rowid,run.accession,experiment.accession,sample.accession,study.accession,bioproject,study.title,study.alias,study.type,study.abstract,study.attributes,study.PMIDs,sample.description,sample.title,sample.alias,sample.centername,sample.attributes,GEOsample.title,GEOsample.dataprocessing,GEOsample.source,GEOsample.treatmentprotocol,GEOsample.extractprotocol,GEOsample.growthprotocol,GEOsample.characteristics,GEOsample.accession,experiment.title,experiment.alias,experiment.library_name,experiment.design_description,experiment.library_construction_protocol,experiment.attributes,experiment.library_strategy,experiment.library_source,experiment.library_selection,experiment.library_layout,experiment.platform,experiment.instrument_model,experiment.spot_descriptor,experiment.study_ref,run.title,run.attributes,run.filename,run.semantic_name,run.total_bases,run.total_spots,run.alias,run.read_lengths,run.base_counts,run.r1_length,run.r2_length,run.r3_length,run.r4_length,run.Acount,run.Ccount,run.Gcount,run.Tcount,run.Ncount,run.experiment,run.pool_member,submission.accession,submission.srasource,submission.bioprojectsource,seqdetective.n_mates,seqdetective.mapping_rate.mate1,seqdetective.mapping_rate.mate2,seqdetective.nofeature_rate.mate1,seqdetective.nofeature_rate.mate2,seqdetective.sparsity.mate1,seqdetective.sparsity.mate2,seqdetective.pos_strand_rate.mate1,seqdetective.pos_strand_rate.mate2,seqdetective.readlen.mate1,seqdetective.readlen.mate2,seqdetective.judgement.mate1,seqdetective.judgement.mate2,seqdetective.judgement.reason,platform_family,instrument_generation,read_bias,selection_class,prep_kit,sc_or_bulk,tech_class,technology,tech_variant,submission.bioprojectsource.country,earliest_date,devstage_curation,devstage_curation_coarse,tissue_curation,tissue_curation_coarse
24784,SRR25502048,SRX21232930,SRS18488024,SRP453114,PRJNA1001808,The Pu.1 target gene Zbtb11 regulates neutrophil development through its integrase like HHCC zinc finger,GSE239949,Transcriptome Analysis,From a forward genetic screen in zebrafish  we identified the transcription factor  ZBTB11  as critical for basal and emergency granulopoiesis and showed that ZBTB11 sits in a pathway directly downstream of master myeloid regulators including PU.1  GFI1 and CEBPa. To better understand target genes regulated by Zbtb11  RNAseq profiling was performed in neutrophils from WT and Zbtb11 mutant zebrafish. Overall design: At 48 hpf  single cell suspensions were prepared from either pooled WT embryos or from pooled phenotype sorted zbtb11 mutant embryos. Neutrophils were FACS sorted on the basis of bright fluorescence for the transgenic neutrophil markers mpx:EGFP or lyz:dsRed into RNALater. N=3 biologically independent pools of neutrophils were obtained from WT and from zbtb11 mutant embryos and used for preparation of RNA and sequencing libraries.,,pubmed:28382966,,Sample 15 05316 MCK mut3,GSM7678168,,tissue:lyz+  mpx+ granulocytes|cell type:lyz+  mpx+ granulocytes|genotype:zbtb11 mutant mne|age:48 hpf|geo loc name:missing|collection date:missing,Sample 15 05316 MCK mut3,Data were QC’d using FastQC  ends trimmed using Trimgalore and trimmed sequence aligned to the zebrafish genome GRCz10 using STAR. Counts were derived using HTseq count and differentially expressed genes determined using limma + voom using Degust v0.21 David R. Powell  Victorian Bioinformatics Consortium  Australia. Assembly: genome GRCz10 Supplementary files format and content: Excel spreadsheet includes HT Seq counts for each sample,lyz+  mpx+ granulocytes,,RNA was extracted from sorted cells using RNeasy Micro Qiagen. Unstranded barcoded libraries were prepared using total RNA and Nugen Ovation RNA Seq system V2 for amplification and cDNA generation  followed by Ovation Ultralow System V2 for library preparation.,,cell type:lyz+  mpx+ granulocytes|genotype:zbtb11 mutant mne|age:48 hpf,GSM7678168,GSM7678168: Sample 15 05316 MCK mut3; Danio rerio; RNA Seq,GSM7678168 r1,GSM7678168,1,RNA was extracted from sorted cells using RNeasy Micro Qiagen. Unstranded barcoded libraries were prepared using total RNA and Nugen Ovation RNA Seq system V2 for amplification and cDNA generation  followed by Ovation Ultralow System V2 for library preparation.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 1500,,SRP453114,,,15-05316_MCK_mut3_GTGCTT_L002_R1_001.fastq.gz 15-05316_MCK_mut3_GTGCTT_L002_R2_001.fastq.gz,fastq fastq,4329868620.0,20618422.0,GSM7678168 r1,0:105 1:105,A:1075032412;C:1077085067;G:1119735718;T:1057797736;N:217687,105,105,,,1075032412,1077085067,1119735718,1057797736,217687,SRX21232930,SRS18488024,SRA1685493,"Rural Clinical Sciences, La Trobe University","Rural Clinical Sciences, La Trobe University",2,0.78961,0.91048,0.20166,0.23232,0.81556,0.81115,0.59478,0.59379,105,105,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Australia,2023-08-03,Hatching,Embryo,Blood,Hematopoietic System
24785,SRR25502049,SRX21232929,SRS18488023,SRP453114,PRJNA1001808,The Pu.1 target gene Zbtb11 regulates neutrophil development through its integrase like HHCC zinc finger,GSE239949,Transcriptome Analysis,From a forward genetic screen in zebrafish  we identified the transcription factor  ZBTB11  as critical for basal and emergency granulopoiesis and showed that ZBTB11 sits in a pathway directly downstream of master myeloid regulators including PU.1  GFI1 and CEBPa. To better understand target genes regulated by Zbtb11  RNAseq profiling was performed in neutrophils from WT and Zbtb11 mutant zebrafish. Overall design: At 48 hpf  single cell suspensions were prepared from either pooled WT embryos or from pooled phenotype sorted zbtb11 mutant embryos. Neutrophils were FACS sorted on the basis of bright fluorescence for the transgenic neutrophil markers mpx:EGFP or lyz:dsRed into RNALater. N=3 biologically independent pools of neutrophils were obtained from WT and from zbtb11 mutant embryos and used for preparation of RNA and sequencing libraries.,,pubmed:28382966,,Sample 15 05316 MCK mut2,GSM7678167,,tissue:lyz+  mpx+ granulocytes|cell type:lyz+  mpx+ granulocytes|genotype:zbtb11 mutant mne|age:48 hpf|geo loc name:missing|collection date:missing,Sample 15 05316 MCK mut2,Data were QC’d using FastQC  ends trimmed using Trimgalore and trimmed sequence aligned to the zebrafish genome GRCz10 using STAR. Counts were derived using HTseq count and differentially expressed genes determined using limma + voom using Degust v0.21 David R. Powell  Victorian Bioinformatics Consortium  Australia. Assembly: genome GRCz10 Supplementary files format and content: Excel spreadsheet includes HT Seq counts for each sample,lyz+  mpx+ granulocytes,,RNA was extracted from sorted cells using RNeasy Micro Qiagen. Unstranded barcoded libraries were prepared using total RNA and Nugen Ovation RNA Seq system V2 for amplification and cDNA generation  followed by Ovation Ultralow System V2 for library preparation.,,cell type:lyz+  mpx+ granulocytes|genotype:zbtb11 mutant mne|age:48 hpf,GSM7678167,GSM7678167: Sample 15 05316 MCK mut2; Danio rerio; RNA Seq,GSM7678167 r1,GSM7678167,1,RNA was extracted from sorted cells using RNeasy Micro Qiagen. Unstranded barcoded libraries were prepared using total RNA and Nugen Ovation RNA Seq system V2 for amplification and cDNA generation  followed by Ovation Ultralow System V2 for library preparation.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 1500,,SRP453114,,,15-05316_MCK_mut2_ACCTCA_L002_R1_001.fastq.gz 15-05316_MCK_mut2_ACCTCA_L002_R2_001.fastq.gz,fastq fastq,4444374270.0,21163687.0,GSM7678167 r1,0:105 1:105,A:1114919906;C:1098541058;G:1145427151;T:1085262902;N:223253,105,105,,,1114919906,1098541058,1145427151,1085262902,223253,SRX21232929,SRS18488023,SRA1685493,"Rural Clinical Sciences, La Trobe University","Rural Clinical Sciences, La Trobe University",2,0.74961,0.90068,0.18596,0.22057,0.81115,0.80754,0.5829,0.58615,105,105,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Australia,2023-08-03,Hatching,Embryo,Blood,Hematopoietic System
24786,SRR25502050,SRX21232928,SRS18488022,SRP453114,PRJNA1001808,The Pu.1 target gene Zbtb11 regulates neutrophil development through its integrase like HHCC zinc finger,GSE239949,Transcriptome Analysis,From a forward genetic screen in zebrafish  we identified the transcription factor  ZBTB11  as critical for basal and emergency granulopoiesis and showed that ZBTB11 sits in a pathway directly downstream of master myeloid regulators including PU.1  GFI1 and CEBPa. To better understand target genes regulated by Zbtb11  RNAseq profiling was performed in neutrophils from WT and Zbtb11 mutant zebrafish. Overall design: At 48 hpf  single cell suspensions were prepared from either pooled WT embryos or from pooled phenotype sorted zbtb11 mutant embryos. Neutrophils were FACS sorted on the basis of bright fluorescence for the transgenic neutrophil markers mpx:EGFP or lyz:dsRed into RNALater. N=3 biologically independent pools of neutrophils were obtained from WT and from zbtb11 mutant embryos and used for preparation of RNA and sequencing libraries.,,pubmed:28382966,,Sample 15 05316 MCK mut1,GSM7678166,,tissue:lyz+  mpx+ granulocytes|cell type:lyz+  mpx+ granulocytes|genotype:zbtb11 mutant mne|age:48 hpf|geo loc name:missing|collection date:missing,Sample 15 05316 MCK mut1,Data were QC’d using FastQC  ends trimmed using Trimgalore and trimmed sequence aligned to the zebrafish genome GRCz10 using STAR. Counts were derived using HTseq count and differentially expressed genes determined using limma + voom using Degust v0.21 David R. Powell  Victorian Bioinformatics Consortium  Australia. Assembly: genome GRCz10 Supplementary files format and content: Excel spreadsheet includes HT Seq counts for each sample,lyz+  mpx+ granulocytes,,RNA was extracted from sorted cells using RNeasy Micro Qiagen. Unstranded barcoded libraries were prepared using total RNA and Nugen Ovation RNA Seq system V2 for amplification and cDNA generation  followed by Ovation Ultralow System V2 for library preparation.,,cell type:lyz+  mpx+ granulocytes|genotype:zbtb11 mutant mne|age:48 hpf,GSM7678166,GSM7678166: Sample 15 05316 MCK mut1; Danio rerio; RNA Seq,GSM7678166 r1,GSM7678166,1,RNA was extracted from sorted cells using RNeasy Micro Qiagen. Unstranded barcoded libraries were prepared using total RNA and Nugen Ovation RNA Seq system V2 for amplification and cDNA generation  followed by Ovation Ultralow System V2 for library preparation.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 1500,,SRP453114,,,15-05316_MCK_mut1_GCACTA_L002_R1_001.fastq.gz 15-05316_MCK_mut1_GCACTA_L002_R2_001.fastq.gz,fastq fastq,4459467180.0,21235558.0,GSM7678166 r1,0:105 1:105,A:1206908747;C:1012207561;G:1060393698;T:1179731376;N:225798,105,105,,,1206908747,1012207561,1060393698,1179731376,225798,SRX21232928,SRS18488022,SRA1685493,"Rural Clinical Sciences, La Trobe University","Rural Clinical Sciences, La Trobe University",2,0.75719,0.88462,0.20719,0.24095,0.78559,0.77914,0.50538,0.55691,105,105,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Australia,2023-08-03,Hatching,Embryo,Blood,Hematopoietic System
24787,SRR25502051,SRX21232927,SRS18488021,SRP453114,PRJNA1001808,The Pu.1 target gene Zbtb11 regulates neutrophil development through its integrase like HHCC zinc finger,GSE239949,Transcriptome Analysis,From a forward genetic screen in zebrafish  we identified the transcription factor  ZBTB11  as critical for basal and emergency granulopoiesis and showed that ZBTB11 sits in a pathway directly downstream of master myeloid regulators including PU.1  GFI1 and CEBPa. To better understand target genes regulated by Zbtb11  RNAseq profiling was performed in neutrophils from WT and Zbtb11 mutant zebrafish. Overall design: At 48 hpf  single cell suspensions were prepared from either pooled WT embryos or from pooled phenotype sorted zbtb11 mutant embryos. Neutrophils were FACS sorted on the basis of bright fluorescence for the transgenic neutrophil markers mpx:EGFP or lyz:dsRed into RNALater. N=3 biologically independent pools of neutrophils were obtained from WT and from zbtb11 mutant embryos and used for preparation of RNA and sequencing libraries.,,pubmed:28382966,,Sample 15 05315 MCK WT3,GSM7678165,,tissue:lyz+  mpx+ granulocytes|cell type:lyz+  mpx+ granulocytes|genotype:wild type|age:48 hpf|geo loc name:missing|collection date:missing,Sample 15 05315 MCK WT3,Data were QC’d using FastQC  ends trimmed using Trimgalore and trimmed sequence aligned to the zebrafish genome GRCz10 using STAR. Counts were derived using HTseq count and differentially expressed genes determined using limma + voom using Degust v0.21 David R. Powell  Victorian Bioinformatics Consortium  Australia. Assembly: genome GRCz10 Supplementary files format and content: Excel spreadsheet includes HT Seq counts for each sample,lyz+  mpx+ granulocytes,,RNA was extracted from sorted cells using RNeasy Micro Qiagen. Unstranded barcoded libraries were prepared using total RNA and Nugen Ovation RNA Seq system V2 for amplification and cDNA generation  followed by Ovation Ultralow System V2 for library preparation.,,cell type:lyz+  mpx+ granulocytes|genotype:wild type|age:48 hpf,GSM7678165,GSM7678165: Sample 15 05315 MCK WT3; Danio rerio; RNA Seq,GSM7678165 r1,GSM7678165,1,RNA was extracted from sorted cells using RNeasy Micro Qiagen. Unstranded barcoded libraries were prepared using total RNA and Nugen Ovation RNA Seq system V2 for amplification and cDNA generation  followed by Ovation Ultralow System V2 for library preparation.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 1500,,SRP453114,,,15-05315_MCK_WT3_AGTGAG_L002_R1_001.fastq.gz 15-05315_MCK_WT3_AGTGAG_L002_R2_001.fastq.gz,fastq fastq,3925329240.0,18692044.0,GSM7678165 r1,0:105 1:105,A:1022654212;C:930239389;G:973328942;T:998905803;N:200894,105,105,,,1022654212,930239389,973328942,998905803,200894,SRX21232927,SRS18488021,SRA1685493,"Rural Clinical Sciences, La Trobe University","Rural Clinical Sciences, La Trobe University",2,0.75647,0.89377,0.19165,0.22718,0.81057,0.80501,0.51173,0.54819,105,105,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Australia,2023-08-03,Hatching,Embryo,Blood,Hematopoietic System
24788,SRR25502052,SRX21232926,SRS18488020,SRP453114,PRJNA1001808,The Pu.1 target gene Zbtb11 regulates neutrophil development through its integrase like HHCC zinc finger,GSE239949,Transcriptome Analysis,From a forward genetic screen in zebrafish  we identified the transcription factor  ZBTB11  as critical for basal and emergency granulopoiesis and showed that ZBTB11 sits in a pathway directly downstream of master myeloid regulators including PU.1  GFI1 and CEBPa. To better understand target genes regulated by Zbtb11  RNAseq profiling was performed in neutrophils from WT and Zbtb11 mutant zebrafish. Overall design: At 48 hpf  single cell suspensions were prepared from either pooled WT embryos or from pooled phenotype sorted zbtb11 mutant embryos. Neutrophils were FACS sorted on the basis of bright fluorescence for the transgenic neutrophil markers mpx:EGFP or lyz:dsRed into RNALater. N=3 biologically independent pools of neutrophils were obtained from WT and from zbtb11 mutant embryos and used for preparation of RNA and sequencing libraries.,,pubmed:28382966,,Sample 15 05314 MCK WT2,GSM7678164,,tissue:lyz+  mpx+ granulocytes|cell type:lyz+  mpx+ granulocytes|genotype:wild type|age:48 hpf|geo loc name:missing|collection date:missing,Sample 15 05314 MCK WT2,Data were QC’d using FastQC  ends trimmed using Trimgalore and trimmed sequence aligned to the zebrafish genome GRCz10 using STAR. Counts were derived using HTseq count and differentially expressed genes determined using limma + voom using Degust v0.21 David R. Powell  Victorian Bioinformatics Consortium  Australia. Assembly: genome GRCz10 Supplementary files format and content: Excel spreadsheet includes HT Seq counts for each sample,lyz+  mpx+ granulocytes,,RNA was extracted from sorted cells using RNeasy Micro Qiagen. Unstranded barcoded libraries were prepared using total RNA and Nugen Ovation RNA Seq system V2 for amplification and cDNA generation  followed by Ovation Ultralow System V2 for library preparation.,,cell type:lyz+  mpx+ granulocytes|genotype:wild type|age:48 hpf,GSM7678164,GSM7678164: Sample 15 05314 MCK WT2; Danio rerio; RNA Seq,GSM7678164 r1,GSM7678164,1,RNA was extracted from sorted cells using RNeasy Micro Qiagen. Unstranded barcoded libraries were prepared using total RNA and Nugen Ovation RNA Seq system V2 for amplification and cDNA generation  followed by Ovation Ultralow System V2 for library preparation.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 1500,,SRP453114,,,15-05314_MCK_WT2_TGGTGA_L002_R2_001.fastq.gz 15-05314_MCK_WT2_TGGTGA_L002_R1_001.fastq.gz,fastq fastq,4100489820.0,19526142.0,GSM7678164 r1,0:105 1:105,A:1022482319;C:1016090490;G:1063619365;T:998086417;N:211229,105,105,,,1022482319,1016090490,1063619365,998086417,211229,SRX21232926,SRS18488020,SRA1685493,"Rural Clinical Sciences, La Trobe University","Rural Clinical Sciences, La Trobe University",2,0.76378,0.90522,0.20093,0.23619,0.82467,0.82049,0.57261,0.562,105,105,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Australia,2023-08-03,Hatching,Embryo,Blood,Hematopoietic System
24789,SRR25502053,SRX21232925,SRS18488019,SRP453114,PRJNA1001808,The Pu.1 target gene Zbtb11 regulates neutrophil development through its integrase like HHCC zinc finger,GSE239949,Transcriptome Analysis,From a forward genetic screen in zebrafish  we identified the transcription factor  ZBTB11  as critical for basal and emergency granulopoiesis and showed that ZBTB11 sits in a pathway directly downstream of master myeloid regulators including PU.1  GFI1 and CEBPa. To better understand target genes regulated by Zbtb11  RNAseq profiling was performed in neutrophils from WT and Zbtb11 mutant zebrafish. Overall design: At 48 hpf  single cell suspensions were prepared from either pooled WT embryos or from pooled phenotype sorted zbtb11 mutant embryos. Neutrophils were FACS sorted on the basis of bright fluorescence for the transgenic neutrophil markers mpx:EGFP or lyz:dsRed into RNALater. N=3 biologically independent pools of neutrophils were obtained from WT and from zbtb11 mutant embryos and used for preparation of RNA and sequencing libraries.,,pubmed:28382966,,Sample 15 05313 MCK WT1,GSM7678163,,tissue:lyz+  mpx+ granulocytes|cell type:lyz+  mpx+ granulocytes|genotype:wild type|age:48 hpf|geo loc name:missing|collection date:missing,Sample 15 05313 MCK WT1,Data were QC’d using FastQC  ends trimmed using Trimgalore and trimmed sequence aligned to the zebrafish genome GRCz10 using STAR. Counts were derived using HTseq count and differentially expressed genes determined using limma + voom using Degust v0.21 David R. Powell  Victorian Bioinformatics Consortium  Australia. Assembly: genome GRCz10 Supplementary files format and content: Excel spreadsheet includes HT Seq counts for each sample,lyz+  mpx+ granulocytes,,RNA was extracted from sorted cells using RNeasy Micro Qiagen. Unstranded barcoded libraries were prepared using total RNA and Nugen Ovation RNA Seq system V2 for amplification and cDNA generation  followed by Ovation Ultralow System V2 for library preparation.,,cell type:lyz+  mpx+ granulocytes|genotype:wild type|age:48 hpf,GSM7678163,GSM7678163: Sample 15 05313 MCK WT1; Danio rerio; RNA Seq,GSM7678163 r1,GSM7678163,1,RNA was extracted from sorted cells using RNeasy Micro Qiagen. Unstranded barcoded libraries were prepared using total RNA and Nugen Ovation RNA Seq system V2 for amplification and cDNA generation  followed by Ovation Ultralow System V2 for library preparation.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 1500,,SRP453114,,,15-05313_MCK_WT1_AACCAG_L002_R1_001.fastq.gz 15-05313_MCK_WT1_AACCAG_L002_R2_001.fastq.gz,fastq fastq,4135721100.0,19693910.0,GSM7678163 r1,0:105 1:105,A:1048700719;C:1014162128;G:1070155053;T:1002495763;N:207437,105,105,,,1048700719,1014162128,1070155053,1002495763,207437,SRX21232925,SRS18488019,SRA1685493,"Rural Clinical Sciences, La Trobe University","Rural Clinical Sciences, La Trobe University",2,0.70974,0.9073,0.1771,0.22534,0.82483,0.81625,0.56311,0.55183,105,105,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Australia,2023-08-03,Hatching,Embryo,Blood,Hematopoietic System
31522,SRR28418937,SRX24023264,SRS20817617,SRP497230,PRJNA1090848,Reprogramming of 3D genome structure underlying HSPC development in zebrafish [RNA seq],GSE262188,Transcriptome Analysis,Development of hematopoietic stem and progenitor cells HSPC is a multi staged complex process that conserved between zebrafish and mammals; however  the mechanism underlying HSPC development is not fully understood. Chromatin conformation plays important roles in transcriptional regulation and cell fate decision  its dynamic and role in HSPC development is poorly investigated. Here  we performed chromatin structure and multi omics dissection across different stages of HSPC developmental trajectory in zebrafish. Chromatin organization of zebrafish HSPC resemble mammalian cells with similar hierarchical structure and characteristics. We revealed the multi scale reorganization of 3D genome and its influence on transcriptional regulation and transition of cell function during HSPC development. Nascent HSPC is featured by loose conformation with obscure structure at all layers. Notably  PU.1 was identified as a potential factor mediating formation of promoter involved loops and regulating gene expression as well as HSPC function. Our results provided a global view of chromatin structure dynamics associated with development of zebrafish HSPC and discovered key transcription factor involved in HSPC chromatin interactions  which will provide new insights into the epigenetic regulatory mechanisms underlying vertebrate HSPC fate decision. Overall design: To comprehensively dissect 3D genome rearrangement and its relation to transcriptional changes of zebrafish HSPC we get RNA seq results from adult sample. Then  conjoint analysis of RNA seq with other datas can reveal the function of transcriptional factors  such as PU.1 .,,pubmed:38886858,,HPSC rep3 RNA seq 3month,GSM8159257,,source name:hematopoietic stem cell|tissue:hematopoietic stem cell|cell line:TgCD41:GFP gata1:dsRed|cell type:hematopoietic stem cell|genotype:CD41+gata1 |time:3month|treatment:flow cytometry|geo loc name:missing|collection date:missing,HPSC rep3 RNA seq 3month,The library is evaluated by FastQC. Readswith mean quality score less than orequal to 30 are removed. Raw reads were trimmed and removed for adapter sequences by fatspv.0.23.2 withpaired end default parameters. Extremely short fragment with length less than or equal to 30bp were also removed. post filtering  high quality reads were aligned to GRCz10 zebrafish genome using HISAT2 with default parameters. FeatureCounts wasused to quantify gene expression and obtain reads count. Fold changes in gene transcription levels were estimated using DESeq2.Enrichment analysis of gene function was performed in the Metascape platform. Assembly: GRCz10 Supplementary files format and content: tab delimited text file includes raw counts for each Sample,hematopoietic stem cell,,Briefly  ∼10 ng of total RNA for each sample was utilized for first strand cDNA reverse transcription in a 30 μl RT buffer containing SuperScript II RTase 100 U  RNase inhibitor 10 U  dNTP mix 10 mM each  SS III first strand buffer 1×  DTT 5 mM  betaine 1 M  MgCl2 6 mM and TSO 1 μM. The RNA library was prepared using TruePrep DNA Library Prep Kit V2 for Illumina,,tissue:hematopoietic stem cell|cell line:TgCD41:GFP gata1:dsRed|cell type:hematopoietic stem cell|genotype:CD41+gata1 |time:3month|treatment:flow cytometry,GSM8159257,GSM8159257: HPSC rep3 RNA seq 3month; Danio rerio; RNA Seq,GSM8159257 r1,GSM8159257,1,Briefly  ∼10 ng of total RNA for each sample was utilized for first strand cDNA reverse transcription in a 30 μl RT buffer containing SuperScript II RTase 100 U  RNase inhibitor 10 U  dNTP mix 10 mM each  SS III first strand buffer 1×  DTT 5 mM  betaine 1 M  MgCl2 6 mM and TSO 1 μM. The RNA library was prepared using TruePrep DNA Library Prep Kit V2 for Illumina,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP497230,,loader:fastq load.py,RNA-seq_Adult_HPSC_rep3_R1.fq.gz RNA-seq_Adult_HPSC_rep3_R2.fq.gz,fastq fastq,11621758500.0,38739195.0,GSM8159257 r1,0:150 1:150,A:3144084931;C:2632272493;G:2693165513;T:3151802925;N:432638,150,150,,,3144084931,2632272493,2693165513,3151802925,432638,SRX24023264,SRS20817617,SRA1831889,South China University of Technology,South China University of Technology,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,China,2024-03-21,Adult,Adult,Blood,Hematopoietic System
31523,SRR28418938,SRX24023263,SRS20817616,SRP497230,PRJNA1090848,Reprogramming of 3D genome structure underlying HSPC development in zebrafish [RNA seq],GSE262188,Transcriptome Analysis,Development of hematopoietic stem and progenitor cells HSPC is a multi staged complex process that conserved between zebrafish and mammals; however  the mechanism underlying HSPC development is not fully understood. Chromatin conformation plays important roles in transcriptional regulation and cell fate decision  its dynamic and role in HSPC development is poorly investigated. Here  we performed chromatin structure and multi omics dissection across different stages of HSPC developmental trajectory in zebrafish. Chromatin organization of zebrafish HSPC resemble mammalian cells with similar hierarchical structure and characteristics. We revealed the multi scale reorganization of 3D genome and its influence on transcriptional regulation and transition of cell function during HSPC development. Nascent HSPC is featured by loose conformation with obscure structure at all layers. Notably  PU.1 was identified as a potential factor mediating formation of promoter involved loops and regulating gene expression as well as HSPC function. Our results provided a global view of chromatin structure dynamics associated with development of zebrafish HSPC and discovered key transcription factor involved in HSPC chromatin interactions  which will provide new insights into the epigenetic regulatory mechanisms underlying vertebrate HSPC fate decision. Overall design: To comprehensively dissect 3D genome rearrangement and its relation to transcriptional changes of zebrafish HSPC we get RNA seq results from adult sample. Then  conjoint analysis of RNA seq with other datas can reveal the function of transcriptional factors  such as PU.1 .,,pubmed:38886858,,HPSC rep2 RNA seq 3month,GSM8159256,,source name:hematopoietic stem cell|tissue:hematopoietic stem cell|cell line:TgCD41:GFP gata1:dsRed|cell type:hematopoietic stem cell|genotype:CD41+gata1 |time:3month|treatment:flow cytometry|geo loc name:missing|collection date:missing,HPSC rep2 RNA seq 3month,The library is evaluated by FastQC. Readswith mean quality score less than orequal to 30 are removed. Raw reads were trimmed and removed for adapter sequences by fatspv.0.23.2 withpaired end default parameters. Extremely short fragment with length less than or equal to 30bp were also removed. post filtering  high quality reads were aligned to GRCz10 zebrafish genome using HISAT2 with default parameters. FeatureCounts wasused to quantify gene expression and obtain reads count. Fold changes in gene transcription levels were estimated using DESeq2.Enrichment analysis of gene function was performed in the Metascape platform. Assembly: GRCz10 Supplementary files format and content: tab delimited text file includes raw counts for each Sample,hematopoietic stem cell,,Briefly  ∼10 ng of total RNA for each sample was utilized for first strand cDNA reverse transcription in a 30 μl RT buffer containing SuperScript II RTase 100 U  RNase inhibitor 10 U  dNTP mix 10 mM each  SS III first strand buffer 1×  DTT 5 mM  betaine 1 M  MgCl2 6 mM and TSO 1 μM. The RNA library was prepared using TruePrep DNA Library Prep Kit V2 for Illumina,,tissue:hematopoietic stem cell|cell line:TgCD41:GFP gata1:dsRed|cell type:hematopoietic stem cell|genotype:CD41+gata1 |time:3month|treatment:flow cytometry,GSM8159256,GSM8159256: HPSC rep2 RNA seq 3month; Danio rerio; RNA Seq,GSM8159256 r1,GSM8159256,1,Briefly  ∼10 ng of total RNA for each sample was utilized for first strand cDNA reverse transcription in a 30 μl RT buffer containing SuperScript II RTase 100 U  RNase inhibitor 10 U  dNTP mix 10 mM each  SS III first strand buffer 1×  DTT 5 mM  betaine 1 M  MgCl2 6 mM and TSO 1 μM. The RNA library was prepared using TruePrep DNA Library Prep Kit V2 for Illumina,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP497230,,loader:fastq load.py,RNA-seq_Adult_HPSC_rep2_R1.fq.gz RNA-seq_Adult_HPSC_rep2_R2.fq.gz,fastq fastq,9951217200.0,33170724.0,GSM8159256 r1,0:150 1:150,A:2755384814;C:2209586340;G:2237522365;T:2748523249;N:200432,150,150,,,2755384814,2209586340,2237522365,2748523249,200432,SRX24023263,SRS20817616,SRA1831889,South China University of Technology,South China University of Technology,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,China,2024-03-21,Adult,Adult,Blood,Hematopoietic System
31524,SRR28418939,SRX24023262,SRS20817615,SRP497230,PRJNA1090848,Reprogramming of 3D genome structure underlying HSPC development in zebrafish [RNA seq],GSE262188,Transcriptome Analysis,Development of hematopoietic stem and progenitor cells HSPC is a multi staged complex process that conserved between zebrafish and mammals; however  the mechanism underlying HSPC development is not fully understood. Chromatin conformation plays important roles in transcriptional regulation and cell fate decision  its dynamic and role in HSPC development is poorly investigated. Here  we performed chromatin structure and multi omics dissection across different stages of HSPC developmental trajectory in zebrafish. Chromatin organization of zebrafish HSPC resemble mammalian cells with similar hierarchical structure and characteristics. We revealed the multi scale reorganization of 3D genome and its influence on transcriptional regulation and transition of cell function during HSPC development. Nascent HSPC is featured by loose conformation with obscure structure at all layers. Notably  PU.1 was identified as a potential factor mediating formation of promoter involved loops and regulating gene expression as well as HSPC function. Our results provided a global view of chromatin structure dynamics associated with development of zebrafish HSPC and discovered key transcription factor involved in HSPC chromatin interactions  which will provide new insights into the epigenetic regulatory mechanisms underlying vertebrate HSPC fate decision. Overall design: To comprehensively dissect 3D genome rearrangement and its relation to transcriptional changes of zebrafish HSPC we get RNA seq results from adult sample. Then  conjoint analysis of RNA seq with other datas can reveal the function of transcriptional factors  such as PU.1 .,,pubmed:38886858,,HPSC rep1 RNA seq 3month,GSM8159255,,source name:hematopoietic stem cell|tissue:hematopoietic stem cell|cell line:TgCD41:GFP gata1:dsRed|cell type:hematopoietic stem cell|genotype:CD41+gata1 |time:3month|treatment:flow cytometry|geo loc name:missing|collection date:missing,HPSC rep1 RNA seq 3month,The library is evaluated by FastQC. Readswith mean quality score less than orequal to 30 are removed. Raw reads were trimmed and removed for adapter sequences by fatspv.0.23.2 withpaired end default parameters. Extremely short fragment with length less than or equal to 30bp were also removed. post filtering  high quality reads were aligned to GRCz10 zebrafish genome using HISAT2 with default parameters. FeatureCounts wasused to quantify gene expression and obtain reads count. Fold changes in gene transcription levels were estimated using DESeq2.Enrichment analysis of gene function was performed in the Metascape platform. Assembly: GRCz10 Supplementary files format and content: tab delimited text file includes raw counts for each Sample,hematopoietic stem cell,,Briefly  ∼10 ng of total RNA for each sample was utilized for first strand cDNA reverse transcription in a 30 μl RT buffer containing SuperScript II RTase 100 U  RNase inhibitor 10 U  dNTP mix 10 mM each  SS III first strand buffer 1×  DTT 5 mM  betaine 1 M  MgCl2 6 mM and TSO 1 μM. The RNA library was prepared using TruePrep DNA Library Prep Kit V2 for Illumina,,tissue:hematopoietic stem cell|cell line:TgCD41:GFP gata1:dsRed|cell type:hematopoietic stem cell|genotype:CD41+gata1 |time:3month|treatment:flow cytometry,GSM8159255,GSM8159255: HPSC rep1 RNA seq 3month; Danio rerio; RNA Seq,GSM8159255 r1,GSM8159255,1,Briefly  ∼10 ng of total RNA for each sample was utilized for first strand cDNA reverse transcription in a 30 μl RT buffer containing SuperScript II RTase 100 U  RNase inhibitor 10 U  dNTP mix 10 mM each  SS III first strand buffer 1×  DTT 5 mM  betaine 1 M  MgCl2 6 mM and TSO 1 μM. The RNA library was prepared using TruePrep DNA Library Prep Kit V2 for Illumina,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP497230,,loader:fastq load.py,RNA-seq_Adult_HPSC_rep1_R1.fq.gz RNA-seq_Adult_HPSC_rep1_R2.fq.gz,fastq fastq,11096617200.0,36988724.0,GSM8159255 r1,0:150 1:150,A:3071303610;C:2460399138;G:2510824334;T:3053621175;N:468943,150,150,,,3071303610,2460399138,2510824334,3053621175,468943,SRX24023262,SRS20817615,SRA1831889,South China University of Technology,South China University of Technology,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,China,2024-03-21,Adult,Adult,Blood,Hematopoietic System
39665,SRR2027911,SRX1029315,SRS937775,SRP058376,PRJNA284108,RNAseq profiling of zebrafish larval macrophages reveals similarities with human M1 and M2 transcriptome signatures,GSE68920,Transcriptome Analysis,We used different zebrafish transgenic lines to sort macrophages  neutrophils and immature lymphoid cells from 5 dpf 6 dpf zebrafish larvae and analyzed their transcriptomes. Comparison between the different transcriptomes and gene ontology analysis revealed specificities for each cell population. Comparison with previously published data showed that zebrafish larval macrophages expressed several known human M1 and M2 macrophages. Transcriptome analysis of uninfected and infected macrophages from embryos infected by of Mycobacterium marinum revealed infection induced transcriptional changes and a shift towards M1 transcriptomic signature. Overall design: For infection experiments  zebrafish embryos were manually dechorionated at 24 hpf and were infected by injection in the caudal vein of 125 colony forming unit of Mycobacterium marinum M strain expressing GFP. Embryos were grown into egg water refresh every day and incubated for 5 days at 28°C. 0.003% 1 phenyl 2 thiourea Sigma Aldrich was added post 1 day to prevent melanisation. post the incubation period  embryos were dissociated into single cell suspension by Trypsin treatment and 20 fluorescent cells per condition were sorted by FACS directly into cDNA synthesis buffer. cDNA synthesis  amplification and library preparation were performed as previously described. Rougeot et al.  2014  Methods Mol Biol 1197:41 66.,,pubmed:31832066,,6dpf mpeg1:mCherryPosMmarinumGFPPos rep3,GSM1686459,,source name:zebra fish larvae|tissue:20 mpeg1 positive macrophages|cell population:GFP positive|developmental stage:6dpf|caudal vain infection:M marinum M strain 125cfu,6dpf mpeg1:mCherryPosMmarinumGFPPos rep3,Image analysis and base calling was done by the Illumina HCS version 1.15.1 Quality trimmed reads were aligned to the Ensembl zebrafish genome Zv9 using Bowtie and reads were mapped to zebrafish transcripts using TopHat and a modified version of the Ensembl Zv9 79 annotation containing few additional genes. Genome build: Zv9 Supplementary files format and content: tab separated value files include gene counts for each sample,zebra fish larvae,Zebrafish embryos were manually dechorionated at 24 hpf and at 28 hpf they were micro injected into the caudal vein with 125 CFU of M. marinum M strain bacteria suspended in PBS/2%PVP.,Between 200 and 300 larvae per condition were collected at 6 dpf. Larvae were dissociated into single cell suspension by Trypsin treatment and fluorescent and 20 fluorescent cells per condition were sorted by FACS directly into cDNA synthesis buffer  without xxx extraction. cDNA were synthetized and amplified with the SMARTer cDNA synthesis kit for Illumina Sequencing Clonetech according to the manufacturer’s instructions. The integrity of the cDNA was confirmed by Lab on chip analysis using the 2100 Bioanalyzer Agilent Technologies. The sheared amplified cDNA  were used to make RNAseq libraries using the Illumina TruSeq RNA Sample Preparation Kit v2 Illumina Inc.  San Diego  USA. In the manufacturer’s instructions two modifications were made. In the adapter ligation step 1 µl instead of 2.5 µl adapter was used. In the library size selection step the library fragments were isolated with a double Ampure XP purification with a 0.7x beads to library ratio. The resulting mRNA Seq library was sequenced using an Illumina HiSeq2000 instrument according to the manufacturer’s description with a read length of 1 x 50 nucleotides.,Zebrafish were handled in compliance with the local animal welfare regulations and maintained according to standard protocols http://ZFIN.org. Embryos were grown at 28 5°C in egg water 60µg/ml Instant Ocean sea salts containing 0.003% 1 phenyl 2 thiourea SigmaFor infected samples. Zebrafish embryos were manually dechorionated at 24 hpf and at 28 hpf they were micro injected into the caudal vein with 125 CFU of M. marinum M strain bacteria suspended in PBS/2%PVP. Aldrich,tissue:20 mpeg1 positive macrophages|cell population:GFP positive|developmental stage:6dpf|caudal vain infection:M marinum M strain 125cfu,GSM1686459,GSM1686459: 6dpf mpeg1:mCherryPosMmarinumGFPPos rep3; Danio rerio; RNA Seq,GSM1686459,,1,Between 200 and 300 larvae per condition were collected at 6 dpf. Larvae were dissociated into single cell suspension by Trypsin treatment and fluorescent and 20 fluorescent cells per condition were sorted by FACS directly into cDNA synthesis buffer  without xxx extraction. cDNA were synthetized and amplified with the SMARTer cDNA synthesis kit for Illumina Sequencing Clonetech according to the manufacturer’s instructions. The integrity of the cDNA was confirmed by Lab on chip analysis using the 2100 Bioanalyzer Agilent Technologies. The sheared amplified cDNA  were used to make RNAseq libraries using the Illumina TruSeq RNA Sample Preparation Kit v2 Illumina Inc.  San Diego  USA. In the manufacturer’s instructions two modifications were made. In the adapter ligation step 1 µl instead of 2.5 µl adapter was used. In the library size selection step the library fragments were isolated with a double Ampure XP purification with a 0.7x beads to library ratio. The resulting mRNA Seq library was sequenced using an Illumina HiSeq2000 instrument according to the manufacturer’s description with a read length of 1 x 50 nucleotides.,GEO Accession:GSM1686459,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP058376,,,ZFG-14-09_06_ATTCCT_L003_R1_001.fastq.gz,fastq,988427889.0,19380939.0,GSM1686459 r1,0:51,A:322268594;C:166925867;G:171531103;T:327506982;N:195343,51,,,,322268594,166925867,171531103,327506982,195343,SRX1029315,SRS937775,SRA268539,GEO,"Institute of Biology, Leiden University",1,0.6999,,0.24019,,0.85358,,0.56832,,51,,B,,usable mapping rate,illumina,hiseq_era,full_length,poly_a,smarter,bulk,unknown,unknown,,Netherlands,2015-05-15,Larval,Larval,Blood,Hematopoietic System
