth_protocol: Immortalized human gingival epithelial cells (OKG4, purchased from Applied Biological Materials Inc. [ABM]) that were cultured in DermaLife K serum-free growth medium (Lifeline Cell Technology) supplemented with and 1% penicillin-streptomycin. Cells were seeded at 180,000 cells per 6-well (TPP Techno Plastic Products) before E. gingivalis infection with and cultured for 2 days to reach around 80% confluence.

extract_protocol:
Growth medium was carefully removed and 500 µl 2.5% paraformaldehyde was added and incubated for 1 hour at room temperature. Subsequently, 2ml pure water was added to dilute the fixation solution to 0.5%. The samples were kept in 24-well-plate and sealed with paraffin film. Total RNA was extracted from the cells using the RNeasy Mini Kit (Qiagen) according to the manufacturer’s instructions.
500-1000 ng of total RNA of the transfected cell cultures of pGECs and pGFs was sequenced with 16 million reads (75 bp single end) on a NextSeq 500 using the NextSeq 500/550 High Output Kit v2.5 (75 Cycles).
Single-end, 75 bp

treatment_protocol: For the infection experiments, petri dishes containing the amoebic cultures were placed on ice for 8 minutes to detach amoebae from the bottom. Subsequently, the cultures were collected and transferred to sterile 2 ml Eppendorf tubes and centrifuged for 10 min at 275g. The supernatant was discarded and the remaining pellet was washed with 1ml sterile 1 ×PBS by gentle pipetting. The washing was repeated 4 times to reduce bacterial contamination from the culture and after the last washing step, the E. gingivalis pellets were pooled. For RNA-Sequencing (RNA-Seq) experiments, after the last washing step, 10 uL PBS containing pooled E. gingivalis at a multiplicity of infection (MOI) 0.2 was added to human primary epithelial cells (pGECs) and primary fibroblasts (pFBs) cultured in 6-well plates (TPP Techno Plastic Products) and co-incubated for 2 hours. To generate the mock infection medium, we used 10µl of the supernatant of the last washing step. For the raster electron microscopy, E. gingivalis was washed and pooled as described above. Immortalized gingival epithelial cells (OKG4/bmi1/TERT)  were grown on coverslips in 24-well-plates to ~ 80% confluence and infected as described above.

tag: treatment

value: E.g. stimulated

value: primary fibroblasts


title: Human primary fibroblasts, E.g. stimulated, rep1

description:
Human primary fibroblasts, E.g. stimulated
S10


title: Human primary fibroblasts, control, rep2

description:
Human primary fibroblasts, control
S08

source_name: Human primary fibroblasts, control

value: control


title: Human primary fibroblasts, control, rep1

description:
Human primary fibroblasts, control
S07


title: Human primary fibroblasts, control, rep3

description:
Human primary fibroblasts, control
S09


title: Human primary epithelial cells, E.g. stimulated, rep3

description:
Human primary epithelial cells, E.g. stimulated
S06

value: primary epithelial cells


title: Human primary epithelial cells, control, rep1

description:
Human primary epithelial cells, control
S01

source_name: Human primary epithelial cells, control


title: Human primary epithelial cells, E.g. stimulated, rep1

description:
Human primary epithelial cells, E.g. stimulated
S04


title: Human primary epithelial cells, E.g. stimulated, rep2

description:
Human primary epithelial cells, E.g. stimulated
S05


title: Human primary epithelial cells, control, rep3

description:
Human primary epithelial cells, control
S03


title: 7dpt Nrg1 RNAseq rep2

value: positive


title: S10598: Epidermal sheet-2


title: WT_R3_60

status: Public on Jan 15 2021

first: Javier

last: Avalos

address: Av. Reina Mercedes sn

department: Genetics

institute: University of Seville

description: Wild type 60 min illumination, replicate 3

data_processing:
Raw reads for all samples were trimmed, filtered and quality controlled with AfterQC (Chen et al., 2017; doi:10.1186/s12859-017-1469-3)
Read mapping to the reference genome was performed using Tophat 2.1.1 (https://ccb.jhu.edu/software/tophat/index.shtml)
Transcript assembly was performed using Cufflinks and Cuffmerge (Roberts, 2011; doi:10.1093/bioinformatics/btr355. http://cole-trapnell-lab.github.io/cufflinks/)
Mapped sequences were analyzed using SeqMonk (version 1.45.4, https://github.com/s-andrews/SeqMonk)
Quantification was performed using the RNAseq quantitation pipeline with the improved mRNA annotation generated by Cuffmerge, merging transcripts and counting reads over exons.
Deseq2 tool (Love et al., 2014; doi:10.1186/s13059-014-0550-8), implemented in SeqMonk, which needs raw counts for quantitation, was used to compare among conditions.
Genome_build: FMJU01;
https://www.ebi.ac.uk/ena/browser/view/FMJU01000001-FMJU01000086
Supplementary_files_format_and_content: Processed data are described in a single tab-delimited text file that includes raw counts for all samples, indicating probe, chromosome, start and end positions, and feature. Transcripts with no equivalent in FFUJ annotation are indicated as "null"

organism: Fusarium fujikuroi

source_name: Wild type 60 min illumination

growth_protocol: the strains were grown in 100 ml of DG medium in 500 ml Erlenmeyer flasks, inoculated with 1000000 conidia. The flasks were kept in total darkness for three days at 30°C in an orbital shaker (150 rpm). Then, the cultures were transferred to four 25-ml Petri dishes under safe red light and kept in static conditions in the dark for 240 min. Subsequently, the Petri dishes were either kept in the dark or illuminated for 15, 60, or 240 min.

extract_protocol:
RNA samples were extracted with Trizol (Invitrogen, Paisley, UK) using the protocol described by the manufacturer
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Illumination was provided by a set of four fluorescent tubes (Philips TL-D 18 W/840) at a distance of 60 cm, yielding a light intensity of 7 W/m2.

tag: genotype/variation

value: wild type

value: 60 min illumination

value: mycelium


title: WT_R3_0

description: Wild type dark, replicate 3

source_name: Wild type dark

value: dark

tag: tissue


title: 7dpt Nrg1 RNAseq rep1


title: S10600: Epidermal sheet-3


title: WT_R1_60

description: Wild type 60 min illumination, replicate 1


title: S10597: ETA sheet-1


title: WT_R2_60

description: Wild type 60 min illumination, replicate 2


title: Human primary fibroblasts, E.g. stimulated, rep3

description:
Human primary fibroblasts, E.g. stimulated
S12


title: high Erk activity; rep1

status: Public on Sep 23 2020

data_processing:
Reads were trimmed by Trim Galore (0.4.1, with -q 15 --paired) and then mapped with TopHat (v 2.1.1, with parameters --b2-very-sensitive --no-coverage-search and supplying the UCSC danRer10 refSeq annotation).
Gene-level read counts were obtained using the featureCounts (v1.6.1) by the reads with MAPQ greater than 30
Genome_build: danRer10
Supplementary_files_format_and_content: raw counts of sequencing reads for the features of interest for RNAseq

source_name: high Erk activity

growth_protocol: Scale regeneration was induced by plucking about 50 scales, in three rows, from each side of osx:H2A-mCherry osx:Venus-hGeminin fish. At 4 days post plucking (dpp), all regenerating scales were plucked  and collected in PBS on ice. About 3-5 fish were used per sample. Tissue was pelleted by centrifugation (5 min at 600g) and resuspended in 600 µl of 13U/ml Liberase (DH-Research Grade - Sigma #5401054001) in HBSS (Gibso #14025-092) and incubated at 37 C for 1 h. Every 15 min, 500 µl of supernatant was removed, quenched with 65µl sheep serum (Sigma S2263) on ice, and 500 µl of fresh Liberase was added to the primary tube. All collected supernatant was filtered using 50 µl filters (Corning #431750), pelleted (5 min at 600 g) and resuspended in 1 ml DMEM + 1% BSA (UltraPure - Invitrogen AM2616).  Before sorting, 1 µg/ml DAPI (Sigma D9542) was added to the tube.

extract_protocol:
RNA was extracted using TriReagent followed by RNAeasy microKit (Qiagen #74004)
Library preparation was performed by BGI Genomics (Low Input Library Preparation – BT01)

treatment_protocol: Cells were analyzed and sorted using a SH800S Sony Cell Sorter using a 100 µm disposable chip. Initially, events were gated using Forward versus Side Scatter Areas (488 nm laser). Then, single cells were enriched by gating Forward Scatter Height versus Forward Scatter Area (488 nm excitation laser). Live cells were enriched by selecting a population with low DAPI emission (405 nm excitation laser). Finally, H2A-mCherry+ Venus-hGeminin- and H2A-mCherry+ Venus-hGeminin+ were sorted by gating Venus-hGeminin (488 nm excitation laser) versus mCherry (561 nm excitation laser). Cells were collected in PBS or TriReagent (Sigma T9424)

tag: fluorescence

value: osx:H2A-mCherry+ osx:Venus-hGeminin+

value: osteoblasts of regenerating zebrafish scales


title: high Erk activity; rep2


title: WT_R2_0

description: Wild type dark, replicate 2


title: 6C2 cells, cell sample s2, Total RNAseq

status: Public on Dec 31 2020

data_processing:
XSQ files generated from SOLiD machine were mapped on reference genome gal3 using LifeScope v2.5.1 software
Whole.transcriptome.pe workflow of LifeScope was used with 2 mismatch penalty settings
Adaptor and barcode sequences were removed
Read counts and rpkm were aligned to RefSeq genes from the WUGSC 2.1/galGal3 Assembly using the WT count module of LifeScope v2.5.1
Genome_build: galGal3
Supplementary_files_format_and_content: TEXT, ensembl gene ID, chr, strand, start, end, count, length, RPKM, gene symbol

organism: Gallus gallus

source_name: 6C2 cell

extract_protocol:
RNA from 6C2 cells were isolated using RNeasy plus mini kit (Qiagen) following manufacturer's instruction. DNase digestion was performed (Promega) to remove any genomic DNA in the purified RNA.
SOLiD Total RNA-Seq kit was used to prepare whole transcriptome libraries. RNA quality and integrity was assessed using the RNA pico Kit and 2000 Bioanalyzer  (Agilent technologies). 4-6 ug of Total RNA was subjected to rRibosomal depletion (RiboMinus eukaryote system v2, Life technologies) followed by RNAse III fragmentation, adaptor hybridization and reverse transcription. Reversed transcribed DNA was size selected and PCR amplified. Libraries were sequenced in a multiplex manner, pooling two libraries per lane.

tag: cell line

value: chicken erythroleukemia line 6C2

tag: cell cycle

value: Cycling cells

value: cells arrested at the erythroid colony-forming unit stage of hematopoietic development


title: 6C2 cells, cell sample s1, Total RNAseq


title: high Erk activity; rep3


title: WT_R1_0

description: Wild type dark, replicate 1


title: H3K27ac ChIP-seq

data_processing:
XSQ files generated from SOLiD machine were mapped on reference genome gal3 using LifeScope v2.5.1 software
ChIPseq workflow of LifeScope was used
Adaptor and barcode sequences were removed
peaks were called using the bed files  by MACS1.4 program
peak  pvalue cutoff = 1.00e-05
Genome_build: gal3
Supplementary_files_format_and_content: peaks.bigwig

source_name: Erythrocyte cell

extract_protocol:
Chicken immature erythrocyte nuclei were treated  with 0.5% formaldehyde and chromatin was sheared into 200bp fragments.Immunoprecipitation was performed with respective antibody.
ChIPSeq libraries for H3K4me3 and H3K27ac antibodies (Abcam) were prepared according to the 5500 SOLiD fragment library protocol (Life technologies). 5 ug of sheared genomic DNA and 30 ng of ChIP DNA were end-repaired and size selected (100-250bp), followed by dA tailing, ligation of SOLiD barcodes and library PCR amplification. Libraries were subjected to emulsion PCR (ePCR) and loaded on the flowchip for sequencing.

tag: breed

value: Lohmann

value: G0 phase Immature erythrocyte cells

value: White leghorn

tag: chip antibody


title: low Erk activity; rep1

source_name: low Erk activity

value: osx:H2A-mCherry+ osx:Venus-hGeminin-


title: low Erk activity; rep2


title: Human primary epithelial cells, control, rep2

description:
Human primary epithelial cells, control
S02


title: H3K4me3 ChIP-seq


title: low Erk activity; rep3


title: S.pombe-wildtype+3AT-(rep3)-f7

type: RNA

city: Kobe

first: Atsushi

last: Matsuda

address: 588-2, Iwaoka, Iwaoka-cho, Nishi-ku

institute: National Institute of Information and Communications Technology

description: SAMPLE 63

hyb_protocol: Hybridization was done by using the Gene Expression Hybridization Kit (Agilent Technologies) according to manufacturer's instructions except for amount of Cy3-labelled cRNA (37.5 ng was used for each hybridization). After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 8 x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3 micro-m, Dye channel is set to Green and Green PMT is set to 100%).

data_processing:
The scanned images were analyzed with Feature Extraction Software (ver 10.7.3.1, Agilent) using default parameters (protocol GE1-107_Sep09 and Grid: 038274_D_F_20120123) to obtain background subtracted and spatially detrended Processed Signal intensities. 6767 probes (including 56 control probes: indicated by “control” in the comment columns) are spotted multiply to fill 62976 spots in each array. A median of the gProcessedsignals of the spots for each probe was calculated to make a data set for 6767 probes. The median was normalized by the 75 percentile method (the value at 75% was set to 2500). When the average of the gIsWellAboveBG of the spots for each probe is higher than 0.55, the probe signal is considered more than the detection limit, ranked with “a” in the Rank columns. The values of probes that represent duplicated genes were divided by the number of duplicated genes to give corrected values in the Value columns (indicated by “corrected” in the comment columns). The values of probes that were cross-hybridized with paralogs were corrected with the correction probes (indicated as “correction” in the comment columns) as described in the supplemental file with GPL18374 to give corrected values in the Value columns (indicated by “corrected” in the comment columns). “combined” and “deleted” in the comment columns mean the genes were combined with other genes or deleted.
6767 probes (including 56 control probes) are spotted multiply to fill 62976 spots in each array. A median of the gProcessedsignals of the spots for each probe was calculated to make a data set for 6767 probes. The median was normalized by the 75 percentile method (the value at 75% was set to 2500.) to get the value in the Matrix sheet. ID_REF in the Matrix sheet match the identifiers in the SPOT ID column in the 038274_D_GEO_20120123.txt file. When the average of the gIsWellAboveBG of the spots for each probe is higher than 0.55, the probe signal is considered more than the detection limit, ranked with “a” in the Rank columns. The values of probes that represent duplicated genes were divided by the number of duplicated genes to give corrected values in the Corrected columns. The values of probes that were cross-hybridized with paralogs were corrected as described in the supplemental file with GPL18374 to give corrected values in the Corrected columns.

organism: Schizosaccharomyces pombe

source_name: wildtype with 3AT:fraction7

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 200 ng RNA using the Low Input Quick Amp Labeling Kit, one-color including Cy3-CTP (Agilent Technologies) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: The mRNA in every gradient fraction was precipitated by TRIzol.Total. The total RNA was isolated as follows: the cell pellet was frozen with liquid nitrogen and thawed on ice. Cells were washed once with pre-chilled water. The cell pellet was resuspended in 720 micro-l of TES(10mM Tris pH7.5, 10mM EDTA pH8, 0.5% SDS) on ice. 720 micro-l of acidic phenol-chloroform was added to the cell suspension and mixed immediately. The sample was incubated at 65°C for 1 hour, and then placed on ice for 1 min. The sample was centrifuged for 15 min. at 14000rpm at 4°C. 700 micro-l of water phase of the sample was added to 700 micro-l of acidic phenol-chloroform prepared in a phase lock tube (MaXtractTM HighDensity 2ml Qiagen), then mixed. The sample was centrifuged for 5min at 14000rpm at 4°C. 700 micro-l of water phase of the sample was added to 700 micro-l of chloroform prepared in a new phase lock tube, then mixed. The tube was centrifuged for 5 min at 14000rpm at 4°C. Total RNA from the 500 micro-l of the water phase was purified by ethanol precipitation.

treatment_protocol: Cells were grown in EMM-Complete (EMMC) (2) or EMMC-His till A600=0.3-0.5, and then 10 mM 3AT (inhibitor of histidine synthesis) was added to the latter medium for 30 min. Cell extracts containing poly-ribosomes (polysomes) were prepared after cycloheximide (CHX) treatment of the cells, and resolved by 10-45% sucrose gradient-velocity sedimentation (at 41,000 rpm for 2 hrs) into seven fractions.