39666,SRR2027910,SRX1029314,SRS937773,SRP058376,PRJNA284108,RNAseq profiling of zebrafish larval macrophages reveals similarities with human M1 and M2 transcriptome signatures,GSE68920,Transcriptome Analysis,We used different zebrafish transgenic lines to sort macrophages  neutrophils and immature lymphoid cells from 5 dpf 6 dpf zebrafish larvae and analyzed their transcriptomes. Comparison between the different transcriptomes and gene ontology analysis revealed specificities for each cell population. Comparison with previously published data showed that zebrafish larval macrophages expressed several known human M1 and M2 macrophages. Transcriptome analysis of uninfected and infected macrophages from embryos infected by of Mycobacterium marinum revealed infection induced transcriptional changes and a shift towards M1 transcriptomic signature. Overall design: For infection experiments  zebrafish embryos were manually dechorionated at 24 hpf and were infected by injection in the caudal vein of 125 colony forming unit of Mycobacterium marinum M strain expressing GFP. Embryos were grown into egg water refresh every day and incubated for 5 days at 28°C. 0.003% 1 phenyl 2 thiourea Sigma Aldrich was added post 1 day to prevent melanisation. post the incubation period  embryos were dissociated into single cell suspension by Trypsin treatment and 20 fluorescent cells per condition were sorted by FACS directly into cDNA synthesis buffer. cDNA synthesis  amplification and library preparation were performed as previously described. Rougeot et al.  2014  Methods Mol Biol 1197:41 66.,,pubmed:31832066,,6dpf mpeg1:mCherryPosMmarinumGFPPos rep2,GSM1686458,,source name:zebra fish larvae|tissue:20 mpeg1 positive macrophages|cell population:GFP positive|developmental stage:6dpf|caudal vain infection:M marinum M strain 125cfu,6dpf mpeg1:mCherryPosMmarinumGFPPos rep2,Image analysis and base calling was done by the Illumina HCS version 1.15.1 Quality trimmed reads were aligned to the Ensembl zebrafish genome Zv9 using Bowtie and reads were mapped to zebrafish transcripts using TopHat and a modified version of the Ensembl Zv9 79 annotation containing few additional genes. Genome build: Zv9 Supplementary files format and content: tab separated value files include gene counts for each sample,zebra fish larvae,Zebrafish embryos were manually dechorionated at 24 hpf and at 28 hpf they were micro injected into the caudal vein with 125 CFU of M. marinum M strain bacteria suspended in PBS/2%PVP.,Between 200 and 300 larvae per condition were collected at 6 dpf. Larvae were dissociated into single cell suspension by Trypsin treatment and fluorescent and 20 fluorescent cells per condition were sorted by FACS directly into cDNA synthesis buffer  without xxx extraction. cDNA were synthetized and amplified with the SMARTer cDNA synthesis kit for Illumina Sequencing Clonetech according to the manufacturer’s instructions. The integrity of the cDNA was confirmed by Lab on chip analysis using the 2100 Bioanalyzer Agilent Technologies. The sheared amplified cDNA  were used to make RNAseq libraries using the Illumina TruSeq RNA Sample Preparation Kit v2 Illumina Inc.  San Diego  USA. In the manufacturer’s instructions two modifications were made. In the adapter ligation step 1 µl instead of 2.5 µl adapter was used. In the library size selection step the library fragments were isolated with a double Ampure XP purification with a 0.7x beads to library ratio. The resulting mRNA Seq library was sequenced using an Illumina HiSeq2000 instrument according to the manufacturer’s description with a read length of 1 x 50 nucleotides.,Zebrafish were handled in compliance with the local animal welfare regulations and maintained according to standard protocols http://ZFIN.org. Embryos were grown at 28 5°C in egg water 60µg/ml Instant Ocean sea salts containing 0.003% 1 phenyl 2 thiourea SigmaFor infected samples. Zebrafish embryos were manually dechorionated at 24 hpf and at 28 hpf they were micro injected into the caudal vein with 125 CFU of M. marinum M strain bacteria suspended in PBS/2%PVP. Aldrich,tissue:20 mpeg1 positive macrophages|cell population:GFP positive|developmental stage:6dpf|caudal vain infection:M marinum M strain 125cfu,GSM1686458,GSM1686458: 6dpf mpeg1:mCherryPosMmarinumGFPPos rep2; Danio rerio; RNA Seq,GSM1686458,,1,Between 200 and 300 larvae per condition were collected at 6 dpf. Larvae were dissociated into single cell suspension by Trypsin treatment and fluorescent and 20 fluorescent cells per condition were sorted by FACS directly into cDNA synthesis buffer  without xxx extraction. cDNA were synthetized and amplified with the SMARTer cDNA synthesis kit for Illumina Sequencing Clonetech according to the manufacturer’s instructions. The integrity of the cDNA was confirmed by Lab on chip analysis using the 2100 Bioanalyzer Agilent Technologies. The sheared amplified cDNA  were used to make RNAseq libraries using the Illumina TruSeq RNA Sample Preparation Kit v2 Illumina Inc.  San Diego  USA. In the manufacturer’s instructions two modifications were made. In the adapter ligation step 1 µl instead of 2.5 µl adapter was used. In the library size selection step the library fragments were isolated with a double Ampure XP purification with a 0.7x beads to library ratio. The resulting mRNA Seq library was sequenced using an Illumina HiSeq2000 instrument according to the manufacturer’s description with a read length of 1 x 50 nucleotides.,GEO Accession:GSM1686458,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP058376,,,ZFG-14-09_05_ACTGAT_L003_R1_001.fastq.gz,fastq,846771207.0,16603357.0,GSM1686458 r1,0:51,A:268435928;C:150903620;G:153931870;T:273331733;N:168056,51,,,,268435928,150903620,153931870,273331733,168056,SRX1029314,SRS937773,SRA268539,GEO,"Institute of Biology, Leiden University",1,0.72025,,0.17943,,0.87937,,0.5683,,51,,B,,usable mapping rate,illumina,hiseq_era,full_length,poly_a,smarter,bulk,unknown,unknown,,Netherlands,2015-05-15,Larval,Larval,Blood,Hematopoietic System
39667,SRR2027909,SRX1029313,SRS937774,SRP058376,PRJNA284108,RNAseq profiling of zebrafish larval macrophages reveals similarities with human M1 and M2 transcriptome signatures,GSE68920,Transcriptome Analysis,We used different zebrafish transgenic lines to sort macrophages  neutrophils and immature lymphoid cells from 5 dpf 6 dpf zebrafish larvae and analyzed their transcriptomes. Comparison between the different transcriptomes and gene ontology analysis revealed specificities for each cell population. Comparison with previously published data showed that zebrafish larval macrophages expressed several known human M1 and M2 macrophages. Transcriptome analysis of uninfected and infected macrophages from embryos infected by of Mycobacterium marinum revealed infection induced transcriptional changes and a shift towards M1 transcriptomic signature. Overall design: For infection experiments  zebrafish embryos were manually dechorionated at 24 hpf and were infected by injection in the caudal vein of 125 colony forming unit of Mycobacterium marinum M strain expressing GFP. Embryos were grown into egg water refresh every day and incubated for 5 days at 28°C. 0.003% 1 phenyl 2 thiourea Sigma Aldrich was added post 1 day to prevent melanisation. post the incubation period  embryos were dissociated into single cell suspension by Trypsin treatment and 20 fluorescent cells per condition were sorted by FACS directly into cDNA synthesis buffer. cDNA synthesis  amplification and library preparation were performed as previously described. Rougeot et al.  2014  Methods Mol Biol 1197:41 66.,,pubmed:31832066,,6dpf mpeg1:mCherryPosMmarinumGFPPos rep1,GSM1686457,,source name:zebra fish larvae|tissue:20 mpeg1 positive macrophages|cell population:GFP positive|developmental stage:6dpf|caudal vain infection:M marinum M strain 125cfu,6dpf mpeg1:mCherryPosMmarinumGFPPos rep1,Image analysis and base calling was done by the Illumina HCS version 1.15.1 Quality trimmed reads were aligned to the Ensembl zebrafish genome Zv9 using Bowtie and reads were mapped to zebrafish transcripts using TopHat and a modified version of the Ensembl Zv9 79 annotation containing few additional genes. Genome build: Zv9 Supplementary files format and content: tab separated value files include gene counts for each sample,zebra fish larvae,Zebrafish embryos were manually dechorionated at 24 hpf and at 28 hpf they were micro injected into the caudal vein with 125 CFU of M. marinum M strain bacteria suspended in PBS/2%PVP.,Between 200 and 300 larvae per condition were collected at 6 dpf. Larvae were dissociated into single cell suspension by Trypsin treatment and fluorescent and 20 fluorescent cells per condition were sorted by FACS directly into cDNA synthesis buffer  without xxx extraction. cDNA were synthetized and amplified with the SMARTer cDNA synthesis kit for Illumina Sequencing Clonetech according to the manufacturer’s instructions. The integrity of the cDNA was confirmed by Lab on chip analysis using the 2100 Bioanalyzer Agilent Technologies. The sheared amplified cDNA  were used to make RNAseq libraries using the Illumina TruSeq RNA Sample Preparation Kit v2 Illumina Inc.  San Diego  USA. In the manufacturer’s instructions two modifications were made. In the adapter ligation step 1 µl instead of 2.5 µl adapter was used. In the library size selection step the library fragments were isolated with a double Ampure XP purification with a 0.7x beads to library ratio. The resulting mRNA Seq library was sequenced using an Illumina HiSeq2000 instrument according to the manufacturer’s description with a read length of 1 x 50 nucleotides.,Zebrafish were handled in compliance with the local animal welfare regulations and maintained according to standard protocols http://ZFIN.org. Embryos were grown at 28 5°C in egg water 60µg/ml Instant Ocean sea salts containing 0.003% 1 phenyl 2 thiourea SigmaFor infected samples. Zebrafish embryos were manually dechorionated at 24 hpf and at 28 hpf they were micro injected into the caudal vein with 125 CFU of M. marinum M strain bacteria suspended in PBS/2%PVP. Aldrich,tissue:20 mpeg1 positive macrophages|cell population:GFP positive|developmental stage:6dpf|caudal vain infection:M marinum M strain 125cfu,GSM1686457,GSM1686457: 6dpf mpeg1:mCherryPosMmarinumGFPPos rep1; Danio rerio; RNA Seq,GSM1686457,,1,Between 200 and 300 larvae per condition were collected at 6 dpf. Larvae were dissociated into single cell suspension by Trypsin treatment and fluorescent and 20 fluorescent cells per condition were sorted by FACS directly into cDNA synthesis buffer  without xxx extraction. cDNA were synthetized and amplified with the SMARTer cDNA synthesis kit for Illumina Sequencing Clonetech according to the manufacturer’s instructions. The integrity of the cDNA was confirmed by Lab on chip analysis using the 2100 Bioanalyzer Agilent Technologies. The sheared amplified cDNA  were used to make RNAseq libraries using the Illumina TruSeq RNA Sample Preparation Kit v2 Illumina Inc.  San Diego  USA. In the manufacturer’s instructions two modifications were made. In the adapter ligation step 1 µl instead of 2.5 µl adapter was used. In the library size selection step the library fragments were isolated with a double Ampure XP purification with a 0.7x beads to library ratio. The resulting mRNA Seq library was sequenced using an Illumina HiSeq2000 instrument according to the manufacturer’s description with a read length of 1 x 50 nucleotides.,GEO Accession:GSM1686457,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP058376,,,ZFG-14-09_04_GAGTGG_L003_R1_001.fastq.gz,fastq,807459642.0,15832542.0,GSM1686457 r1,0:51,A:260516660;C:140425216;G:145411663;T:260942267;N:163836,51,,,,260516660,140425216,145411663,260942267,163836,SRX1029313,SRS937774,SRA268539,GEO,"Institute of Biology, Leiden University",1,0.7097,,0.17187,,0.93304,,0.64092,,51,,B,,usable mapping rate,illumina,hiseq_era,full_length,poly_a,smarter,bulk,unknown,unknown,,Netherlands,2015-05-15,Larval,Larval,Blood,Hematopoietic System
39668,SRR2027908,SRX1029312,SRS937776,SRP058376,PRJNA284108,RNAseq profiling of zebrafish larval macrophages reveals similarities with human M1 and M2 transcriptome signatures,GSE68920,Transcriptome Analysis,We used different zebrafish transgenic lines to sort macrophages  neutrophils and immature lymphoid cells from 5 dpf 6 dpf zebrafish larvae and analyzed their transcriptomes. Comparison between the different transcriptomes and gene ontology analysis revealed specificities for each cell population. Comparison with previously published data showed that zebrafish larval macrophages expressed several known human M1 and M2 macrophages. Transcriptome analysis of uninfected and infected macrophages from embryos infected by of Mycobacterium marinum revealed infection induced transcriptional changes and a shift towards M1 transcriptomic signature. Overall design: For infection experiments  zebrafish embryos were manually dechorionated at 24 hpf and were infected by injection in the caudal vein of 125 colony forming unit of Mycobacterium marinum M strain expressing GFP. Embryos were grown into egg water refresh every day and incubated for 5 days at 28°C. 0.003% 1 phenyl 2 thiourea Sigma Aldrich was added post 1 day to prevent melanisation. post the incubation period  embryos were dissociated into single cell suspension by Trypsin treatment and 20 fluorescent cells per condition were sorted by FACS directly into cDNA synthesis buffer. cDNA synthesis  amplification and library preparation were performed as previously described. Rougeot et al.  2014  Methods Mol Biol 1197:41 66.,,pubmed:31832066,,6dpf mpeg1:mCherryPos MmarinumGFPNeg rep3,GSM1686456,,source name:zebra fish larvae|tissue:20 mpeg1 positive macrophages|cell population:GFP negative|developmental stage:6dpf|caudal vain infection:M marinum M strain 125cfu,6dpf mpeg1:mCherryPos MmarinumGFPNeg rep3,Image analysis and base calling was done by the Illumina HCS version 1.15.1 Quality trimmed reads were aligned to the Ensembl zebrafish genome Zv9 using Bowtie and reads were mapped to zebrafish transcripts using TopHat and a modified version of the Ensembl Zv9 79 annotation containing few additional genes. Genome build: Zv9 Supplementary files format and content: tab separated value files include gene counts for each sample,zebra fish larvae,Zebrafish embryos were manually dechorionated at 24 hpf and at 28 hpf they were micro injected into the caudal vein with 125 CFU of M. marinum M strain bacteria suspended in PBS/2%PVP.,Between 200 and 300 larvae per condition were collected at 6 dpf. Larvae were dissociated into single cell suspension by Trypsin treatment and fluorescent and 20 fluorescent cells per condition were sorted by FACS directly into cDNA synthesis buffer  without xxx extraction. cDNA were synthetized and amplified with the SMARTer cDNA synthesis kit for Illumina Sequencing Clonetech according to the manufacturer’s instructions. The integrity of the cDNA was confirmed by Lab on chip analysis using the 2100 Bioanalyzer Agilent Technologies. The sheared amplified cDNA  were used to make RNAseq libraries using the Illumina TruSeq RNA Sample Preparation Kit v2 Illumina Inc.  San Diego  USA. In the manufacturer’s instructions two modifications were made. In the adapter ligation step 1 µl instead of 2.5 µl adapter was used. In the library size selection step the library fragments were isolated with a double Ampure XP purification with a 0.7x beads to library ratio. The resulting mRNA Seq library was sequenced using an Illumina HiSeq2000 instrument according to the manufacturer’s description with a read length of 1 x 50 nucleotides.,Zebrafish were handled in compliance with the local animal welfare regulations and maintained according to standard protocols http://ZFIN.org. Embryos were grown at 28 5°C in egg water 60µg/ml Instant Ocean sea salts containing 0.003% 1 phenyl 2 thiourea SigmaFor infected samples. Zebrafish embryos were manually dechorionated at 24 hpf and at 28 hpf they were micro injected into the caudal vein with 125 CFU of M. marinum M strain bacteria suspended in PBS/2%PVP. Aldrich,tissue:20 mpeg1 positive macrophages|cell population:GFP negative|developmental stage:6dpf|caudal vain infection:M marinum M strain 125cfu,GSM1686456,GSM1686456: 6dpf mpeg1:mCherryPos MmarinumGFPNeg rep3; Danio rerio; RNA Seq,GSM1686456,,1,Between 200 and 300 larvae per condition were collected at 6 dpf. Larvae were dissociated into single cell suspension by Trypsin treatment and fluorescent and 20 fluorescent cells per condition were sorted by FACS directly into cDNA synthesis buffer  without xxx extraction. cDNA were synthetized and amplified with the SMARTer cDNA synthesis kit for Illumina Sequencing Clonetech according to the manufacturer’s instructions. The integrity of the cDNA was confirmed by Lab on chip analysis using the 2100 Bioanalyzer Agilent Technologies. The sheared amplified cDNA  were used to make RNAseq libraries using the Illumina TruSeq RNA Sample Preparation Kit v2 Illumina Inc.  San Diego  USA. In the manufacturer’s instructions two modifications were made. In the adapter ligation step 1 µl instead of 2.5 µl adapter was used. In the library size selection step the library fragments were isolated with a double Ampure XP purification with a 0.7x beads to library ratio. The resulting mRNA Seq library was sequenced using an Illumina HiSeq2000 instrument according to the manufacturer’s description with a read length of 1 x 50 nucleotides.,GEO Accession:GSM1686456,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP058376,,,ZFG-14-09_03_CGTACG_L003_R1_001.fastq.gz,fastq,1523483526.0,29872226.0,GSM1686456 r1,0:51,A:499019794;C:267493952;G:277264815;T:479405699;N:299266,51,,,,499019794,267493952,277264815,479405699,299266,SRX1029312,SRS937776,SRA268539,GEO,"Institute of Biology, Leiden University",1,0.67328,,0.15117,,0.91179,,0.54858,,51,,B,,usable mapping rate,illumina,hiseq_era,full_length,poly_a,smarter,bulk,unknown,unknown,,Netherlands,2015-05-15,Larval,Larval,Blood,Hematopoietic System
39669,SRR2027907,SRX1029311,SRS937777,SRP058376,PRJNA284108,RNAseq profiling of zebrafish larval macrophages reveals similarities with human M1 and M2 transcriptome signatures,GSE68920,Transcriptome Analysis,We used different zebrafish transgenic lines to sort macrophages  neutrophils and immature lymphoid cells from 5 dpf 6 dpf zebrafish larvae and analyzed their transcriptomes. Comparison between the different transcriptomes and gene ontology analysis revealed specificities for each cell population. Comparison with previously published data showed that zebrafish larval macrophages expressed several known human M1 and M2 macrophages. Transcriptome analysis of uninfected and infected macrophages from embryos infected by of Mycobacterium marinum revealed infection induced transcriptional changes and a shift towards M1 transcriptomic signature. Overall design: For infection experiments  zebrafish embryos were manually dechorionated at 24 hpf and were infected by injection in the caudal vein of 125 colony forming unit of Mycobacterium marinum M strain expressing GFP. Embryos were grown into egg water refresh every day and incubated for 5 days at 28°C. 0.003% 1 phenyl 2 thiourea Sigma Aldrich was added post 1 day to prevent melanisation. post the incubation period  embryos were dissociated into single cell suspension by Trypsin treatment and 20 fluorescent cells per condition were sorted by FACS directly into cDNA synthesis buffer. cDNA synthesis  amplification and library preparation were performed as previously described. Rougeot et al.  2014  Methods Mol Biol 1197:41 66.,,pubmed:31832066,,6dpf mpeg1:mCherryPos MmarinumGFPNeg rep2,GSM1686455,,source name:zebra fish larvae|tissue:20 mpeg1 positive macrophages|cell population:GFP negative|developmental stage:6dpf|caudal vain infection:M marinum M strain 125cfu,6dpf mpeg1:mCherryPos MmarinumGFPNeg rep2,Image analysis and base calling was done by the Illumina HCS version 1.15.1 Quality trimmed reads were aligned to the Ensembl zebrafish genome Zv9 using Bowtie and reads were mapped to zebrafish transcripts using TopHat and a modified version of the Ensembl Zv9 79 annotation containing few additional genes. Genome build: Zv9 Supplementary files format and content: tab separated value files include gene counts for each sample,zebra fish larvae,Zebrafish embryos were manually dechorionated at 24 hpf and at 28 hpf they were micro injected into the caudal vein with 125 CFU of M. marinum M strain bacteria suspended in PBS/2%PVP.,Between 200 and 300 larvae per condition were collected at 6 dpf. Larvae were dissociated into single cell suspension by Trypsin treatment and fluorescent and 20 fluorescent cells per condition were sorted by FACS directly into cDNA synthesis buffer  without xxx extraction. cDNA were synthetized and amplified with the SMARTer cDNA synthesis kit for Illumina Sequencing Clonetech according to the manufacturer’s instructions. The integrity of the cDNA was confirmed by Lab on chip analysis using the 2100 Bioanalyzer Agilent Technologies. The sheared amplified cDNA  were used to make RNAseq libraries using the Illumina TruSeq RNA Sample Preparation Kit v2 Illumina Inc.  San Diego  USA. In the manufacturer’s instructions two modifications were made. In the adapter ligation step 1 µl instead of 2.5 µl adapter was used. In the library size selection step the library fragments were isolated with a double Ampure XP purification with a 0.7x beads to library ratio. The resulting mRNA Seq library was sequenced using an Illumina HiSeq2000 instrument according to the manufacturer’s description with a read length of 1 x 50 nucleotides.,Zebrafish were handled in compliance with the local animal welfare regulations and maintained according to standard protocols http://ZFIN.org. Embryos were grown at 28 5°C in egg water 60µg/ml Instant Ocean sea salts containing 0.003% 1 phenyl 2 thiourea SigmaFor infected samples. Zebrafish embryos were manually dechorionated at 24 hpf and at 28 hpf they were micro injected into the caudal vein with 125 CFU of M. marinum M strain bacteria suspended in PBS/2%PVP. Aldrich,tissue:20 mpeg1 positive macrophages|cell population:GFP negative|developmental stage:6dpf|caudal vain infection:M marinum M strain 125cfu,GSM1686455,GSM1686455: 6dpf mpeg1:mCherryPos MmarinumGFPNeg rep2; Danio rerio; RNA Seq,GSM1686455,,1,Between 200 and 300 larvae per condition were collected at 6 dpf. Larvae were dissociated into single cell suspension by Trypsin treatment and fluorescent and 20 fluorescent cells per condition were sorted by FACS directly into cDNA synthesis buffer  without xxx extraction. cDNA were synthetized and amplified with the SMARTer cDNA synthesis kit for Illumina Sequencing Clonetech according to the manufacturer’s instructions. The integrity of the cDNA was confirmed by Lab on chip analysis using the 2100 Bioanalyzer Agilent Technologies. The sheared amplified cDNA  were used to make RNAseq libraries using the Illumina TruSeq RNA Sample Preparation Kit v2 Illumina Inc.  San Diego  USA. In the manufacturer’s instructions two modifications were made. In the adapter ligation step 1 µl instead of 2.5 µl adapter was used. In the library size selection step the library fragments were isolated with a double Ampure XP purification with a 0.7x beads to library ratio. The resulting mRNA Seq library was sequenced using an Illumina HiSeq2000 instrument according to the manufacturer’s description with a read length of 1 x 50 nucleotides.,GEO Accession:GSM1686455,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP058376,,,ZFG-14-09_02_GTTTCG_L003_R1_001.fastq.gz,fastq,938675094.0,18405394.0,GSM1686455 r1,0:51,A:284384359;C:173449465;G:178039777;T:302612825;N:188668,51,,,,284384359,173449465,178039777,302612825,188668,SRX1029311,SRS937777,SRA268539,GEO,"Institute of Biology, Leiden University",1,0.72884,,0.14723,,0.90767,,0.57414,,51,,B,,usable mapping rate,illumina,hiseq_era,full_length,poly_a,smarter,bulk,unknown,unknown,,Netherlands,2015-05-15,Larval,Larval,Blood,Hematopoietic System
39670,SRR2027906,SRX1029310,SRS937778,SRP058376,PRJNA284108,RNAseq profiling of zebrafish larval macrophages reveals similarities with human M1 and M2 transcriptome signatures,GSE68920,Transcriptome Analysis,We used different zebrafish transgenic lines to sort macrophages  neutrophils and immature lymphoid cells from 5 dpf 6 dpf zebrafish larvae and analyzed their transcriptomes. Comparison between the different transcriptomes and gene ontology analysis revealed specificities for each cell population. Comparison with previously published data showed that zebrafish larval macrophages expressed several known human M1 and M2 macrophages. Transcriptome analysis of uninfected and infected macrophages from embryos infected by of Mycobacterium marinum revealed infection induced transcriptional changes and a shift towards M1 transcriptomic signature. Overall design: For infection experiments  zebrafish embryos were manually dechorionated at 24 hpf and were infected by injection in the caudal vein of 125 colony forming unit of Mycobacterium marinum M strain expressing GFP. Embryos were grown into egg water refresh every day and incubated for 5 days at 28°C. 0.003% 1 phenyl 2 thiourea Sigma Aldrich was added post 1 day to prevent melanisation. post the incubation period  embryos were dissociated into single cell suspension by Trypsin treatment and 20 fluorescent cells per condition were sorted by FACS directly into cDNA synthesis buffer. cDNA synthesis  amplification and library preparation were performed as previously described. Rougeot et al.  2014  Methods Mol Biol 1197:41 66.,,pubmed:31832066,,6dpf mpeg1:mCherryPos MmarinumGFPNeg rep1,GSM1686454,,source name:zebra fish larvae|tissue:20 mpeg1 positive macrophages|cell population:GFP negative|developmental stage:6dpf|caudal vain infection:M marinum M strain 125cfu,6dpf mpeg1:mCherryPos MmarinumGFPNeg rep1,Image analysis and base calling was done by the Illumina HCS version 1.15.1 Quality trimmed reads were aligned to the Ensembl zebrafish genome Zv9 using Bowtie and reads were mapped to zebrafish transcripts using TopHat and a modified version of the Ensembl Zv9 79 annotation containing few additional genes. Genome build: Zv9 Supplementary files format and content: tab separated value files include gene counts for each sample,zebra fish larvae,Zebrafish embryos were manually dechorionated at 24 hpf and at 28 hpf they were micro injected into the caudal vein with 125 CFU of M. marinum M strain bacteria suspended in PBS/2%PVP.,Between 200 and 300 larvae per condition were collected at 6 dpf. Larvae were dissociated into single cell suspension by Trypsin treatment and fluorescent and 20 fluorescent cells per condition were sorted by FACS directly into cDNA synthesis buffer  without xxx extraction. cDNA were synthetized and amplified with the SMARTer cDNA synthesis kit for Illumina Sequencing Clonetech according to the manufacturer’s instructions. The integrity of the cDNA was confirmed by Lab on chip analysis using the 2100 Bioanalyzer Agilent Technologies. The sheared amplified cDNA  were used to make RNAseq libraries using the Illumina TruSeq RNA Sample Preparation Kit v2 Illumina Inc.  San Diego  USA. In the manufacturer’s instructions two modifications were made. In the adapter ligation step 1 µl instead of 2.5 µl adapter was used. In the library size selection step the library fragments were isolated with a double Ampure XP purification with a 0.7x beads to library ratio. The resulting mRNA Seq library was sequenced using an Illumina HiSeq2000 instrument according to the manufacturer’s description with a read length of 1 x 50 nucleotides.,Zebrafish were handled in compliance with the local animal welfare regulations and maintained according to standard protocols http://ZFIN.org. Embryos were grown at 28 5°C in egg water 60µg/ml Instant Ocean sea salts containing 0.003% 1 phenyl 2 thiourea SigmaFor infected samples. Zebrafish embryos were manually dechorionated at 24 hpf and at 28 hpf they were micro injected into the caudal vein with 125 CFU of M. marinum M strain bacteria suspended in PBS/2%PVP. Aldrich,tissue:20 mpeg1 positive macrophages|cell population:GFP negative|developmental stage:6dpf|caudal vain infection:M marinum M strain 125cfu,GSM1686454,GSM1686454: 6dpf mpeg1:mCherryPos MmarinumGFPNeg rep1; Danio rerio; RNA Seq,GSM1686454,,1,Between 200 and 300 larvae per condition were collected at 6 dpf. Larvae were dissociated into single cell suspension by Trypsin treatment and fluorescent and 20 fluorescent cells per condition were sorted by FACS directly into cDNA synthesis buffer  without xxx extraction. cDNA were synthetized and amplified with the SMARTer cDNA synthesis kit for Illumina Sequencing Clonetech according to the manufacturer’s instructions. The integrity of the cDNA was confirmed by Lab on chip analysis using the 2100 Bioanalyzer Agilent Technologies. The sheared amplified cDNA  were used to make RNAseq libraries using the Illumina TruSeq RNA Sample Preparation Kit v2 Illumina Inc.  San Diego  USA. In the manufacturer’s instructions two modifications were made. In the adapter ligation step 1 µl instead of 2.5 µl adapter was used. In the library size selection step the library fragments were isolated with a double Ampure XP purification with a 0.7x beads to library ratio. The resulting mRNA Seq library was sequenced using an Illumina HiSeq2000 instrument according to the manufacturer’s description with a read length of 1 x 50 nucleotides.,GEO Accession:GSM1686454,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP058376,,,ZFG-14-09_01_GTGGCC_L003_R1_001.fastq.gz,fastq,1248324348.0,24476948.0,GSM1686454 r1,0:51,A:391067882;C:223380294;G:229132022;T:404526410;N:217740,51,,,,391067882,223380294,229132022,404526410,217740,SRX1029310,SRS937778,SRA268539,GEO,"Institute of Biology, Leiden University",1,0.70232,,0.14257,,0.92894,,0.59305,,51,,B,,usable mapping rate,illumina,hiseq_era,full_length,poly_a,smarter,bulk,unknown,unknown,,Netherlands,2015-05-15,Larval,Larval,Blood,Hematopoietic System
40807,SRR3381847,SRX1704280,SRS1396343,SRP073272,PRJNA318414,Cortisol treated zebrafish embryos develop into pro inflammatory adults with aberrant immune gene regulation [adults],GSE80260,Transcriptome Analysis,Chronic early life stress increases adult susceptibility to numerous health problems linked to chronic inflammation. One way that this may occur is via glucocorticoid induced developmental programming. To gain insight into such programming  we treated zebrafish embryos with cortisol and examined the effects on adults. In maturity  the treated fish maintained elevated basal cortisol levels in the absence of exogenous cortisol  and constitutively mis expressed genes involved in defense response and its regulation. Adults derived from cortisol treated embryos displayed defective tailfin regeneration  heightened basal expression of pro inflammatory genes  and failure to appropriately regulate those genes following injury or immunological challenge. These results support the hypothesis that chronically elevated glucocorticoid signaling early in life directs development of a pro inflammatory adult phenotype  at the expense of immunoregulation and somatic regenerative capacity. Overall design: 30 samples total were analyzed. 9 caudal fins samples 0  2 and 4dpa  3 blood samples and 3 muscle samples from adults exposed to DMSO control as embryos. 9 caudal fins samples 0  2 and 4dpa  3 blood samples and 3 muscle samples from adults exposed to cortisol 1 micromolar as embryos.,parent bioproject:PRJNA318502,pubmed:27444789,,Treated 3 blood,GSM2122871,,source name:whole blood  cortisol|strain/background:AB|tissue:whole blood|age:adult|embryonic treatment:cortisol,Treated 3 blood,Sequence quality was assessed using Fastqc QC v0.11.2; http://www.bioinformatics.babraham.ac.uk/projects/fastqc. Reads were trimmed using Trimmomatic v 0.3; Bolger et al.  2014. Trimmed reads were aligned to the zebrafish Danio rerio transcriptome annotated by Ensembl version 83 of the GRCz10 genome assembly using RSEM version 1.2.25 Li and Dewey  2011 and Bowtie 1.1.2 Langmead et al.  2009. Differentially expressed transcripts were determined using R/edgeR version 3.10.2 Robinson et al.  2010. Genome build: Danio rerio GRCz10 Supplementary files format and content: Tab delimited text files with read counts counts per million per sample.,whole blood  cortisol,DMSO or 1 micromolar cortisol was added to larval medium for first 5 days of development  and then maintained to 4.5 month under normal conditions.,RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.,AB zebrafish were maintained at 28 degrees Celsius at the MDI Biological Laboratory Animal Core.,strain/background:AB|tissue:whole blood|age:adult|embryonic treatment:cortisol,GSM2122871,GSM2122871: Treated 3 blood; Danio rerio; RNA Seq,GSM2122871,,1,RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.,GEO Accession:GSM2122871,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP073272,,,C8DY1ANXX_s6_1_GSLv3-7_38_SL139795.fastq.gz C8DY1ANXX_s6_2_GSLv3-7_38_SL139795.fastq.gz,fastq fastq,1349428600.0,13494286.0,GSM2122871 r1,0:50 1:50,A:391483366;C:283353944;G:288253777;T:386190051;N:147462,50,50,,,391483366,283353944,288253777,386190051,147462,SRX1704280,SRS1396343,SRA411416,GEO,"Molecular and Biomedical Sciences, University of Maine",2,0.88853,0.89204,0.22815,0.23941,0.73917,0.73979,0.53637,0.53893,50,50,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,United States,2016-04-13,Adult,Adult,Blood,Hematopoietic System