value: wildtype

tag: medium

tag: fraction

tag: temperature


title: S.pombe-wildtype+3AT-(rep3)-f6

description: SAMPLE 62

source_name: wildtype with 3AT:fraction6


title: S.pombe-wildtype+3AT-(rep3)-TotalRNA

description: SAMPLE 64

source_name: wildtype with 3AT:total RNA

value: TotalRNA


title: S.pombe-wildtype+3AT-(rep3)-f2

description: SAMPLE 58

source_name: wildtype with 3AT:fraction2


title: S.pombe-wildtype+3AT-(rep3)-f5

description: SAMPLE 61

source_name: wildtype with 3AT:fraction5


title: S.pombe-wildtype+3AT-(rep3)-f4

description: SAMPLE 60

source_name: wildtype with 3AT:fraction4


title: S.pombe-wildtype-(rep3)-TotalRNA

description: SAMPLE 56

source_name: wildtype at exponentially-growing phase:total RNA


title: S.pombe-wildtype+3AT-(rep3)-f1

description: SAMPLE 57

source_name: wildtype with 3AT:fraction1


title: S.pombe-wildtype+3AT-(rep2)-f4

description: SAMPLE 44


title: S.pombe-wildtype-(rep3)-f1

description: SAMPLE 49

source_name: wildtype at exponentially-growing phase:fraction1


title: S.pombe-wildtype-(rep3)-f2

description: SAMPLE 50

source_name: wildtype at exponentially-growing phase:fraction2


title: S.pombe-wildtype-(rep3)-f5

description: SAMPLE 53

source_name: wildtype at exponentially-growing phase:fraction5


title: S.pombe-wildtype+3AT-(rep2)-f2

description: SAMPLE 42


title: S.pombe-wildtype+3AT-(rep2)-f6

description: SAMPLE 46


title: S.pombe-wildtype+3AT-(rep3)-f3

description: SAMPLE 59

source_name: wildtype with 3AT:fraction3


title: S.pombe-wildtype+3AT-(rep2)-TotalRNA

description: SAMPLE 48


title: S.pombe-wildtype-(rep3)-f4

description: SAMPLE 52

source_name: wildtype at exponentially-growing phase:fraction4


title: S.pombe-wildtype+3AT-(rep2)-f7

description: SAMPLE 47


title: S.pombe-wildtype-(rep3)-f3

description: SAMPLE 51

source_name: wildtype at exponentially-growing phase:fraction3


title: S.pombe-wildtype-(rep2)-TotalRNA

description: SAMPLE 40


title: S.pombe-wildtype-(rep2)-f7

description: SAMPLE 39

source_name: wildtype at exponentially-growing phase:fraction7


title: S.pombe-wildtype-(rep3)-f6

description: SAMPLE 54

source_name: wildtype at exponentially-growing phase:fraction6


title: S.pombe-wildtype-(rep2)-f6

description: SAMPLE 38


title: S.pombe-wildtype+3AT-(rep2)-f1

description: SAMPLE 41


title: S.pombe-wildtype-(rep3)-f7

description: SAMPLE 55


title: S.pombe-wildtype-(rep2)-f5

description: SAMPLE 37


title: S.pombe-wildtype+3AT-(rep2)-f5

description: SAMPLE 45


title: S.pombe-wildtype+3AT-(rep2)-f3

description: SAMPLE 43


title: S.pombe-wildtype-(rep2)-f4

description: SAMPLE 36


title: S.pombe-wildtype-(rep2)-f3

description: SAMPLE 35


title: S.pombe-wildtype-(rep2)-f2

description: SAMPLE 34


title: S.pombe-wildtype-(rep2)-f1

description: SAMPLE 33


title: S.pombe-gcn2D+3AT-f6

description: SAMPLE 30

source_name: gcn2D with 3AT:fraction6


title: S.pombe-gcn2D-f3

description: SAMPLE 19

source_name: gcn2D at exponentially-growing phase:fraction3


title: S.pombe-gcn2D+3AT-f5

description: SAMPLE 29

source_name: gcn2D with 3AT:fraction5


title: S.pombe-gcn2D+3AT-f4

description: SAMPLE 28

source_name: gcn2D with 3AT:fraction4


title: S.pombe-wildtype+3AT-(rep1)-f6

description: SAMPLE 14

source_name: wildtype with 3AT:fraction6


title: S.pombe-gcn2D-TotalRNA

description: SAMPLE 24

source_name: gcn2D at exponentially-growing phase:total RNA


title: S.pombe-gcn2D-f2

description: SAMPLE 18

source_name: gcn2D at exponentially-growing phase:fraction2


title: S.pombe-gcn2D-f5

description: SAMPLE 21

source_name: gcn2D at exponentially-growing phase:fraction5


title: S.pombe-gcn2D-f4

description: SAMPLE 20

source_name: gcn2D at exponentially-growing phase:fraction4


title: S.pombe-gcn2D+3AT-TotalRNA

description: SAMPLE 32

source_name: gcn2D with 3AT:total RNA


title: S.pombe-gcn2D+3AT-f2

description: SAMPLE 26

source_name: gcn2D with 3AT:fraction2


title: S.pombe-gcn2D-f7

description: SAMPLE 23

source_name: gcn2D at exponentially-growing phase:fraction7


title: S.pombe-gcn2D+3AT-f7

description: SAMPLE 31

source_name: gcn2D with 3AT:fraction7


title: S.pombe-gcn2D-f6

description: SAMPLE 22

source_name: gcn2D at exponentially-growing phase:fraction6


title: S.pombe-gcn2D+3AT-f1

description: SAMPLE 25

source_name: gcn2D with 3AT:fraction1


title: S.pombe-gcn2D+3AT-f3

description: SAMPLE 27

source_name: gcn2D with 3AT:fraction3


title: S.pombe-wildtype+3AT-(rep1)-f3

description: SAMPLE 11

source_name: wildtype with 3AT:fraction3


title: S.pombe-wildtype+3AT-(rep1)-f4

description: SAMPLE 12

source_name: wildtype with 3AT:fraction4


title: S.pombe-wildtype+3AT-(rep1)-f7

description: SAMPLE 15

source_name: wildtype with 3AT:fraction7


title: S.pombe-wildtype+3AT-(rep1)-f5

description: SAMPLE 13

source_name: wildtype with 3AT:fraction5


title: S.pombe-wildtype+3AT-(rep1)-f2

description: SAMPLE 10

source_name: wildtype with 3AT:fraction2


title: S.pombe-wildtype-(rep1)-f6

description: SAMPLE 6

source_name: wildtype at exponentially-growing phase:fraction6


title: S.pombe-wildtype-(rep1)-TotalRNA

description: SAMPLE 8

source_name: wildtype at exponentially-growing phase:total RNA


title: S.pombe-wildtype-(rep1)-f7

description: SAMPLE 7

source_name: wildtype at exponentially-growing phase:fraction7


title: S.pombe-wildtype+3AT-(rep1)-f1

description: SAMPLE 9

source_name: wildtype with 3AT:fraction1


title: S.pombe-wildtype+3AT-(rep1)-TotalRNA

description: SAMPLE 16

source_name: wildtype with 3AT:total RNA


title: S.pombe-gcn2D-f1

description: SAMPLE 17

source_name: gcn2D at exponentially-growing phase:fraction1


title: S.pombe-wildtype-(rep1)-f5

description: SAMPLE 5

source_name: wildtype at exponentially-growing phase:fraction5


title: Ventricles, inj_p53_pos.rep2

status: Public on Sep 21 2020

data_processing:
RNA-Seq reads were trimmed by Trim Galore (0.6.4, with -q 15) and then mapped with TopHat (v 2.1.1, with parameters --b2-very-sensitive --no-coverage-search and supplying the UCSC danRer10 refSeq gene annotation).
Gene-level read counts were obtained using the htseq-count (v1.6.1) by the reads with MAPQ greater than 30.
Genome_build: danRer10
Supplementary_files_format_and_content: raw counts of sequencing reads for the features of interest

source_name: Ventricles of  Tg(Cmlc2:CreER; β-actin2:loxp-mCherry-STOP-loxp-DTA) zebrafish 7 days after tamoxifen-induced genetic ablation of cardiomyocytes

growth_protocol: Fish were grown at 28 degrees.  Male and female animals between 6 and 12 months and of ~2 cm in length were used.

extract_protocol:
Zebrafish ventricles were collected and placed in cold PBS while still pumping to help decrease intra-ventricular blood. Atrium and outflow tract were removed and ventricles (5 per sample) were homogenized in Trizol using a Tissue Lyser II (QIAGEN). RNA was extracted using the standard Trizol protocol, genomic DNA removed using RNA clean and Concentrator Kit (Zymo Research) and processed for libraries preparation.
Libraries were constructed by single-end 50-bp sequencing, with 30 M reads/sample was performed at BGI. RNA-Seq reads were trimmed by Trim Galore (0.6.4, with -q 15) and then mapped with TopHat (v 2.1.1, with parameters --b2-very-sensitive --no-coverage-search and supplying the UCSC danRer10 refSeq gene annotation). Gene-level read counts were obtained using the htseq-count (v1.6.1) by the reads with MAPQ greater than 30. DESeq2 (v 1.26.0) was employed for differential expression analysis.

treatment_protocol: Fish were treated ~ 17 hours  with 0.5 μM tamoxifen to ablate cardiomyocytes. Control fish were equally treated.