40808,SRR3381848,SRX1704280,SRS1396343,SRP073272,PRJNA318414,Cortisol treated zebrafish embryos develop into pro inflammatory adults with aberrant immune gene regulation [adults],GSE80260,Transcriptome Analysis,Chronic early life stress increases adult susceptibility to numerous health problems linked to chronic inflammation. One way that this may occur is via glucocorticoid induced developmental programming. To gain insight into such programming  we treated zebrafish embryos with cortisol and examined the effects on adults. In maturity  the treated fish maintained elevated basal cortisol levels in the absence of exogenous cortisol  and constitutively mis expressed genes involved in defense response and its regulation. Adults derived from cortisol treated embryos displayed defective tailfin regeneration  heightened basal expression of pro inflammatory genes  and failure to appropriately regulate those genes following injury or immunological challenge. These results support the hypothesis that chronically elevated glucocorticoid signaling early in life directs development of a pro inflammatory adult phenotype  at the expense of immunoregulation and somatic regenerative capacity. Overall design: 30 samples total were analyzed. 9 caudal fins samples 0  2 and 4dpa  3 blood samples and 3 muscle samples from adults exposed to DMSO control as embryos. 9 caudal fins samples 0  2 and 4dpa  3 blood samples and 3 muscle samples from adults exposed to cortisol 1 micromolar as embryos.,parent bioproject:PRJNA318502,pubmed:27444789,,Treated 3 blood,GSM2122871,,source name:whole blood  cortisol|strain/background:AB|tissue:whole blood|age:adult|embryonic treatment:cortisol,Treated 3 blood,Sequence quality was assessed using Fastqc QC v0.11.2; http://www.bioinformatics.babraham.ac.uk/projects/fastqc. Reads were trimmed using Trimmomatic v 0.3; Bolger et al.  2014. Trimmed reads were aligned to the zebrafish Danio rerio transcriptome annotated by Ensembl version 83 of the GRCz10 genome assembly using RSEM version 1.2.25 Li and Dewey  2011 and Bowtie 1.1.2 Langmead et al.  2009. Differentially expressed transcripts were determined using R/edgeR version 3.10.2 Robinson et al.  2010. Genome build: Danio rerio GRCz10 Supplementary files format and content: Tab delimited text files with read counts counts per million per sample.,whole blood  cortisol,DMSO or 1 micromolar cortisol was added to larval medium for first 5 days of development  and then maintained to 4.5 month under normal conditions.,RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.,AB zebrafish were maintained at 28 degrees Celsius at the MDI Biological Laboratory Animal Core.,strain/background:AB|tissue:whole blood|age:adult|embryonic treatment:cortisol,GSM2122871,GSM2122871: Treated 3 blood; Danio rerio; RNA Seq,GSM2122871,,1,RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.,GEO Accession:GSM2122871,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP073272,,,C8BH2ANXX_s5_1_GSLv3-7_38_SL139795.fastq.gz C8BH2ANXX_s5_2_GSLv3-7_38_SL139795.fastq.gz,fastq fastq,1020366100.0,10203661.0,GSM2122871 r2,0:50 1:50,A:296023946;C:213173706;G:215342808;T:295806226;N:19414,50,50,,,296023946,213173706,215342808,295806226,19414,SRX1704280,SRS1396343,SRA411416,GEO,"Molecular and Biomedical Sciences, University of Maine",2,0.88792,0.89203,0.21382,0.24279,0.7652,0.7444,0.53618,0.54254,50,50,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,United States,2016-04-13,Adult,Adult,Blood,Hematopoietic System
40809,SRR3381849,SRX1704280,SRS1396343,SRP073272,PRJNA318414,Cortisol treated zebrafish embryos develop into pro inflammatory adults with aberrant immune gene regulation [adults],GSE80260,Transcriptome Analysis,Chronic early life stress increases adult susceptibility to numerous health problems linked to chronic inflammation. One way that this may occur is via glucocorticoid induced developmental programming. To gain insight into such programming  we treated zebrafish embryos with cortisol and examined the effects on adults. In maturity  the treated fish maintained elevated basal cortisol levels in the absence of exogenous cortisol  and constitutively mis expressed genes involved in defense response and its regulation. Adults derived from cortisol treated embryos displayed defective tailfin regeneration  heightened basal expression of pro inflammatory genes  and failure to appropriately regulate those genes following injury or immunological challenge. These results support the hypothesis that chronically elevated glucocorticoid signaling early in life directs development of a pro inflammatory adult phenotype  at the expense of immunoregulation and somatic regenerative capacity. Overall design: 30 samples total were analyzed. 9 caudal fins samples 0  2 and 4dpa  3 blood samples and 3 muscle samples from adults exposed to DMSO control as embryos. 9 caudal fins samples 0  2 and 4dpa  3 blood samples and 3 muscle samples from adults exposed to cortisol 1 micromolar as embryos.,parent bioproject:PRJNA318502,pubmed:27444789,,Treated 3 blood,GSM2122871,,source name:whole blood  cortisol|strain/background:AB|tissue:whole blood|age:adult|embryonic treatment:cortisol,Treated 3 blood,Sequence quality was assessed using Fastqc QC v0.11.2; http://www.bioinformatics.babraham.ac.uk/projects/fastqc. Reads were trimmed using Trimmomatic v 0.3; Bolger et al.  2014. Trimmed reads were aligned to the zebrafish Danio rerio transcriptome annotated by Ensembl version 83 of the GRCz10 genome assembly using RSEM version 1.2.25 Li and Dewey  2011 and Bowtie 1.1.2 Langmead et al.  2009. Differentially expressed transcripts were determined using R/edgeR version 3.10.2 Robinson et al.  2010. Genome build: Danio rerio GRCz10 Supplementary files format and content: Tab delimited text files with read counts counts per million per sample.,whole blood  cortisol,DMSO or 1 micromolar cortisol was added to larval medium for first 5 days of development  and then maintained to 4.5 month under normal conditions.,RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.,AB zebrafish were maintained at 28 degrees Celsius at the MDI Biological Laboratory Animal Core.,strain/background:AB|tissue:whole blood|age:adult|embryonic treatment:cortisol,GSM2122871,GSM2122871: Treated 3 blood; Danio rerio; RNA Seq,GSM2122871,,1,RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.,GEO Accession:GSM2122871,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP073272,,,C8BH2ANXX_s6_1_GSLv3-7_38_SL139795.fastq.gz C8BH2ANXX_s6_2_GSLv3-7_38_SL139795.fastq.gz,fastq fastq,1008129000.0,10081290.0,GSM2122871 r3,0:50 1:50,A:292536545;C:210308039;G:212529262;T:292736486;N:18668,50,50,,,292536545,210308039,212529262,292736486,18668,SRX1704280,SRS1396343,SRA411416,GEO,"Molecular and Biomedical Sciences, University of Maine",2,0.88682,0.89249,0.21573,0.24321,0.7657,0.74456,0.53948,0.54456,50,50,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,United States,2016-04-13,Adult,Adult,Blood,Hematopoietic System
40810,SRR3381850,SRX1704280,SRS1396343,SRP073272,PRJNA318414,Cortisol treated zebrafish embryos develop into pro inflammatory adults with aberrant immune gene regulation [adults],GSE80260,Transcriptome Analysis,Chronic early life stress increases adult susceptibility to numerous health problems linked to chronic inflammation. One way that this may occur is via glucocorticoid induced developmental programming. To gain insight into such programming  we treated zebrafish embryos with cortisol and examined the effects on adults. In maturity  the treated fish maintained elevated basal cortisol levels in the absence of exogenous cortisol  and constitutively mis expressed genes involved in defense response and its regulation. Adults derived from cortisol treated embryos displayed defective tailfin regeneration  heightened basal expression of pro inflammatory genes  and failure to appropriately regulate those genes following injury or immunological challenge. These results support the hypothesis that chronically elevated glucocorticoid signaling early in life directs development of a pro inflammatory adult phenotype  at the expense of immunoregulation and somatic regenerative capacity. Overall design: 30 samples total were analyzed. 9 caudal fins samples 0  2 and 4dpa  3 blood samples and 3 muscle samples from adults exposed to DMSO control as embryos. 9 caudal fins samples 0  2 and 4dpa  3 blood samples and 3 muscle samples from adults exposed to cortisol 1 micromolar as embryos.,parent bioproject:PRJNA318502,pubmed:27444789,,Treated 3 blood,GSM2122871,,source name:whole blood  cortisol|strain/background:AB|tissue:whole blood|age:adult|embryonic treatment:cortisol,Treated 3 blood,Sequence quality was assessed using Fastqc QC v0.11.2; http://www.bioinformatics.babraham.ac.uk/projects/fastqc. Reads were trimmed using Trimmomatic v 0.3; Bolger et al.  2014. Trimmed reads were aligned to the zebrafish Danio rerio transcriptome annotated by Ensembl version 83 of the GRCz10 genome assembly using RSEM version 1.2.25 Li and Dewey  2011 and Bowtie 1.1.2 Langmead et al.  2009. Differentially expressed transcripts were determined using R/edgeR version 3.10.2 Robinson et al.  2010. Genome build: Danio rerio GRCz10 Supplementary files format and content: Tab delimited text files with read counts counts per million per sample.,whole blood  cortisol,DMSO or 1 micromolar cortisol was added to larval medium for first 5 days of development  and then maintained to 4.5 month under normal conditions.,RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.,AB zebrafish were maintained at 28 degrees Celsius at the MDI Biological Laboratory Animal Core.,strain/background:AB|tissue:whole blood|age:adult|embryonic treatment:cortisol,GSM2122871,GSM2122871: Treated 3 blood; Danio rerio; RNA Seq,GSM2122871,,1,RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.,GEO Accession:GSM2122871,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP073272,,,C8DY1ANXX_s5_1_GSLv3-7_38_SL139795.fastq.gz C8DY1ANXX_s5_2_GSLv3-7_38_SL139795.fastq.gz,fastq fastq,1348814000.0,13488140.0,GSM2122871 r4,0:50 1:50,A:391186639;C:283404571;G:288274584;T:385756613;N:191593,50,50,,,391186639,283404571,288274584,385756613,191593,SRX1704280,SRS1396343,SRA411416,GEO,"Molecular and Biomedical Sciences, University of Maine",2,0.88673,0.89303,0.22875,0.24107,0.74276,0.74134,0.53585,0.54514,50,50,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,United States,2016-04-13,Adult,Adult,Blood,Hematopoietic System
40811,SRR3381843,SRX1704279,SRS1396344,SRP073272,PRJNA318414,Cortisol treated zebrafish embryos develop into pro inflammatory adults with aberrant immune gene regulation [adults],GSE80260,Transcriptome Analysis,Chronic early life stress increases adult susceptibility to numerous health problems linked to chronic inflammation. One way that this may occur is via glucocorticoid induced developmental programming. To gain insight into such programming  we treated zebrafish embryos with cortisol and examined the effects on adults. In maturity  the treated fish maintained elevated basal cortisol levels in the absence of exogenous cortisol  and constitutively mis expressed genes involved in defense response and its regulation. Adults derived from cortisol treated embryos displayed defective tailfin regeneration  heightened basal expression of pro inflammatory genes  and failure to appropriately regulate those genes following injury or immunological challenge. These results support the hypothesis that chronically elevated glucocorticoid signaling early in life directs development of a pro inflammatory adult phenotype  at the expense of immunoregulation and somatic regenerative capacity. Overall design: 30 samples total were analyzed. 9 caudal fins samples 0  2 and 4dpa  3 blood samples and 3 muscle samples from adults exposed to DMSO control as embryos. 9 caudal fins samples 0  2 and 4dpa  3 blood samples and 3 muscle samples from adults exposed to cortisol 1 micromolar as embryos.,parent bioproject:PRJNA318502,pubmed:27444789,,Treated 2 blood,GSM2122870,,source name:whole blood  cortisol|strain/background:AB|tissue:whole blood|age:adult|embryonic treatment:cortisol,Treated 2 blood,Sequence quality was assessed using Fastqc QC v0.11.2; http://www.bioinformatics.babraham.ac.uk/projects/fastqc. Reads were trimmed using Trimmomatic v 0.3; Bolger et al.  2014. Trimmed reads were aligned to the zebrafish Danio rerio transcriptome annotated by Ensembl version 83 of the GRCz10 genome assembly using RSEM version 1.2.25 Li and Dewey  2011 and Bowtie 1.1.2 Langmead et al.  2009. Differentially expressed transcripts were determined using R/edgeR version 3.10.2 Robinson et al.  2010. Genome build: Danio rerio GRCz10 Supplementary files format and content: Tab delimited text files with read counts counts per million per sample.,whole blood  cortisol,DMSO or 1 micromolar cortisol was added to larval medium for first 5 days of development  and then maintained to 4.5 month under normal conditions.,RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.,AB zebrafish were maintained at 28 degrees Celsius at the MDI Biological Laboratory Animal Core.,strain/background:AB|tissue:whole blood|age:adult|embryonic treatment:cortisol,GSM2122870,GSM2122870: Treated 2 blood; Danio rerio; RNA Seq,GSM2122870,,1,RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.,GEO Accession:GSM2122870,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP073272,,,C8DY1ANXX_s6_1_GSLv3-7_37_SL139794.fastq.gz C8DY1ANXX_s6_2_GSLv3-7_37_SL139794.fastq.gz,fastq fastq,1251398700.0,12513987.0,GSM2122870 r1,0:50 1:50,A:383059535;C:243111832;G:248681985;T:376401618;N:143730,50,50,,,383059535,243111832,248681985,376401618,143730,SRX1704279,SRS1396344,SRA411416,GEO,"Molecular and Biomedical Sciences, University of Maine",2,0.86725,0.86597,0.35725,0.37228,0.74312,0.73961,0.53136,0.53663,50,50,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,United States,2016-04-13,Adult,Adult,Blood,Hematopoietic System
40812,SRR3381844,SRX1704279,SRS1396344,SRP073272,PRJNA318414,Cortisol treated zebrafish embryos develop into pro inflammatory adults with aberrant immune gene regulation [adults],GSE80260,Transcriptome Analysis,Chronic early life stress increases adult susceptibility to numerous health problems linked to chronic inflammation. One way that this may occur is via glucocorticoid induced developmental programming. To gain insight into such programming  we treated zebrafish embryos with cortisol and examined the effects on adults. In maturity  the treated fish maintained elevated basal cortisol levels in the absence of exogenous cortisol  and constitutively mis expressed genes involved in defense response and its regulation. Adults derived from cortisol treated embryos displayed defective tailfin regeneration  heightened basal expression of pro inflammatory genes  and failure to appropriately regulate those genes following injury or immunological challenge. These results support the hypothesis that chronically elevated glucocorticoid signaling early in life directs development of a pro inflammatory adult phenotype  at the expense of immunoregulation and somatic regenerative capacity. Overall design: 30 samples total were analyzed. 9 caudal fins samples 0  2 and 4dpa  3 blood samples and 3 muscle samples from adults exposed to DMSO control as embryos. 9 caudal fins samples 0  2 and 4dpa  3 blood samples and 3 muscle samples from adults exposed to cortisol 1 micromolar as embryos.,parent bioproject:PRJNA318502,pubmed:27444789,,Treated 2 blood,GSM2122870,,source name:whole blood  cortisol|strain/background:AB|tissue:whole blood|age:adult|embryonic treatment:cortisol,Treated 2 blood,Sequence quality was assessed using Fastqc QC v0.11.2; http://www.bioinformatics.babraham.ac.uk/projects/fastqc. Reads were trimmed using Trimmomatic v 0.3; Bolger et al.  2014. Trimmed reads were aligned to the zebrafish Danio rerio transcriptome annotated by Ensembl version 83 of the GRCz10 genome assembly using RSEM version 1.2.25 Li and Dewey  2011 and Bowtie 1.1.2 Langmead et al.  2009. Differentially expressed transcripts were determined using R/edgeR version 3.10.2 Robinson et al.  2010. Genome build: Danio rerio GRCz10 Supplementary files format and content: Tab delimited text files with read counts counts per million per sample.,whole blood  cortisol,DMSO or 1 micromolar cortisol was added to larval medium for first 5 days of development  and then maintained to 4.5 month under normal conditions.,RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.,AB zebrafish were maintained at 28 degrees Celsius at the MDI Biological Laboratory Animal Core.,strain/background:AB|tissue:whole blood|age:adult|embryonic treatment:cortisol,GSM2122870,GSM2122870: Treated 2 blood; Danio rerio; RNA Seq,GSM2122870,,1,RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.,GEO Accession:GSM2122870,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP073272,,,C8BH2ANXX_s5_1_GSLv3-7_37_SL139794.fastq.gz C8BH2ANXX_s5_2_GSLv3-7_37_SL139794.fastq.gz,fastq fastq,959597100.0,9595971.0,GSM2122870 r2,0:50 1:50,A:294644349;C:184893976;G:188222172;T:291818696;N:17907,50,50,,,294644349,184893976,188222172,291818696,17907,SRX1704279,SRS1396344,SRA411416,GEO,"Molecular and Biomedical Sciences, University of Maine",2,0.86953,0.86626,0.33903,0.3765,0.77264,0.74432,0.53426,0.53782,50,50,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,United States,2016-04-13,Adult,Adult,Blood,Hematopoietic System
40813,SRR3381845,SRX1704279,SRS1396344,SRP073272,PRJNA318414,Cortisol treated zebrafish embryos develop into pro inflammatory adults with aberrant immune gene regulation [adults],GSE80260,Transcriptome Analysis,Chronic early life stress increases adult susceptibility to numerous health problems linked to chronic inflammation. One way that this may occur is via glucocorticoid induced developmental programming. To gain insight into such programming  we treated zebrafish embryos with cortisol and examined the effects on adults. In maturity  the treated fish maintained elevated basal cortisol levels in the absence of exogenous cortisol  and constitutively mis expressed genes involved in defense response and its regulation. Adults derived from cortisol treated embryos displayed defective tailfin regeneration  heightened basal expression of pro inflammatory genes  and failure to appropriately regulate those genes following injury or immunological challenge. These results support the hypothesis that chronically elevated glucocorticoid signaling early in life directs development of a pro inflammatory adult phenotype  at the expense of immunoregulation and somatic regenerative capacity. Overall design: 30 samples total were analyzed. 9 caudal fins samples 0  2 and 4dpa  3 blood samples and 3 muscle samples from adults exposed to DMSO control as embryos. 9 caudal fins samples 0  2 and 4dpa  3 blood samples and 3 muscle samples from adults exposed to cortisol 1 micromolar as embryos.,parent bioproject:PRJNA318502,pubmed:27444789,,Treated 2 blood,GSM2122870,,source name:whole blood  cortisol|strain/background:AB|tissue:whole blood|age:adult|embryonic treatment:cortisol,Treated 2 blood,Sequence quality was assessed using Fastqc QC v0.11.2; http://www.bioinformatics.babraham.ac.uk/projects/fastqc. Reads were trimmed using Trimmomatic v 0.3; Bolger et al.  2014. Trimmed reads were aligned to the zebrafish Danio rerio transcriptome annotated by Ensembl version 83 of the GRCz10 genome assembly using RSEM version 1.2.25 Li and Dewey  2011 and Bowtie 1.1.2 Langmead et al.  2009. Differentially expressed transcripts were determined using R/edgeR version 3.10.2 Robinson et al.  2010. Genome build: Danio rerio GRCz10 Supplementary files format and content: Tab delimited text files with read counts counts per million per sample.,whole blood  cortisol,DMSO or 1 micromolar cortisol was added to larval medium for first 5 days of development  and then maintained to 4.5 month under normal conditions.,RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.,AB zebrafish were maintained at 28 degrees Celsius at the MDI Biological Laboratory Animal Core.,strain/background:AB|tissue:whole blood|age:adult|embryonic treatment:cortisol,GSM2122870,GSM2122870: Treated 2 blood; Danio rerio; RNA Seq,GSM2122870,,1,RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.,GEO Accession:GSM2122870,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP073272,,,C8DY1ANXX_s5_1_GSLv3-7_37_SL139794.fastq.gz C8DY1ANXX_s5_2_GSLv3-7_37_SL139794.fastq.gz,fastq fastq,1245250000.0,12452500.0,GSM2122870 r3,0:50 1:50,A:381219052;C:241987476;G:247543915;T:374295403;N:204154,50,50,,,381219052,241987476,247543915,374295403,204154,SRX1704279,SRS1396344,SRA411416,GEO,"Molecular and Biomedical Sciences, University of Maine",2,0.86789,0.86686,0.35484,0.37206,0.74119,0.73679,0.50299,0.53759,50,50,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,United States,2016-04-13,Adult,Adult,Blood,Hematopoietic System
40814,SRR3381846,SRX1704279,SRS1396344,SRP073272,PRJNA318414,Cortisol treated zebrafish embryos develop into pro inflammatory adults with aberrant immune gene regulation [adults],GSE80260,Transcriptome Analysis,Chronic early life stress increases adult susceptibility to numerous health problems linked to chronic inflammation. One way that this may occur is via glucocorticoid induced developmental programming. To gain insight into such programming  we treated zebrafish embryos with cortisol and examined the effects on adults. In maturity  the treated fish maintained elevated basal cortisol levels in the absence of exogenous cortisol  and constitutively mis expressed genes involved in defense response and its regulation. Adults derived from cortisol treated embryos displayed defective tailfin regeneration  heightened basal expression of pro inflammatory genes  and failure to appropriately regulate those genes following injury or immunological challenge. These results support the hypothesis that chronically elevated glucocorticoid signaling early in life directs development of a pro inflammatory adult phenotype  at the expense of immunoregulation and somatic regenerative capacity. Overall design: 30 samples total were analyzed. 9 caudal fins samples 0  2 and 4dpa  3 blood samples and 3 muscle samples from adults exposed to DMSO control as embryos. 9 caudal fins samples 0  2 and 4dpa  3 blood samples and 3 muscle samples from adults exposed to cortisol 1 micromolar as embryos.,parent bioproject:PRJNA318502,pubmed:27444789,,Treated 2 blood,GSM2122870,,source name:whole blood  cortisol|strain/background:AB|tissue:whole blood|age:adult|embryonic treatment:cortisol,Treated 2 blood,Sequence quality was assessed using Fastqc QC v0.11.2; http://www.bioinformatics.babraham.ac.uk/projects/fastqc. Reads were trimmed using Trimmomatic v 0.3; Bolger et al.  2014. Trimmed reads were aligned to the zebrafish Danio rerio transcriptome annotated by Ensembl version 83 of the GRCz10 genome assembly using RSEM version 1.2.25 Li and Dewey  2011 and Bowtie 1.1.2 Langmead et al.  2009. Differentially expressed transcripts were determined using R/edgeR version 3.10.2 Robinson et al.  2010. Genome build: Danio rerio GRCz10 Supplementary files format and content: Tab delimited text files with read counts counts per million per sample.,whole blood  cortisol,DMSO or 1 micromolar cortisol was added to larval medium for first 5 days of development  and then maintained to 4.5 month under normal conditions.,RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.,AB zebrafish were maintained at 28 degrees Celsius at the MDI Biological Laboratory Animal Core.,strain/background:AB|tissue:whole blood|age:adult|embryonic treatment:cortisol,GSM2122870,GSM2122870: Treated 2 blood; Danio rerio; RNA Seq,GSM2122870,,1,RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.,GEO Accession:GSM2122870,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP073272,,,C8BH2ANXX_s6_1_GSLv3-7_37_SL139794.fastq.gz C8BH2ANXX_s6_2_GSLv3-7_37_SL139794.fastq.gz,fastq fastq,950337100.0,9503371.0,GSM2122870 r4,0:50 1:50,A:291821125;C:182753545;G:186179426;T:289565320;N:17684,50,50,,,291821125,182753545,186179426,289565320,17684,SRX1704279,SRS1396344,SRA411416,GEO,"Molecular and Biomedical Sciences, University of Maine",2,0.86635,0.86476,0.34245,0.3786,0.77309,0.74474,0.50694,0.53099,50,50,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,United States,2016-04-13,Adult,Adult,Blood,Hematopoietic System
40815,SRR3381839,SRX1704278,SRS1396345,SRP073272,PRJNA318414,Cortisol treated zebrafish embryos develop into pro inflammatory adults with aberrant immune gene regulation [adults],GSE80260,Transcriptome Analysis,Chronic early life stress increases adult susceptibility to numerous health problems linked to chronic inflammation. One way that this may occur is via glucocorticoid induced developmental programming. To gain insight into such programming  we treated zebrafish embryos with cortisol and examined the effects on adults. In maturity  the treated fish maintained elevated basal cortisol levels in the absence of exogenous cortisol  and constitutively mis expressed genes involved in defense response and its regulation. Adults derived from cortisol treated embryos displayed defective tailfin regeneration  heightened basal expression of pro inflammatory genes  and failure to appropriately regulate those genes following injury or immunological challenge. These results support the hypothesis that chronically elevated glucocorticoid signaling early in life directs development of a pro inflammatory adult phenotype  at the expense of immunoregulation and somatic regenerative capacity. Overall design: 30 samples total were analyzed. 9 caudal fins samples 0  2 and 4dpa  3 blood samples and 3 muscle samples from adults exposed to DMSO control as embryos. 9 caudal fins samples 0  2 and 4dpa  3 blood samples and 3 muscle samples from adults exposed to cortisol 1 micromolar as embryos.,parent bioproject:PRJNA318502,pubmed:27444789,,Treated 1 blood,GSM2122869,,source name:whole blood  cortisol|strain/background:AB|tissue:whole blood|age:adult|embryonic treatment:cortisol,Treated 1 blood,Sequence quality was assessed using Fastqc QC v0.11.2; http://www.bioinformatics.babraham.ac.uk/projects/fastqc. Reads were trimmed using Trimmomatic v 0.3; Bolger et al.  2014. Trimmed reads were aligned to the zebrafish Danio rerio transcriptome annotated by Ensembl version 83 of the GRCz10 genome assembly using RSEM version 1.2.25 Li and Dewey  2011 and Bowtie 1.1.2 Langmead et al.  2009. Differentially expressed transcripts were determined using R/edgeR version 3.10.2 Robinson et al.  2010. Genome build: Danio rerio GRCz10 Supplementary files format and content: Tab delimited text files with read counts counts per million per sample.,whole blood  cortisol,DMSO or 1 micromolar cortisol was added to larval medium for first 5 days of development  and then maintained to 4.5 month under normal conditions.,RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.,AB zebrafish were maintained at 28 degrees Celsius at the MDI Biological Laboratory Animal Core.,strain/background:AB|tissue:whole blood|age:adult|embryonic treatment:cortisol,GSM2122869,GSM2122869: Treated 1 blood; Danio rerio; RNA Seq,GSM2122869,,1,RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.,GEO Accession:GSM2122869,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP073272,,,C8DY1ANXX_s5_1_GSLv3-7_36_SL139793.fastq.gz C8DY1ANXX_s5_2_GSLv3-7_36_SL139793.fastq.gz,fastq fastq,1067516000.0,10675160.0,GSM2122869 r1,0:50 1:50,A:289362409;C:244764167;G:247658920;T:285596522;N:133982,50,50,,,289362409,244764167,247658920,285596522,133982,SRX1704278,SRS1396345,SRA411416,GEO,"Molecular and Biomedical Sciences, University of Maine",2,0.90704,0.92219,0.1113,0.11316,0.73645,0.73746,0.52358,0.53128,50,50,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,United States,2016-04-13,Adult,Adult,Blood,Hematopoietic System
40816,SRR3381840,SRX1704278,SRS1396345,SRP073272,PRJNA318414,Cortisol treated zebrafish embryos develop into pro inflammatory adults with aberrant immune gene regulation [adults],GSE80260,Transcriptome Analysis,Chronic early life stress increases adult susceptibility to numerous health problems linked to chronic inflammation. One way that this may occur is via glucocorticoid induced developmental programming. To gain insight into such programming  we treated zebrafish embryos with cortisol and examined the effects on adults. In maturity  the treated fish maintained elevated basal cortisol levels in the absence of exogenous cortisol  and constitutively mis expressed genes involved in defense response and its regulation. Adults derived from cortisol treated embryos displayed defective tailfin regeneration  heightened basal expression of pro inflammatory genes  and failure to appropriately regulate those genes following injury or immunological challenge. These results support the hypothesis that chronically elevated glucocorticoid signaling early in life directs development of a pro inflammatory adult phenotype  at the expense of immunoregulation and somatic regenerative capacity. Overall design: 30 samples total were analyzed. 9 caudal fins samples 0  2 and 4dpa  3 blood samples and 3 muscle samples from adults exposed to DMSO control as embryos. 9 caudal fins samples 0  2 and 4dpa  3 blood samples and 3 muscle samples from adults exposed to cortisol 1 micromolar as embryos.,parent bioproject:PRJNA318502,pubmed:27444789,,Treated 1 blood,GSM2122869,,source name:whole blood  cortisol|strain/background:AB|tissue:whole blood|age:adult|embryonic treatment:cortisol,Treated 1 blood,Sequence quality was assessed using Fastqc QC v0.11.2; http://www.bioinformatics.babraham.ac.uk/projects/fastqc. Reads were trimmed using Trimmomatic v 0.3; Bolger et al.  2014. Trimmed reads were aligned to the zebrafish Danio rerio transcriptome annotated by Ensembl version 83 of the GRCz10 genome assembly using RSEM version 1.2.25 Li and Dewey  2011 and Bowtie 1.1.2 Langmead et al.  2009. Differentially expressed transcripts were determined using R/edgeR version 3.10.2 Robinson et al.  2010. Genome build: Danio rerio GRCz10 Supplementary files format and content: Tab delimited text files with read counts counts per million per sample.,whole blood  cortisol,DMSO or 1 micromolar cortisol was added to larval medium for first 5 days of development  and then maintained to 4.5 month under normal conditions.,RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.,AB zebrafish were maintained at 28 degrees Celsius at the MDI Biological Laboratory Animal Core.,strain/background:AB|tissue:whole blood|age:adult|embryonic treatment:cortisol,GSM2122869,GSM2122869: Treated 1 blood; Danio rerio; RNA Seq,GSM2122869,,1,RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.,GEO Accession:GSM2122869,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP073272,,,C8BH2ANXX_s5_1_GSLv3-7_36_SL139793.fastq.gz C8BH2ANXX_s5_2_GSLv3-7_36_SL139793.fastq.gz,fastq fastq,802301400.0,8023014.0,GSM2122869 r2,0:50 1:50,A:216222361;C:183743858;G:183958773;T:218361744;N:14664,50,50,,,216222361,183743858,183958773,218361744,14664,SRX1704278,SRS1396345,SRA411416,GEO,"Molecular and Biomedical Sciences, University of Maine",2,0.90734,0.92073,0.10828,0.11414,0.75816,0.74156,0.52518,0.53162,50,50,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,United States,2016-04-13,Adult,Adult,Blood,Hematopoietic System
40817,SRR3381841,SRX1704278,SRS1396345,SRP073272,PRJNA318414,Cortisol treated zebrafish embryos develop into pro inflammatory adults with aberrant immune gene regulation [adults],GSE80260,Transcriptome Analysis,Chronic early life stress increases adult susceptibility to numerous health problems linked to chronic inflammation. One way that this may occur is via glucocorticoid induced developmental programming. To gain insight into such programming  we treated zebrafish embryos with cortisol and examined the effects on adults. In maturity  the treated fish maintained elevated basal cortisol levels in the absence of exogenous cortisol  and constitutively mis expressed genes involved in defense response and its regulation. Adults derived from cortisol treated embryos displayed defective tailfin regeneration  heightened basal expression of pro inflammatory genes  and failure to appropriately regulate those genes following injury or immunological challenge. These results support the hypothesis that chronically elevated glucocorticoid signaling early in life directs development of a pro inflammatory adult phenotype  at the expense of immunoregulation and somatic regenerative capacity. Overall design: 30 samples total were analyzed. 9 caudal fins samples 0  2 and 4dpa  3 blood samples and 3 muscle samples from adults exposed to DMSO control as embryos. 9 caudal fins samples 0  2 and 4dpa  3 blood samples and 3 muscle samples from adults exposed to cortisol 1 micromolar as embryos.,parent bioproject:PRJNA318502,pubmed:27444789,,Treated 1 blood,GSM2122869,,source name:whole blood  cortisol|strain/background:AB|tissue:whole blood|age:adult|embryonic treatment:cortisol,Treated 1 blood,Sequence quality was assessed using Fastqc QC v0.11.2; http://www.bioinformatics.babraham.ac.uk/projects/fastqc. Reads were trimmed using Trimmomatic v 0.3; Bolger et al.  2014. Trimmed reads were aligned to the zebrafish Danio rerio transcriptome annotated by Ensembl version 83 of the GRCz10 genome assembly using RSEM version 1.2.25 Li and Dewey  2011 and Bowtie 1.1.2 Langmead et al.  2009. Differentially expressed transcripts were determined using R/edgeR version 3.10.2 Robinson et al.  2010. Genome build: Danio rerio GRCz10 Supplementary files format and content: Tab delimited text files with read counts counts per million per sample.,whole blood  cortisol,DMSO or 1 micromolar cortisol was added to larval medium for first 5 days of development  and then maintained to 4.5 month under normal conditions.,RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.,AB zebrafish were maintained at 28 degrees Celsius at the MDI Biological Laboratory Animal Core.,strain/background:AB|tissue:whole blood|age:adult|embryonic treatment:cortisol,GSM2122869,GSM2122869: Treated 1 blood; Danio rerio; RNA Seq,GSM2122869,,1,RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.,GEO Accession:GSM2122869,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP073272,,,C8DY1ANXX_s6_1_GSLv3-7_36_SL139793.fastq.gz C8DY1ANXX_s6_2_GSLv3-7_36_SL139793.fastq.gz,fastq fastq,1068410400.0,10684104.0,GSM2122869 r3,0:50 1:50,A:289709397;C:244889156;G:247758297;T:285941886;N:111664,50,50,,,289709397,244889156,247758297,285941886,111664,SRX1704278,SRS1396345,SRA411416,GEO,"Molecular and Biomedical Sciences, University of Maine",2,0.90673,0.9217,0.11124,0.11262,0.73779,0.73819,0.52628,0.53419,50,50,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,United States,2016-04-13,Adult,Adult,Blood,Hematopoietic System
40818,SRR3381842,SRX1704278,SRS1396345,SRP073272,PRJNA318414,Cortisol treated zebrafish embryos develop into pro inflammatory adults with aberrant immune gene regulation [adults],GSE80260,Transcriptome Analysis,Chronic early life stress increases adult susceptibility to numerous health problems linked to chronic inflammation. One way that this may occur is via glucocorticoid induced developmental programming. To gain insight into such programming  we treated zebrafish embryos with cortisol and examined the effects on adults. In maturity  the treated fish maintained elevated basal cortisol levels in the absence of exogenous cortisol  and constitutively mis expressed genes involved in defense response and its regulation. Adults derived from cortisol treated embryos displayed defective tailfin regeneration  heightened basal expression of pro inflammatory genes  and failure to appropriately regulate those genes following injury or immunological challenge. These results support the hypothesis that chronically elevated glucocorticoid signaling early in life directs development of a pro inflammatory adult phenotype  at the expense of immunoregulation and somatic regenerative capacity. Overall design: 30 samples total were analyzed. 9 caudal fins samples 0  2 and 4dpa  3 blood samples and 3 muscle samples from adults exposed to DMSO control as embryos. 9 caudal fins samples 0  2 and 4dpa  3 blood samples and 3 muscle samples from adults exposed to cortisol 1 micromolar as embryos.,parent bioproject:PRJNA318502,pubmed:27444789,,Treated 1 blood,GSM2122869,,source name:whole blood  cortisol|strain/background:AB|tissue:whole blood|age:adult|embryonic treatment:cortisol,Treated 1 blood,Sequence quality was assessed using Fastqc QC v0.11.2; http://www.bioinformatics.babraham.ac.uk/projects/fastqc. Reads were trimmed using Trimmomatic v 0.3; Bolger et al.  2014. Trimmed reads were aligned to the zebrafish Danio rerio transcriptome annotated by Ensembl version 83 of the GRCz10 genome assembly using RSEM version 1.2.25 Li and Dewey  2011 and Bowtie 1.1.2 Langmead et al.  2009. Differentially expressed transcripts were determined using R/edgeR version 3.10.2 Robinson et al.  2010. Genome build: Danio rerio GRCz10 Supplementary files format and content: Tab delimited text files with read counts counts per million per sample.,whole blood  cortisol,DMSO or 1 micromolar cortisol was added to larval medium for first 5 days of development  and then maintained to 4.5 month under normal conditions.,RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.,AB zebrafish were maintained at 28 degrees Celsius at the MDI Biological Laboratory Animal Core.,strain/background:AB|tissue:whole blood|age:adult|embryonic treatment:cortisol,GSM2122869,GSM2122869: Treated 1 blood; Danio rerio; RNA Seq,GSM2122869,,1,RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.,GEO Accession:GSM2122869,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP073272,,,C8BH2ANXX_s6_1_GSLv3-7_36_SL139793.fastq.gz C8BH2ANXX_s6_2_GSLv3-7_36_SL139793.fastq.gz,fastq fastq,792180400.0,7921804.0,GSM2122869 r4,0:50 1:50,A:213515752;C:181199374;G:181507201;T:215943851;N:14222,50,50,,,213515752,181199374,181507201,215943851,14222,SRX1704278,SRS1396345,SRA411416,GEO,"Molecular and Biomedical Sciences, University of Maine",2,0.90574,0.92099,0.11022,0.11558,0.75773,0.74158,0.52565,0.52697,50,50,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,United States,2016-04-13,Adult,Adult,Blood,Hematopoietic System
40819,SRR3381835,SRX1704277,SRS1396346,SRP073272,PRJNA318414,Cortisol treated zebrafish embryos develop into pro inflammatory adults with aberrant immune gene regulation [adults],GSE80260,Transcriptome Analysis,Chronic early life stress increases adult susceptibility to numerous health problems linked to chronic inflammation. One way that this may occur is via glucocorticoid induced developmental programming. To gain insight into such programming  we treated zebrafish embryos with cortisol and examined the effects on adults. In maturity  the treated fish maintained elevated basal cortisol levels in the absence of exogenous cortisol  and constitutively mis expressed genes involved in defense response and its regulation. Adults derived from cortisol treated embryos displayed defective tailfin regeneration  heightened basal expression of pro inflammatory genes  and failure to appropriately regulate those genes following injury or immunological challenge. These results support the hypothesis that chronically elevated glucocorticoid signaling early in life directs development of a pro inflammatory adult phenotype  at the expense of immunoregulation and somatic regenerative capacity. Overall design: 30 samples total were analyzed. 9 caudal fins samples 0  2 and 4dpa  3 blood samples and 3 muscle samples from adults exposed to DMSO control as embryos. 9 caudal fins samples 0  2 and 4dpa  3 blood samples and 3 muscle samples from adults exposed to cortisol 1 micromolar as embryos.,parent bioproject:PRJNA318502,pubmed:27444789,,Control 3 blood,GSM2122868,,source name:whole blood  DMSO control|strain/background:AB|tissue:whole blood|age:adult|embryonic treatment:DMSO,Control 3 blood,Sequence quality was assessed using Fastqc QC v0.11.2; http://www.bioinformatics.babraham.ac.uk/projects/fastqc. Reads were trimmed using Trimmomatic v 0.3; Bolger et al.  2014. Trimmed reads were aligned to the zebrafish Danio rerio transcriptome annotated by Ensembl version 83 of the GRCz10 genome assembly using RSEM version 1.2.25 Li and Dewey  2011 and Bowtie 1.1.2 Langmead et al.  2009. Differentially expressed transcripts were determined using R/edgeR version 3.10.2 Robinson et al.  2010. Genome build: Danio rerio GRCz10 Supplementary files format and content: Tab delimited text files with read counts counts per million per sample.,whole blood  DMSO control,DMSO or 1 micromolar cortisol was added to larval medium for first 5 days of development  and then maintained to 4.5 month under normal conditions.,RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.,AB zebrafish were maintained at 28 degrees Celsius at the MDI Biological Laboratory Animal Core.,strain/background:AB|tissue:whole blood|age:adult|embryonic treatment:DMSO,GSM2122868,GSM2122868: Control 3 blood; Danio rerio; RNA Seq,GSM2122868,,1,RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.,GEO Accession:GSM2122868,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP073272,,,C8BH2ANXX_s6_1_GSLv3-7_35_SL139792.fastq.gz C8BH2ANXX_s6_2_GSLv3-7_35_SL139792.fastq.gz,fastq fastq,1006437300.0,10064373.0,GSM2122868 r1,0:50 1:50,A:270736589;C:231073543;G:230348781;T:274259695;N:18692,50,50,,,270736589,231073543,230348781,274259695,18692,SRX1704277,SRS1396346,SRA411416,GEO,"Molecular and Biomedical Sciences, University of Maine",2,0.89576,0.91552,0.11015,0.11108,0.77108,0.75708,0.52238,0.55295,50,50,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,United States,2016-04-13,Adult,Adult,Blood,Hematopoietic System
40820,SRR3381836,SRX1704277,SRS1396346,SRP073272,PRJNA318414,Cortisol treated zebrafish embryos develop into pro inflammatory adults with aberrant immune gene regulation [adults],GSE80260,Transcriptome Analysis,Chronic early life stress increases adult susceptibility to numerous health problems linked to chronic inflammation. One way that this may occur is via glucocorticoid induced developmental programming. To gain insight into such programming  we treated zebrafish embryos with cortisol and examined the effects on adults. In maturity  the treated fish maintained elevated basal cortisol levels in the absence of exogenous cortisol  and constitutively mis expressed genes involved in defense response and its regulation. Adults derived from cortisol treated embryos displayed defective tailfin regeneration  heightened basal expression of pro inflammatory genes  and failure to appropriately regulate those genes following injury or immunological challenge. These results support the hypothesis that chronically elevated glucocorticoid signaling early in life directs development of a pro inflammatory adult phenotype  at the expense of immunoregulation and somatic regenerative capacity. Overall design: 30 samples total were analyzed. 9 caudal fins samples 0  2 and 4dpa  3 blood samples and 3 muscle samples from adults exposed to DMSO control as embryos. 9 caudal fins samples 0  2 and 4dpa  3 blood samples and 3 muscle samples from adults exposed to cortisol 1 micromolar as embryos.,parent bioproject:PRJNA318502,pubmed:27444789,,Control 3 blood,GSM2122868,,source name:whole blood  DMSO control|strain/background:AB|tissue:whole blood|age:adult|embryonic treatment:DMSO,Control 3 blood,Sequence quality was assessed using Fastqc QC v0.11.2; http://www.bioinformatics.babraham.ac.uk/projects/fastqc. Reads were trimmed using Trimmomatic v 0.3; Bolger et al.  2014. Trimmed reads were aligned to the zebrafish Danio rerio transcriptome annotated by Ensembl version 83 of the GRCz10 genome assembly using RSEM version 1.2.25 Li and Dewey  2011 and Bowtie 1.1.2 Langmead et al.  2009. Differentially expressed transcripts were determined using R/edgeR version 3.10.2 Robinson et al.  2010. Genome build: Danio rerio GRCz10 Supplementary files format and content: Tab delimited text files with read counts counts per million per sample.,whole blood  DMSO control,DMSO or 1 micromolar cortisol was added to larval medium for first 5 days of development  and then maintained to 4.5 month under normal conditions.,RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.,AB zebrafish were maintained at 28 degrees Celsius at the MDI Biological Laboratory Animal Core.,strain/background:AB|tissue:whole blood|age:adult|embryonic treatment:DMSO,GSM2122868,GSM2122868: Control 3 blood; Danio rerio; RNA Seq,GSM2122868,,1,RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.,GEO Accession:GSM2122868,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP073272,,,C8BH2ANXX_s5_1_GSLv3-7_35_SL139792.fastq.gz C8BH2ANXX_s5_2_GSLv3-7_35_SL139792.fastq.gz,fastq fastq,1019872300.0,10198723.0,GSM2122868 r2,0:50 1:50,A:274310405;C:234397316;G:233653220;T:277492635;N:18724,50,50,,,274310405,234397316,233653220,277492635,18724,SRX1704277,SRS1396346,SRA411416,GEO,"Molecular and Biomedical Sciences, University of Maine",2,0.89872,0.91671,0.10908,0.10998,0.76848,0.7559,0.55678,0.52913,50,50,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,United States,2016-04-13,Adult,Adult,Blood,Hematopoietic System
40821,SRR3381837,SRX1704277,SRS1396346,SRP073272,PRJNA318414,Cortisol treated zebrafish embryos develop into pro inflammatory adults with aberrant immune gene regulation [adults],GSE80260,Transcriptome Analysis,Chronic early life stress increases adult susceptibility to numerous health problems linked to chronic inflammation. One way that this may occur is via glucocorticoid induced developmental programming. To gain insight into such programming  we treated zebrafish embryos with cortisol and examined the effects on adults. In maturity  the treated fish maintained elevated basal cortisol levels in the absence of exogenous cortisol  and constitutively mis expressed genes involved in defense response and its regulation. Adults derived from cortisol treated embryos displayed defective tailfin regeneration  heightened basal expression of pro inflammatory genes  and failure to appropriately regulate those genes following injury or immunological challenge. These results support the hypothesis that chronically elevated glucocorticoid signaling early in life directs development of a pro inflammatory adult phenotype  at the expense of immunoregulation and somatic regenerative capacity. Overall design: 30 samples total were analyzed. 9 caudal fins samples 0  2 and 4dpa  3 blood samples and 3 muscle samples from adults exposed to DMSO control as embryos. 9 caudal fins samples 0  2 and 4dpa  3 blood samples and 3 muscle samples from adults exposed to cortisol 1 micromolar as embryos.,parent bioproject:PRJNA318502,pubmed:27444789,,Control 3 blood,GSM2122868,,source name:whole blood  DMSO control|strain/background:AB|tissue:whole blood|age:adult|embryonic treatment:DMSO,Control 3 blood,Sequence quality was assessed using Fastqc QC v0.11.2; http://www.bioinformatics.babraham.ac.uk/projects/fastqc. Reads were trimmed using Trimmomatic v 0.3; Bolger et al.  2014. Trimmed reads were aligned to the zebrafish Danio rerio transcriptome annotated by Ensembl version 83 of the GRCz10 genome assembly using RSEM version 1.2.25 Li and Dewey  2011 and Bowtie 1.1.2 Langmead et al.  2009. Differentially expressed transcripts were determined using R/edgeR version 3.10.2 Robinson et al.  2010. Genome build: Danio rerio GRCz10 Supplementary files format and content: Tab delimited text files with read counts counts per million per sample.,whole blood  DMSO control,DMSO or 1 micromolar cortisol was added to larval medium for first 5 days of development  and then maintained to 4.5 month under normal conditions.,RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.,AB zebrafish were maintained at 28 degrees Celsius at the MDI Biological Laboratory Animal Core.,strain/background:AB|tissue:whole blood|age:adult|embryonic treatment:DMSO,GSM2122868,GSM2122868: Control 3 blood; Danio rerio; RNA Seq,GSM2122868,,1,RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.,GEO Accession:GSM2122868,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP073272,,,C8DY1ANXX_s6_1_GSLv3-7_35_SL139792.fastq.gz C8DY1ANXX_s6_2_GSLv3-7_35_SL139792.fastq.gz,fastq fastq,1350419100.0,13504191.0,GSM2122868 r3,0:50 1:50,A:365416324;C:310498635;G:312632921;T:361739733;N:131487,50,50,,,365416324,310498635,312632921,361739733,131487,SRX1704277,SRS1396346,SRA411416,GEO,"Molecular and Biomedical Sciences, University of Maine",2,0.89828,0.91602,0.11147,0.11073,0.74941,0.75053,0.54012,0.53979,50,50,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,United States,2016-04-13,Adult,Adult,Blood,Hematopoietic System
40822,SRR3381838,SRX1704277,SRS1396346,SRP073272,PRJNA318414,Cortisol treated zebrafish embryos develop into pro inflammatory adults with aberrant immune gene regulation [adults],GSE80260,Transcriptome Analysis,Chronic early life stress increases adult susceptibility to numerous health problems linked to chronic inflammation. One way that this may occur is via glucocorticoid induced developmental programming. To gain insight into such programming  we treated zebrafish embryos with cortisol and examined the effects on adults. In maturity  the treated fish maintained elevated basal cortisol levels in the absence of exogenous cortisol  and constitutively mis expressed genes involved in defense response and its regulation. Adults derived from cortisol treated embryos displayed defective tailfin regeneration  heightened basal expression of pro inflammatory genes  and failure to appropriately regulate those genes following injury or immunological challenge. These results support the hypothesis that chronically elevated glucocorticoid signaling early in life directs development of a pro inflammatory adult phenotype  at the expense of immunoregulation and somatic regenerative capacity. Overall design: 30 samples total were analyzed. 9 caudal fins samples 0  2 and 4dpa  3 blood samples and 3 muscle samples from adults exposed to DMSO control as embryos. 9 caudal fins samples 0  2 and 4dpa  3 blood samples and 3 muscle samples from adults exposed to cortisol 1 micromolar as embryos.,parent bioproject:PRJNA318502,pubmed:27444789,,Control 3 blood,GSM2122868,,source name:whole blood  DMSO control|strain/background:AB|tissue:whole blood|age:adult|embryonic treatment:DMSO,Control 3 blood,Sequence quality was assessed using Fastqc QC v0.11.2; http://www.bioinformatics.babraham.ac.uk/projects/fastqc. Reads were trimmed using Trimmomatic v 0.3; Bolger et al.  2014. Trimmed reads were aligned to the zebrafish Danio rerio transcriptome annotated by Ensembl version 83 of the GRCz10 genome assembly using RSEM version 1.2.25 Li and Dewey  2011 and Bowtie 1.1.2 Langmead et al.  2009. Differentially expressed transcripts were determined using R/edgeR version 3.10.2 Robinson et al.  2010. Genome build: Danio rerio GRCz10 Supplementary files format and content: Tab delimited text files with read counts counts per million per sample.,whole blood  DMSO control,DMSO or 1 micromolar cortisol was added to larval medium for first 5 days of development  and then maintained to 4.5 month under normal conditions.,RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.,AB zebrafish were maintained at 28 degrees Celsius at the MDI Biological Laboratory Animal Core.,strain/background:AB|tissue:whole blood|age:adult|embryonic treatment:DMSO,GSM2122868,GSM2122868: Control 3 blood; Danio rerio; RNA Seq,GSM2122868,,1,RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.,GEO Accession:GSM2122868,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP073272,,,C8DY1ANXX_s5_1_GSLv3-7_35_SL139792.fastq.gz C8DY1ANXX_s5_2_GSLv3-7_35_SL139792.fastq.gz,fastq fastq,1352817900.0,13528179.0,GSM2122868 r4,0:50 1:50,A:366001448;C:311109301;G:313269573;T:362247619;N:189959,50,50,,,366001448,311109301,313269573,362247619,189959,SRX1704277,SRS1396346,SRA411416,GEO,"Molecular and Biomedical Sciences, University of Maine",2,0.89762,0.91702,0.11094,0.1109,0.74864,0.7498,0.53153,0.55731,50,50,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,United States,2016-04-13,Adult,Adult,Blood,Hematopoietic System
40823,SRR3381831,SRX1704276,SRS1396347,SRP073272,PRJNA318414,Cortisol treated zebrafish embryos develop into pro inflammatory adults with aberrant immune gene regulation [adults],GSE80260,Transcriptome Analysis,Chronic early life stress increases adult susceptibility to numerous health problems linked to chronic inflammation. One way that this may occur is via glucocorticoid induced developmental programming. To gain insight into such programming  we treated zebrafish embryos with cortisol and examined the effects on adults. In maturity  the treated fish maintained elevated basal cortisol levels in the absence of exogenous cortisol  and constitutively mis expressed genes involved in defense response and its regulation. Adults derived from cortisol treated embryos displayed defective tailfin regeneration  heightened basal expression of pro inflammatory genes  and failure to appropriately regulate those genes following injury or immunological challenge. These results support the hypothesis that chronically elevated glucocorticoid signaling early in life directs development of a pro inflammatory adult phenotype  at the expense of immunoregulation and somatic regenerative capacity. Overall design: 30 samples total were analyzed. 9 caudal fins samples 0  2 and 4dpa  3 blood samples and 3 muscle samples from adults exposed to DMSO control as embryos. 9 caudal fins samples 0  2 and 4dpa  3 blood samples and 3 muscle samples from adults exposed to cortisol 1 micromolar as embryos.,parent bioproject:PRJNA318502,pubmed:27444789,,Control 2 blood,GSM2122867,,source name:whole blood  DMSO control|strain/background:AB|tissue:whole blood|age:adult|embryonic treatment:DMSO,Control 2 blood,Sequence quality was assessed using Fastqc QC v0.11.2; http://www.bioinformatics.babraham.ac.uk/projects/fastqc. Reads were trimmed using Trimmomatic v 0.3; Bolger et al.  2014. Trimmed reads were aligned to the zebrafish Danio rerio transcriptome annotated by Ensembl version 83 of the GRCz10 genome assembly using RSEM version 1.2.25 Li and Dewey  2011 and Bowtie 1.1.2 Langmead et al.  2009. Differentially expressed transcripts were determined using R/edgeR version 3.10.2 Robinson et al.  2010. Genome build: Danio rerio GRCz10 Supplementary files format and content: Tab delimited text files with read counts counts per million per sample.,whole blood  DMSO control,DMSO or 1 micromolar cortisol was added to larval medium for first 5 days of development  and then maintained to 4.5 month under normal conditions.,RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.,AB zebrafish were maintained at 28 degrees Celsius at the MDI Biological Laboratory Animal Core.,strain/background:AB|tissue:whole blood|age:adult|embryonic treatment:DMSO,GSM2122867,GSM2122867: Control 2 blood; Danio rerio; RNA Seq,GSM2122867,,1,RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.,GEO Accession:GSM2122867,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP073272,,,C8DY1ANXX_s5_1_GSLv3-7_34_SL139791.fastq.gz C8DY1ANXX_s5_2_GSLv3-7_34_SL139791.fastq.gz,fastq fastq,1320276500.0,13202765.0,GSM2122867 r1,0:50 1:50,A:347340148;C:314346533;G:315984111;T:342435896;N:169812,50,50,,,347340148,314346533,315984111,342435896,169812,SRX1704276,SRS1396347,SRA411416,GEO,"Molecular and Biomedical Sciences, University of Maine",2,0.92673,0.93522,0.1474,0.1486,0.77695,0.77822,0.5491,0.55404,50,50,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,United States,2016-04-13,Adult,Adult,Blood,Hematopoietic System
40824,SRR3381832,SRX1704276,SRS1396347,SRP073272,PRJNA318414,Cortisol treated zebrafish embryos develop into pro inflammatory adults with aberrant immune gene regulation [adults],GSE80260,Transcriptome Analysis,Chronic early life stress increases adult susceptibility to numerous health problems linked to chronic inflammation. One way that this may occur is via glucocorticoid induced developmental programming. To gain insight into such programming  we treated zebrafish embryos with cortisol and examined the effects on adults. In maturity  the treated fish maintained elevated basal cortisol levels in the absence of exogenous cortisol  and constitutively mis expressed genes involved in defense response and its regulation. Adults derived from cortisol treated embryos displayed defective tailfin regeneration  heightened basal expression of pro inflammatory genes  and failure to appropriately regulate those genes following injury or immunological challenge. These results support the hypothesis that chronically elevated glucocorticoid signaling early in life directs development of a pro inflammatory adult phenotype  at the expense of immunoregulation and somatic regenerative capacity. Overall design: 30 samples total were analyzed. 9 caudal fins samples 0  2 and 4dpa  3 blood samples and 3 muscle samples from adults exposed to DMSO control as embryos. 9 caudal fins samples 0  2 and 4dpa  3 blood samples and 3 muscle samples from adults exposed to cortisol 1 micromolar as embryos.,parent bioproject:PRJNA318502,pubmed:27444789,,Control 2 blood,GSM2122867,,source name:whole blood  DMSO control|strain/background:AB|tissue:whole blood|age:adult|embryonic treatment:DMSO,Control 2 blood,Sequence quality was assessed using Fastqc QC v0.11.2; http://www.bioinformatics.babraham.ac.uk/projects/fastqc. Reads were trimmed using Trimmomatic v 0.3; Bolger et al.  2014. Trimmed reads were aligned to the zebrafish Danio rerio transcriptome annotated by Ensembl version 83 of the GRCz10 genome assembly using RSEM version 1.2.25 Li and Dewey  2011 and Bowtie 1.1.2 Langmead et al.  2009. Differentially expressed transcripts were determined using R/edgeR version 3.10.2 Robinson et al.  2010. Genome build: Danio rerio GRCz10 Supplementary files format and content: Tab delimited text files with read counts counts per million per sample.,whole blood  DMSO control,DMSO or 1 micromolar cortisol was added to larval medium for first 5 days of development  and then maintained to 4.5 month under normal conditions.,RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.,AB zebrafish were maintained at 28 degrees Celsius at the MDI Biological Laboratory Animal Core.,strain/background:AB|tissue:whole blood|age:adult|embryonic treatment:DMSO,GSM2122867,GSM2122867: Control 2 blood; Danio rerio; RNA Seq,GSM2122867,,1,RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.,GEO Accession:GSM2122867,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP073272,,,C8BH2ANXX_s6_1_GSLv3-7_34_SL139791.fastq.gz C8BH2ANXX_s6_2_GSLv3-7_34_SL139791.fastq.gz,fastq fastq,980312400.0,9803124.0,GSM2122867 r2,0:50 1:50,A:256051139;C:233456025;G:232307447;T:258480444;N:17345,50,50,,,256051139,233456025,232307447,258480444,17345,SRX1704276,SRS1396347,SRA411416,GEO,"Molecular and Biomedical Sciences, University of Maine",2,0.92686,0.9359,0.1445,0.14733,0.79537,0.78244,0.55823,0.5607,50,50,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,United States,2016-04-13,Adult,Adult,Blood,Hematopoietic System
40825,SRR3381833,SRX1704276,SRS1396347,SRP073272,PRJNA318414,Cortisol treated zebrafish embryos develop into pro inflammatory adults with aberrant immune gene regulation [adults],GSE80260,Transcriptome Analysis,Chronic early life stress increases adult susceptibility to numerous health problems linked to chronic inflammation. One way that this may occur is via glucocorticoid induced developmental programming. To gain insight into such programming  we treated zebrafish embryos with cortisol and examined the effects on adults. In maturity  the treated fish maintained elevated basal cortisol levels in the absence of exogenous cortisol  and constitutively mis expressed genes involved in defense response and its regulation. Adults derived from cortisol treated embryos displayed defective tailfin regeneration  heightened basal expression of pro inflammatory genes  and failure to appropriately regulate those genes following injury or immunological challenge. These results support the hypothesis that chronically elevated glucocorticoid signaling early in life directs development of a pro inflammatory adult phenotype  at the expense of immunoregulation and somatic regenerative capacity. Overall design: 30 samples total were analyzed. 9 caudal fins samples 0  2 and 4dpa  3 blood samples and 3 muscle samples from adults exposed to DMSO control as embryos. 9 caudal fins samples 0  2 and 4dpa  3 blood samples and 3 muscle samples from adults exposed to cortisol 1 micromolar as embryos.,parent bioproject:PRJNA318502,pubmed:27444789,,Control 2 blood,GSM2122867,,source name:whole blood  DMSO control|strain/background:AB|tissue:whole blood|age:adult|embryonic treatment:DMSO,Control 2 blood,Sequence quality was assessed using Fastqc QC v0.11.2; http://www.bioinformatics.babraham.ac.uk/projects/fastqc. Reads were trimmed using Trimmomatic v 0.3; Bolger et al.  2014. Trimmed reads were aligned to the zebrafish Danio rerio transcriptome annotated by Ensembl version 83 of the GRCz10 genome assembly using RSEM version 1.2.25 Li and Dewey  2011 and Bowtie 1.1.2 Langmead et al.  2009. Differentially expressed transcripts were determined using R/edgeR version 3.10.2 Robinson et al.  2010. Genome build: Danio rerio GRCz10 Supplementary files format and content: Tab delimited text files with read counts counts per million per sample.,whole blood  DMSO control,DMSO or 1 micromolar cortisol was added to larval medium for first 5 days of development  and then maintained to 4.5 month under normal conditions.,RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.,AB zebrafish were maintained at 28 degrees Celsius at the MDI Biological Laboratory Animal Core.,strain/background:AB|tissue:whole blood|age:adult|embryonic treatment:DMSO,GSM2122867,GSM2122867: Control 2 blood; Danio rerio; RNA Seq,GSM2122867,,1,RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.,GEO Accession:GSM2122867,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP073272,,,C8BH2ANXX_s5_1_GSLv3-7_34_SL139791.fastq.gz C8BH2ANXX_s5_2_GSLv3-7_34_SL139791.fastq.gz,fastq fastq,996477700.0,9964777.0,GSM2122867 r3,0:50 1:50,A:260257795;C:237526121;G:236299803;T:262375630;N:18351,50,50,,,260257795,237526121,236299803,262375630,18351,SRX1704276,SRS1396347,SRA411416,GEO,"Molecular and Biomedical Sciences, University of Maine",2,0.9292,0.93713,0.143,0.14889,0.79531,0.7834,0.55615,0.55279,50,50,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,United States,2016-04-13,Adult,Adult,Blood,Hematopoietic System
40826,SRR3381834,SRX1704276,SRS1396347,SRP073272,PRJNA318414,Cortisol treated zebrafish embryos develop into pro inflammatory adults with aberrant immune gene regulation [adults],GSE80260,Transcriptome Analysis,Chronic early life stress increases adult susceptibility to numerous health problems linked to chronic inflammation. One way that this may occur is via glucocorticoid induced developmental programming. To gain insight into such programming  we treated zebrafish embryos with cortisol and examined the effects on adults. In maturity  the treated fish maintained elevated basal cortisol levels in the absence of exogenous cortisol  and constitutively mis expressed genes involved in defense response and its regulation. Adults derived from cortisol treated embryos displayed defective tailfin regeneration  heightened basal expression of pro inflammatory genes  and failure to appropriately regulate those genes following injury or immunological challenge. These results support the hypothesis that chronically elevated glucocorticoid signaling early in life directs development of a pro inflammatory adult phenotype  at the expense of immunoregulation and somatic regenerative capacity. Overall design: 30 samples total were analyzed. 9 caudal fins samples 0  2 and 4dpa  3 blood samples and 3 muscle samples from adults exposed to DMSO control as embryos. 9 caudal fins samples 0  2 and 4dpa  3 blood samples and 3 muscle samples from adults exposed to cortisol 1 micromolar as embryos.,parent bioproject:PRJNA318502,pubmed:27444789,,Control 2 blood,GSM2122867,,source name:whole blood  DMSO control|strain/background:AB|tissue:whole blood|age:adult|embryonic treatment:DMSO,Control 2 blood,Sequence quality was assessed using Fastqc QC v0.11.2; http://www.bioinformatics.babraham.ac.uk/projects/fastqc. Reads were trimmed using Trimmomatic v 0.3; Bolger et al.  2014. Trimmed reads were aligned to the zebrafish Danio rerio transcriptome annotated by Ensembl version 83 of the GRCz10 genome assembly using RSEM version 1.2.25 Li and Dewey  2011 and Bowtie 1.1.2 Langmead et al.  2009. Differentially expressed transcripts were determined using R/edgeR version 3.10.2 Robinson et al.  2010. Genome build: Danio rerio GRCz10 Supplementary files format and content: Tab delimited text files with read counts counts per million per sample.,whole blood  DMSO control,DMSO or 1 micromolar cortisol was added to larval medium for first 5 days of development  and then maintained to 4.5 month under normal conditions.,RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.,AB zebrafish were maintained at 28 degrees Celsius at the MDI Biological Laboratory Animal Core.,strain/background:AB|tissue:whole blood|age:adult|embryonic treatment:DMSO,GSM2122867,GSM2122867: Control 2 blood; Danio rerio; RNA Seq,GSM2122867,,1,RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.,GEO Accession:GSM2122867,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP073272,,,C8DY1ANXX_s6_1_GSLv3-7_34_SL139791.fastq.gz C8DY1ANXX_s6_2_GSLv3-7_34_SL139791.fastq.gz,fastq fastq,1319184300.0,13191843.0,GSM2122867 r4,0:50 1:50,A:347098468;C:314043165;G:315610117;T:342302442;N:130108,50,50,,,347098468,314043165,315610117,342302442,130108,SRX1704276,SRS1396347,SRA411416,GEO,"Molecular and Biomedical Sciences, University of Maine",2,0.92671,0.93595,0.14826,0.14877,0.77792,0.77873,0.55524,0.5557,50,50,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,United States,2016-04-13,Adult,Adult,Blood,Hematopoietic System
40827,SRR3381825,SRX1704275,SRS1396348,SRP073272,PRJNA318414,Cortisol treated zebrafish embryos develop into pro inflammatory adults with aberrant immune gene regulation [adults],GSE80260,Transcriptome Analysis,Chronic early life stress increases adult susceptibility to numerous health problems linked to chronic inflammation. One way that this may occur is via glucocorticoid induced developmental programming. To gain insight into such programming  we treated zebrafish embryos with cortisol and examined the effects on adults. In maturity  the treated fish maintained elevated basal cortisol levels in the absence of exogenous cortisol  and constitutively mis expressed genes involved in defense response and its regulation. Adults derived from cortisol treated embryos displayed defective tailfin regeneration  heightened basal expression of pro inflammatory genes  and failure to appropriately regulate those genes following injury or immunological challenge. These results support the hypothesis that chronically elevated glucocorticoid signaling early in life directs development of a pro inflammatory adult phenotype  at the expense of immunoregulation and somatic regenerative capacity. Overall design: 30 samples total were analyzed. 9 caudal fins samples 0  2 and 4dpa  3 blood samples and 3 muscle samples from adults exposed to DMSO control as embryos. 9 caudal fins samples 0  2 and 4dpa  3 blood samples and 3 muscle samples from adults exposed to cortisol 1 micromolar as embryos.,parent bioproject:PRJNA318502,pubmed:27444789,,Control 1 blood,GSM2122866,,source name:whole blood  DMSO control|strain/background:AB|tissue:whole blood|age:adult|embryonic treatment:DMSO,Control 1 blood,Sequence quality was assessed using Fastqc QC v0.11.2; http://www.bioinformatics.babraham.ac.uk/projects/fastqc. Reads were trimmed using Trimmomatic v 0.3; Bolger et al.  2014. Trimmed reads were aligned to the zebrafish Danio rerio transcriptome annotated by Ensembl version 83 of the GRCz10 genome assembly using RSEM version 1.2.25 Li and Dewey  2011 and Bowtie 1.1.2 Langmead et al.  2009. Differentially expressed transcripts were determined using R/edgeR version 3.10.2 Robinson et al.  2010. Genome build: Danio rerio GRCz10 Supplementary files format and content: Tab delimited text files with read counts counts per million per sample.,whole blood  DMSO control,DMSO or 1 micromolar cortisol was added to larval medium for first 5 days of development  and then maintained to 4.5 month under normal conditions.,RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.,AB zebrafish were maintained at 28 degrees Celsius at the MDI Biological Laboratory Animal Core.,strain/background:AB|tissue:whole blood|age:adult|embryonic treatment:DMSO,GSM2122866,GSM2122866: Control 1 blood; Danio rerio; RNA Seq,GSM2122866,,1,RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.,GEO Accession:GSM2122866,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP073272,,,C8BH2ANXX_s6_1_GSLv3-7_33_SL139790.fastq.gz C8BH2ANXX_s6_2_GSLv3-7_33_SL139790.fastq.gz,fastq fastq,692276000.0,6922760.0,GSM2122866 r1,0:50 1:50,A:191405813;C:153586292;G:152965257;T:194306049;N:12589,50,50,,,191405813,153586292,152965257,194306049,12589,SRX1704275,SRS1396348,SRA411416,GEO,"Molecular and Biomedical Sciences, University of Maine",2,0.9083,0.91142,0.16578,0.17743,0.75789,0.74221,0.55181,0.54476,50,50,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,United States,2016-04-13,Adult,Adult,Blood,Hematopoietic System
40828,SRR3381826,SRX1704275,SRS1396348,SRP073272,PRJNA318414,Cortisol treated zebrafish embryos develop into pro inflammatory adults with aberrant immune gene regulation [adults],GSE80260,Transcriptome Analysis,Chronic early life stress increases adult susceptibility to numerous health problems linked to chronic inflammation. One way that this may occur is via glucocorticoid induced developmental programming. To gain insight into such programming  we treated zebrafish embryos with cortisol and examined the effects on adults. In maturity  the treated fish maintained elevated basal cortisol levels in the absence of exogenous cortisol  and constitutively mis expressed genes involved in defense response and its regulation. Adults derived from cortisol treated embryos displayed defective tailfin regeneration  heightened basal expression of pro inflammatory genes  and failure to appropriately regulate those genes following injury or immunological challenge. These results support the hypothesis that chronically elevated glucocorticoid signaling early in life directs development of a pro inflammatory adult phenotype  at the expense of immunoregulation and somatic regenerative capacity. Overall design: 30 samples total were analyzed. 9 caudal fins samples 0  2 and 4dpa  3 blood samples and 3 muscle samples from adults exposed to DMSO control as embryos. 9 caudal fins samples 0  2 and 4dpa  3 blood samples and 3 muscle samples from adults exposed to cortisol 1 micromolar as embryos.,parent bioproject:PRJNA318502,pubmed:27444789,,Control 1 blood,GSM2122866,,source name:whole blood  DMSO control|strain/background:AB|tissue:whole blood|age:adult|embryonic treatment:DMSO,Control 1 blood,Sequence quality was assessed using Fastqc QC v0.11.2; http://www.bioinformatics.babraham.ac.uk/projects/fastqc. Reads were trimmed using Trimmomatic v 0.3; Bolger et al.  2014. Trimmed reads were aligned to the zebrafish Danio rerio transcriptome annotated by Ensembl version 83 of the GRCz10 genome assembly using RSEM version 1.2.25 Li and Dewey  2011 and Bowtie 1.1.2 Langmead et al.  2009. Differentially expressed transcripts were determined using R/edgeR version 3.10.2 Robinson et al.  2010. Genome build: Danio rerio GRCz10 Supplementary files format and content: Tab delimited text files with read counts counts per million per sample.,whole blood  DMSO control,DMSO or 1 micromolar cortisol was added to larval medium for first 5 days of development  and then maintained to 4.5 month under normal conditions.,RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.,AB zebrafish were maintained at 28 degrees Celsius at the MDI Biological Laboratory Animal Core.,strain/background:AB|tissue:whole blood|age:adult|embryonic treatment:DMSO,GSM2122866,GSM2122866: Control 1 blood; Danio rerio; RNA Seq,GSM2122866,,1,RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.,GEO Accession:GSM2122866,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP073272,,,C8DY1ANXX_s5_1_GSLv3-7_33_SL139790.fastq.gz C8DY1ANXX_s5_2_GSLv3-7_33_SL139790.fastq.gz,fastq fastq,911479300.0,9114793.0,GSM2122866 r2,0:50 1:50,A:253240601;C:202627238;G:203390297;T:252105631;N:115533,50,50,,,253240601,202627238,203390297,252105631,115533,SRX1704275,SRS1396348,SRA411416,GEO,"Molecular and Biomedical Sciences, University of Maine",2,0.90729,0.91334,0.17307,0.1777,0.73316,0.73419,0.55981,0.56826,50,50,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,United States,2016-04-13,Adult,Adult,Blood,Hematopoietic System
40829,SRR3381827,SRX1704275,SRS1396348,SRP073272,PRJNA318414,Cortisol treated zebrafish embryos develop into pro inflammatory adults with aberrant immune gene regulation [adults],GSE80260,Transcriptome Analysis,Chronic early life stress increases adult susceptibility to numerous health problems linked to chronic inflammation. One way that this may occur is via glucocorticoid induced developmental programming. To gain insight into such programming  we treated zebrafish embryos with cortisol and examined the effects on adults. In maturity  the treated fish maintained elevated basal cortisol levels in the absence of exogenous cortisol  and constitutively mis expressed genes involved in defense response and its regulation. Adults derived from cortisol treated embryos displayed defective tailfin regeneration  heightened basal expression of pro inflammatory genes  and failure to appropriately regulate those genes following injury or immunological challenge. These results support the hypothesis that chronically elevated glucocorticoid signaling early in life directs development of a pro inflammatory adult phenotype  at the expense of immunoregulation and somatic regenerative capacity. Overall design: 30 samples total were analyzed. 9 caudal fins samples 0  2 and 4dpa  3 blood samples and 3 muscle samples from adults exposed to DMSO control as embryos. 9 caudal fins samples 0  2 and 4dpa  3 blood samples and 3 muscle samples from adults exposed to cortisol 1 micromolar as embryos.,parent bioproject:PRJNA318502,pubmed:27444789,,Control 1 blood,GSM2122866,,source name:whole blood  DMSO control|strain/background:AB|tissue:whole blood|age:adult|embryonic treatment:DMSO,Control 1 blood,Sequence quality was assessed using Fastqc QC v0.11.2; http://www.bioinformatics.babraham.ac.uk/projects/fastqc. Reads were trimmed using Trimmomatic v 0.3; Bolger et al.  2014. Trimmed reads were aligned to the zebrafish Danio rerio transcriptome annotated by Ensembl version 83 of the GRCz10 genome assembly using RSEM version 1.2.25 Li and Dewey  2011 and Bowtie 1.1.2 Langmead et al.  2009. Differentially expressed transcripts were determined using R/edgeR version 3.10.2 Robinson et al.  2010. Genome build: Danio rerio GRCz10 Supplementary files format and content: Tab delimited text files with read counts counts per million per sample.,whole blood  DMSO control,DMSO or 1 micromolar cortisol was added to larval medium for first 5 days of development  and then maintained to 4.5 month under normal conditions.,RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.,AB zebrafish were maintained at 28 degrees Celsius at the MDI Biological Laboratory Animal Core.,strain/background:AB|tissue:whole blood|age:adult|embryonic treatment:DMSO,GSM2122866,GSM2122866: Control 1 blood; Danio rerio; RNA Seq,GSM2122866,,1,RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.,GEO Accession:GSM2122866,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP073272,,,C8DY1ANXX_s6_1_GSLv3-7_33_SL139790.fastq.gz C8DY1ANXX_s6_2_GSLv3-7_33_SL139790.fastq.gz,fastq fastq,910041600.0,9100416.0,GSM2122866 r3,0:50 1:50,A:252924440;C:202200821;G:202972517;T:251856107;N:87715,50,50,,,252924440,202200821,202972517,251856107,87715,SRX1704275,SRS1396348,SRA411416,GEO,"Molecular and Biomedical Sciences, University of Maine",2,0.90819,0.91345,0.17288,0.17678,0.73582,0.73448,0.55482,0.56579,50,50,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,United States,2016-04-13,Adult,Adult,Blood,Hematopoietic System