value: EK /AB strain

value: ~ 17 hours treatment with 0.5 μM tamoxifen

value: Ventricles


title: Ventricles, uninj_p53_neg.rep3

source_name: Ventricles of uninjured Tg(tp53M214K) zebrafish


title: Ventricles, uninj_p53_pos.rep2

source_name: Ventricles of uninjured Tg(tpWT) zebrafish


title: Ventricles, uninj_p53_pos.rep3


title: Ventricles, uninj_p53_pos.rep1


title: Ventricles, uninj_p53_neg.rep2


title: Ventricles, uninj_p53_neg.rep1


title: Ventricles, inj_p53_neg.rep2

source_name: Ventricles of  Tg(Cmlc2:CreER; β-actin2:loxp-mCherry-STOP-loxp-DTA; tp53M214K) zebrafish 7 days after tamoxifen-induced genetic ablation of cardiomyocytes


title: RNAseq; LEN deletion; 2dpa; injured; batch 3; rep1

status: Public on Jul 19 2020

data_processing:
RNA-Seq reads were trimmed by Trim Galore (0.6.4, with -q 15) and then mapped with TopHat (v 2.1.1, with parameters --b2-very-sensitive --no-coverage-search and supplying the UCSC danRer10 refSeq gene annotation).
Gene-level read counts were obtained using the htseq-count (v1.6.1) by the reads with MAPQ greater than 30.
Genome_build: danRer10
Supplementary_files_format_and_content: raw counts of sequencing reads for the features of interest for RNAseq

source_name: whole fin

growth_protocol: D. rerio from the outbred Ekkwill (EK) strain ranging from 4 to 12 months were used for whole fin library preparations, Tg(tph1b:mCherry-NTR;ubi:switch) fish were used for fibroblast library preparation (Tornini et al 2016). Water temperature was maintained at 27.5°C, and fish were kept on a 14/10 light/dark cycle. Fish were anesthetized in 0.75% v/v 2-phenoxyethanol (Sigma-Aldrich) in fish water. Work with D. rerio was performed in accordance with Duke University guidelines.

extract_protocol:
For RNA-seq, biological triplicate D. rerio caudal fin clip  pools were collected at 0 dpa, 1 dpa, or 4 dpa time points via razor blade (VWR) from 15 fish aged between 3-12 months. Fin tissue was collected in Tri-Reagent (Sigma) and isolated by ethanol precipitation. RNA was further purified with the RNA Clean & Concentrator Kit-5 (Zymo).
RNA-seq libraries were prepared using a Stranded mRNA-seq Kit (KAPA).

treatment_protocol: For fibroblast libraries, triplicate Tg(tph1b:creER;ubi:switch) caudal fins were clipped and treated at 2dpa for 12 hours in 4uM Tamoxifen (Sigma-Aldritch) (Tornini et al., 2016). Fins were allowed to regenerate fully for two months and 75 fish fin samples were pooled for each biological replicate pool.

tag: date

value: 2 dpa

value: whole fin


title: RNAseq; whole fin; 2dpa; injured; batch 3; rep1


title: RNAseq; LEN deletion; 0dpa; uninjured; batch 3; rep1

value: 0 dpa


title: Ventricles, inj_p53_pos.rep1


title: Ventricles, inj_p53_neg.rep3


title: S.pombe-wildtype-(rep1)-f2

description: SAMPLE 2

source_name: wildtype at exponentially-growing phase:fraction2


title: ATACseq; Fibroblast; 0dpa; uninjured; batch 3; rep3

data_processing:
RNA-Seq reads were trimmed by Trim Galore (0.6.4, with -q 15) and then mapped with TopHat (v 2.1.1, with parameters --b2-very-sensitive --no-coverage-search and supplying the UCSC danRer10 refSeq gene annotation).
Gene-level read counts were obtained using the htseq-count (v1.6.1) by the reads with MAPQ greater than 30.
ATAC-Seq reads were trimmed by Trim Galore (0.4.1, with -q 15) and then mapped with bowtie2(2.2.5, with parameters --very-sensitive) to zebrafish genome (UCSC danRer10 refSeq annotation).
The mapped reads were filtered by MAPQ greater than 30 by samtools (v 1.5) and duplicated reads were removed by picard (v 1.91). Bigwig files were generated by kentUtils.
Genome_build: danRer10
Supplementary_files_format_and_content: raw counts of sequencing reads for the features of interest for RNAseq; bigwig files were generated using kentUtils by converting the output of macs2 bedgraph

source_name: ATACseq; Fibroblast; 0dpi; uninjured

growth_protocol: D. rerio from the outbred Ekkwill (EK) strain ranging from 4 to 12 months were used for whole fin library preparations, Tg(tph1b:mCherry-NTR;ubi:switch) fish were used for fibroblast library preparation (Tornini et al 2016), and homozygous evx1 knockout fish were used for evx1 libraries (Schulte et al 2011). Water temperature was maintained at 27.5°C, and fish were kept on a 14/10 light/dark cycle. Fish were anesthetized in 0.75% v/v 2-phenoxyethanol (Sigma-Aldrich) in fish water. Work with D. rerio was performed in accordance with Duke University guidelines.

extract_protocol:
For RNA-seq, biological triplicate D. rerio caudal fin clip  pools were collected at 0 dpa, 1 dpa, or 4 dpa time points via razor blade (VWR) from 15 fish aged between 3-12 months. Homozygous evx1 knockout fish were used for evx1 knockout libraries. Fin tissue was collected in Tri-Reagent (Sigma) and isolated by ethanol precipitation. RNA was further purified with the RNA Clean & Concentrator Kit-5 (Zymo).
For ATAC-seq libraries, biological triplicate D. rerio caudal fin clip pools were collected at 0 dpa, 1 dpa, or 4 dpa time points via razor blade (VWR) from 15 fish aged 3-12 months. Homozygous Evx1 knockout fish (screened visually by jointless phenotype) (Borday et al., 2001) were used for Evx1 knockout libraries. Cells were dissociated using 1.18 U/mL Liberase DH (Roche) in Hank’s Balanced Salt Solution (Gibco) stirring at 37°C for 2 hours, collected in 15 minute increments, then strained through a 70 μm nylon cell strainer (Corning). Samples were quantitated for 100K live cells using the Countess Automated Cell Counter (Thermo Fisher Scientific).Fibroblast samples were sorted for 100K mCherry+ fluorescent cells on a B-C Astrios cell sorter insead of quaitized for 100K live cells on a Contess SCell Conter.
RNA-seq libraries were prepared using a Stranded mRNA-seq Kit (KAPA).
ATAC-seq library preparation was performed as detailed in (Buenrostro et al., 2013).

tag: time

value: fibroblast

value: wild type


title: ATACseq; whole fin; 1dpa; injured; batch 2; rep3

source_name: ATACseq; whole fin; 1dpi; injured

value: 4 dpa


title: S.pombe-wildtype-(rep1)-f3

description: SAMPLE 3

source_name: wildtype at exponentially-growing phase:fraction3


title: ATACseq; Fibroblast; 0dpa; uninjured; batch 3; rep1


title: S.pombe-wildtype-(rep1)-f1

description: SAMPLE 1

source_name: wildtype at exponentially-growing phase:fraction1


title: ATACseq; Fibroblast; 4dpa; injured; batch 3; rep1

source_name: ATACseq; Fibroblast; 4dpi; injured


title: ATACseq; whole fin; 1dpa; injured; batch 2; rep1


title: ATACseq; Fibroblast; 4dpa; injured; batch 3; rep3


title: ATACseq; whole fin; 1dpa; injured; batch 2; rep2


title: ATACseq; Fibroblast; 0dpa; uninjured; batch 3; rep2


title: S.pombe-wildtype-(rep1)-f4

description: SAMPLE 4

source_name: wildtype at exponentially-growing phase:fraction4


title: Ventricles, inj_p53_pos.rep3


title: Ventricles, inj_p53_neg.rep1


title: RNAseq; whole fin; 0dpa; uninjured; batch 3; rep1


title: ATACseq; whole fin; 0dpa; uninjured; batch 2; rep3

source_name: ATACseq; whole fin; 0dpi; uninjured


title: ATACseq; Fibroblast; 4dpa; injured; batch 3; rep2


title: ATACseq; whole fin; 0dpa; uninjured; batch 2; rep2


title: ATACseq; whole fin; 0dpa; uninjured; batch 2; rep1


title: ATACseq; whole fin; 4dpa; injured; batch 1; rep3

source_name: ATACseq; whole fin; 4dpi; injured


title: ATACseq; whole fin; 0dpa; uninjured; batch 1; rep1


title: RNAseq; Fibroblast; 4dpa; injured; batch 3; rep2

source_name: RNAseq; Fibroblast; 4dpi; injured


title: RNAseq; Fibroblast; 0dpa; uninjured; batch 3; rep2

source_name: RNAseq; Fibroblast; 0dpi; uninjured


title: ATACseq; whole fin; 0dpa; uninjured; batch 1; rep2


title: ATACseq; whole fin; 4dpa; injured; batch 1; rep2


title: RNAseq; Fibroblast; 4dpa; injured; batch 3; rep1


title: ATACseq; whole fin; 4dpa; injured; batch 1; rep1


title: ATACseq; whole fin; 0dpa; uninjured; batch 1; rep3


title: RNAseq; Fibroblast; 0dpa; uninjured; batch 3; rep1


title: RNAseq; whole fin; 1dpa; injured; batch 2; rep1

source_name: RNAseq; whole fin; 1dpi; injured

value: 1 dpa


title: RNAseq; whole fin; 1dpa; injured; batch 2; rep3


title: RNAseq; whole fin; 1dpa; injured; batch 2; rep2


title: RNAseq; whole fin; 0dpa; uninjured; batch 2; rep3

source_name: RNAseq; whole fin; 0dpi; uninjured


title: RNAseq; whole fin; 0dpa; uninjured; batch 2; rep2


title: RNAseq; whole fin; 0dpa; uninjured; batch 2; rep1


title: RNAseq; whole fin; 4dpa; injured; batch 1; rep1

source_name: RNAseq; whole fin; 4dpi; injured


title: RNAseq; whole fin; 4dpa; injured; batch 1; rep2


title: RNAseq; whole fin; 0dpa; uninjured; batch 1; rep2


title: G3KO_BMP4_48h_scRNA

status: Public on Apr 19 2020

city: London

first: Silvia

middle: DM

last: Santos

address: 1 Midland Road

country: United Kingdom

institute: The Francis Crick Institute

description: single cell RNA

data_processing:
We used cell-ranger version 3.0.2 to deconvolve, align and quantify the per-cell transcriptomes. Reads were aligned to human transcriptome GRCh38-3.0.0 (software and data available from 10x genomics).
From these alignments we were able to identify 6,221 high quality cells with a mean reads per cell value of 102,867 and a median genes per cell count of 6,487.  All other QC metrics were within thresholds set by 10x Genomics
Genome_build: human GRCh38 (GRCh38-3.0.0 from 10x Genomics)
Supplementary_files_format_and_content: 10x counts matrix, features and barcode data

source_name: embryonic stem cells

growth_protocol: The hESC line KO-GATA3-06 was grown on growth factor-reduced Matrigel and maintained in mTeSR1 media

extract_protocol:
Cells were washed with DPBS and dissociated with Gentle Cell Dissociation Buffer (Stem Cell Technologies) for a maximum of 20 minutes at 37 degrees, then triturated in mTeSR1. Cells were pelleted and resupended in 1% BSA in DPBS, and filtered using a 35 um cell strainer.
The quality and concentration of each single cell suspension was measured using Trypan blue and the Eve automatic cell counter. Where necessary samples were diluted to a concentration of ~1000 cells/ul and approximately 10 000 cells were loaded for each sample into a separate channel of a Chromium Chip B for use in the 10X Chromium Controller. The cells were partitioned into nanoliter scale Gel Beads in emulsions (GEMs) and lysed using the Chromium Single cell 3’ v3 GEM, Library and Gel Bead Kit (cat: 1000075). The RNA was reversed transcribed and amplified using 11 cycles of PCR. Libraries were prepared from the cDNA using a further 12 cycles of amplification and QC’d using the Agilent TapeStation. The libraries were pooled and sequenced on the HiSeq 4000
10x Chromium Single Cell 3' Capture v3

treatment_protocol: BMP4 (50 ng/ml; Life Technologies, PHC9534) was added to mTeSR1 media (Stem Cell Technologies) for 48 hours.

tag: cell type

value: human embryonic stem cells (hESCs)

value: 48 hrs


title: RNAseq; whole fin; 0dpa; uninjured; batch 1; rep1


title: Erythrocyte cell, H4R3me2a

status: Public on Mar 09 2020

description:
Bovan
H4R3me2a

data_processing:
XSQ files generated from SOLiD machine and fastq files from Illumina HiSeq 4000 (Génome Québec)  were mapped on reference genome gal3 using LifeScope v2.5.1 software
ChIPseq workflow of LifeScope was used
Adaptor and barcode sequences were removed
peaks were called using the bed files  by MACS1.4 program
peak  pvalue cutoff = 1.00e-05
Genome_build: gal3
Supplementary_files_format_and_content: peaks.xls, chr, start, end, length, summit, tags, -10*log10(pvalue),fold_enrichment FDR(%)

source_name: Erythrocyte

extract_protocol:
Chicken immature (polychromatic) erythrocyte nuclei were treated  with 0.5% formaldehyde and chromatin was sheared into 200bp fragments.Immunoprecipitation was performed with respective antibody.
ChIP-seq libraries for inputi, H3R2me2si and H4R3me2ai were prepared according to  Illumina and Génome Québec library construction guideline
ChIPSeq libraries for H3R2me2s and H4R3me2a were prepared according to the 5500 SOLiD fragment library protocol (Life technologies). 5 ug of sheared genomic DNA and 30 ng of ChIP DNA were end-repaired and size selected (100-250bp), followed by dA tailing, ligation of SOLiD barcodes and library PCR amplification. Libraries were subjected to emulsion PCR (ePCR) and loaded on the flowchip for sequencing.

value: Lohmann

value: G0 phase Immature erythrocyte cells

value: H4R3me2a (Active motif) 39705


title: Erythrocyte cell, H3R2me2s

description:
Bovan
H3R2me2s

value: H3R2me2s (Millipore) ABE-460


title: Erythrocyte cell, H4R3me2ai

description:
Bovan
srt_SJ11

value: H4R3me2a (Active motif) 39705 (2nd replicate)


title: Erythrocyte cell, H3R2me2si

description:
Bovan
srt_SJ10

value: H3R2me2s (Millipore) ABE-460 (2nd replicate)


title: Erythrocyte cell, Inputi

description:
Bovan
srt_SJ12


title: H1hESC_BMP4_48h_scRNA

data_processing:
We used cell-ranger version 3.0.2 to deconvolve, align and quantify the per-cell transcriptomes. Reads were aligned to human transcriptome GRCh38-3.0.0 (software and data available from 10x genomics).
From these alignments we were able to identify 3,744 high quality cells with a mean reads per cell value of 111,517 and a median genes per cell count of 5,948.  All other QC metrics were within thresholds set by 10x Genomics
Genome_build: human GRCh38 (GRCh38-3.0.0 from 10x Genomics)
Supplementary_files_format_and_content: 10x counts matrix, features and barcode data

growth_protocol: The hESC line H1 was grown on growth factor-reduced Matrigel and maintained in mTeSR1 media

treatment_protocol: BMP4 was added to mTeSR1 media (50 ng/ml) for 1 hour.


title: S.706_D01: day 1 post vaccination, not pregnant

status: Public on Jan 31 2020

description:
day 1 post vaccination, not pregnant
S.706_D01

hyb_protocol: According to manufacturers instructions.

scan_protocol: Image analysis and data extraction were performed with Agilent's Feature Extraction software (version 11.5) to generate the raw expression data.

data_processing: Data analysis was performed in R version 3.6.0 (2019-04-26). Microarray data were pre-processed, normalised and analysed for differential expression using R package limma v3.41.15 13. The raw data were first background corrected using the normexp method. Background corrected signals were quantile normalised between arrays.

source_name: peripherial blood RNA day 1 post vaccination

label_protocol: Microarray experiments were performed as single-color hybridization, and RNA was labeled with the Low Input Quick-Amp Labeling Kit (Agilent Technologies). In brief, mRNA was reverse transcribed and amplified using an oligo-dT-T7 promoter primer, and labeled with cyanine 3-CTP by T7 in vitro transcription. After precipitation, purification and quantification, 0.75 μg labeled cRNA was fragmented and hybridized to custom whole genome human 8 × 60 K multipack microarrays (Agilent-048908) according to the supplier’s protocol (Agilent Technologies).

extract_protocol: Peripheral blood was drawn into PAXgene tubes (PreAnalytiX) and RNA was extracted on the automated QIAcube system (Qiagen) using the PAXgene Blood RNA kit (Qiagen) according to the manufacturer’s instructions. Quality control and quantification of isolated RNA was analyzed with an Agilent 2100 Bioanalyzer (Agilent Technologies) and a NanoDrop 1000 UV-Vis spectrophotometer (Thermo Fisher Scientific).

treatment_protocol: After informed consent had been obtained the first study visit was arranged to take place between 16 and 32 weeks of pregnancy. At this visit all participants had a blood sample collected into a PAXgene tube followed by administration of 1 dose (0.5mls) Boostrix-IPV into the deltoid muscle of their non-dominant arm. A second blood sample was collected into a Paxgene tube 24 hours after vaccine administration and information collected about any adverse events which they had experienced.