40830,SRR3381828,SRX1704275,SRS1396348,SRP073272,PRJNA318414,Cortisol treated zebrafish embryos develop into pro inflammatory adults with aberrant immune gene regulation [adults],GSE80260,Transcriptome Analysis,Chronic early life stress increases adult susceptibility to numerous health problems linked to chronic inflammation. One way that this may occur is via glucocorticoid induced developmental programming. To gain insight into such programming  we treated zebrafish embryos with cortisol and examined the effects on adults. In maturity  the treated fish maintained elevated basal cortisol levels in the absence of exogenous cortisol  and constitutively mis expressed genes involved in defense response and its regulation. Adults derived from cortisol treated embryos displayed defective tailfin regeneration  heightened basal expression of pro inflammatory genes  and failure to appropriately regulate those genes following injury or immunological challenge. These results support the hypothesis that chronically elevated glucocorticoid signaling early in life directs development of a pro inflammatory adult phenotype  at the expense of immunoregulation and somatic regenerative capacity. Overall design: 30 samples total were analyzed. 9 caudal fins samples 0  2 and 4dpa  3 blood samples and 3 muscle samples from adults exposed to DMSO control as embryos. 9 caudal fins samples 0  2 and 4dpa  3 blood samples and 3 muscle samples from adults exposed to cortisol 1 micromolar as embryos.,parent bioproject:PRJNA318502,pubmed:27444789,,Control 1 blood,GSM2122866,,source name:whole blood  DMSO control|strain/background:AB|tissue:whole blood|age:adult|embryonic treatment:DMSO,Control 1 blood,Sequence quality was assessed using Fastqc QC v0.11.2; http://www.bioinformatics.babraham.ac.uk/projects/fastqc. Reads were trimmed using Trimmomatic v 0.3; Bolger et al.  2014. Trimmed reads were aligned to the zebrafish Danio rerio transcriptome annotated by Ensembl version 83 of the GRCz10 genome assembly using RSEM version 1.2.25 Li and Dewey  2011 and Bowtie 1.1.2 Langmead et al.  2009. Differentially expressed transcripts were determined using R/edgeR version 3.10.2 Robinson et al.  2010. Genome build: Danio rerio GRCz10 Supplementary files format and content: Tab delimited text files with read counts counts per million per sample.,whole blood  DMSO control,DMSO or 1 micromolar cortisol was added to larval medium for first 5 days of development  and then maintained to 4.5 month under normal conditions.,RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.,AB zebrafish were maintained at 28 degrees Celsius at the MDI Biological Laboratory Animal Core.,strain/background:AB|tissue:whole blood|age:adult|embryonic treatment:DMSO,GSM2122866,GSM2122866: Control 1 blood; Danio rerio; RNA Seq,GSM2122866,,1,RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.,GEO Accession:GSM2122866,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP073272,,,C8BH2ANXX_s5_1_GSLv3-7_33_SL139790.fastq.gz C8BH2ANXX_s5_2_GSLv3-7_33_SL139790.fastq.gz,fastq fastq,701940200.0,7019402.0,GSM2122866 r4,0:50 1:50,A:194036996;C:155992188;G:155284640;T:196613376;N:13000,50,50,,,194036996,155992188,155284640,196613376,13000,SRX1704275,SRS1396348,SRA411416,GEO,"Molecular and Biomedical Sciences, University of Maine",2,0.90959,0.91386,0.16429,0.17705,0.75544,0.7391,0.548,0.57224,50,50,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,United States,2016-04-13,Adult,Adult,Blood,Hematopoietic System
40831,SRR3381829,SRX1704275,SRS1396348,SRP073272,PRJNA318414,Cortisol treated zebrafish embryos develop into pro inflammatory adults with aberrant immune gene regulation [adults],GSE80260,Transcriptome Analysis,Chronic early life stress increases adult susceptibility to numerous health problems linked to chronic inflammation. One way that this may occur is via glucocorticoid induced developmental programming. To gain insight into such programming  we treated zebrafish embryos with cortisol and examined the effects on adults. In maturity  the treated fish maintained elevated basal cortisol levels in the absence of exogenous cortisol  and constitutively mis expressed genes involved in defense response and its regulation. Adults derived from cortisol treated embryos displayed defective tailfin regeneration  heightened basal expression of pro inflammatory genes  and failure to appropriately regulate those genes following injury or immunological challenge. These results support the hypothesis that chronically elevated glucocorticoid signaling early in life directs development of a pro inflammatory adult phenotype  at the expense of immunoregulation and somatic regenerative capacity. Overall design: 30 samples total were analyzed. 9 caudal fins samples 0  2 and 4dpa  3 blood samples and 3 muscle samples from adults exposed to DMSO control as embryos. 9 caudal fins samples 0  2 and 4dpa  3 blood samples and 3 muscle samples from adults exposed to cortisol 1 micromolar as embryos.,parent bioproject:PRJNA318502,pubmed:27444789,,Control 1 blood,GSM2122866,,source name:whole blood  DMSO control|strain/background:AB|tissue:whole blood|age:adult|embryonic treatment:DMSO,Control 1 blood,Sequence quality was assessed using Fastqc QC v0.11.2; http://www.bioinformatics.babraham.ac.uk/projects/fastqc. Reads were trimmed using Trimmomatic v 0.3; Bolger et al.  2014. Trimmed reads were aligned to the zebrafish Danio rerio transcriptome annotated by Ensembl version 83 of the GRCz10 genome assembly using RSEM version 1.2.25 Li and Dewey  2011 and Bowtie 1.1.2 Langmead et al.  2009. Differentially expressed transcripts were determined using R/edgeR version 3.10.2 Robinson et al.  2010. Genome build: Danio rerio GRCz10 Supplementary files format and content: Tab delimited text files with read counts counts per million per sample.,whole blood  DMSO control,DMSO or 1 micromolar cortisol was added to larval medium for first 5 days of development  and then maintained to 4.5 month under normal conditions.,RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.,AB zebrafish were maintained at 28 degrees Celsius at the MDI Biological Laboratory Animal Core.,strain/background:AB|tissue:whole blood|age:adult|embryonic treatment:DMSO,GSM2122866,GSM2122866: Control 1 blood; Danio rerio; RNA Seq,GSM2122866,,1,RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.,GEO Accession:GSM2122866,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP073272,,,C8DKGANXX_s8_1_GSLv3-7_33_SL139790.fastq.gz C8DKGANXX_s8_2_GSLv3-7_33_SL139790.fastq.gz,fastq fastq,1596331500.0,15963315.0,GSM2122866 r5,0:50 1:50,A:444854958;C:353331559;G:354367449;T:442888766;N:888768,50,50,,,444854958,353331559,354367449,442888766,888768,SRX1704275,SRS1396348,SRA411416,GEO,"Molecular and Biomedical Sciences, University of Maine",2,0.90554,0.91175,0.17327,0.17968,0.73669,0.73728,0.55044,0.5651,50,50,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,United States,2016-04-13,Adult,Adult,Blood,Hematopoietic System
40832,SRR3381830,SRX1704275,SRS1396348,SRP073272,PRJNA318414,Cortisol treated zebrafish embryos develop into pro inflammatory adults with aberrant immune gene regulation [adults],GSE80260,Transcriptome Analysis,Chronic early life stress increases adult susceptibility to numerous health problems linked to chronic inflammation. One way that this may occur is via glucocorticoid induced developmental programming. To gain insight into such programming  we treated zebrafish embryos with cortisol and examined the effects on adults. In maturity  the treated fish maintained elevated basal cortisol levels in the absence of exogenous cortisol  and constitutively mis expressed genes involved in defense response and its regulation. Adults derived from cortisol treated embryos displayed defective tailfin regeneration  heightened basal expression of pro inflammatory genes  and failure to appropriately regulate those genes following injury or immunological challenge. These results support the hypothesis that chronically elevated glucocorticoid signaling early in life directs development of a pro inflammatory adult phenotype  at the expense of immunoregulation and somatic regenerative capacity. Overall design: 30 samples total were analyzed. 9 caudal fins samples 0  2 and 4dpa  3 blood samples and 3 muscle samples from adults exposed to DMSO control as embryos. 9 caudal fins samples 0  2 and 4dpa  3 blood samples and 3 muscle samples from adults exposed to cortisol 1 micromolar as embryos.,parent bioproject:PRJNA318502,pubmed:27444789,,Control 1 blood,GSM2122866,,source name:whole blood  DMSO control|strain/background:AB|tissue:whole blood|age:adult|embryonic treatment:DMSO,Control 1 blood,Sequence quality was assessed using Fastqc QC v0.11.2; http://www.bioinformatics.babraham.ac.uk/projects/fastqc. Reads were trimmed using Trimmomatic v 0.3; Bolger et al.  2014. Trimmed reads were aligned to the zebrafish Danio rerio transcriptome annotated by Ensembl version 83 of the GRCz10 genome assembly using RSEM version 1.2.25 Li and Dewey  2011 and Bowtie 1.1.2 Langmead et al.  2009. Differentially expressed transcripts were determined using R/edgeR version 3.10.2 Robinson et al.  2010. Genome build: Danio rerio GRCz10 Supplementary files format and content: Tab delimited text files with read counts counts per million per sample.,whole blood  DMSO control,DMSO or 1 micromolar cortisol was added to larval medium for first 5 days of development  and then maintained to 4.5 month under normal conditions.,RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.,AB zebrafish were maintained at 28 degrees Celsius at the MDI Biological Laboratory Animal Core.,strain/background:AB|tissue:whole blood|age:adult|embryonic treatment:DMSO,GSM2122866,GSM2122866: Control 1 blood; Danio rerio; RNA Seq,GSM2122866,,1,RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.,GEO Accession:GSM2122866,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP073272,,,C8DKGANXX_s7_1_GSLv3-7_33_SL139790.fastq.gz C8DKGANXX_s7_2_GSLv3-7_33_SL139790.fastq.gz,fastq fastq,1600754600.0,16007546.0,GSM2122866 r6,0:50 1:50,A:446178544;C:354456079;G:355435947;T:443937350;N:746680,50,50,,,446178544,354456079,355435947,443937350,746680,SRX1704275,SRS1396348,SRA411416,GEO,"Molecular and Biomedical Sciences, University of Maine",2,0.90709,0.91238,0.17011,0.17723,0.74054,0.73994,0.55938,0.55607,50,50,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,United States,2016-04-13,Adult,Adult,Blood,Hematopoietic System
49188,SRR7785379,SRX4640375,SRS3738589,SRP159583,PRJNA489308,Over expression of EVI 1 oncogene regulate multi pathway to affect zebrafish embryogenesis and hemopoiesis,PRJNA489308,Other,Our group established Tg Tol GFP EVI 1 zebrafish line and detected survival rate and developmental abnormality in injected embryos. And we found Tg Tol GFP EVI 1 zebrafish embryos underwent abnormal hematopoiesis and aberrant expression of human EVI 1 perturbs hematopoiesis to promote myeloid myeloid and suppress erythroid lineage fates. Moreover  overexpression of human EVI 1 induced immature hematopoietic cells emerged in blood circulation. We used whole genome transcriptome analysis RNA Seq to determine differential gene expression in peripheral blood between wildtype larvae and EVI 1 transgenic zebrafish larvae.,,,,,H67,,breed:AB strain|age:3 month|sex:male|tissue:Peripheral blood|genotype:wild type|replicate:replicate2|BioSampleModel:Model organism or animal,,,,,,,,,H67,H67,H67,Wild type zebrafish control 2,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP159583,,,H67_S2_L001_R2_001.fastq.gz H67_S2_L001_R1_001.fastq.gz,fastq fastq,18477819300.0,61592731.0,H67 S2 L001 R2 001.fastq.gz,0:150 1:150,A:4887782016;C:4375793599;G:4438933003;T:4775205744;N:104938,150,150,,,4887782016,4375793599,4438933003,4775205744,104938,SRX4640375,SRS3738589,SRA766519,"Department of Haematology, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University|Department: Department of Haematology","Department of Haematology, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University",2,0.93322,0.93319,0.06946,0.06963,0.6747,0.68083,0.47183,0.47148,150,150,B,B,biological fallback assumption,illumina,hiseq_era,full_length,random_priming,unknown,bulk,unknown,unknown,,China,2019-09-20,Adult,Adult,Blood,Hematopoietic System
49189,SRR7785380,SRX4640374,SRS3738594,SRP159583,PRJNA489308,Over expression of EVI 1 oncogene regulate multi pathway to affect zebrafish embryogenesis and hemopoiesis,PRJNA489308,Other,Our group established Tg Tol GFP EVI 1 zebrafish line and detected survival rate and developmental abnormality in injected embryos. And we found Tg Tol GFP EVI 1 zebrafish embryos underwent abnormal hematopoiesis and aberrant expression of human EVI 1 perturbs hematopoiesis to promote myeloid myeloid and suppress erythroid lineage fates. Moreover  overexpression of human EVI 1 induced immature hematopoietic cells emerged in blood circulation. We used whole genome transcriptome analysis RNA Seq to determine differential gene expression in peripheral blood between wildtype larvae and EVI 1 transgenic zebrafish larvae.,,,,,H66,,breed:AB strain|age:3 month|sex:male|tissue:Peripheral blood|genotype:wild type|replicate:replicate1|BioSampleModel:Model organism or animal,,,,,,,,,H66,H66,H66,Wild type zebrafish control 1,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP159583,,,H66_S1_L001_R2_001.fastq.gz H66_S1_L001_R1_001.fastq.gz,fastq fastq,20487126300.0,68290421.0,H66 S1 L001 R2 001.fastq.gz,0:150 1:150,A:5445452582;C:4824876569;G:4904146081;T:5312533433;N:117635,150,150,,,5445452582,4824876569,4904146081,5312533433,117635,SRX4640374,SRS3738594,SRA766519,"Department of Haematology, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University|Department: Department of Haematology","Department of Haematology, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University",2,0.93306,0.9336,0.08694,0.08764,0.66687,0.6734,0.46489,0.47008,150,150,B,B,biological fallback assumption,illumina,hiseq_era,full_length,random_priming,unknown,bulk,unknown,unknown,,China,2019-09-20,Adult,Adult,Blood,Hematopoietic System
49190,SRR7785381,SRX4640373,SRS3738593,SRP159583,PRJNA489308,Over expression of EVI 1 oncogene regulate multi pathway to affect zebrafish embryogenesis and hemopoiesis,PRJNA489308,Other,Our group established Tg Tol GFP EVI 1 zebrafish line and detected survival rate and developmental abnormality in injected embryos. And we found Tg Tol GFP EVI 1 zebrafish embryos underwent abnormal hematopoiesis and aberrant expression of human EVI 1 perturbs hematopoiesis to promote myeloid myeloid and suppress erythroid lineage fates. Moreover  overexpression of human EVI 1 induced immature hematopoietic cells emerged in blood circulation. We used whole genome transcriptome analysis RNA Seq to determine differential gene expression in peripheral blood between wildtype larvae and EVI 1 transgenic zebrafish larvae.,,,,,H124,,breed:AB strain|age:3 month|sex:male|tissue:Peripheral blood|genotype:Tol2 EVI 1 EGFP transgenic|replicate:replicate1|BioSampleModel:Model organism or animal,,,,,,,,,H124,H124,H124,Tol2 EVI 1 EGFP transgenic zebrafish sample 1,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP159583,,,H124_S1_L001_R1_001.fastq.gz H124_S1_L001_R2_001.fastq.gz,fastq fastq,13178593800.0,43928646.0,H124 S1 L001 R1 001.fastq.gz,0:150 1:150,A:3507220604;C:3103991247;G:3164157369;T:3403051995;N:172585,150,150,,,3507220604,3103991247,3164157369,3403051995,172585,SRX4640373,SRS3738593,SRA766519,"Department of Haematology, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University|Department: Department of Haematology","Department of Haematology, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University",2,0.94147,0.94277,0.08109,0.08136,0.69483,0.70011,0.47542,0.47593,150,150,B,B,biological fallback assumption,illumina,hiseq_era,full_length,random_priming,unknown,bulk,unknown,unknown,,China,2019-09-20,Adult,Adult,Blood,Hematopoietic System
49191,SRR7785382,SRX4640372,SRS3738592,SRP159583,PRJNA489308,Over expression of EVI 1 oncogene regulate multi pathway to affect zebrafish embryogenesis and hemopoiesis,PRJNA489308,Other,Our group established Tg Tol GFP EVI 1 zebrafish line and detected survival rate and developmental abnormality in injected embryos. And we found Tg Tol GFP EVI 1 zebrafish embryos underwent abnormal hematopoiesis and aberrant expression of human EVI 1 perturbs hematopoiesis to promote myeloid myeloid and suppress erythroid lineage fates. Moreover  overexpression of human EVI 1 induced immature hematopoietic cells emerged in blood circulation. We used whole genome transcriptome analysis RNA Seq to determine differential gene expression in peripheral blood between wildtype larvae and EVI 1 transgenic zebrafish larvae.,,,,,H93,,breed:AB strain|age:3 month|sex:male|tissue:Peripheral blood|genotype:wild type|replicate:replicate3|BioSampleModel:Model organism or animal,,,,,,,,,H93,H93,H93,Wild type zebrafish control 3,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP159583,,,H93_S3_L001_R1_001.fastq.gz H93_S3_L001_R2_001.fastq.gz,fastq fastq,18197379600.0,60657932.0,H93 S3 L001 R1 001.fastq.gz,0:150 1:150,A:4814246240;C:4308418881;G:4375398316;T:4699211054;N:105109,150,150,,,4814246240,4308418881,4375398316,4699211054,105109,SRX4640372,SRS3738592,SRA766519,"Department of Haematology, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University|Department: Department of Haematology","Department of Haematology, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University",2,0.9312,0.93173,0.07454,0.07498,0.67065,0.6773,0.46807,0.47334,150,150,B,B,biological fallback assumption,illumina,hiseq_era,full_length,random_priming,unknown,bulk,unknown,unknown,,China,2019-09-20,Adult,Adult,Blood,Hematopoietic System
49192,SRR7785383,SRX4640371,SRS3738590,SRP159583,PRJNA489308,Over expression of EVI 1 oncogene regulate multi pathway to affect zebrafish embryogenesis and hemopoiesis,PRJNA489308,Other,Our group established Tg Tol GFP EVI 1 zebrafish line and detected survival rate and developmental abnormality in injected embryos. And we found Tg Tol GFP EVI 1 zebrafish embryos underwent abnormal hematopoiesis and aberrant expression of human EVI 1 perturbs hematopoiesis to promote myeloid myeloid and suppress erythroid lineage fates. Moreover  overexpression of human EVI 1 induced immature hematopoietic cells emerged in blood circulation. We used whole genome transcriptome analysis RNA Seq to determine differential gene expression in peripheral blood between wildtype larvae and EVI 1 transgenic zebrafish larvae.,,,,,H126,,breed:AB strain|age:3 month|sex:male|tissue:Peripheral blood|genotype:Tol2 EVI 1 EGFP transgenic|replicate:replicate3|BioSampleModel:Model organism or animal,,,,,,,,,H126,H126,H126,Tol2 EVI 1 EGFP transgenic zebrafish sample 3,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP159583,,,H126_S3_L001_R1_001.fastq.gz H126_S3_L001_R2_001.fastq.gz,fastq fastq,14979601800.0,49932006.0,H126 S3 L001 R2 001.fastq.gz,0:150 1:150,A:3961375940;C:3551410264;G:3640700651;T:3825918931;N:196014,150,150,,,3961375940,3551410264,3640700651,3825918931,196014,SRX4640371,SRS3738590,SRA766519,"Department of Haematology, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University|Department: Department of Haematology","Department of Haematology, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University",2,0.93717,0.93908,0.05823,0.05891,0.70552,0.71256,0.46146,0.45779,150,150,B,B,biological fallback assumption,illumina,hiseq_era,full_length,random_priming,unknown,bulk,unknown,unknown,,China,2019-09-20,Adult,Adult,Blood,Hematopoietic System
49193,SRR7785384,SRX4640370,SRS3738588,SRP159583,PRJNA489308,Over expression of EVI 1 oncogene regulate multi pathway to affect zebrafish embryogenesis and hemopoiesis,PRJNA489308,Other,Our group established Tg Tol GFP EVI 1 zebrafish line and detected survival rate and developmental abnormality in injected embryos. And we found Tg Tol GFP EVI 1 zebrafish embryos underwent abnormal hematopoiesis and aberrant expression of human EVI 1 perturbs hematopoiesis to promote myeloid myeloid and suppress erythroid lineage fates. Moreover  overexpression of human EVI 1 induced immature hematopoietic cells emerged in blood circulation. We used whole genome transcriptome analysis RNA Seq to determine differential gene expression in peripheral blood between wildtype larvae and EVI 1 transgenic zebrafish larvae.,,,,,H125,,breed:AB strain|age:3 month|sex:male|tissue:Peripheral blood|genotype:Tol2 EVI 1 EGFP transgenic|replicate:replicate2|BioSampleModel:Model organism or animal,,,,,,,,,H125,H125,H125,Tol2 EVI 1 EGFP transgenic zebrafish sample 2,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP159583,,,H125_S2_L001_R1_001.fastq.gz H125_S2_L001_R2_001.fastq.gz,fastq fastq,16012998000.0,53376660.0,H125 S2 L001 R1 001.fastq.gz,0:150 1:150,A:4365269809;C:3662731840;G:3768367416;T:4216409682;N:219253,150,150,,,4365269809,3662731840,3768367416,4216409682,219253,SRX4640370,SRS3738588,SRA766519,"Department of Haematology, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University|Department: Department of Haematology","Department of Haematology, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University",2,0.9402,0.94198,0.09449,0.09528,0.71999,0.72512,0.46106,0.47624,150,150,B,B,biological fallback assumption,illumina,hiseq_era,full_length,random_priming,unknown,bulk,unknown,unknown,,China,2018-09-04,Adult,Adult,Blood,Hematopoietic System
51876,SRR8922974,SRX5704273,SRS4643334,SRP192854,PRJNA533283,RNA seq of erythroid cells from 24 hpf sf3b1 mutant and sibling zebrafish,GSE129952,Transcriptome Analysis,The purpose of the experiment was to define the gene expression and splicing alterations occurring when the levels of the splicing factor Sf3b1 are lowered in embryonic zebrafish. Results provide insight the role of Sf3b1 in erythropoietic development. Overall design: mRNA profiling of gata1 positive erythroid cells isolated from 24 hpf sf3b1 mutant and sibling zebrafish using Illumina NextSeq500. Five samples were sequenced for each.,,,,erythroid cells: WT6,GSM3728533,,tissue:erythroid cells|age:24 hpf type:gata1 positive erythroid cells|genotype/variation:wild type,erythroid cells: WT6,basecalling was done with the Picard module IlluminaBasecallsToFastq Reads were trimmed using TRIM GALORE software to check for quality of 150bp reads. These paired end reads were mapped using STAR aligner version 2.4.2a to the reference genome. Differential expression analysis was done using DESeq220 and EdgeR21 Bioconductor packages. To calculate FPKM  Cufflinks version 2.2.1 was used. Genome build: GRcz10 Supplementary files format and content: tab delimited text file includeS FPKM values for each Sample,erythroid cells,,Gata1 positive cells were isolated from zebrafish embryos. RNA was extracted with the quick RNA microprep Zymo. Ribosomal RNA was depleted with Ribogone Clontech. Libraries were made following the protocol and using the reagents from the SMARTer Stranded RNA Seq Kit Clontech.,,age:24 hpf type:gata1 positive erythroid cells|genotype/variation:wild type,GSM3728533,GSM3728533: erythroid cells: WT6; Danio rerio; RNA Seq,GSM3728533,,1,Gata1 positive cells were isolated from zebrafish embryos. RNA was extracted with the quick RNA microprep Zymo. Ribosomal RNA was depleted with Ribogone Clontech. Libraries were made following the protocol and using the reagents from the SMARTer Stranded RNA Seq Kit Clontech.,GEO Accession:GSM3728533,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP192854,,,J633_AHFHNLBGX2_TAGCTT_LWT6.1_val_1.fq.gz J633_AHFHNLBGX2_TAGCTT_LWT6.2_val_2.fq.gz,fastq fastq,8611605345.0,32335443.0,GSM3728533 r1,0:133.59 1:132.74,A:1724489451;C:2542199793;G:2626828499;T:1716562999;N:1524603,133,132,,,1724489451,2542199793,2626828499,1716562999,1524603,SRX5704273,SRS4643334,SRA875634,GEO,Albert Einstein College of Medicine,2,0.91241,0.96131,0.10384,0.10826,0.77761,0.7767,0.69985,0.69519,128,128,B,B,biological fallback assumption,illumina,nextseq,full_length,rrna_depletion,smarter,bulk,unknown,unknown,,United States,2019-04-17,Pharyngula,Embryo,Blood,Hematopoietic System
51877,SRR8922973,SRX5704272,SRS4643333,SRP192854,PRJNA533283,RNA seq of erythroid cells from 24 hpf sf3b1 mutant and sibling zebrafish,GSE129952,Transcriptome Analysis,The purpose of the experiment was to define the gene expression and splicing alterations occurring when the levels of the splicing factor Sf3b1 are lowered in embryonic zebrafish. Results provide insight the role of Sf3b1 in erythropoietic development. Overall design: mRNA profiling of gata1 positive erythroid cells isolated from 24 hpf sf3b1 mutant and sibling zebrafish using Illumina NextSeq500. Five samples were sequenced for each.,,,,erythroid cells: WT5,GSM3728532,,tissue:erythroid cells|age:24 hpf type:gata1 positive erythroid cells|genotype/variation:wild type,erythroid cells: WT5,basecalling was done with the Picard module IlluminaBasecallsToFastq Reads were trimmed using TRIM GALORE software to check for quality of 150bp reads. These paired end reads were mapped using STAR aligner version 2.4.2a to the reference genome. Differential expression analysis was done using DESeq220 and EdgeR21 Bioconductor packages. To calculate FPKM  Cufflinks version 2.2.1 was used. Genome build: GRcz10 Supplementary files format and content: tab delimited text file includeS FPKM values for each Sample,erythroid cells,,Gata1 positive cells were isolated from zebrafish embryos. RNA was extracted with the quick RNA microprep Zymo. Ribosomal RNA was depleted with Ribogone Clontech. Libraries were made following the protocol and using the reagents from the SMARTer Stranded RNA Seq Kit Clontech.,,age:24 hpf type:gata1 positive erythroid cells|genotype/variation:wild type,GSM3728532,GSM3728532: erythroid cells: WT5; Danio rerio; RNA Seq,GSM3728532,,1,Gata1 positive cells were isolated from zebrafish embryos. RNA was extracted with the quick RNA microprep Zymo. Ribosomal RNA was depleted with Ribogone Clontech. Libraries were made following the protocol and using the reagents from the SMARTer Stranded RNA Seq Kit Clontech.,GEO Accession:GSM3728532,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP192854,,,J633_AHFHNLBGX2_TGACCA_LWT5.1_val_1.fq.gz J633_AHFHNLBGX2_TGACCA_LWT5.2_val_2.fq.gz,fastq fastq,8110446942.0,28906836.0,GSM3728532 r1,0:140.70 1:139.87,A:1479901358;C:2533764326;G:2613647627;T:1481710129;N:1423502,140,139,,,1479901358,2533764326,2613647627,1481710129,1423502,SRX5704272,SRS4643333,SRA875634,GEO,Albert Einstein College of Medicine,2,0.92578,0.97511,0.09182,0.09201,0.80503,0.80324,0.76985,0.7675,150,150,B,B,biological fallback assumption,illumina,nextseq,full_length,rrna_depletion,smarter,bulk,unknown,unknown,,United States,2019-04-17,Pharyngula,Embryo,Blood,Hematopoietic System
51878,SRR8922972,SRX5704271,SRS4643332,SRP192854,PRJNA533283,RNA seq of erythroid cells from 24 hpf sf3b1 mutant and sibling zebrafish,GSE129952,Transcriptome Analysis,The purpose of the experiment was to define the gene expression and splicing alterations occurring when the levels of the splicing factor Sf3b1 are lowered in embryonic zebrafish. Results provide insight the role of Sf3b1 in erythropoietic development. Overall design: mRNA profiling of gata1 positive erythroid cells isolated from 24 hpf sf3b1 mutant and sibling zebrafish using Illumina NextSeq500. Five samples were sequenced for each.,,,,erythroid cells: WT4,GSM3728531,,tissue:erythroid cells|age:24 hpf type:gata1 positive erythroid cells|genotype/variation:wild type,erythroid cells: WT4,basecalling was done with the Picard module IlluminaBasecallsToFastq Reads were trimmed using TRIM GALORE software to check for quality of 150bp reads. These paired end reads were mapped using STAR aligner version 2.4.2a to the reference genome. Differential expression analysis was done using DESeq220 and EdgeR21 Bioconductor packages. To calculate FPKM  Cufflinks version 2.2.1 was used. Genome build: GRcz10 Supplementary files format and content: tab delimited text file includeS FPKM values for each Sample,erythroid cells,,Gata1 positive cells were isolated from zebrafish embryos. RNA was extracted with the quick RNA microprep Zymo. Ribosomal RNA was depleted with Ribogone Clontech. Libraries were made following the protocol and using the reagents from the SMARTer Stranded RNA Seq Kit Clontech.,,age:24 hpf type:gata1 positive erythroid cells|genotype/variation:wild type,GSM3728531,GSM3728531: erythroid cells: WT4; Danio rerio; RNA Seq,GSM3728531,,1,Gata1 positive cells were isolated from zebrafish embryos. RNA was extracted with the quick RNA microprep Zymo. Ribosomal RNA was depleted with Ribogone Clontech. Libraries were made following the protocol and using the reagents from the SMARTer Stranded RNA Seq Kit Clontech.,GEO Accession:GSM3728531,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP192854,,,J633_AHFHNLBGX2_TTAGGC_LWT4.2_val_2.fq.gz J633_AHFHNLBGX2_TTAGGC_LWT4.1_val_1.fq.gz,fastq fastq,8627466135.0,32957109.0,GSM3728531 r1,0:131.12 1:130.66,A:1686521982;C:2592728511;G:2670950174;T:1675745501;N:1519967,131,130,,,1686521982,2592728511,2670950174,1675745501,1519967,SRX5704271,SRS4643332,SRA875634,GEO,Albert Einstein College of Medicine,2,0.91773,0.96731,0.11151,0.1134,0.78792,0.78597,0.73657,0.73692,104,104,B,B,biological fallback assumption,illumina,nextseq,full_length,rrna_depletion,smarter,bulk,unknown,unknown,,United States,2019-04-17,Pharyngula,Embryo,Blood,Hematopoietic System
51879,SRR8922971,SRX5704270,SRS4643331,SRP192854,PRJNA533283,RNA seq of erythroid cells from 24 hpf sf3b1 mutant and sibling zebrafish,GSE129952,Transcriptome Analysis,The purpose of the experiment was to define the gene expression and splicing alterations occurring when the levels of the splicing factor Sf3b1 are lowered in embryonic zebrafish. Results provide insight the role of Sf3b1 in erythropoietic development. Overall design: mRNA profiling of gata1 positive erythroid cells isolated from 24 hpf sf3b1 mutant and sibling zebrafish using Illumina NextSeq500. Five samples were sequenced for each.,,,,erythroid cells: WT3,GSM3728530,,tissue:erythroid cells|age:24 hpf type:gata1 positive erythroid cells|genotype/variation:wild type,erythroid cells: WT3,basecalling was done with the Picard module IlluminaBasecallsToFastq Reads were trimmed using TRIM GALORE software to check for quality of 150bp reads. These paired end reads were mapped using STAR aligner version 2.4.2a to the reference genome. Differential expression analysis was done using DESeq220 and EdgeR21 Bioconductor packages. To calculate FPKM  Cufflinks version 2.2.1 was used. Genome build: GRcz10 Supplementary files format and content: tab delimited text file includeS FPKM values for each Sample,erythroid cells,,Gata1 positive cells were isolated from zebrafish embryos. RNA was extracted with the quick RNA microprep Zymo. Ribosomal RNA was depleted with Ribogone Clontech. Libraries were made following the protocol and using the reagents from the SMARTer Stranded RNA Seq Kit Clontech.,,age:24 hpf type:gata1 positive erythroid cells|genotype/variation:wild type,GSM3728530,GSM3728530: erythroid cells: WT3; Danio rerio; RNA Seq,GSM3728530,,1,Gata1 positive cells were isolated from zebrafish embryos. RNA was extracted with the quick RNA microprep Zymo. Ribosomal RNA was depleted with Ribogone Clontech. Libraries were made following the protocol and using the reagents from the SMARTer Stranded RNA Seq Kit Clontech.,GEO Accession:GSM3728530,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP192854,,,J633_AHFHNLBGX2_CGATGT_LWT3.2_val_2.fq.gz J633_AHFHNLBGX2_CGATGT_LWT3.1_val_1.fq.gz,fastq fastq,7675701402.0,28099783.0,GSM3728530 r1,0:136.90 1:136.26,A:1496106079;C:2307580110;G:2386093773;T:1484556287;N:1365153,136,136,,,1496106079,2307580110,2386093773,1484556287,1365153,SRX5704270,SRS4643331,SRA875634,GEO,Albert Einstein College of Medicine,2,0.91833,0.96754,0.10771,0.10822,0.80135,0.80158,0.76757,0.7524,150,150,B,B,biological fallback assumption,illumina,nextseq,full_length,rrna_depletion,smarter,bulk,unknown,unknown,,United States,2019-04-17,Pharyngula,Embryo,Blood,Hematopoietic System
51880,SRR8922970,SRX5704269,SRS4643330,SRP192854,PRJNA533283,RNA seq of erythroid cells from 24 hpf sf3b1 mutant and sibling zebrafish,GSE129952,Transcriptome Analysis,The purpose of the experiment was to define the gene expression and splicing alterations occurring when the levels of the splicing factor Sf3b1 are lowered in embryonic zebrafish. Results provide insight the role of Sf3b1 in erythropoietic development. Overall design: mRNA profiling of gata1 positive erythroid cells isolated from 24 hpf sf3b1 mutant and sibling zebrafish using Illumina NextSeq500. Five samples were sequenced for each.,,,,erythroid cells: WT2,GSM3728529,,tissue:erythroid cells|age:24 hpf type:gata1 positive erythroid cells|genotype/variation:sf3b1 mutant,erythroid cells: WT2,basecalling was done with the Picard module IlluminaBasecallsToFastq Reads were trimmed using TRIM GALORE software to check for quality of 150bp reads. These paired end reads were mapped using STAR aligner version 2.4.2a to the reference genome. Differential expression analysis was done using DESeq220 and EdgeR21 Bioconductor packages. To calculate FPKM  Cufflinks version 2.2.1 was used. Genome build: GRcz10 Supplementary files format and content: tab delimited text file includeS FPKM values for each Sample,erythroid cells,,Gata1 positive cells were isolated from zebrafish embryos. RNA was extracted with the quick RNA microprep Zymo. Ribosomal RNA was depleted with Ribogone Clontech. Libraries were made following the protocol and using the reagents from the SMARTer Stranded RNA Seq Kit Clontech.,,age:24 hpf type:gata1 positive erythroid cells|genotype/variation:sf3b1 mutant,GSM3728529,GSM3728529: erythroid cells: WT2; Danio rerio; RNA Seq,GSM3728529,,1,Gata1 positive cells were isolated from zebrafish embryos. RNA was extracted with the quick RNA microprep Zymo. Ribosomal RNA was depleted with Ribogone Clontech. Libraries were made following the protocol and using the reagents from the SMARTer Stranded RNA Seq Kit Clontech.,GEO Accession:GSM3728529,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP192854,,,J633_AHFHNLBGX2_ATCACG_LWT2.2_val_2.fq.gz J633_AHFHNLBGX2_ATCACG_LWT2.1_val_1.fq.gz,fastq fastq,8749226933.0,32236600.0,GSM3728529 r1,0:135.97 1:135.43,A:1818348438;C:2523018672;G:2595068272;T:1811215171;N:1576380,135,135,,,1818348438,2523018672,2595068272,1811215171,1576380,SRX5704269,SRS4643330,SRA875634,GEO,Albert Einstein College of Medicine,2,0.91533,0.96543,0.12825,0.13005,0.77394,0.77344,0.70772,0.67993,143,143,B,B,biological fallback assumption,illumina,nextseq,full_length,rrna_depletion,smarter,bulk,unknown,unknown,,United States,2019-04-17,Pharyngula,Embryo,Blood,Hematopoietic System
51881,SRR8922969,SRX5704268,SRS4643329,SRP192854,PRJNA533283,RNA seq of erythroid cells from 24 hpf sf3b1 mutant and sibling zebrafish,GSE129952,Transcriptome Analysis,The purpose of the experiment was to define the gene expression and splicing alterations occurring when the levels of the splicing factor Sf3b1 are lowered in embryonic zebrafish. Results provide insight the role of Sf3b1 in erythropoietic development. Overall design: mRNA profiling of gata1 positive erythroid cells isolated from 24 hpf sf3b1 mutant and sibling zebrafish using Illumina NextSeq500. Five samples were sequenced for each.,,,,erythroid cells: Mut6,GSM3728528,,tissue:erythroid cells|age:24 hpf type:gata1 positive erythroid cells|genotype/variation:sf3b1 mutant,erythroid cells: Mut6,basecalling was done with the Picard module IlluminaBasecallsToFastq Reads were trimmed using TRIM GALORE software to check for quality of 150bp reads. These paired end reads were mapped using STAR aligner version 2.4.2a to the reference genome. Differential expression analysis was done using DESeq220 and EdgeR21 Bioconductor packages. To calculate FPKM  Cufflinks version 2.2.1 was used. Genome build: GRcz10 Supplementary files format and content: tab delimited text file includeS FPKM values for each Sample,erythroid cells,,Gata1 positive cells were isolated from zebrafish embryos. RNA was extracted with the quick RNA microprep Zymo. Ribosomal RNA was depleted with Ribogone Clontech. Libraries were made following the protocol and using the reagents from the SMARTer Stranded RNA Seq Kit Clontech.,,age:24 hpf type:gata1 positive erythroid cells|genotype/variation:sf3b1 mutant,GSM3728528,GSM3728528: erythroid cells: Mut6; Danio rerio; RNA Seq,GSM3728528,,1,Gata1 positive cells were isolated from zebrafish embryos. RNA was extracted with the quick RNA microprep Zymo. Ribosomal RNA was depleted with Ribogone Clontech. Libraries were made following the protocol and using the reagents from the SMARTer Stranded RNA Seq Kit Clontech.,GEO Accession:GSM3728528,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP192854,,,J633_AHFHNLBGX2_GGCTAC_LMut6.2_val_2.fq.gz J633_AHFHNLBGX2_GGCTAC_LMut6.1_val_1.fq.gz,fastq fastq,7989745578.0,29813232.0,GSM3728528 r1,0:134.59 1:133.41,A:1487912329;C:2465671654;G:2552013900;T:1482837472;N:1310223,134,133,,,1487912329,2465671654,2552013900,1482837472,1310223,SRX5704268,SRS4643329,SRA875634,GEO,Albert Einstein College of Medicine,2,0.91636,0.96506,0.12513,0.13214,0.80255,0.80277,0.77309,0.77779,106,106,B,B,biological fallback assumption,illumina,nextseq,full_length,rrna_depletion,smarter,bulk,unknown,unknown,,United States,2019-04-17,Pharyngula,Embryo,Blood,Hematopoietic System
51882,SRR8922968,SRX5704267,SRS4643327,SRP192854,PRJNA533283,RNA seq of erythroid cells from 24 hpf sf3b1 mutant and sibling zebrafish,GSE129952,Transcriptome Analysis,The purpose of the experiment was to define the gene expression and splicing alterations occurring when the levels of the splicing factor Sf3b1 are lowered in embryonic zebrafish. Results provide insight the role of Sf3b1 in erythropoietic development. Overall design: mRNA profiling of gata1 positive erythroid cells isolated from 24 hpf sf3b1 mutant and sibling zebrafish using Illumina NextSeq500. Five samples were sequenced for each.,,,,erythroid cells: Mut5,GSM3728527,,tissue:erythroid cells|age:24 hpf type:gata1 positive erythroid cells|genotype/variation:sf3b1 mutant,erythroid cells: Mut5,basecalling was done with the Picard module IlluminaBasecallsToFastq Reads were trimmed using TRIM GALORE software to check for quality of 150bp reads. These paired end reads were mapped using STAR aligner version 2.4.2a to the reference genome. Differential expression analysis was done using DESeq220 and EdgeR21 Bioconductor packages. To calculate FPKM  Cufflinks version 2.2.1 was used. Genome build: GRcz10 Supplementary files format and content: tab delimited text file includeS FPKM values for each Sample,erythroid cells,,Gata1 positive cells were isolated from zebrafish embryos. RNA was extracted with the quick RNA microprep Zymo. Ribosomal RNA was depleted with Ribogone Clontech. Libraries were made following the protocol and using the reagents from the SMARTer Stranded RNA Seq Kit Clontech.,,age:24 hpf type:gata1 positive erythroid cells|genotype/variation:sf3b1 mutant,GSM3728527,GSM3728527: erythroid cells: Mut5; Danio rerio; RNA Seq,GSM3728527,,1,Gata1 positive cells were isolated from zebrafish embryos. RNA was extracted with the quick RNA microprep Zymo. Ribosomal RNA was depleted with Ribogone Clontech. Libraries were made following the protocol and using the reagents from the SMARTer Stranded RNA Seq Kit Clontech.,GEO Accession:GSM3728527,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP192854,,,J633_AHFHNLBGX2_GATCAG_LMut5.2_val_2.fq.gz J633_AHFHNLBGX2_GATCAG_LMut5.1_val_1.fq.gz,fastq fastq,8500296799.0,30812271.0,GSM3728527 r1,0:138.28 1:137.59,A:1566669253;C:2640866820;G:2726747970;T:1564531299;N:1481457,138,137,,,1566669253,2640866820,2726747970,1564531299,1481457,SRX5704267,SRS4643327,SRA875634,GEO,Albert Einstein College of Medicine,2,0.91987,0.9688,0.10388,0.10646,0.80338,0.80176,0.75914,0.71799,52,52,B,B,biological fallback assumption,illumina,nextseq,full_length,rrna_depletion,smarter,bulk,unknown,unknown,,United States,2019-04-17,Pharyngula,Embryo,Blood,Hematopoietic System
51883,SRR8922967,SRX5704266,SRS4643328,SRP192854,PRJNA533283,RNA seq of erythroid cells from 24 hpf sf3b1 mutant and sibling zebrafish,GSE129952,Transcriptome Analysis,The purpose of the experiment was to define the gene expression and splicing alterations occurring when the levels of the splicing factor Sf3b1 are lowered in embryonic zebrafish. Results provide insight the role of Sf3b1 in erythropoietic development. Overall design: mRNA profiling of gata1 positive erythroid cells isolated from 24 hpf sf3b1 mutant and sibling zebrafish using Illumina NextSeq500. Five samples were sequenced for each.,,,,erythroid cells: Mut4,GSM3728526,,tissue:erythroid cells|age:24 hpf type:gata1 positive erythroid cells|genotype/variation:sf3b1 mutant,erythroid cells: Mut4,basecalling was done with the Picard module IlluminaBasecallsToFastq Reads were trimmed using TRIM GALORE software to check for quality of 150bp reads. These paired end reads were mapped using STAR aligner version 2.4.2a to the reference genome. Differential expression analysis was done using DESeq220 and EdgeR21 Bioconductor packages. To calculate FPKM  Cufflinks version 2.2.1 was used. Genome build: GRcz10 Supplementary files format and content: tab delimited text file includeS FPKM values for each Sample,erythroid cells,,Gata1 positive cells were isolated from zebrafish embryos. RNA was extracted with the quick RNA microprep Zymo. Ribosomal RNA was depleted with Ribogone Clontech. Libraries were made following the protocol and using the reagents from the SMARTer Stranded RNA Seq Kit Clontech.,,age:24 hpf type:gata1 positive erythroid cells|genotype/variation:sf3b1 mutant,GSM3728526,GSM3728526: erythroid cells: Mut4; Danio rerio; RNA Seq,GSM3728526,,1,Gata1 positive cells were isolated from zebrafish embryos. RNA was extracted with the quick RNA microprep Zymo. Ribosomal RNA was depleted with Ribogone Clontech. Libraries were made following the protocol and using the reagents from the SMARTer Stranded RNA Seq Kit Clontech.,GEO Accession:GSM3728526,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP192854,,,J633_AHFHNLBGX2_ACTTGA_LMut4.2_val_2.fq.gz J633_AHFHNLBGX2_ACTTGA_LMut4.1_val_1.fq.gz,fastq fastq,8415322795.0,32199684.0,GSM3728526 r1,0:130.80 1:130.55,A:1593557159;C:2583771193;G:2657553064;T:1578891748;N:1549631,130,130,,,1593557159,2583771193,2657553064,1578891748,1549631,SRX5704266,SRS4643328,SRA875634,GEO,Albert Einstein College of Medicine,2,0.92078,0.97122,0.12063,0.12061,0.81994,0.81822,0.76635,0.7826,149,148,B,B,biological fallback assumption,illumina,nextseq,full_length,rrna_depletion,smarter,bulk,unknown,unknown,,United States,2019-04-17,Pharyngula,Embryo,Blood,Hematopoietic System
51884,SRR8922966,SRX5704265,SRS4643326,SRP192854,PRJNA533283,RNA seq of erythroid cells from 24 hpf sf3b1 mutant and sibling zebrafish,GSE129952,Transcriptome Analysis,The purpose of the experiment was to define the gene expression and splicing alterations occurring when the levels of the splicing factor Sf3b1 are lowered in embryonic zebrafish. Results provide insight the role of Sf3b1 in erythropoietic development. Overall design: mRNA profiling of gata1 positive erythroid cells isolated from 24 hpf sf3b1 mutant and sibling zebrafish using Illumina NextSeq500. Five samples were sequenced for each.,,,,erythroid cells: Mut3,GSM3728525,,tissue:erythroid cells|age:24 hpf type:gata1 positive erythroid cells|genotype/variation:sf3b1 mutant,erythroid cells: Mut3,basecalling was done with the Picard module IlluminaBasecallsToFastq Reads were trimmed using TRIM GALORE software to check for quality of 150bp reads. These paired end reads were mapped using STAR aligner version 2.4.2a to the reference genome. Differential expression analysis was done using DESeq220 and EdgeR21 Bioconductor packages. To calculate FPKM  Cufflinks version 2.2.1 was used. Genome build: GRcz10 Supplementary files format and content: tab delimited text file includeS FPKM values for each Sample,erythroid cells,,Gata1 positive cells were isolated from zebrafish embryos. RNA was extracted with the quick RNA microprep Zymo. Ribosomal RNA was depleted with Ribogone Clontech. Libraries were made following the protocol and using the reagents from the SMARTer Stranded RNA Seq Kit Clontech.,,age:24 hpf type:gata1 positive erythroid cells|genotype/variation:sf3b1 mutant,GSM3728525,GSM3728525: erythroid cells: Mut3; Danio rerio; RNA Seq,GSM3728525,,1,Gata1 positive cells were isolated from zebrafish embryos. RNA was extracted with the quick RNA microprep Zymo. Ribosomal RNA was depleted with Ribogone Clontech. Libraries were made following the protocol and using the reagents from the SMARTer Stranded RNA Seq Kit Clontech.,GEO Accession:GSM3728525,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP192854,,,J633_AHFHNLBGX2_CAGATC_LMut3.2_val_2.fq.gz J633_AHFHNLBGX2_CAGATC_LMut3.1_val_1.fq.gz,fastq fastq,5373096143.0,19350806.0,GSM3728525 r1,0:139.04 1:138.63,A:990313321;C:1667762750;G:1723819167;T:990236765;N:964140,139,138,,,990313321,1667762750,1723819167,990236765,964140,SRX5704265,SRS4643326,SRA875634,GEO,Albert Einstein College of Medicine,2,0.92305,0.97223,0.10386,0.10158,0.8062,0.80415,0.79641,0.78792,150,149,B,B,biological fallback assumption,illumina,nextseq,full_length,rrna_depletion,smarter,bulk,unknown,unknown,,United States,2019-04-17,Pharyngula,Embryo,Blood,Hematopoietic System
51885,SRR8922965,SRX5704264,SRS4643325,SRP192854,PRJNA533283,RNA seq of erythroid cells from 24 hpf sf3b1 mutant and sibling zebrafish,GSE129952,Transcriptome Analysis,The purpose of the experiment was to define the gene expression and splicing alterations occurring when the levels of the splicing factor Sf3b1 are lowered in embryonic zebrafish. Results provide insight the role of Sf3b1 in erythropoietic development. Overall design: mRNA profiling of gata1 positive erythroid cells isolated from 24 hpf sf3b1 mutant and sibling zebrafish using Illumina NextSeq500. Five samples were sequenced for each.,,,,erythroid cells: Mut1,GSM3728524,,tissue:erythroid cells|age:24 hpf type:gata1 positive erythroid cells|genotype/variation:sf3b1 mutant,erythroid cells: Mut1,basecalling was done with the Picard module IlluminaBasecallsToFastq Reads were trimmed using TRIM GALORE software to check for quality of 150bp reads. These paired end reads were mapped using STAR aligner version 2.4.2a to the reference genome. Differential expression analysis was done using DESeq220 and EdgeR21 Bioconductor packages. To calculate FPKM  Cufflinks version 2.2.1 was used. Genome build: GRcz10 Supplementary files format and content: tab delimited text file includeS FPKM values for each Sample,erythroid cells,,Gata1 positive cells were isolated from zebrafish embryos. RNA was extracted with the quick RNA microprep Zymo. Ribosomal RNA was depleted with Ribogone Clontech. Libraries were made following the protocol and using the reagents from the SMARTer Stranded RNA Seq Kit Clontech.,,age:24 hpf type:gata1 positive erythroid cells|genotype/variation:sf3b1 mutant,GSM3728524,GSM3728524: erythroid cells: Mut1; Danio rerio; RNA Seq,GSM3728524,,1,Gata1 positive cells were isolated from zebrafish embryos. RNA was extracted with the quick RNA microprep Zymo. Ribosomal RNA was depleted with Ribogone Clontech. Libraries were made following the protocol and using the reagents from the SMARTer Stranded RNA Seq Kit Clontech.,GEO Accession:GSM3728524,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP192854,,,J633_AHFHNLBGX2_GCCAAT_LMut1.1_val_1.fq.gz J633_AHFHNLBGX2_GCCAAT_LMut1.2_val_2.fq.gz,fastq fastq,7256147960.0,27513744.0,GSM3728524 r1,0:132.21 1:131.52,A:1506751800;C:2097058291;G:2163719918;T:1487337753;N:1280198,132,131,,,1506751800,2097058291,2163719918,1487337753,1280198,SRX5704264,SRS4643325,SRA875634,GEO,Albert Einstein College of Medicine,2,0.90512,0.95369,0.12564,0.13165,0.77153,0.77098,0.74915,0.74717,122,122,B,B,biological fallback assumption,illumina,nextseq,full_length,rrna_depletion,smarter,bulk,unknown,unknown,,United States,2019-04-17,Pharyngula,Embryo,Blood,Hematopoietic System
54715,SRR10136115,SRX6864204,SRS5401831,SRP222275,PRJNA566103,Next Generation Sequencing to compare gene expression of PC 3M Pro4 in cell culture and in zebrafish metastasis,GSE137629,Other,We report how engrafted human prostate cancer cells respond to zebrafish microenvironment during metasatic colonization. Overall design: RNA was isolated from metastasese in zebrafish 70 fish/group  from  uninjected fish 70fish/group  and from cells in culture  in triplicate. Transcriptomics of human cancer cells were compared between in culture and in metastases. PBS injected fish was set as  control to analyze how engrafted cancer cells modulate gene expression of the host stromal cells,,pubmed:31740783,,24: PBS injected fish3,GSM4083497,,source name:PBS injected fish|tissue:Hematopoietic tissue without xxx cells|FISH strain:TGFli1a:EGFP|age:8 dpf,24: PBS injected fish3,All RNAseq libraries 150–750 bp inserts were sequenced on an Illumina HiSeq2500 sequencer as 1 × 50 nucleotides single end reads according to the manufacturer’s protocol. Image analysis and basecalling were done using the Illumina pipeline. Total yield varied from 10 to 26 Mreads per sample. Illumina reads were aligned against the human GRCh38.p3 and zebrafish GRCz10.80 reference genome sequences using TopHat version 2.0.5. Secondary alignments of reads were excluded by filtering the files using SAMtools version 0.1.18 Aligned fragments per predicted gene were counted from SAM alignment files using the Python package HTSeq version 0.5.3p9. To make comparisons across samples possible  these fragment counts were corrected for the total amount of sequencing performed for each sample. As a correction scaling factor  library size estimates determined using the R/Bioconductor release 2.11 package DESeq were employed Read counts were normalized by dividing the raw counts obtained from HTSeq by its scale factor. Detailed read coverage for individual genes was extracted from the TopHat alignments using SAMtools. Supplementary files format and content: tab delimited text files include gene name  ID  reads and normalized comparision between each groups,PBS injected fish,,Metastasis samples in zebrafish embryos and uninjected control were isolated by cutting the whole metastatic area 80 fish per group randomly chosen from >100 engrafted fish at 6dpi 8dpf with a micro dissection scissor WPI. The samples were immediately washed with cold PBS and stored in TRIzol Sigma at  80 ˚C. The whole process was finished within 30 min.  1000000 Cells in culture were lysized with TRIzol and stored at   80 ˚C. RNA isolation was further performed using RNeasy mini kit qiagen then Illumina RNAseq libraries were prepared using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer’s instructions Illumina  San Diego CA  USA.,PC 3M Pro4 cells were cultured in DMEM complemented with 10% Fetal Clone II. 200 400 PC 3M Pro4 cells were injected into the duct of cuvier DoC of the zebrafish embryos using a Pneumatic Picopump and a manipulator WPI. post transplantation  120 well engrafted embryos were selected using fluorescent microscope and incubated in a 34 ˚C incubator for 6 days.,tissue:Hematopoietic tissue without xxx cells|FISH strain:TGFli1a:EGFP|age:8 dpf,GSM4083497,GSM4083497: 24: PBS injected fish3; Danio rerio; RNA Seq,GSM4083497,,1,Metastasis samples in zebrafish embryos and uninjected control were isolated by cutting the whole metastatic area 80 fish per group randomly chosen from >100 engrafted fish at 6dpi 8dpf with a micro dissection scissor WPI. The samples were immediately washed with cold PBS and stored in TRIzol Sigma at  80 ˚C. The whole process was finished within 30 min.  1000000 Cells in culture were lysized with TRIzol and stored at   80 ˚C. RNA isolation was further performed using RNeasy mini kit qiagen then Illumina RNAseq libraries were prepared using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer's instructions Illumina  San Diego CA  USA.,GEO Accession:GSM4083497,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP222275,,,ZFG-16-03_24_18845_TGACCA_L001_R1_001.fastq.gz,fastq,175231359.0,3435909.0,GSM4083497 r1,0:51,A:43536404;C:41827219;G:40775397;T:49039258;N:53081,51,,,,43536404,41827219,40775397,49039258,53081,SRX6864204,SRS5401831,SRA963954,GEO,"Institute of Biology, Leiden University",1,0.92557,,0.08034,,0.71354,,0.48221,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Netherlands,2019-09-18,Larval,Larval,Blood,Hematopoietic System
54716,SRR10136116,SRX6864204,SRS5401831,SRP222275,PRJNA566103,Next Generation Sequencing to compare gene expression of PC 3M Pro4 in cell culture and in zebrafish metastasis,GSE137629,Other,We report how engrafted human prostate cancer cells respond to zebrafish microenvironment during metasatic colonization. Overall design: RNA was isolated from metastasese in zebrafish 70 fish/group  from  uninjected fish 70fish/group  and from cells in culture  in triplicate. Transcriptomics of human cancer cells were compared between in culture and in metastases. PBS injected fish was set as  control to analyze how engrafted cancer cells modulate gene expression of the host stromal cells,,pubmed:31740783,,24: PBS injected fish3,GSM4083497,,source name:PBS injected fish|tissue:Hematopoietic tissue without xxx cells|FISH strain:TGFli1a:EGFP|age:8 dpf,24: PBS injected fish3,All RNAseq libraries 150–750 bp inserts were sequenced on an Illumina HiSeq2500 sequencer as 1 × 50 nucleotides single end reads according to the manufacturer’s protocol. Image analysis and basecalling were done using the Illumina pipeline. Total yield varied from 10 to 26 Mreads per sample. Illumina reads were aligned against the human GRCh38.p3 and zebrafish GRCz10.80 reference genome sequences using TopHat version 2.0.5. Secondary alignments of reads were excluded by filtering the files using SAMtools version 0.1.18 Aligned fragments per predicted gene were counted from SAM alignment files using the Python package HTSeq version 0.5.3p9. To make comparisons across samples possible  these fragment counts were corrected for the total amount of sequencing performed for each sample. As a correction scaling factor  library size estimates determined using the R/Bioconductor release 2.11 package DESeq were employed Read counts were normalized by dividing the raw counts obtained from HTSeq by its scale factor. Detailed read coverage for individual genes was extracted from the TopHat alignments using SAMtools. Supplementary files format and content: tab delimited text files include gene name  ID  reads and normalized comparision between each groups,PBS injected fish,,Metastasis samples in zebrafish embryos and uninjected control were isolated by cutting the whole metastatic area 80 fish per group randomly chosen from >100 engrafted fish at 6dpi 8dpf with a micro dissection scissor WPI. The samples were immediately washed with cold PBS and stored in TRIzol Sigma at  80 ˚C. The whole process was finished within 30 min.  1000000 Cells in culture were lysized with TRIzol and stored at   80 ˚C. RNA isolation was further performed using RNeasy mini kit qiagen then Illumina RNAseq libraries were prepared using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer’s instructions Illumina  San Diego CA  USA.,PC 3M Pro4 cells were cultured in DMEM complemented with 10% Fetal Clone II. 200 400 PC 3M Pro4 cells were injected into the duct of cuvier DoC of the zebrafish embryos using a Pneumatic Picopump and a manipulator WPI. post transplantation  120 well engrafted embryos were selected using fluorescent microscope and incubated in a 34 ˚C incubator for 6 days.,tissue:Hematopoietic tissue without xxx cells|FISH strain:TGFli1a:EGFP|age:8 dpf,GSM4083497,GSM4083497: 24: PBS injected fish3; Danio rerio; RNA Seq,GSM4083497,,1,Metastasis samples in zebrafish embryos and uninjected control were isolated by cutting the whole metastatic area 80 fish per group randomly chosen from >100 engrafted fish at 6dpi 8dpf with a micro dissection scissor WPI. The samples were immediately washed with cold PBS and stored in TRIzol Sigma at  80 ˚C. The whole process was finished within 30 min.  1000000 Cells in culture were lysized with TRIzol and stored at   80 ˚C. RNA isolation was further performed using RNeasy mini kit qiagen then Illumina RNAseq libraries were prepared using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer's instructions Illumina  San Diego CA  USA.,GEO Accession:GSM4083497,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP222275,,,ZFG-16-03_24_18845_TGACCA_L002_R1_001.fastq.gz,fastq,183497490.0,3597990.0,GSM4083497 r2,0:51,A:45576151;C:43814900;G:42692291;T:51382292;N:31856,51,,,,45576151,43814900,42692291,51382292,31856,SRX6864204,SRS5401831,SRA963954,GEO,"Institute of Biology, Leiden University",1,0.92775,,0.08176,,0.71305,,0.47131,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Netherlands,2019-09-18,Larval,Larval,Blood,Hematopoietic System
54717,SRR10136113,SRX6864203,SRS5401830,SRP222275,PRJNA566103,Next Generation Sequencing to compare gene expression of PC 3M Pro4 in cell culture and in zebrafish metastasis,GSE137629,Other,We report how engrafted human prostate cancer cells respond to zebrafish microenvironment during metasatic colonization. Overall design: RNA was isolated from metastasese in zebrafish 70 fish/group  from  uninjected fish 70fish/group  and from cells in culture  in triplicate. Transcriptomics of human cancer cells were compared between in culture and in metastases. PBS injected fish was set as  control to analyze how engrafted cancer cells modulate gene expression of the host stromal cells,,pubmed:31740783,,23: PBS injected fish2,GSM4083496,,source name:PBS injected fish|tissue:Hematopoietic tissue without xxx cells|FISH strain:TGFli1a:EGFP|age:8 dpf,23: PBS injected fish2,All RNAseq libraries 150–750 bp inserts were sequenced on an Illumina HiSeq2500 sequencer as 1 × 50 nucleotides single end reads according to the manufacturer’s protocol. Image analysis and basecalling were done using the Illumina pipeline. Total yield varied from 10 to 26 Mreads per sample. Illumina reads were aligned against the human GRCh38.p3 and zebrafish GRCz10.80 reference genome sequences using TopHat version 2.0.5. Secondary alignments of reads were excluded by filtering the files using SAMtools version 0.1.18 Aligned fragments per predicted gene were counted from SAM alignment files using the Python package HTSeq version 0.5.3p9. To make comparisons across samples possible  these fragment counts were corrected for the total amount of sequencing performed for each sample. As a correction scaling factor  library size estimates determined using the R/Bioconductor release 2.11 package DESeq were employed Read counts were normalized by dividing the raw counts obtained from HTSeq by its scale factor. Detailed read coverage for individual genes was extracted from the TopHat alignments using SAMtools. Supplementary files format and content: tab delimited text files include gene name  ID  reads and normalized comparision between each groups,PBS injected fish,,Metastasis samples in zebrafish embryos and uninjected control were isolated by cutting the whole metastatic area 80 fish per group randomly chosen from >100 engrafted fish at 6dpi 8dpf with a micro dissection scissor WPI. The samples were immediately washed with cold PBS and stored in TRIzol Sigma at  80 ˚C. The whole process was finished within 30 min.  1000000 Cells in culture were lysized with TRIzol and stored at   80 ˚C. RNA isolation was further performed using RNeasy mini kit qiagen then Illumina RNAseq libraries were prepared using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer’s instructions Illumina  San Diego CA  USA.,PC 3M Pro4 cells were cultured in DMEM complemented with 10% Fetal Clone II. 200 400 PC 3M Pro4 cells were injected into the duct of cuvier DoC of the zebrafish embryos using a Pneumatic Picopump and a manipulator WPI. post transplantation  120 well engrafted embryos were selected using fluorescent microscope and incubated in a 34 ˚C incubator for 6 days.,tissue:Hematopoietic tissue without xxx cells|FISH strain:TGFli1a:EGFP|age:8 dpf,GSM4083496,GSM4083496: 23: PBS injected fish2; Danio rerio; RNA Seq,GSM4083496,,1,Metastasis samples in zebrafish embryos and uninjected control were isolated by cutting the whole metastatic area 80 fish per group randomly chosen from >100 engrafted fish at 6dpi 8dpf with a micro dissection scissor WPI. The samples were immediately washed with cold PBS and stored in TRIzol Sigma at  80 ˚C. The whole process was finished within 30 min.  1000000 Cells in culture were lysized with TRIzol and stored at   80 ˚C. RNA isolation was further performed using RNeasy mini kit qiagen then Illumina RNAseq libraries were prepared using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer's instructions Illumina  San Diego CA  USA.,GEO Accession:GSM4083496,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP222275,,,ZFG-16-03_23_18844_CGATGT_L001_R1_001.fastq.gz,fastq,178603683.0,3502033.0,GSM4083496 r1,0:51,A:43615081;C:43303795;G:41835813;T:49795688;N:53306,51,,,,43615081,43303795,41835813,49795688,53306,SRX6864203,SRS5401830,SRA963954,GEO,"Institute of Biology, Leiden University",1,0.9227,,0.06923,,0.72547,,0.45761,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Netherlands,2019-09-18,Larval,Larval,Blood,Hematopoietic System
54718,SRR10136114,SRX6864203,SRS5401830,SRP222275,PRJNA566103,Next Generation Sequencing to compare gene expression of PC 3M Pro4 in cell culture and in zebrafish metastasis,GSE137629,Other,We report how engrafted human prostate cancer cells respond to zebrafish microenvironment during metasatic colonization. Overall design: RNA was isolated from metastasese in zebrafish 70 fish/group  from  uninjected fish 70fish/group  and from cells in culture  in triplicate. Transcriptomics of human cancer cells were compared between in culture and in metastases. PBS injected fish was set as  control to analyze how engrafted cancer cells modulate gene expression of the host stromal cells,,pubmed:31740783,,23: PBS injected fish2,GSM4083496,,source name:PBS injected fish|tissue:Hematopoietic tissue without xxx cells|FISH strain:TGFli1a:EGFP|age:8 dpf,23: PBS injected fish2,All RNAseq libraries 150–750 bp inserts were sequenced on an Illumina HiSeq2500 sequencer as 1 × 50 nucleotides single end reads according to the manufacturer’s protocol. Image analysis and basecalling were done using the Illumina pipeline. Total yield varied from 10 to 26 Mreads per sample. Illumina reads were aligned against the human GRCh38.p3 and zebrafish GRCz10.80 reference genome sequences using TopHat version 2.0.5. Secondary alignments of reads were excluded by filtering the files using SAMtools version 0.1.18 Aligned fragments per predicted gene were counted from SAM alignment files using the Python package HTSeq version 0.5.3p9. To make comparisons across samples possible  these fragment counts were corrected for the total amount of sequencing performed for each sample. As a correction scaling factor  library size estimates determined using the R/Bioconductor release 2.11 package DESeq were employed Read counts were normalized by dividing the raw counts obtained from HTSeq by its scale factor. Detailed read coverage for individual genes was extracted from the TopHat alignments using SAMtools. Supplementary files format and content: tab delimited text files include gene name  ID  reads and normalized comparision between each groups,PBS injected fish,,Metastasis samples in zebrafish embryos and uninjected control were isolated by cutting the whole metastatic area 80 fish per group randomly chosen from >100 engrafted fish at 6dpi 8dpf with a micro dissection scissor WPI. The samples were immediately washed with cold PBS and stored in TRIzol Sigma at  80 ˚C. The whole process was finished within 30 min.  1000000 Cells in culture were lysized with TRIzol and stored at   80 ˚C. RNA isolation was further performed using RNeasy mini kit qiagen then Illumina RNAseq libraries were prepared using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer’s instructions Illumina  San Diego CA  USA.,PC 3M Pro4 cells were cultured in DMEM complemented with 10% Fetal Clone II. 200 400 PC 3M Pro4 cells were injected into the duct of cuvier DoC of the zebrafish embryos using a Pneumatic Picopump and a manipulator WPI. post transplantation  120 well engrafted embryos were selected using fluorescent microscope and incubated in a 34 ˚C incubator for 6 days.,tissue:Hematopoietic tissue without xxx cells|FISH strain:TGFli1a:EGFP|age:8 dpf,GSM4083496,GSM4083496: 23: PBS injected fish2; Danio rerio; RNA Seq,GSM4083496,,1,Metastasis samples in zebrafish embryos and uninjected control were isolated by cutting the whole metastatic area 80 fish per group randomly chosen from >100 engrafted fish at 6dpi 8dpf with a micro dissection scissor WPI. The samples were immediately washed with cold PBS and stored in TRIzol Sigma at  80 ˚C. The whole process was finished within 30 min.  1000000 Cells in culture were lysized with TRIzol and stored at   80 ˚C. RNA isolation was further performed using RNeasy mini kit qiagen then Illumina RNAseq libraries were prepared using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer's instructions Illumina  San Diego CA  USA.,GEO Accession:GSM4083496,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP222275,,,ZFG-16-03_23_18844_CGATGT_L002_R1_001.fastq.gz,fastq,186816264.0,3663064.0,GSM4083496 r2,0:51,A:45642596;C:45311565;G:43750888;T:52078681;N:32534,51,,,,45642596,45311565,43750888,52078681,32534,SRX6864203,SRS5401830,SRA963954,GEO,"Institute of Biology, Leiden University",1,0.92517,,0.07013,,0.72561,,0.4586,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Netherlands,2019-09-18,Larval,Larval,Blood,Hematopoietic System
54719,SRR10136111,SRX6864202,SRS5401829,SRP222275,PRJNA566103,Next Generation Sequencing to compare gene expression of PC 3M Pro4 in cell culture and in zebrafish metastasis,GSE137629,Other,We report how engrafted human prostate cancer cells respond to zebrafish microenvironment during metasatic colonization. Overall design: RNA was isolated from metastasese in zebrafish 70 fish/group  from  uninjected fish 70fish/group  and from cells in culture  in triplicate. Transcriptomics of human cancer cells were compared between in culture and in metastases. PBS injected fish was set as  control to analyze how engrafted cancer cells modulate gene expression of the host stromal cells,,pubmed:31740783,,22: PBS injected fish1,GSM4083495,,source name:PBS injected fish|tissue:Hematopoietic tissue without xxx cells|FISH strain:TGFli1a:EGFP|age:8 dpf,22: PBS injected fish1,All RNAseq libraries 150–750 bp inserts were sequenced on an Illumina HiSeq2500 sequencer as 1 × 50 nucleotides single end reads according to the manufacturer’s protocol. Image analysis and basecalling were done using the Illumina pipeline. Total yield varied from 10 to 26 Mreads per sample. Illumina reads were aligned against the human GRCh38.p3 and zebrafish GRCz10.80 reference genome sequences using TopHat version 2.0.5. Secondary alignments of reads were excluded by filtering the files using SAMtools version 0.1.18 Aligned fragments per predicted gene were counted from SAM alignment files using the Python package HTSeq version 0.5.3p9. To make comparisons across samples possible  these fragment counts were corrected for the total amount of sequencing performed for each sample. As a correction scaling factor  library size estimates determined using the R/Bioconductor release 2.11 package DESeq were employed Read counts were normalized by dividing the raw counts obtained from HTSeq by its scale factor. Detailed read coverage for individual genes was extracted from the TopHat alignments using SAMtools. Supplementary files format and content: tab delimited text files include gene name  ID  reads and normalized comparision between each groups,PBS injected fish,,Metastasis samples in zebrafish embryos and uninjected control were isolated by cutting the whole metastatic area 80 fish per group randomly chosen from >100 engrafted fish at 6dpi 8dpf with a micro dissection scissor WPI. The samples were immediately washed with cold PBS and stored in TRIzol Sigma at  80 ˚C. The whole process was finished within 30 min.  1000000 Cells in culture were lysized with TRIzol and stored at   80 ˚C. RNA isolation was further performed using RNeasy mini kit qiagen then Illumina RNAseq libraries were prepared using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer’s instructions Illumina  San Diego CA  USA.,PC 3M Pro4 cells were cultured in DMEM complemented with 10% Fetal Clone II. 200 400 PC 3M Pro4 cells were injected into the duct of cuvier DoC of the zebrafish embryos using a Pneumatic Picopump and a manipulator WPI. post transplantation  120 well engrafted embryos were selected using fluorescent microscope and incubated in a 34 ˚C incubator for 6 days.,tissue:Hematopoietic tissue without xxx cells|FISH strain:TGFli1a:EGFP|age:8 dpf,GSM4083495,GSM4083495: 22: PBS injected fish1; Danio rerio; RNA Seq,GSM4083495,,1,Metastasis samples in zebrafish embryos and uninjected control were isolated by cutting the whole metastatic area 80 fish per group randomly chosen from >100 engrafted fish at 6dpi 8dpf with a micro dissection scissor WPI. The samples were immediately washed with cold PBS and stored in TRIzol Sigma at  80 ˚C. The whole process was finished within 30 min.  1000000 Cells in culture were lysized with TRIzol and stored at   80 ˚C. RNA isolation was further performed using RNeasy mini kit qiagen then Illumina RNAseq libraries were prepared using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer's instructions Illumina  San Diego CA  USA.,GEO Accession:GSM4083495,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP222275,,,ZFG-16-03_22_18843_ATTCCT_L001_R1_001.fastq.gz,fastq,338607105.0,6639355.0,GSM4083495 r1,0:51,A:83848769;C:81493095;G:77979951;T:95181006;N:104284,51,,,,83848769,81493095,77979951,95181006,104284,SRX6864202,SRS5401829,SRA963954,GEO,"Institute of Biology, Leiden University",1,0.93231,,0.07583,,0.70784,,0.47906,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Netherlands,2019-09-18,Larval,Larval,Blood,Hematopoietic System
54720,SRR10136112,SRX6864202,SRS5401829,SRP222275,PRJNA566103,Next Generation Sequencing to compare gene expression of PC 3M Pro4 in cell culture and in zebrafish metastasis,GSE137629,Other,We report how engrafted human prostate cancer cells respond to zebrafish microenvironment during metasatic colonization. Overall design: RNA was isolated from metastasese in zebrafish 70 fish/group  from  uninjected fish 70fish/group  and from cells in culture  in triplicate. Transcriptomics of human cancer cells were compared between in culture and in metastases. PBS injected fish was set as  control to analyze how engrafted cancer cells modulate gene expression of the host stromal cells,,pubmed:31740783,,22: PBS injected fish1,GSM4083495,,source name:PBS injected fish|tissue:Hematopoietic tissue without xxx cells|FISH strain:TGFli1a:EGFP|age:8 dpf,22: PBS injected fish1,All RNAseq libraries 150–750 bp inserts were sequenced on an Illumina HiSeq2500 sequencer as 1 × 50 nucleotides single end reads according to the manufacturer’s protocol. Image analysis and basecalling were done using the Illumina pipeline. Total yield varied from 10 to 26 Mreads per sample. Illumina reads were aligned against the human GRCh38.p3 and zebrafish GRCz10.80 reference genome sequences using TopHat version 2.0.5. Secondary alignments of reads were excluded by filtering the files using SAMtools version 0.1.18 Aligned fragments per predicted gene were counted from SAM alignment files using the Python package HTSeq version 0.5.3p9. To make comparisons across samples possible  these fragment counts were corrected for the total amount of sequencing performed for each sample. As a correction scaling factor  library size estimates determined using the R/Bioconductor release 2.11 package DESeq were employed Read counts were normalized by dividing the raw counts obtained from HTSeq by its scale factor. Detailed read coverage for individual genes was extracted from the TopHat alignments using SAMtools. Supplementary files format and content: tab delimited text files include gene name  ID  reads and normalized comparision between each groups,PBS injected fish,,Metastasis samples in zebrafish embryos and uninjected control were isolated by cutting the whole metastatic area 80 fish per group randomly chosen from >100 engrafted fish at 6dpi 8dpf with a micro dissection scissor WPI. The samples were immediately washed with cold PBS and stored in TRIzol Sigma at  80 ˚C. The whole process was finished within 30 min.  1000000 Cells in culture were lysized with TRIzol and stored at   80 ˚C. RNA isolation was further performed using RNeasy mini kit qiagen then Illumina RNAseq libraries were prepared using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer’s instructions Illumina  San Diego CA  USA.,PC 3M Pro4 cells were cultured in DMEM complemented with 10% Fetal Clone II. 200 400 PC 3M Pro4 cells were injected into the duct of cuvier DoC of the zebrafish embryos using a Pneumatic Picopump and a manipulator WPI. post transplantation  120 well engrafted embryos were selected using fluorescent microscope and incubated in a 34 ˚C incubator for 6 days.,tissue:Hematopoietic tissue without xxx cells|FISH strain:TGFli1a:EGFP|age:8 dpf,GSM4083495,GSM4083495: 22: PBS injected fish1; Danio rerio; RNA Seq,GSM4083495,,1,Metastasis samples in zebrafish embryos and uninjected control were isolated by cutting the whole metastatic area 80 fish per group randomly chosen from >100 engrafted fish at 6dpi 8dpf with a micro dissection scissor WPI. The samples were immediately washed with cold PBS and stored in TRIzol Sigma at  80 ˚C. The whole process was finished within 30 min.  1000000 Cells in culture were lysized with TRIzol and stored at   80 ˚C. RNA isolation was further performed using RNeasy mini kit qiagen then Illumina RNAseq libraries were prepared using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer's instructions Illumina  San Diego CA  USA.,GEO Accession:GSM4083495,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP222275,,,ZFG-16-03_22_18843_ATTCCT_L002_R1_001.fastq.gz,fastq,351800346.0,6898046.0,GSM4083495 r2,0:51,A:87109106;C:84668841;G:81026500;T:98935234;N:60665,51,,,,87109106,84668841,81026500,98935234,60665,SRX6864202,SRS5401829,SRA963954,GEO,"Institute of Biology, Leiden University",1,0.93354,,0.07513,,0.7049,,0.47898,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Netherlands,2019-09-18,Larval,Larval,Blood,Hematopoietic System