value: day 1 post vaccination

value: peripheral blood

tag: timepoint

tag: status

value: not pregnant


title: S.615_D00: prior to vaccination, not pregnant

description:
prior to vaccination, not pregnant
S.615_D00

source_name: peripherial blood RNA prior to vaccination

value: prior to vaccination


title: S.611_D01: day 1 post vaccination, not pregnant

description:
day 1 post vaccination, not pregnant
S.611_D01


title: S.720_D00: prior to vaccination, not pregnant

description:
prior to vaccination, not pregnant
S.720_D00


title: S.513_D01: day 1 post vaccination, not pregnant

description:
day 1 post vaccination, not pregnant
S.513_D01


title: S.505_D01: day 1 post vaccination, not pregnant

description:
day 1 post vaccination, not pregnant
S.505_D01


title: S.815_D01: day 1 post vaccination, not pregnant

description:
day 1 post vaccination, not pregnant
S.815_D01


title: S.514_D00: prior to vaccination, not pregnant

description:
prior to vaccination, not pregnant
S.514_D00


title: S.819_D01: day 1 post vaccination, not pregnant

description:
day 1 post vaccination, not pregnant
S.819_D01


title: S.719_D01: day 1 post vaccination, not pregnant

description:
day 1 post vaccination, not pregnant
S.719_D01


title: S.720_D01: day 1 post vaccination, not pregnant

description:
day 1 post vaccination, not pregnant
S.720_D01


title: S.815_D00: prior to vaccination, not pregnant

description:
prior to vaccination, not pregnant
S.815_D00


title: S.619_D01: day 1 post vaccination, not pregnant

description:
day 1 post vaccination, not pregnant
S.619_D01


title: S.726_D01: day 1 post vaccination, not pregnant

description:
day 1 post vaccination, not pregnant
S.726_D01


title: S.830_D01: day 1 post vaccination, not pregnant

description:
day 1 post vaccination, not pregnant
S.830_D01


title: S.614_D01: day 1 post vaccination, not pregnant

description:
day 1 post vaccination, not pregnant
S.614_D01


title: S.514_D01: day 1 post vaccination, not pregnant

description:
day 1 post vaccination, not pregnant
S.514_D01


title: S.515_D01: day 1 post vaccination, not pregnant

description:
day 1 post vaccination, not pregnant
S.515_D01


title: S.625_D01: day 1 post vaccination, not pregnant

description:
day 1 post vaccination, not pregnant
S.625_D01


title: S.823_D01: day 1 post vaccination, not pregnant

description:
day 1 post vaccination, not pregnant
S.823_D01


title: S.819_D00: prior to vaccination, not pregnant

description:
prior to vaccination, not pregnant
S.819_D00


title: S.817_D01: day 1 post vaccination, not pregnant

description:
day 1 post vaccination, not pregnant
S.817_D01


title: S.803_D01: day 1 post vaccination, not pregnant

description:
day 1 post vaccination, not pregnant
S.803_D01


title: S.716_D01: day 1 post vaccination, not pregnant

description:
day 1 post vaccination, not pregnant
S.716_D01


title: S.818_D01: day 1 post vaccination, not pregnant

description:
day 1 post vaccination, not pregnant
S.818_D01


title: S.615_D01: day 1 post vaccination, not pregnant

description:
day 1 post vaccination, not pregnant
S.615_D01


title: S.817_D00: prior to vaccination, not pregnant

description:
prior to vaccination, not pregnant
S.817_D00


title: S.719_D00: prior to vaccination, not pregnant

description:
prior to vaccination, not pregnant
S.719_D00


title: S.818_D00: prior to vaccination, not pregnant

description:
prior to vaccination, not pregnant
S.818_D00


title: S.612_D01: day 1 post vaccination, not pregnant

description:
day 1 post vaccination, not pregnant
S.612_D01


title: S.609_D00: prior to vaccination, not pregnant

description:
prior to vaccination, not pregnant
S.609_D00


title: S.611_D00: prior to vaccination, not pregnant

description:
prior to vaccination, not pregnant
S.611_D00


title: S.608_D00: prior to vaccination, not pregnant

description:
prior to vaccination, not pregnant
S.608_D00


title: S.512_D00: prior to vaccination, not pregnant

description:
prior to vaccination, not pregnant
S.512_D00


title: S.612_D00: prior to vaccination, not pregnant

description:
prior to vaccination, not pregnant
S.612_D00


title: S.813_D00: prior to vaccination, not pregnant

description:
prior to vaccination, not pregnant
S.813_D00


title: S.814_D01: day 1 post vaccination, not pregnant

description:
day 1 post vaccination, not pregnant
S.814_D01


title: S.609_D01: day 1 post vaccination, not pregnant

description:
day 1 post vaccination, not pregnant
S.609_D01


title: S.813_D01: day 1 post vaccination, not pregnant

description:
day 1 post vaccination, not pregnant
S.813_D01


title: S.515_D00: prior to vaccination, not pregnant

description:
prior to vaccination, not pregnant
S.515_D00


title: S.614_D00: prior to vaccination, not pregnant

description:
prior to vaccination, not pregnant
S.614_D00


title: S.513_D00: prior to vaccination, not pregnant

description:
prior to vaccination, not pregnant
S.513_D00


title: S.608_D01: day 1 post vaccination, not pregnant

description:
day 1 post vaccination, not pregnant
S.608_D01


title: S.814_D00: prior to vaccination, not pregnant

description:
prior to vaccination, not pregnant
S.814_D00


title: S.715_D01: day 1 post vaccination, not pregnant

description:
day 1 post vaccination, not pregnant
S.715_D01


title: S.714_D01: day 1 post vaccination, not pregnant

description:
day 1 post vaccination, not pregnant
S.714_D01


title: S.715_D00: prior to vaccination, not pregnant

description:
prior to vaccination, not pregnant
S.715_D00


title: S.511_D01: day 1 post vaccination, not pregnant

description:
day 1 post vaccination, not pregnant
S.511_D01


title: S.509_D00: prior to vaccination, not pregnant

description:
prior to vaccination, not pregnant
S.509_D00


title: S.512_D01: day 1 post vaccination, not pregnant

description:
day 1 post vaccination, not pregnant
S.512_D01


title: S.508_D00: prior to vaccination, not pregnant

description:
prior to vaccination, not pregnant
S.508_D00


title: S.717_D01: day 1 post vaccination, not pregnant

description:
day 1 post vaccination, not pregnant
S.717_D01


title: S.713_D01: day 1 post vaccination, not pregnant

description:
day 1 post vaccination, not pregnant
S.713_D01


title: S.508_D01: day 1 post vaccination, not pregnant

description:
day 1 post vaccination, not pregnant
S.508_D01


title: S.716_D00: prior to vaccination, not pregnant

description:
prior to vaccination, not pregnant
S.716_D00


title: S.717_D00: prior to vaccination, not pregnant

description:
prior to vaccination, not pregnant
S.717_D00


title: S.511_D00: prior to vaccination, not pregnant

description:
prior to vaccination, not pregnant
S.511_D00


title: S.712_D01: day 1 post vaccination, not pregnant

description:
day 1 post vaccination, not pregnant
S.712_D01


title: S.509_D01: day 1 post vaccination, not pregnant

description:
day 1 post vaccination, not pregnant
S.509_D01


title: S.713_D00: prior to vaccination, not pregnant

description:
prior to vaccination, not pregnant
S.713_D00


title: S.714_D00: prior to vaccination, not pregnant

description:
prior to vaccination, not pregnant
S.714_D00


title: S.712_D00: prior to vaccination, not pregnant

description:
prior to vaccination, not pregnant
S.712_D00


title: S.809_D01: day 1 post vaccination, not pregnant

description:
day 1 post vaccination, not pregnant
S.809_D01


title: S.506_D00: prior to vaccination, not pregnant

description:
prior to vaccination, not pregnant
S.506_D00


title: S.807_D01: day 1 post vaccination, not pregnant

description:
day 1 post vaccination, not pregnant
S.807_D01


title: S.711_D01: day 1 post vaccination, not pregnant

description:
day 1 post vaccination, not pregnant
S.711_D01


title: S.806_D00: prior to vaccination, not pregnant

description:
prior to vaccination, not pregnant
S.806_D00


title: S.711_D00: prior to vaccination, not pregnant

description:
prior to vaccination, not pregnant
S.711_D00


title: S.601_D00: prior to vaccination, not pregnant

description:
prior to vaccination, not pregnant
S.601_D00


title: S.709_D00: prior to vaccination, not pregnant

description:
prior to vaccination, not pregnant
S.709_D00


title: S.503_D01: day 1 post vaccination, not pregnant

description:
day 1 post vaccination, not pregnant
S.503_D01


title: S.505_D00: prior to vaccination, not pregnant