54721,SRR10136109,SRX6864201,SRS5401828,SRP222275,PRJNA566103,Next Generation Sequencing to compare gene expression of PC 3M Pro4 in cell culture and in zebrafish metastasis,GSE137629,Other,We report how engrafted human prostate cancer cells respond to zebrafish microenvironment during metasatic colonization. Overall design: RNA was isolated from metastasese in zebrafish 70 fish/group  from  uninjected fish 70fish/group  and from cells in culture  in triplicate. Transcriptomics of human cancer cells were compared between in culture and in metastases. PBS injected fish was set as  control to analyze how engrafted cancer cells modulate gene expression of the host stromal cells,,pubmed:31740783,,27: Metastases3,GSM4083494,,source name:PC 3M Pro4 injected fish|tissue:Metastases at zebrafish caudal hematopoietic tissue|FISH strain:TGFli1a:EGFP|age:8 dpf,27: Metastases3,All RNAseq libraries 150–750 bp inserts were sequenced on an Illumina HiSeq2500 sequencer as 1 × 50 nucleotides single end reads according to the manufacturer’s protocol. Image analysis and basecalling were done using the Illumina pipeline. Total yield varied from 10 to 26 Mreads per sample. Illumina reads were aligned against the human GRCh38.p3 and zebrafish GRCz10.80 reference genome sequences using TopHat version 2.0.5. Secondary alignments of reads were excluded by filtering the files using SAMtools version 0.1.18 Aligned fragments per predicted gene were counted from SAM alignment files using the Python package HTSeq version 0.5.3p9. To make comparisons across samples possible  these fragment counts were corrected for the total amount of sequencing performed for each sample. As a correction scaling factor  library size estimates determined using the R/Bioconductor release 2.11 package DESeq were employed Read counts were normalized by dividing the raw counts obtained from HTSeq by its scale factor. Detailed read coverage for individual genes was extracted from the TopHat alignments using SAMtools. Supplementary files format and content: tab delimited text files include gene name  ID  reads and normalized comparision between each groups,PC 3M Pro4 injected fish,,Metastasis samples in zebrafish embryos and uninjected control were isolated by cutting the whole metastatic area 80 fish per group randomly chosen from >100 engrafted fish at 6dpi 8dpf with a micro dissection scissor WPI. The samples were immediately washed with cold PBS and stored in TRIzol Sigma at  80 ˚C. The whole process was finished within 30 min.  1000000 Cells in culture were lysized with TRIzol and stored at   80 ˚C. RNA isolation was further performed using RNeasy mini kit qiagen then Illumina RNAseq libraries were prepared using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer’s instructions Illumina  San Diego CA  USA.,PC 3M Pro4 cells were cultured in DMEM complemented with 10% Fetal Clone II. 200 400 PC 3M Pro4 cells were injected into the duct of cuvier DoC of the zebrafish embryos using a Pneumatic Picopump and a manipulator WPI. post transplantation  120 well engrafted embryos were selected using fluorescent microscope and incubated in a 34 ˚C incubator for 6 days.,tissue:Metastases at zebrafish caudal hematopoietic tissue|FISH strain:TGFli1a:EGFP|age:8 dpf,GSM4083494,GSM4083494: 27: Metastases3; Danio rerio; Homo sapiens; RNA Seq,GSM4083494,,1,Metastasis samples in zebrafish embryos and uninjected control were isolated by cutting the whole metastatic area 80 fish per group randomly chosen from >100 engrafted fish at 6dpi 8dpf with a micro dissection scissor WPI. The samples were immediately washed with cold PBS and stored in TRIzol Sigma at  80 ˚C. The whole process was finished within 30 min.  1000000 Cells in culture were lysized with TRIzol and stored at   80 ˚C. RNA isolation was further performed using RNeasy mini kit qiagen then Illumina RNAseq libraries were prepared using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer's instructions Illumina  San Diego CA  USA.,GEO Accession:GSM4083494,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP222275,,,ZFG-16-03_27_19265_CAGATC_L001_R1_001.fastq.gz,fastq,331816863.0,6506213.0,GSM4083494 r1,0:51,A:82933253;C:78905859;G:76570035;T:93218124;N:189592,51,,,,82933253,78905859,76570035,93218124,189592,SRX6864201,SRS5401828,SRA963954,GEO,"Institute of Biology, Leiden University",1,0.81726,,0.07727,,0.71928,,0.47447,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Netherlands,2019-09-18,Larval,Larval,Blood,Hematopoietic System
54722,SRR10136110,SRX6864201,SRS5401828,SRP222275,PRJNA566103,Next Generation Sequencing to compare gene expression of PC 3M Pro4 in cell culture and in zebrafish metastasis,GSE137629,Other,We report how engrafted human prostate cancer cells respond to zebrafish microenvironment during metasatic colonization. Overall design: RNA was isolated from metastasese in zebrafish 70 fish/group  from  uninjected fish 70fish/group  and from cells in culture  in triplicate. Transcriptomics of human cancer cells were compared between in culture and in metastases. PBS injected fish was set as  control to analyze how engrafted cancer cells modulate gene expression of the host stromal cells,,pubmed:31740783,,27: Metastases3,GSM4083494,,source name:PC 3M Pro4 injected fish|tissue:Metastases at zebrafish caudal hematopoietic tissue|FISH strain:TGFli1a:EGFP|age:8 dpf,27: Metastases3,All RNAseq libraries 150–750 bp inserts were sequenced on an Illumina HiSeq2500 sequencer as 1 × 50 nucleotides single end reads according to the manufacturer’s protocol. Image analysis and basecalling were done using the Illumina pipeline. Total yield varied from 10 to 26 Mreads per sample. Illumina reads were aligned against the human GRCh38.p3 and zebrafish GRCz10.80 reference genome sequences using TopHat version 2.0.5. Secondary alignments of reads were excluded by filtering the files using SAMtools version 0.1.18 Aligned fragments per predicted gene were counted from SAM alignment files using the Python package HTSeq version 0.5.3p9. To make comparisons across samples possible  these fragment counts were corrected for the total amount of sequencing performed for each sample. As a correction scaling factor  library size estimates determined using the R/Bioconductor release 2.11 package DESeq were employed Read counts were normalized by dividing the raw counts obtained from HTSeq by its scale factor. Detailed read coverage for individual genes was extracted from the TopHat alignments using SAMtools. Supplementary files format and content: tab delimited text files include gene name  ID  reads and normalized comparision between each groups,PC 3M Pro4 injected fish,,Metastasis samples in zebrafish embryos and uninjected control were isolated by cutting the whole metastatic area 80 fish per group randomly chosen from >100 engrafted fish at 6dpi 8dpf with a micro dissection scissor WPI. The samples were immediately washed with cold PBS and stored in TRIzol Sigma at  80 ˚C. The whole process was finished within 30 min.  1000000 Cells in culture were lysized with TRIzol and stored at   80 ˚C. RNA isolation was further performed using RNeasy mini kit qiagen then Illumina RNAseq libraries were prepared using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer’s instructions Illumina  San Diego CA  USA.,PC 3M Pro4 cells were cultured in DMEM complemented with 10% Fetal Clone II. 200 400 PC 3M Pro4 cells were injected into the duct of cuvier DoC of the zebrafish embryos using a Pneumatic Picopump and a manipulator WPI. post transplantation  120 well engrafted embryos were selected using fluorescent microscope and incubated in a 34 ˚C incubator for 6 days.,tissue:Metastases at zebrafish caudal hematopoietic tissue|FISH strain:TGFli1a:EGFP|age:8 dpf,GSM4083494,GSM4083494: 27: Metastases3; Danio rerio; Homo sapiens; RNA Seq,GSM4083494,,1,Metastasis samples in zebrafish embryos and uninjected control were isolated by cutting the whole metastatic area 80 fish per group randomly chosen from >100 engrafted fish at 6dpi 8dpf with a micro dissection scissor WPI. The samples were immediately washed with cold PBS and stored in TRIzol Sigma at  80 ˚C. The whole process was finished within 30 min.  1000000 Cells in culture were lysized with TRIzol and stored at   80 ˚C. RNA isolation was further performed using RNeasy mini kit qiagen then Illumina RNAseq libraries were prepared using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer's instructions Illumina  San Diego CA  USA.,GEO Accession:GSM4083494,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP222275,,,ZFG-16-03_27_19265_CAGATC_L002_R1_001.fastq.gz,fastq,345788568.0,6780168.0,GSM4083494 r2,0:51,A:86481669;C:82220901;G:79836085;T:97146784;N:103129,51,,,,86481669,82220901,79836085,97146784,103129,SRX6864201,SRS5401828,SRA963954,GEO,"Institute of Biology, Leiden University",1,0.81844,,0.07678,,0.7189,,0.4755,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Netherlands,2019-09-18,Larval,Larval,Blood,Hematopoietic System
54723,SRR10136107,SRX6864200,SRS5401827,SRP222275,PRJNA566103,Next Generation Sequencing to compare gene expression of PC 3M Pro4 in cell culture and in zebrafish metastasis,GSE137629,Other,We report how engrafted human prostate cancer cells respond to zebrafish microenvironment during metasatic colonization. Overall design: RNA was isolated from metastasese in zebrafish 70 fish/group  from  uninjected fish 70fish/group  and from cells in culture  in triplicate. Transcriptomics of human cancer cells were compared between in culture and in metastases. PBS injected fish was set as  control to analyze how engrafted cancer cells modulate gene expression of the host stromal cells,,pubmed:31740783,,26: Metastases2,GSM4083493,,source name:PC 3M Pro4 injected fish|tissue:Metastases at zebrafish caudal hematopoietic tissue|FISH strain:TGFli1a:EGFP|age:8 dpf,26: Metastases2,All RNAseq libraries 150–750 bp inserts were sequenced on an Illumina HiSeq2500 sequencer as 1 × 50 nucleotides single end reads according to the manufacturer’s protocol. Image analysis and basecalling were done using the Illumina pipeline. Total yield varied from 10 to 26 Mreads per sample. Illumina reads were aligned against the human GRCh38.p3 and zebrafish GRCz10.80 reference genome sequences using TopHat version 2.0.5. Secondary alignments of reads were excluded by filtering the files using SAMtools version 0.1.18 Aligned fragments per predicted gene were counted from SAM alignment files using the Python package HTSeq version 0.5.3p9. To make comparisons across samples possible  these fragment counts were corrected for the total amount of sequencing performed for each sample. As a correction scaling factor  library size estimates determined using the R/Bioconductor release 2.11 package DESeq were employed Read counts were normalized by dividing the raw counts obtained from HTSeq by its scale factor. Detailed read coverage for individual genes was extracted from the TopHat alignments using SAMtools. Supplementary files format and content: tab delimited text files include gene name  ID  reads and normalized comparision between each groups,PC 3M Pro4 injected fish,,Metastasis samples in zebrafish embryos and uninjected control were isolated by cutting the whole metastatic area 80 fish per group randomly chosen from >100 engrafted fish at 6dpi 8dpf with a micro dissection scissor WPI. The samples were immediately washed with cold PBS and stored in TRIzol Sigma at  80 ˚C. The whole process was finished within 30 min.  1000000 Cells in culture were lysized with TRIzol and stored at   80 ˚C. RNA isolation was further performed using RNeasy mini kit qiagen then Illumina RNAseq libraries were prepared using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer’s instructions Illumina  San Diego CA  USA.,PC 3M Pro4 cells were cultured in DMEM complemented with 10% Fetal Clone II. 200 400 PC 3M Pro4 cells were injected into the duct of cuvier DoC of the zebrafish embryos using a Pneumatic Picopump and a manipulator WPI. post transplantation  120 well engrafted embryos were selected using fluorescent microscope and incubated in a 34 ˚C incubator for 6 days.,tissue:Metastases at zebrafish caudal hematopoietic tissue|FISH strain:TGFli1a:EGFP|age:8 dpf,GSM4083493,GSM4083493: 26: Metastases2; Danio rerio; Homo sapiens; RNA Seq,GSM4083493,,1,Metastasis samples in zebrafish embryos and uninjected control were isolated by cutting the whole metastatic area 80 fish per group randomly chosen from >100 engrafted fish at 6dpi 8dpf with a micro dissection scissor WPI. The samples were immediately washed with cold PBS and stored in TRIzol Sigma at  80 ˚C. The whole process was finished within 30 min.  1000000 Cells in culture were lysized with TRIzol and stored at   80 ˚C. RNA isolation was further performed using RNeasy mini kit qiagen then Illumina RNAseq libraries were prepared using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer's instructions Illumina  San Diego CA  USA.,GEO Accession:GSM4083493,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP222275,,,ZFG-16-03_26_19264_GCCAAT_L001_R1_001.fastq.gz,fastq,381088575.0,7472325.0,GSM4083493 r1,0:51,A:93834091;C:91635540;G:89019328;T:106380009;N:219607,51,,,,93834091,91635540,89019328,106380009,219607,SRX6864200,SRS5401827,SRA963954,GEO,"Institute of Biology, Leiden University",1,0.79302,,0.0612,,0.72803,,0.47524,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Netherlands,2019-09-18,Larval,Larval,Blood,Hematopoietic System
54724,SRR10136108,SRX6864200,SRS5401827,SRP222275,PRJNA566103,Next Generation Sequencing to compare gene expression of PC 3M Pro4 in cell culture and in zebrafish metastasis,GSE137629,Other,We report how engrafted human prostate cancer cells respond to zebrafish microenvironment during metasatic colonization. Overall design: RNA was isolated from metastasese in zebrafish 70 fish/group  from  uninjected fish 70fish/group  and from cells in culture  in triplicate. Transcriptomics of human cancer cells were compared between in culture and in metastases. PBS injected fish was set as  control to analyze how engrafted cancer cells modulate gene expression of the host stromal cells,,pubmed:31740783,,26: Metastases2,GSM4083493,,source name:PC 3M Pro4 injected fish|tissue:Metastases at zebrafish caudal hematopoietic tissue|FISH strain:TGFli1a:EGFP|age:8 dpf,26: Metastases2,All RNAseq libraries 150–750 bp inserts were sequenced on an Illumina HiSeq2500 sequencer as 1 × 50 nucleotides single end reads according to the manufacturer’s protocol. Image analysis and basecalling were done using the Illumina pipeline. Total yield varied from 10 to 26 Mreads per sample. Illumina reads were aligned against the human GRCh38.p3 and zebrafish GRCz10.80 reference genome sequences using TopHat version 2.0.5. Secondary alignments of reads were excluded by filtering the files using SAMtools version 0.1.18 Aligned fragments per predicted gene were counted from SAM alignment files using the Python package HTSeq version 0.5.3p9. To make comparisons across samples possible  these fragment counts were corrected for the total amount of sequencing performed for each sample. As a correction scaling factor  library size estimates determined using the R/Bioconductor release 2.11 package DESeq were employed Read counts were normalized by dividing the raw counts obtained from HTSeq by its scale factor. Detailed read coverage for individual genes was extracted from the TopHat alignments using SAMtools. Supplementary files format and content: tab delimited text files include gene name  ID  reads and normalized comparision between each groups,PC 3M Pro4 injected fish,,Metastasis samples in zebrafish embryos and uninjected control were isolated by cutting the whole metastatic area 80 fish per group randomly chosen from >100 engrafted fish at 6dpi 8dpf with a micro dissection scissor WPI. The samples were immediately washed with cold PBS and stored in TRIzol Sigma at  80 ˚C. The whole process was finished within 30 min.  1000000 Cells in culture were lysized with TRIzol and stored at   80 ˚C. RNA isolation was further performed using RNeasy mini kit qiagen then Illumina RNAseq libraries were prepared using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer’s instructions Illumina  San Diego CA  USA.,PC 3M Pro4 cells were cultured in DMEM complemented with 10% Fetal Clone II. 200 400 PC 3M Pro4 cells were injected into the duct of cuvier DoC of the zebrafish embryos using a Pneumatic Picopump and a manipulator WPI. post transplantation  120 well engrafted embryos were selected using fluorescent microscope and incubated in a 34 ˚C incubator for 6 days.,tissue:Metastases at zebrafish caudal hematopoietic tissue|FISH strain:TGFli1a:EGFP|age:8 dpf,GSM4083493,GSM4083493: 26: Metastases2; Danio rerio; Homo sapiens; RNA Seq,GSM4083493,,1,Metastasis samples in zebrafish embryos and uninjected control were isolated by cutting the whole metastatic area 80 fish per group randomly chosen from >100 engrafted fish at 6dpi 8dpf with a micro dissection scissor WPI. The samples were immediately washed with cold PBS and stored in TRIzol Sigma at  80 ˚C. The whole process was finished within 30 min.  1000000 Cells in culture were lysized with TRIzol and stored at   80 ˚C. RNA isolation was further performed using RNeasy mini kit qiagen then Illumina RNAseq libraries were prepared using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer's instructions Illumina  San Diego CA  USA.,GEO Accession:GSM4083493,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP222275,,,ZFG-16-03_26_19264_GCCAAT_L002_R1_001.fastq.gz,fastq,396777450.0,7779950.0,GSM4083493 r2,0:51,A:97747141;C:95409433;G:92718325;T:110778709;N:123842,51,,,,97747141,95409433,92718325,110778709,123842,SRX6864200,SRS5401827,SRA963954,GEO,"Institute of Biology, Leiden University",1,0.79294,,0.06073,,0.72636,,0.47389,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Netherlands,2019-09-18,Larval,Larval,Blood,Hematopoietic System
54725,SRR10136105,SRX6864199,SRS5401826,SRP222275,PRJNA566103,Next Generation Sequencing to compare gene expression of PC 3M Pro4 in cell culture and in zebrafish metastasis,GSE137629,Other,We report how engrafted human prostate cancer cells respond to zebrafish microenvironment during metasatic colonization. Overall design: RNA was isolated from metastasese in zebrafish 70 fish/group  from  uninjected fish 70fish/group  and from cells in culture  in triplicate. Transcriptomics of human cancer cells were compared between in culture and in metastases. PBS injected fish was set as  control to analyze how engrafted cancer cells modulate gene expression of the host stromal cells,,pubmed:31740783,,25: Metastases1,GSM4083492,,source name:PC 3M Pro4 injected fish|tissue:Metastases at zebrafish caudal hematopoietic tissue|FISH strain:TGFli1a:EGFP|age:8 dpf,25: Metastases1,All RNAseq libraries 150–750 bp inserts were sequenced on an Illumina HiSeq2500 sequencer as 1 × 50 nucleotides single end reads according to the manufacturer’s protocol. Image analysis and basecalling were done using the Illumina pipeline. Total yield varied from 10 to 26 Mreads per sample. Illumina reads were aligned against the human GRCh38.p3 and zebrafish GRCz10.80 reference genome sequences using TopHat version 2.0.5. Secondary alignments of reads were excluded by filtering the files using SAMtools version 0.1.18 Aligned fragments per predicted gene were counted from SAM alignment files using the Python package HTSeq version 0.5.3p9. To make comparisons across samples possible  these fragment counts were corrected for the total amount of sequencing performed for each sample. As a correction scaling factor  library size estimates determined using the R/Bioconductor release 2.11 package DESeq were employed Read counts were normalized by dividing the raw counts obtained from HTSeq by its scale factor. Detailed read coverage for individual genes was extracted from the TopHat alignments using SAMtools. Supplementary files format and content: tab delimited text files include gene name  ID  reads and normalized comparision between each groups,PC 3M Pro4 injected fish,,Metastasis samples in zebrafish embryos and uninjected control were isolated by cutting the whole metastatic area 80 fish per group randomly chosen from >100 engrafted fish at 6dpi 8dpf with a micro dissection scissor WPI. The samples were immediately washed with cold PBS and stored in TRIzol Sigma at  80 ˚C. The whole process was finished within 30 min.  1000000 Cells in culture were lysized with TRIzol and stored at   80 ˚C. RNA isolation was further performed using RNeasy mini kit qiagen then Illumina RNAseq libraries were prepared using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer’s instructions Illumina  San Diego CA  USA.,PC 3M Pro4 cells were cultured in DMEM complemented with 10% Fetal Clone II. 200 400 PC 3M Pro4 cells were injected into the duct of cuvier DoC of the zebrafish embryos using a Pneumatic Picopump and a manipulator WPI. post transplantation  120 well engrafted embryos were selected using fluorescent microscope and incubated in a 34 ˚C incubator for 6 days.,tissue:Metastases at zebrafish caudal hematopoietic tissue|FISH strain:TGFli1a:EGFP|age:8 dpf,GSM4083492,GSM4083492: 25: Metastases1; Danio rerio; Homo sapiens; RNA Seq,GSM4083492,,1,Metastasis samples in zebrafish embryos and uninjected control were isolated by cutting the whole metastatic area 80 fish per group randomly chosen from >100 engrafted fish at 6dpi 8dpf with a micro dissection scissor WPI. The samples were immediately washed with cold PBS and stored in TRIzol Sigma at  80 ˚C. The whole process was finished within 30 min.  1000000 Cells in culture were lysized with TRIzol and stored at   80 ˚C. RNA isolation was further performed using RNeasy mini kit qiagen then Illumina RNAseq libraries were prepared using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer's instructions Illumina  San Diego CA  USA.,GEO Accession:GSM4083492,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP222275,,,ZFG-16-03_25_19263_ACAGTG_L001_R1_001.fastq.gz,fastq,335771148.0,6583748.0,GSM4083492 r1,0:51,A:82544663;C:80955820;G:79009084;T:93066010;N:195571,51,,,,82544663,80955820,79009084,93066010,195571,SRX6864199,SRS5401826,SRA963954,GEO,"Institute of Biology, Leiden University",1,0.82172,,0.05893,,0.72088,,0.48241,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Netherlands,2019-09-18,Larval,Larval,Blood,Hematopoietic System
54726,SRR10136106,SRX6864199,SRS5401826,SRP222275,PRJNA566103,Next Generation Sequencing to compare gene expression of PC 3M Pro4 in cell culture and in zebrafish metastasis,GSE137629,Other,We report how engrafted human prostate cancer cells respond to zebrafish microenvironment during metasatic colonization. Overall design: RNA was isolated from metastasese in zebrafish 70 fish/group  from  uninjected fish 70fish/group  and from cells in culture  in triplicate. Transcriptomics of human cancer cells were compared between in culture and in metastases. PBS injected fish was set as  control to analyze how engrafted cancer cells modulate gene expression of the host stromal cells,,pubmed:31740783,,25: Metastases1,GSM4083492,,source name:PC 3M Pro4 injected fish|tissue:Metastases at zebrafish caudal hematopoietic tissue|FISH strain:TGFli1a:EGFP|age:8 dpf,25: Metastases1,All RNAseq libraries 150–750 bp inserts were sequenced on an Illumina HiSeq2500 sequencer as 1 × 50 nucleotides single end reads according to the manufacturer’s protocol. Image analysis and basecalling were done using the Illumina pipeline. Total yield varied from 10 to 26 Mreads per sample. Illumina reads were aligned against the human GRCh38.p3 and zebrafish GRCz10.80 reference genome sequences using TopHat version 2.0.5. Secondary alignments of reads were excluded by filtering the files using SAMtools version 0.1.18 Aligned fragments per predicted gene were counted from SAM alignment files using the Python package HTSeq version 0.5.3p9. To make comparisons across samples possible  these fragment counts were corrected for the total amount of sequencing performed for each sample. As a correction scaling factor  library size estimates determined using the R/Bioconductor release 2.11 package DESeq were employed Read counts were normalized by dividing the raw counts obtained from HTSeq by its scale factor. Detailed read coverage for individual genes was extracted from the TopHat alignments using SAMtools. Supplementary files format and content: tab delimited text files include gene name  ID  reads and normalized comparision between each groups,PC 3M Pro4 injected fish,,Metastasis samples in zebrafish embryos and uninjected control were isolated by cutting the whole metastatic area 80 fish per group randomly chosen from >100 engrafted fish at 6dpi 8dpf with a micro dissection scissor WPI. The samples were immediately washed with cold PBS and stored in TRIzol Sigma at  80 ˚C. The whole process was finished within 30 min.  1000000 Cells in culture were lysized with TRIzol and stored at   80 ˚C. RNA isolation was further performed using RNeasy mini kit qiagen then Illumina RNAseq libraries were prepared using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer’s instructions Illumina  San Diego CA  USA.,PC 3M Pro4 cells were cultured in DMEM complemented with 10% Fetal Clone II. 200 400 PC 3M Pro4 cells were injected into the duct of cuvier DoC of the zebrafish embryos using a Pneumatic Picopump and a manipulator WPI. post transplantation  120 well engrafted embryos were selected using fluorescent microscope and incubated in a 34 ˚C incubator for 6 days.,tissue:Metastases at zebrafish caudal hematopoietic tissue|FISH strain:TGFli1a:EGFP|age:8 dpf,GSM4083492,GSM4083492: 25: Metastases1; Danio rerio; Homo sapiens; RNA Seq,GSM4083492,,1,Metastasis samples in zebrafish embryos and uninjected control were isolated by cutting the whole metastatic area 80 fish per group randomly chosen from >100 engrafted fish at 6dpi 8dpf with a micro dissection scissor WPI. The samples were immediately washed with cold PBS and stored in TRIzol Sigma at  80 ˚C. The whole process was finished within 30 min.  1000000 Cells in culture were lysized with TRIzol and stored at   80 ˚C. RNA isolation was further performed using RNeasy mini kit qiagen then Illumina RNAseq libraries were prepared using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer's instructions Illumina  San Diego CA  USA.,GEO Accession:GSM4083492,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP222275,,,ZFG-16-03_25_19263_ACAGTG_L002_R1_001.fastq.gz,fastq,348764061.0,6838511.0,GSM4083492 r2,0:51,A:85790391;C:84069256;G:82076851;T:96714974;N:112589,51,,,,85790391,84069256,82076851,96714974,112589,SRX6864199,SRS5401826,SRA963954,GEO,"Institute of Biology, Leiden University",1,0.82119,,0.06015,,0.72299,,0.47492,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Netherlands,2019-09-18,Larval,Larval,Blood,Hematopoietic System
55483,SRR10510897,SRX7199568,SRS5705123,SRP231168,PRJNA591000,RNA seq analysis of transcriptomic changes in macrophage lineage cells post acute neural injury in larval zebrafish,GSE140810,Transcriptome Analysis,Both brain resident microglia and peripheral macrophages are important cellular effectors of the inflammatory response to neural injury. They respond to neural injury by secreting a wide range of effector molecules including cytokines  chemokines and neurotrophic factors. To identify additional secreted signalling molecules  we used RNA seq gene expression profiling to detect changes in the transcriptome of macrophage lineage cells post acute neural injury in larval zebrafish. GO term analysis was then used to analyse the list of differentially expressed genes and identify secreted signalling molecules among them. Overall design: The transcriptomes of FACS purified macrophage lineage cells from mpeg1:GFP transgenic zebrafish larvae with or without xxx injury were compared.,,pubmed:32366533,,Injury 6,GSM4186881,,tissue:Macrophage lineage cells|age:4 dpf,Injury 6,Reads were trimmed using Cutadapt version cutadapt 1.9.dev2. Reads were trimmed for quality at the 3’ end using a quality threshold of 30 and for adapter sequences of the TruSeq DNA Nano kit AGATCGGAAGAGC. Reads post trimming were required to have a minimum length of 35. The reference used for mapping was the Danio rerio GRCz10 genome from Ensembl. The annotation used for counting was the standard GTF format annotation for that reference annotation version 84. Reads were aligned to the reference genome using STAR version 2.5.2b specifying paired end reads and the option   outSAMtype BAM Unsorted. All other parameters were left at default. Reads were assigned to features of type ‘exon’ in the input annotation grouped by gene id in the reference genome using featureCounts version 1.5.1. Strandness was set to ‘reverse’ and a minimum alignment quality of 10 was specified. Gene names and other fields were derived from input annotation and added to the count/expression matrices. The raw counts table was filtered to remove genes consisting predominantly of near zero counts  filtering on counts per million CPM to avoid artefacts due to library depth. Specifically  a row of the expression matrix was required to have values greater than 0.1 in at least 3 samples  corresponding to the smallest sample group as defined by Group  once any samples were removed where applicable. Reads were normalised using the weighted trimmed mean of M values method  passing ‘TMM’ as the method to the calcNormFactors method of edgeR. A principal components analysis was undertaken on normalised and filtered expression data to explore observed patterns with respect to experimental factors. The cumulative proportion of variance associated with each factor was used to study the level of structure in the data  while associations between continuous value ranges in principal components and categorical experimental factors was assessed with an ANOVA test. Three samples Injury 3  Injury 5 and Injury 6 were identified as having high duplication rate and low mapping rate during bioinformatics QC. The high levels of variation in these three samples caused signal from the remaining samples to be overwhelmed  and it was clear that inclusion of the poor quality samples would negatively affect the results of the analysis. In summary samples Injury 3  Injury 5 and Injury 6 were removed  and filtering and normalisation re performed  prior to generation of subsequent plots and downstream analysis. Differential analysis was carried out with edgeR version 3.20.1. Fold changes were estimated as per the default behaviour of edgeR  to avoid artefacts which occur with empirical calculation. Statistical assessment of differential expression was carried out with the quasi likelihood QL F test. Genome build: GRCz10 Supplementary files format and content: A comma separated value file of normalised gene wise counts  gene wise differential expression log fold changes and false discovery rates for every sample passed to downstream analysis.,Macrophage lineage cells,Neural injury was induced in mpeg1:GFP transgenic zebrafish larvae at 4 dpf by piercing the optic tectum with a fine metal pin. At 2 xxx post injury hpi  sham and injured larvae were anaesthesised  larval heads were transected  the tissue was homogenised  and GFP+ cells were isolated from the resulting cell suspension using FACS. Sorted cells from about 180 larvae were used per sample. Six samples each were generated for 'Sham' and 'Injury' experimental conditions.,RNA was extracted from sorted cells using a RNeasy Plus Micro kit Qiagen. RNA was reverse transcribed and amplified using an Ovation RNA Seq System V2 NuGEN with an input of at least 500 ng RNA per sample. Libraries were prepared using a manual TruSeq DNA Nano gel free library kit Illumina.,,age:4 dpf,GSM4186881,GSM4186881: Injury 6; Danio rerio; RNA Seq,GSM4186881,,1,RNA was extracted from sorted cells using a RNeasy Plus Micro kit Qiagen. RNA was reverse transcribed and amplified using an Ovation RNA Seq System V2 NuGEN with an input of at least 500 ng RNA per sample. Libraries were prepared using a manual TruSeq DNA Nano gel free library kit Illumina.,GEO Accession:GSM4186881,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP231168,,,180809_A00291_0059_BH3FLKDRXX_2_11398HL0012L01_1.fastq.gz 180809_A00291_0059_BH3FLKDRXX_2_11398HL0012L01_2.fastq.gz,fastq fastq,2370267700.0,23702677.0,GSM4186881 r1,0:50 1:50,A:606210613;C:401855240;G:580678813;T:781359784;N:163250,50,50,,,606210613,401855240,580678813,781359784,163250,SRX7199568,SRS5705123,SRA1000323,GEO,"Centre for Discovery Brain Sciences, University of Edinburgh",2,0.71766,0.68121,0.304,0.29349,0.9694,0.97047,0.60698,0.47166,50,50,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,United Kingdom,2019-11-21,Larval,Larval,Blood,Hematopoietic System
55484,SRR10510896,SRX7199567,SRS5705122,SRP231168,PRJNA591000,RNA seq analysis of transcriptomic changes in macrophage lineage cells post acute neural injury in larval zebrafish,GSE140810,Transcriptome Analysis,Both brain resident microglia and peripheral macrophages are important cellular effectors of the inflammatory response to neural injury. They respond to neural injury by secreting a wide range of effector molecules including cytokines  chemokines and neurotrophic factors. To identify additional secreted signalling molecules  we used RNA seq gene expression profiling to detect changes in the transcriptome of macrophage lineage cells post acute neural injury in larval zebrafish. GO term analysis was then used to analyse the list of differentially expressed genes and identify secreted signalling molecules among them. Overall design: The transcriptomes of FACS purified macrophage lineage cells from mpeg1:GFP transgenic zebrafish larvae with or without xxx injury were compared.,,pubmed:32366533,,Injury 5,GSM4186880,,tissue:Macrophage lineage cells|age:4 dpf,Injury 5,Reads were trimmed using Cutadapt version cutadapt 1.9.dev2. Reads were trimmed for quality at the 3’ end using a quality threshold of 30 and for adapter sequences of the TruSeq DNA Nano kit AGATCGGAAGAGC. Reads post trimming were required to have a minimum length of 35. The reference used for mapping was the Danio rerio GRCz10 genome from Ensembl. The annotation used for counting was the standard GTF format annotation for that reference annotation version 84. Reads were aligned to the reference genome using STAR version 2.5.2b specifying paired end reads and the option   outSAMtype BAM Unsorted. All other parameters were left at default. Reads were assigned to features of type ‘exon’ in the input annotation grouped by gene id in the reference genome using featureCounts version 1.5.1. Strandness was set to ‘reverse’ and a minimum alignment quality of 10 was specified. Gene names and other fields were derived from input annotation and added to the count/expression matrices. The raw counts table was filtered to remove genes consisting predominantly of near zero counts  filtering on counts per million CPM to avoid artefacts due to library depth. Specifically  a row of the expression matrix was required to have values greater than 0.1 in at least 3 samples  corresponding to the smallest sample group as defined by Group  once any samples were removed where applicable. Reads were normalised using the weighted trimmed mean of M values method  passing ‘TMM’ as the method to the calcNormFactors method of edgeR. A principal components analysis was undertaken on normalised and filtered expression data to explore observed patterns with respect to experimental factors. The cumulative proportion of variance associated with each factor was used to study the level of structure in the data  while associations between continuous value ranges in principal components and categorical experimental factors was assessed with an ANOVA test. Three samples Injury 3  Injury 5 and Injury 6 were identified as having high duplication rate and low mapping rate during bioinformatics QC. The high levels of variation in these three samples caused signal from the remaining samples to be overwhelmed  and it was clear that inclusion of the poor quality samples would negatively affect the results of the analysis. In summary samples Injury 3  Injury 5 and Injury 6 were removed  and filtering and normalisation re performed  prior to generation of subsequent plots and downstream analysis. Differential analysis was carried out with edgeR version 3.20.1. Fold changes were estimated as per the default behaviour of edgeR  to avoid artefacts which occur with empirical calculation. Statistical assessment of differential expression was carried out with the quasi likelihood QL F test. Genome build: GRCz10 Supplementary files format and content: A comma separated value file of normalised gene wise counts  gene wise differential expression log fold changes and false discovery rates for every sample passed to downstream analysis.,Macrophage lineage cells,Neural injury was induced in mpeg1:GFP transgenic zebrafish larvae at 4 dpf by piercing the optic tectum with a fine metal pin. At 2 xxx post injury hpi  sham and injured larvae were anaesthesised  larval heads were transected  the tissue was homogenised  and GFP+ cells were isolated from the resulting cell suspension using FACS. Sorted cells from about 180 larvae were used per sample. Six samples each were generated for 'Sham' and 'Injury' experimental conditions.,RNA was extracted from sorted cells using a RNeasy Plus Micro kit Qiagen. RNA was reverse transcribed and amplified using an Ovation RNA Seq System V2 NuGEN with an input of at least 500 ng RNA per sample. Libraries were prepared using a manual TruSeq DNA Nano gel free library kit Illumina.,,age:4 dpf,GSM4186880,GSM4186880: Injury 5; Danio rerio; RNA Seq,GSM4186880,,1,RNA was extracted from sorted cells using a RNeasy Plus Micro kit Qiagen. RNA was reverse transcribed and amplified using an Ovation RNA Seq System V2 NuGEN with an input of at least 500 ng RNA per sample. Libraries were prepared using a manual TruSeq DNA Nano gel free library kit Illumina.,GEO Accession:GSM4186880,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP231168,,,180809_A00291_0059_BH3FLKDRXX_2_11398HL0011L01_1.fastq.gz 180809_A00291_0059_BH3FLKDRXX_2_11398HL0011L01_2.fastq.gz,fastq fastq,3104558400.0,31045584.0,GSM4186880 r1,0:50 1:50,A:787529128;C:520514424;G:755538210;T:1040764721;N:211917,50,50,,,787529128,520514424,755538210,1040764721,211917,SRX7199567,SRS5705122,SRA1000323,GEO,"Centre for Discovery Brain Sciences, University of Edinburgh",2,0.71708,0.6862,0.33746,0.32646,0.97104,0.97195,0.57901,0.57237,50,50,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,United Kingdom,2019-11-21,Larval,Larval,Blood,Hematopoietic System