description:
prior to vaccination, not pregnant
S.505_D00


title: S.806_D01: day 1 post vaccination, not pregnant

description:
day 1 post vaccination, not pregnant
S.806_D01


title: S.504_D01: day 1 post vaccination, not pregnant

description:
day 1 post vaccination, not pregnant
S.504_D01


title: S.503_D00: prior to vaccination, not pregnant

description:
prior to vaccination, not pregnant
S.503_D00


title: S.502_D00: prior to vaccination, not pregnant

description:
prior to vaccination, not pregnant
S.502_D00


title: S.708_D00: prior to vaccination, not pregnant

description:
prior to vaccination, not pregnant
S.708_D00


title: S.704_D01: day 1 post vaccination, not pregnant

description:
day 1 post vaccination, not pregnant
S.704_D01


title: S.504_D00: prior to vaccination, not pregnant

description:
prior to vaccination, not pregnant
S.504_D00


title: S.805_D00: prior to vaccination, not pregnant

description:
prior to vaccination, not pregnant
S.805_D00


title: S.607_D01: day 1 post vaccination, not pregnant

description:
day 1 post vaccination, not pregnant
S.607_D01


title: S.502_D01: day 1 post vaccination, not pregnant

description:
day 1 post vaccination, not pregnant
S.502_D01


title: S.804_D00: prior to vaccination, not pregnant

description:
prior to vaccination, not pregnant
S.804_D00


title: S.706_D00: prior to vaccination, not pregnant

description:
prior to vaccination, not pregnant
S.706_D00


title: S.803_D00: prior to vaccination, not pregnant

description:
prior to vaccination, not pregnant
S.803_D00


title: S.802_D00: prior to vaccination, not pregnant

description:
prior to vaccination, not pregnant
S.802_D00


title: S.707_D00: prior to vaccination, not pregnant

description:
prior to vaccination, not pregnant
S.707_D00


title: S.703_D00: prior to vaccination, not pregnant

description:
prior to vaccination, not pregnant
S.703_D00


title: S.705_D00: prior to vaccination, not pregnant

description:
prior to vaccination, not pregnant
S.705_D00


title: S.703_D01: day 1 post vaccination, not pregnant

description:
day 1 post vaccination, not pregnant
S.703_D01


title: S.605_D01: day 1 post vaccination, not pregnant

description:
day 1 post vaccination, not pregnant
S.605_D01


title: S.812_D00: prior to vaccination, not pregnant

description:
prior to vaccination, not pregnant
S.812_D00


title: S.811_D00: prior to vaccination, not pregnant

description:
prior to vaccination, not pregnant
S.811_D00


title: S.810_D01: day 1 post vaccination, not pregnant

description:
day 1 post vaccination, not pregnant
S.810_D01


title: S.604_D01: day 1 post vaccination, not pregnant

description:
day 1 post vaccination, not pregnant
S.604_D01


title: S.507_D00: prior to vaccination, not pregnant

description:
prior to vaccination, not pregnant
S.507_D00


title: S.602_D00: prior to vaccination, not pregnant

description:
prior to vaccination, not pregnant
S.602_D00


title: S.603_D00: prior to vaccination, not pregnant

description:
prior to vaccination, not pregnant
S.603_D00


title: S.605_D00: prior to vaccination, not pregnant

description:
prior to vaccination, not pregnant
S.605_D00


title: S.704_D00: prior to vaccination, not pregnant

description:
prior to vaccination, not pregnant
S.704_D00


title: S.604_D00: prior to vaccination, not pregnant

description:
prior to vaccination, not pregnant
S.604_D00


title: S.506_D01: day 1 post vaccination, not pregnant

description:
day 1 post vaccination, not pregnant
S.506_D01


title: S.507_D01: day 1 post vaccination, not pregnant

description:
day 1 post vaccination, not pregnant
S.507_D01


title: S.607_D00: prior to vaccination, not pregnant

description:
prior to vaccination, not pregnant
S.607_D00


title: S.809_D00: prior to vaccination, not pregnant

description:
prior to vaccination, not pregnant
S.809_D00


title: S.812_D01: day 1 post vaccination, not pregnant

description:
day 1 post vaccination, not pregnant
S.812_D01


title: S.811_D01: day 1 post vaccination, not pregnant

description:
day 1 post vaccination, not pregnant
S.811_D01


title: S.810_D00: prior to vaccination, not pregnant

description:
prior to vaccination, not pregnant
S.810_D00


title: S.705_D01: day 1 post vaccination, not pregnant

description:
day 1 post vaccination, not pregnant
S.705_D01


title: S.603_D01: day 1 post vaccination, not pregnant

description:
day 1 post vaccination, not pregnant
S.603_D01


title: S.807_D00: prior to vaccination, not pregnant

description:
prior to vaccination, not pregnant
S.807_D00


title: S.701_D01: day 1 post vaccination, not pregnant

description:
day 1 post vaccination, not pregnant
S.701_D01


title: S.701_D00: prior to vaccination, not pregnant

description:
prior to vaccination, not pregnant
S.701_D00


title: S.601_D01: day 1 post vaccination, not pregnant

description:
day 1 post vaccination, not pregnant
S.601_D01


title: S.805_D01: day 1 post vaccination, not pregnant

description:
day 1 post vaccination, not pregnant
S.805_D01


title: S.602_D01: day 1 post vaccination, not pregnant

description:
day 1 post vaccination, not pregnant
S.602_D01


title: S.707_D01: day 1 post vaccination, not pregnant

description:
day 1 post vaccination, not pregnant
S.707_D01


title: S.628_D00: prior to vaccination, not pregnant

description:
prior to vaccination, not pregnant
S.628_D00


title: S.804_D01: day 1 post vaccination, not pregnant

description:
day 1 post vaccination, not pregnant
S.804_D01


title: S.727_D01: day 1 post vaccination, not pregnant

description:
day 1 post vaccination, not pregnant
S.727_D01


title: S.829_D01: day 1 post vaccination, not pregnant

description:
day 1 post vaccination, not pregnant
S.829_D01


title: S.709_D01: day 1 post vaccination, not pregnant

description:
day 1 post vaccination, not pregnant
S.709_D01


title: S.627_D00: prior to vaccination, not pregnant

description:
prior to vaccination, not pregnant
S.627_D00


title: S.830_D00: prior to vaccination, not pregnant

description:
prior to vaccination, not pregnant
S.830_D00


title: S.802_D01: day 1 post vaccination, not pregnant

description:
day 1 post vaccination, not pregnant
S.802_D01


title: S.728_D01: day 1 post vaccination, not pregnant

description:
day 1 post vaccination, not pregnant
S.728_D01


title: S.630_D01: day 1 post vaccination, not pregnant

description:
day 1 post vaccination, not pregnant
S.630_D01


title: S.530_D01: day 1 post vaccination, not pregnant

description:
day 1 post vaccination, not pregnant
S.530_D01


title: S.626_D00: prior to vaccination, not pregnant

description:
prior to vaccination, not pregnant
S.626_D00


title: S.829_D00: prior to vaccination, not pregnant

description:
prior to vaccination, not pregnant
S.829_D00


title: S.628_D01: day 1 post vaccination, not pregnant

description:
day 1 post vaccination, not pregnant
S.628_D01


title: S.630_D00: prior to vaccination, not pregnant

description:
prior to vaccination, not pregnant
S.630_D00


title: S.730_D01: day 1 post vaccination, not pregnant

description:
day 1 post vaccination, not pregnant
S.730_D01


title: S.728_D00: prior to vaccination, not pregnant

description:
prior to vaccination, not pregnant
S.728_D00


title: S.727_D00: prior to vaccination, not pregnant

description:
prior to vaccination, not pregnant
S.727_D00


title: S.627_D01: day 1 post vaccination, not pregnant

description:
day 1 post vaccination, not pregnant
S.627_D01


title: S.708_D01: day 1 post vaccination, not pregnant

description:
day 1 post vaccination, not pregnant
S.708_D01


title: S.730_D00: prior to vaccination, not pregnant

description:
prior to vaccination, not pregnant
S.730_D00


title: S.530_D00: prior to vaccination, not pregnant

description:
prior to vaccination, not pregnant
S.530_D00


title: S.625_D00: prior to vaccination, not pregnant

description:
prior to vaccination, not pregnant
S.625_D00


title: S.626_D01: day 1 post vaccination, not pregnant

description:
day 1 post vaccination, not pregnant
S.626_D01


title: S.725_D01: day 1 post vaccination, not pregnant

description:
day 1 post vaccination, not pregnant
S.725_D01


title: S.828_D01: day 1 post vaccination, not pregnant

description:
day 1 post vaccination, not pregnant
S.828_D01


title: S.725_D00: prior to vaccination, not pregnant

description:
prior to vaccination, not pregnant
S.725_D00


title: S.726_D00: prior to vaccination, not pregnant

description:
prior to vaccination, not pregnant
S.726_D00


title: S.620_D01: day 1 post vaccination, not pregnant

description:
day 1 post vaccination, not pregnant
S.620_D01


title: S.529_D01: day 1 post vaccination, not pregnant

description:
day 1 post vaccination, not pregnant
S.529_D01


title: S.527_D01: day 1 post vaccination, not pregnant

description:
day 1 post vaccination, not pregnant
S.527_D01


title: S.526_D01: day 1 post vaccination, not pregnant

description:
day 1 post vaccination, not pregnant
S.526_D01


title: S.827_D00: prior to vaccination, not pregnant

description:
prior to vaccination, not pregnant
S.827_D00


title: S.524_D01: day 1 post vaccination, not pregnant

description:
day 1 post vaccination, not pregnant
S.524_D01


title: S.525_D01: day 1 post vaccination, not pregnant

description:
day 1 post vaccination, not pregnant
S.525_D01


title: S.526_D00: prior to vaccination, not pregnant

description:
prior to vaccination, not pregnant
S.526_D00


title: S.623_D01: day 1 post vaccination, not pregnant

description:
day 1 post vaccination, not pregnant
S.623_D01


title: S.723_D01: day 1 post vaccination, not pregnant

description:
day 1 post vaccination, not pregnant
S.723_D01


title: S.824_D01: day 1 post vaccination, not pregnant

description:
day 1 post vaccination, not pregnant
S.824_D01


title: S.525_D00: prior to vaccination, not pregnant

description:
prior to vaccination, not pregnant
S.525_D00


title: S.529_D00: prior to vaccination, not pregnant

description:
prior to vaccination, not pregnant
S.529_D00


title: S.828_D00: prior to vaccination, not pregnant

description:
prior to vaccination, not pregnant
S.828_D00


title: S.827_D01: day 1 post vaccination, not pregnant

description:
day 1 post vaccination, not pregnant
S.827_D01


title: S.622_D01: day 1 post vaccination, not pregnant

description:
day 1 post vaccination, not pregnant
S.622_D01


title: S.523_D00: prior to vaccination, not pregnant

description:
prior to vaccination, not pregnant
S.523_D00


title: S.826_D00: prior to vaccination, not pregnant

description:
prior to vaccination, not pregnant
S.826_D00


title: S.624_D00: prior to vaccination, not pregnant

description:
prior to vaccination, not pregnant
S.624_D00


title: S.826_D01: day 1 post vaccination, not pregnant

description:
day 1 post vaccination, not pregnant
S.826_D01


title: S.824_D00: prior to vaccination, not pregnant

description:
prior to vaccination, not pregnant
S.824_D00


title: S.523_D01: day 1 post vaccination, not pregnant

description:
day 1 post vaccination, not pregnant
S.523_D01


title: S.724_D00: prior to vaccination, not pregnant

description:
prior to vaccination, not pregnant
S.724_D00


title: S.624_D01: day 1 post vaccination, not pregnant

description:
day 1 post vaccination, not pregnant
S.624_D01


title: S.724_D01: day 1 post vaccination, not pregnant

description:
day 1 post vaccination, not pregnant
S.724_D01


title: S.527_D00: prior to vaccination, not pregnant

description:
prior to vaccination, not pregnant
S.527_D00


title: S.524_D00: prior to vaccination, not pregnant

description:
prior to vaccination, not pregnant
S.524_D00


title: S.623_D00: prior to vaccination, not pregnant

description:
prior to vaccination, not pregnant
S.623_D00


title: S.723_D00: prior to vaccination, not pregnant

description:
prior to vaccination, not pregnant
S.723_D00


title: S.622_D00: prior to vaccination, not pregnant

description:
prior to vaccination, not pregnant
S.622_D00


title: S.520_D01: day 1 post vaccination, not pregnant

description:
day 1 post vaccination, not pregnant
S.520_D01


title: S.519_D00: prior to vaccination, not pregnant

description:
prior to vaccination, not pregnant
S.519_D00


title: S.520_D00: prior to vaccination, not pregnant

description:
prior to vaccination, not pregnant
S.520_D00


title: S.517_D00: prior to vaccination, not pregnant

description:
prior to vaccination, not pregnant
S.517_D00


title: S.517_D01: day 1 post vaccination, not pregnant

description:
day 1 post vaccination, not pregnant
S.517_D01


title: S.620_D00: prior to vaccination, not pregnant

description:
prior to vaccination, not pregnant
S.620_D00


title: S.821_D00: prior to vaccination, not pregnant

description:
prior to vaccination, not pregnant
S.821_D00


title: S.617_D00: prior to vaccination, not pregnant

description:
prior to vaccination, not pregnant
S.617_D00


title: S.516_D00: prior to vaccination, not pregnant

description:
prior to vaccination, not pregnant
S.516_D00


title: VIP30.B: day 1 post vaccination, pregnant

description:
day 1 post vaccination, pregnant
VIP30.B

value: pregnant


title: S.522_D01: day 1 post vaccination, not pregnant

description:
day 1 post vaccination, not pregnant
S.522_D01


title: VIP29.B: day 1 post vaccination, pregnant

description:
day 1 post vaccination, pregnant
VIP29.B


title: S.823_D00: prior to vaccination, not pregnant

description:
prior to vaccination, not pregnant
S.823_D00


title: S.617_D01: day 1 post vaccination, not pregnant

description:
day 1 post vaccination, not pregnant
S.617_D01


title: S.522_D00: prior to vaccination, not pregnant

description:
prior to vaccination, not pregnant
S.522_D00


title: S.820_D00: prior to vaccination, not pregnant

description:
prior to vaccination, not pregnant
S.820_D00


title: S.619_D00: prior to vaccination, not pregnant

description:
prior to vaccination, not pregnant
S.619_D00


title: S.618_D00: prior to vaccination, not pregnant

description:
prior to vaccination, not pregnant
S.618_D00


title: VIP12.B: day 1 post vaccination, pregnant

description:
day 1 post vaccination, pregnant
VIP12.B


title: S.616_D01: day 1 post vaccination, not pregnant

description:
day 1 post vaccination, not pregnant
S.616_D01


title: S.721_D00: prior to vaccination, not pregnant

description:
prior to vaccination, not pregnant
S.721_D00


title: S.618_D01: day 1 post vaccination, not pregnant

description:
day 1 post vaccination, not pregnant
S.618_D01


title: S.821_D01: day 1 post vaccination, not pregnant

description:
day 1 post vaccination, not pregnant
S.821_D01


title: S.820_D01: day 1 post vaccination, not pregnant

description:
day 1 post vaccination, not pregnant
S.820_D01


title: S.516_D01: day 1 post vaccination, not pregnant

description:
day 1 post vaccination, not pregnant
S.516_D01


title: S.616_D00: prior to vaccination, not pregnant

description:
prior to vaccination, not pregnant
S.616_D00


title: S.721_D01: day 1 post vaccination, not pregnant

description:
day 1 post vaccination, not pregnant
S.721_D01


title: VIP30.A: prior to vaccination, pregnant

description:
prior to vaccination, pregnant
VIP30.A


title: S.519_D01: day 1 post vaccination, not pregnant

description:
day 1 post vaccination, not pregnant
S.519_D01


title: VIP29.A: prior to vaccination, pregnant

description:
prior to vaccination, pregnant
VIP29.A


title: VIP19.B: day 1 post vaccination, pregnant

description:
day 1 post vaccination, pregnant
VIP19.B


title: VIP28.A: prior to vaccination, pregnant

description:
prior to vaccination, pregnant
VIP28.A


title: VIP27.A: prior to vaccination, pregnant

description:
prior to vaccination, pregnant
VIP27.A


title: VIP24.B: day 1 post vaccination, pregnant

description:
day 1 post vaccination, pregnant
VIP24.B


title: VIP26.A: prior to vaccination, pregnant

description:
prior to vaccination, pregnant
VIP26.A


title: VIP17.B: day 1 post vaccination, pregnant

description:
day 1 post vaccination, pregnant
VIP17.B


title: VIP22.B: day 1 post vaccination, pregnant

description:
day 1 post vaccination, pregnant
VIP22.B


title: VIP22.A: prior to vaccination, pregnant

description:
prior to vaccination, pregnant
VIP22.A


title: VIP18.B: day 1 post vaccination, pregnant

description:
day 1 post vaccination, pregnant
VIP18.B


title: VIP21.B: day 1 post vaccination, pregnant

description:
day 1 post vaccination, pregnant
VIP21.B


title: VIP25.B: day 1 post vaccination, pregnant

description:
day 1 post vaccination, pregnant
VIP25.B


title: VIP23.B: day 1 post vaccination, pregnant

description:
day 1 post vaccination, pregnant
VIP23.B