55485,SRR10510895,SRX7199566,SRS5705121,SRP231168,PRJNA591000,RNA seq analysis of transcriptomic changes in macrophage lineage cells post acute neural injury in larval zebrafish,GSE140810,Transcriptome Analysis,Both brain resident microglia and peripheral macrophages are important cellular effectors of the inflammatory response to neural injury. They respond to neural injury by secreting a wide range of effector molecules including cytokines  chemokines and neurotrophic factors. To identify additional secreted signalling molecules  we used RNA seq gene expression profiling to detect changes in the transcriptome of macrophage lineage cells post acute neural injury in larval zebrafish. GO term analysis was then used to analyse the list of differentially expressed genes and identify secreted signalling molecules among them. Overall design: The transcriptomes of FACS purified macrophage lineage cells from mpeg1:GFP transgenic zebrafish larvae with or without xxx injury were compared.,,pubmed:32366533,,Injury 4,GSM4186879,,tissue:Macrophage lineage cells|age:4 dpf,Injury 4,Reads were trimmed using Cutadapt version cutadapt 1.9.dev2. Reads were trimmed for quality at the 3’ end using a quality threshold of 30 and for adapter sequences of the TruSeq DNA Nano kit AGATCGGAAGAGC. Reads post trimming were required to have a minimum length of 35. The reference used for mapping was the Danio rerio GRCz10 genome from Ensembl. The annotation used for counting was the standard GTF format annotation for that reference annotation version 84. Reads were aligned to the reference genome using STAR version 2.5.2b specifying paired end reads and the option   outSAMtype BAM Unsorted. All other parameters were left at default. Reads were assigned to features of type ‘exon’ in the input annotation grouped by gene id in the reference genome using featureCounts version 1.5.1. Strandness was set to ‘reverse’ and a minimum alignment quality of 10 was specified. Gene names and other fields were derived from input annotation and added to the count/expression matrices. The raw counts table was filtered to remove genes consisting predominantly of near zero counts  filtering on counts per million CPM to avoid artefacts due to library depth. Specifically  a row of the expression matrix was required to have values greater than 0.1 in at least 3 samples  corresponding to the smallest sample group as defined by Group  once any samples were removed where applicable. Reads were normalised using the weighted trimmed mean of M values method  passing ‘TMM’ as the method to the calcNormFactors method of edgeR. A principal components analysis was undertaken on normalised and filtered expression data to explore observed patterns with respect to experimental factors. The cumulative proportion of variance associated with each factor was used to study the level of structure in the data  while associations between continuous value ranges in principal components and categorical experimental factors was assessed with an ANOVA test. Three samples Injury 3  Injury 5 and Injury 6 were identified as having high duplication rate and low mapping rate during bioinformatics QC. The high levels of variation in these three samples caused signal from the remaining samples to be overwhelmed  and it was clear that inclusion of the poor quality samples would negatively affect the results of the analysis. In summary samples Injury 3  Injury 5 and Injury 6 were removed  and filtering and normalisation re performed  prior to generation of subsequent plots and downstream analysis. Differential analysis was carried out with edgeR version 3.20.1. Fold changes were estimated as per the default behaviour of edgeR  to avoid artefacts which occur with empirical calculation. Statistical assessment of differential expression was carried out with the quasi likelihood QL F test. Genome build: GRCz10 Supplementary files format and content: A comma separated value file of normalised gene wise counts  gene wise differential expression log fold changes and false discovery rates for every sample passed to downstream analysis.,Macrophage lineage cells,Neural injury was induced in mpeg1:GFP transgenic zebrafish larvae at 4 dpf by piercing the optic tectum with a fine metal pin. At 2 xxx post injury hpi  sham and injured larvae were anaesthesised  larval heads were transected  the tissue was homogenised  and GFP+ cells were isolated from the resulting cell suspension using FACS. Sorted cells from about 180 larvae were used per sample. Six samples each were generated for 'Sham' and 'Injury' experimental conditions.,RNA was extracted from sorted cells using a RNeasy Plus Micro kit Qiagen. RNA was reverse transcribed and amplified using an Ovation RNA Seq System V2 NuGEN with an input of at least 500 ng RNA per sample. Libraries were prepared using a manual TruSeq DNA Nano gel free library kit Illumina.,,age:4 dpf,GSM4186879,GSM4186879: Injury 4; Danio rerio; RNA Seq,GSM4186879,,1,RNA was extracted from sorted cells using a RNeasy Plus Micro kit Qiagen. RNA was reverse transcribed and amplified using an Ovation RNA Seq System V2 NuGEN with an input of at least 500 ng RNA per sample. Libraries were prepared using a manual TruSeq DNA Nano gel free library kit Illumina.,GEO Accession:GSM4186879,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP231168,,,180809_A00291_0059_BH3FLKDRXX_2_11398HL0010L01_1.fastq.gz 180809_A00291_0059_BH3FLKDRXX_2_11398HL0010L01_2.fastq.gz,fastq fastq,3141608300.0,31416083.0,GSM4186879 r1,0:50 1:50,A:835441484;C:680585583;G:723722079;T:901640444;N:218710,50,50,,,835441484,680585583,723722079,901640444,218710,SRX7199566,SRS5705121,SRA1000323,GEO,"Centre for Discovery Brain Sciences, University of Edinburgh",2,0.84591,0.82203,0.24837,0.24573,0.76729,0.77287,0.55164,0.55075,50,50,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,United Kingdom,2019-11-21,Larval,Larval,Blood,Hematopoietic System
55486,SRR10510894,SRX7199565,SRS5705120,SRP231168,PRJNA591000,RNA seq analysis of transcriptomic changes in macrophage lineage cells post acute neural injury in larval zebrafish,GSE140810,Transcriptome Analysis,Both brain resident microglia and peripheral macrophages are important cellular effectors of the inflammatory response to neural injury. They respond to neural injury by secreting a wide range of effector molecules including cytokines  chemokines and neurotrophic factors. To identify additional secreted signalling molecules  we used RNA seq gene expression profiling to detect changes in the transcriptome of macrophage lineage cells post acute neural injury in larval zebrafish. GO term analysis was then used to analyse the list of differentially expressed genes and identify secreted signalling molecules among them. Overall design: The transcriptomes of FACS purified macrophage lineage cells from mpeg1:GFP transgenic zebrafish larvae with or without xxx injury were compared.,,pubmed:32366533,,Injury 3,GSM4186878,,tissue:Macrophage lineage cells|age:4 dpf,Injury 3,Reads were trimmed using Cutadapt version cutadapt 1.9.dev2. Reads were trimmed for quality at the 3’ end using a quality threshold of 30 and for adapter sequences of the TruSeq DNA Nano kit AGATCGGAAGAGC. Reads post trimming were required to have a minimum length of 35. The reference used for mapping was the Danio rerio GRCz10 genome from Ensembl. The annotation used for counting was the standard GTF format annotation for that reference annotation version 84. Reads were aligned to the reference genome using STAR version 2.5.2b specifying paired end reads and the option   outSAMtype BAM Unsorted. All other parameters were left at default. Reads were assigned to features of type ‘exon’ in the input annotation grouped by gene id in the reference genome using featureCounts version 1.5.1. Strandness was set to ‘reverse’ and a minimum alignment quality of 10 was specified. Gene names and other fields were derived from input annotation and added to the count/expression matrices. The raw counts table was filtered to remove genes consisting predominantly of near zero counts  filtering on counts per million CPM to avoid artefacts due to library depth. Specifically  a row of the expression matrix was required to have values greater than 0.1 in at least 3 samples  corresponding to the smallest sample group as defined by Group  once any samples were removed where applicable. Reads were normalised using the weighted trimmed mean of M values method  passing ‘TMM’ as the method to the calcNormFactors method of edgeR. A principal components analysis was undertaken on normalised and filtered expression data to explore observed patterns with respect to experimental factors. The cumulative proportion of variance associated with each factor was used to study the level of structure in the data  while associations between continuous value ranges in principal components and categorical experimental factors was assessed with an ANOVA test. Three samples Injury 3  Injury 5 and Injury 6 were identified as having high duplication rate and low mapping rate during bioinformatics QC. The high levels of variation in these three samples caused signal from the remaining samples to be overwhelmed  and it was clear that inclusion of the poor quality samples would negatively affect the results of the analysis. In summary samples Injury 3  Injury 5 and Injury 6 were removed  and filtering and normalisation re performed  prior to generation of subsequent plots and downstream analysis. Differential analysis was carried out with edgeR version 3.20.1. Fold changes were estimated as per the default behaviour of edgeR  to avoid artefacts which occur with empirical calculation. Statistical assessment of differential expression was carried out with the quasi likelihood QL F test. Genome build: GRCz10 Supplementary files format and content: A comma separated value file of normalised gene wise counts  gene wise differential expression log fold changes and false discovery rates for every sample passed to downstream analysis.,Macrophage lineage cells,Neural injury was induced in mpeg1:GFP transgenic zebrafish larvae at 4 dpf by piercing the optic tectum with a fine metal pin. At 2 xxx post injury hpi  sham and injured larvae were anaesthesised  larval heads were transected  the tissue was homogenised  and GFP+ cells were isolated from the resulting cell suspension using FACS. Sorted cells from about 180 larvae were used per sample. Six samples each were generated for 'Sham' and 'Injury' experimental conditions.,RNA was extracted from sorted cells using a RNeasy Plus Micro kit Qiagen. RNA was reverse transcribed and amplified using an Ovation RNA Seq System V2 NuGEN with an input of at least 500 ng RNA per sample. Libraries were prepared using a manual TruSeq DNA Nano gel free library kit Illumina.,,age:4 dpf,GSM4186878,GSM4186878: Injury 3; Danio rerio; RNA Seq,GSM4186878,,1,RNA was extracted from sorted cells using a RNeasy Plus Micro kit Qiagen. RNA was reverse transcribed and amplified using an Ovation RNA Seq System V2 NuGEN with an input of at least 500 ng RNA per sample. Libraries were prepared using a manual TruSeq DNA Nano gel free library kit Illumina.,GEO Accession:GSM4186878,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP231168,,,180809_A00291_0059_BH3FLKDRXX_2_11398HL0009L01_1.fastq.gz 180809_A00291_0059_BH3FLKDRXX_2_11398HL0009L01_2.fastq.gz,fastq fastq,3113500800.0,31135008.0,GSM4186878 r1,0:50 1:50,A:766956694;C:669677107;G:744420894;T:932232213;N:213892,50,50,,,766956694,669677107,744420894,932232213,213892,SRX7199565,SRS5705120,SRA1000323,GEO,"Centre for Discovery Brain Sciences, University of Edinburgh",2,0.71164,0.6754,0.17946,0.17464,0.81734,0.82373,0.53588,0.60496,50,50,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,United Kingdom,2019-11-21,Larval,Larval,Blood,Hematopoietic System
55487,SRR10510893,SRX7199564,SRS5705119,SRP231168,PRJNA591000,RNA seq analysis of transcriptomic changes in macrophage lineage cells post acute neural injury in larval zebrafish,GSE140810,Transcriptome Analysis,Both brain resident microglia and peripheral macrophages are important cellular effectors of the inflammatory response to neural injury. They respond to neural injury by secreting a wide range of effector molecules including cytokines  chemokines and neurotrophic factors. To identify additional secreted signalling molecules  we used RNA seq gene expression profiling to detect changes in the transcriptome of macrophage lineage cells post acute neural injury in larval zebrafish. GO term analysis was then used to analyse the list of differentially expressed genes and identify secreted signalling molecules among them. Overall design: The transcriptomes of FACS purified macrophage lineage cells from mpeg1:GFP transgenic zebrafish larvae with or without xxx injury were compared.,,pubmed:32366533,,Injury 2,GSM4186877,,tissue:Macrophage lineage cells|age:4 dpf,Injury 2,Reads were trimmed using Cutadapt version cutadapt 1.9.dev2. Reads were trimmed for quality at the 3’ end using a quality threshold of 30 and for adapter sequences of the TruSeq DNA Nano kit AGATCGGAAGAGC. Reads post trimming were required to have a minimum length of 35. The reference used for mapping was the Danio rerio GRCz10 genome from Ensembl. The annotation used for counting was the standard GTF format annotation for that reference annotation version 84. Reads were aligned to the reference genome using STAR version 2.5.2b specifying paired end reads and the option   outSAMtype BAM Unsorted. All other parameters were left at default. Reads were assigned to features of type ‘exon’ in the input annotation grouped by gene id in the reference genome using featureCounts version 1.5.1. Strandness was set to ‘reverse’ and a minimum alignment quality of 10 was specified. Gene names and other fields were derived from input annotation and added to the count/expression matrices. The raw counts table was filtered to remove genes consisting predominantly of near zero counts  filtering on counts per million CPM to avoid artefacts due to library depth. Specifically  a row of the expression matrix was required to have values greater than 0.1 in at least 3 samples  corresponding to the smallest sample group as defined by Group  once any samples were removed where applicable. Reads were normalised using the weighted trimmed mean of M values method  passing ‘TMM’ as the method to the calcNormFactors method of edgeR. A principal components analysis was undertaken on normalised and filtered expression data to explore observed patterns with respect to experimental factors. The cumulative proportion of variance associated with each factor was used to study the level of structure in the data  while associations between continuous value ranges in principal components and categorical experimental factors was assessed with an ANOVA test. Three samples Injury 3  Injury 5 and Injury 6 were identified as having high duplication rate and low mapping rate during bioinformatics QC. The high levels of variation in these three samples caused signal from the remaining samples to be overwhelmed  and it was clear that inclusion of the poor quality samples would negatively affect the results of the analysis. In summary samples Injury 3  Injury 5 and Injury 6 were removed  and filtering and normalisation re performed  prior to generation of subsequent plots and downstream analysis. Differential analysis was carried out with edgeR version 3.20.1. Fold changes were estimated as per the default behaviour of edgeR  to avoid artefacts which occur with empirical calculation. Statistical assessment of differential expression was carried out with the quasi likelihood QL F test. Genome build: GRCz10 Supplementary files format and content: A comma separated value file of normalised gene wise counts  gene wise differential expression log fold changes and false discovery rates for every sample passed to downstream analysis.,Macrophage lineage cells,Neural injury was induced in mpeg1:GFP transgenic zebrafish larvae at 4 dpf by piercing the optic tectum with a fine metal pin. At 2 xxx post injury hpi  sham and injured larvae were anaesthesised  larval heads were transected  the tissue was homogenised  and GFP+ cells were isolated from the resulting cell suspension using FACS. Sorted cells from about 180 larvae were used per sample. Six samples each were generated for 'Sham' and 'Injury' experimental conditions.,RNA was extracted from sorted cells using a RNeasy Plus Micro kit Qiagen. RNA was reverse transcribed and amplified using an Ovation RNA Seq System V2 NuGEN with an input of at least 500 ng RNA per sample. Libraries were prepared using a manual TruSeq DNA Nano gel free library kit Illumina.,,age:4 dpf,GSM4186877,GSM4186877: Injury 2; Danio rerio; RNA Seq,GSM4186877,,1,RNA was extracted from sorted cells using a RNeasy Plus Micro kit Qiagen. RNA was reverse transcribed and amplified using an Ovation RNA Seq System V2 NuGEN with an input of at least 500 ng RNA per sample. Libraries were prepared using a manual TruSeq DNA Nano gel free library kit Illumina.,GEO Accession:GSM4186877,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP231168,,,180809_A00291_0059_BH3FLKDRXX_2_11398HL0002L01_1.fastq.gz 180809_A00291_0059_BH3FLKDRXX_2_11398HL0002L01_2.fastq.gz,fastq fastq,2894623100.0,28946231.0,GSM4186877 r1,0:50 1:50,A:761759953;C:626039697;G:669398895;T:837222282;N:202273,50,50,,,761759953,626039697,669398895,837222282,202273,SRX7199564,SRS5705119,SRA1000323,GEO,"Centre for Discovery Brain Sciences, University of Edinburgh",2,0.83047,0.80183,0.22927,0.22366,0.76715,0.77419,0.54395,0.53733,50,50,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,United Kingdom,2019-11-21,Larval,Larval,Blood,Hematopoietic System
55488,SRR10510892,SRX7199563,SRS5705118,SRP231168,PRJNA591000,RNA seq analysis of transcriptomic changes in macrophage lineage cells post acute neural injury in larval zebrafish,GSE140810,Transcriptome Analysis,Both brain resident microglia and peripheral macrophages are important cellular effectors of the inflammatory response to neural injury. They respond to neural injury by secreting a wide range of effector molecules including cytokines  chemokines and neurotrophic factors. To identify additional secreted signalling molecules  we used RNA seq gene expression profiling to detect changes in the transcriptome of macrophage lineage cells post acute neural injury in larval zebrafish. GO term analysis was then used to analyse the list of differentially expressed genes and identify secreted signalling molecules among them. Overall design: The transcriptomes of FACS purified macrophage lineage cells from mpeg1:GFP transgenic zebrafish larvae with or without xxx injury were compared.,,pubmed:32366533,,Injury 1,GSM4186876,,tissue:Macrophage lineage cells|age:4 dpf,Injury 1,Reads were trimmed using Cutadapt version cutadapt 1.9.dev2. Reads were trimmed for quality at the 3’ end using a quality threshold of 30 and for adapter sequences of the TruSeq DNA Nano kit AGATCGGAAGAGC. Reads post trimming were required to have a minimum length of 35. The reference used for mapping was the Danio rerio GRCz10 genome from Ensembl. The annotation used for counting was the standard GTF format annotation for that reference annotation version 84. Reads were aligned to the reference genome using STAR version 2.5.2b specifying paired end reads and the option   outSAMtype BAM Unsorted. All other parameters were left at default. Reads were assigned to features of type ‘exon’ in the input annotation grouped by gene id in the reference genome using featureCounts version 1.5.1. Strandness was set to ‘reverse’ and a minimum alignment quality of 10 was specified. Gene names and other fields were derived from input annotation and added to the count/expression matrices. The raw counts table was filtered to remove genes consisting predominantly of near zero counts  filtering on counts per million CPM to avoid artefacts due to library depth. Specifically  a row of the expression matrix was required to have values greater than 0.1 in at least 3 samples  corresponding to the smallest sample group as defined by Group  once any samples were removed where applicable. Reads were normalised using the weighted trimmed mean of M values method  passing ‘TMM’ as the method to the calcNormFactors method of edgeR. A principal components analysis was undertaken on normalised and filtered expression data to explore observed patterns with respect to experimental factors. The cumulative proportion of variance associated with each factor was used to study the level of structure in the data  while associations between continuous value ranges in principal components and categorical experimental factors was assessed with an ANOVA test. Three samples Injury 3  Injury 5 and Injury 6 were identified as having high duplication rate and low mapping rate during bioinformatics QC. The high levels of variation in these three samples caused signal from the remaining samples to be overwhelmed  and it was clear that inclusion of the poor quality samples would negatively affect the results of the analysis. In summary samples Injury 3  Injury 5 and Injury 6 were removed  and filtering and normalisation re performed  prior to generation of subsequent plots and downstream analysis. Differential analysis was carried out with edgeR version 3.20.1. Fold changes were estimated as per the default behaviour of edgeR  to avoid artefacts which occur with empirical calculation. Statistical assessment of differential expression was carried out with the quasi likelihood QL F test. Genome build: GRCz10 Supplementary files format and content: A comma separated value file of normalised gene wise counts  gene wise differential expression log fold changes and false discovery rates for every sample passed to downstream analysis.,Macrophage lineage cells,Neural injury was induced in mpeg1:GFP transgenic zebrafish larvae at 4 dpf by piercing the optic tectum with a fine metal pin. At 2 xxx post injury hpi  sham and injured larvae were anaesthesised  larval heads were transected  the tissue was homogenised  and GFP+ cells were isolated from the resulting cell suspension using FACS. Sorted cells from about 180 larvae were used per sample. Six samples each were generated for 'Sham' and 'Injury' experimental conditions.,RNA was extracted from sorted cells using a RNeasy Plus Micro kit Qiagen. RNA was reverse transcribed and amplified using an Ovation RNA Seq System V2 NuGEN with an input of at least 500 ng RNA per sample. Libraries were prepared using a manual TruSeq DNA Nano gel free library kit Illumina.,,age:4 dpf,GSM4186876,GSM4186876: Injury 1; Danio rerio; RNA Seq,GSM4186876,,1,RNA was extracted from sorted cells using a RNeasy Plus Micro kit Qiagen. RNA was reverse transcribed and amplified using an Ovation RNA Seq System V2 NuGEN with an input of at least 500 ng RNA per sample. Libraries were prepared using a manual TruSeq DNA Nano gel free library kit Illumina.,GEO Accession:GSM4186876,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP231168,,,180809_A00291_0059_BH3FLKDRXX_2_11398HL0007L01_1.fastq.gz 180809_A00291_0059_BH3FLKDRXX_2_11398HL0007L01_2.fastq.gz,fastq fastq,2953684900.0,29536849.0,GSM4186876 r1,0:50 1:50,A:779744552;C:654064489;G:682109837;T:837563725;N:202297,50,50,,,779744552,654064489,682109837,837563725,202297,SRX7199563,SRS5705118,SRA1000323,GEO,"Centre for Discovery Brain Sciences, University of Edinburgh",2,0.85999,0.8342,0.23302,0.22629,0.76788,0.77664,0.53288,0.54359,50,50,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,United Kingdom,2019-11-21,Larval,Larval,Blood,Hematopoietic System
55489,SRR10510891,SRX7199562,SRS5705117,SRP231168,PRJNA591000,RNA seq analysis of transcriptomic changes in macrophage lineage cells post acute neural injury in larval zebrafish,GSE140810,Transcriptome Analysis,Both brain resident microglia and peripheral macrophages are important cellular effectors of the inflammatory response to neural injury. They respond to neural injury by secreting a wide range of effector molecules including cytokines  chemokines and neurotrophic factors. To identify additional secreted signalling molecules  we used RNA seq gene expression profiling to detect changes in the transcriptome of macrophage lineage cells post acute neural injury in larval zebrafish. GO term analysis was then used to analyse the list of differentially expressed genes and identify secreted signalling molecules among them. Overall design: The transcriptomes of FACS purified macrophage lineage cells from mpeg1:GFP transgenic zebrafish larvae with or without xxx injury were compared.,,pubmed:32366533,,Sham 6,GSM4186875,,tissue:Macrophage lineage cells|age:4 dpf,Sham 6,Reads were trimmed using Cutadapt version cutadapt 1.9.dev2. Reads were trimmed for quality at the 3’ end using a quality threshold of 30 and for adapter sequences of the TruSeq DNA Nano kit AGATCGGAAGAGC. Reads post trimming were required to have a minimum length of 35. The reference used for mapping was the Danio rerio GRCz10 genome from Ensembl. The annotation used for counting was the standard GTF format annotation for that reference annotation version 84. Reads were aligned to the reference genome using STAR version 2.5.2b specifying paired end reads and the option   outSAMtype BAM Unsorted. All other parameters were left at default. Reads were assigned to features of type ‘exon’ in the input annotation grouped by gene id in the reference genome using featureCounts version 1.5.1. Strandness was set to ‘reverse’ and a minimum alignment quality of 10 was specified. Gene names and other fields were derived from input annotation and added to the count/expression matrices. The raw counts table was filtered to remove genes consisting predominantly of near zero counts  filtering on counts per million CPM to avoid artefacts due to library depth. Specifically  a row of the expression matrix was required to have values greater than 0.1 in at least 3 samples  corresponding to the smallest sample group as defined by Group  once any samples were removed where applicable. Reads were normalised using the weighted trimmed mean of M values method  passing ‘TMM’ as the method to the calcNormFactors method of edgeR. A principal components analysis was undertaken on normalised and filtered expression data to explore observed patterns with respect to experimental factors. The cumulative proportion of variance associated with each factor was used to study the level of structure in the data  while associations between continuous value ranges in principal components and categorical experimental factors was assessed with an ANOVA test. Three samples Injury 3  Injury 5 and Injury 6 were identified as having high duplication rate and low mapping rate during bioinformatics QC. The high levels of variation in these three samples caused signal from the remaining samples to be overwhelmed  and it was clear that inclusion of the poor quality samples would negatively affect the results of the analysis. In summary samples Injury 3  Injury 5 and Injury 6 were removed  and filtering and normalisation re performed  prior to generation of subsequent plots and downstream analysis. Differential analysis was carried out with edgeR version 3.20.1. Fold changes were estimated as per the default behaviour of edgeR  to avoid artefacts which occur with empirical calculation. Statistical assessment of differential expression was carried out with the quasi likelihood QL F test. Genome build: GRCz10 Supplementary files format and content: A comma separated value file of normalised gene wise counts  gene wise differential expression log fold changes and false discovery rates for every sample passed to downstream analysis.,Macrophage lineage cells,Neural injury was induced in mpeg1:GFP transgenic zebrafish larvae at 4 dpf by piercing the optic tectum with a fine metal pin. At 2 xxx post injury hpi  sham and injured larvae were anaesthesised  larval heads were transected  the tissue was homogenised  and GFP+ cells were isolated from the resulting cell suspension using FACS. Sorted cells from about 180 larvae were used per sample. Six samples each were generated for 'Sham' and 'Injury' experimental conditions.,RNA was extracted from sorted cells using a RNeasy Plus Micro kit Qiagen. RNA was reverse transcribed and amplified using an Ovation RNA Seq System V2 NuGEN with an input of at least 500 ng RNA per sample. Libraries were prepared using a manual TruSeq DNA Nano gel free library kit Illumina.,,age:4 dpf,GSM4186875,GSM4186875: Sham 6; Danio rerio; RNA Seq,GSM4186875,,1,RNA was extracted from sorted cells using a RNeasy Plus Micro kit Qiagen. RNA was reverse transcribed and amplified using an Ovation RNA Seq System V2 NuGEN with an input of at least 500 ng RNA per sample. Libraries were prepared using a manual TruSeq DNA Nano gel free library kit Illumina.,GEO Accession:GSM4186875,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP231168,,,180809_A00291_0059_BH3FLKDRXX_2_11398HL0006L01_1.fastq.gz 180809_A00291_0059_BH3FLKDRXX_2_11398HL0006L01_2.fastq.gz,fastq fastq,3041448600.0,30414486.0,GSM4186875 r1,0:50 1:50,A:814525300;C:665527185;G:697073297;T:864112866;N:209952,50,50,,,814525300,665527185,697073297,864112866,209952,SRX7199562,SRS5705117,SRA1000323,GEO,"Centre for Discovery Brain Sciences, University of Edinburgh",2,0.8565,0.83045,0.26068,0.25484,0.75998,0.76828,0.53257,0.51687,50,50,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,United Kingdom,2019-11-21,Larval,Larval,Blood,Hematopoietic System
55490,SRR10510890,SRX7199561,SRS5705116,SRP231168,PRJNA591000,RNA seq analysis of transcriptomic changes in macrophage lineage cells post acute neural injury in larval zebrafish,GSE140810,Transcriptome Analysis,Both brain resident microglia and peripheral macrophages are important cellular effectors of the inflammatory response to neural injury. They respond to neural injury by secreting a wide range of effector molecules including cytokines  chemokines and neurotrophic factors. To identify additional secreted signalling molecules  we used RNA seq gene expression profiling to detect changes in the transcriptome of macrophage lineage cells post acute neural injury in larval zebrafish. GO term analysis was then used to analyse the list of differentially expressed genes and identify secreted signalling molecules among them. Overall design: The transcriptomes of FACS purified macrophage lineage cells from mpeg1:GFP transgenic zebrafish larvae with or without xxx injury were compared.,,pubmed:32366533,,Sham 5,GSM4186874,,tissue:Macrophage lineage cells|age:4 dpf,Sham 5,Reads were trimmed using Cutadapt version cutadapt 1.9.dev2. Reads were trimmed for quality at the 3’ end using a quality threshold of 30 and for adapter sequences of the TruSeq DNA Nano kit AGATCGGAAGAGC. Reads post trimming were required to have a minimum length of 35. The reference used for mapping was the Danio rerio GRCz10 genome from Ensembl. The annotation used for counting was the standard GTF format annotation for that reference annotation version 84. Reads were aligned to the reference genome using STAR version 2.5.2b specifying paired end reads and the option   outSAMtype BAM Unsorted. All other parameters were left at default. Reads were assigned to features of type ‘exon’ in the input annotation grouped by gene id in the reference genome using featureCounts version 1.5.1. Strandness was set to ‘reverse’ and a minimum alignment quality of 10 was specified. Gene names and other fields were derived from input annotation and added to the count/expression matrices. The raw counts table was filtered to remove genes consisting predominantly of near zero counts  filtering on counts per million CPM to avoid artefacts due to library depth. Specifically  a row of the expression matrix was required to have values greater than 0.1 in at least 3 samples  corresponding to the smallest sample group as defined by Group  once any samples were removed where applicable. Reads were normalised using the weighted trimmed mean of M values method  passing ‘TMM’ as the method to the calcNormFactors method of edgeR. A principal components analysis was undertaken on normalised and filtered expression data to explore observed patterns with respect to experimental factors. The cumulative proportion of variance associated with each factor was used to study the level of structure in the data  while associations between continuous value ranges in principal components and categorical experimental factors was assessed with an ANOVA test. Three samples Injury 3  Injury 5 and Injury 6 were identified as having high duplication rate and low mapping rate during bioinformatics QC. The high levels of variation in these three samples caused signal from the remaining samples to be overwhelmed  and it was clear that inclusion of the poor quality samples would negatively affect the results of the analysis. In summary samples Injury 3  Injury 5 and Injury 6 were removed  and filtering and normalisation re performed  prior to generation of subsequent plots and downstream analysis. Differential analysis was carried out with edgeR version 3.20.1. Fold changes were estimated as per the default behaviour of edgeR  to avoid artefacts which occur with empirical calculation. Statistical assessment of differential expression was carried out with the quasi likelihood QL F test. Genome build: GRCz10 Supplementary files format and content: A comma separated value file of normalised gene wise counts  gene wise differential expression log fold changes and false discovery rates for every sample passed to downstream analysis.,Macrophage lineage cells,Neural injury was induced in mpeg1:GFP transgenic zebrafish larvae at 4 dpf by piercing the optic tectum with a fine metal pin. At 2 xxx post injury hpi  sham and injured larvae were anaesthesised  larval heads were transected  the tissue was homogenised  and GFP+ cells were isolated from the resulting cell suspension using FACS. Sorted cells from about 180 larvae were used per sample. Six samples each were generated for 'Sham' and 'Injury' experimental conditions.,RNA was extracted from sorted cells using a RNeasy Plus Micro kit Qiagen. RNA was reverse transcribed and amplified using an Ovation RNA Seq System V2 NuGEN with an input of at least 500 ng RNA per sample. Libraries were prepared using a manual TruSeq DNA Nano gel free library kit Illumina.,,age:4 dpf,GSM4186874,GSM4186874: Sham 5; Danio rerio; RNA Seq,GSM4186874,,1,RNA was extracted from sorted cells using a RNeasy Plus Micro kit Qiagen. RNA was reverse transcribed and amplified using an Ovation RNA Seq System V2 NuGEN with an input of at least 500 ng RNA per sample. Libraries were prepared using a manual TruSeq DNA Nano gel free library kit Illumina.,GEO Accession:GSM4186874,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP231168,,,180809_A00291_0059_BH3FLKDRXX_2_11398HL0005L01_1.fastq.gz 180809_A00291_0059_BH3FLKDRXX_2_11398HL0005L01_2.fastq.gz,fastq fastq,2978747900.0,29787479.0,GSM4186874 r1,0:50 1:50,A:790529419;C:644687609;G:687572262;T:855752767;N:205843,50,50,,,790529419,644687609,687572262,855752767,205843,SRX7199561,SRS5705116,SRA1000323,GEO,"Centre for Discovery Brain Sciences, University of Edinburgh",2,0.84039,0.81667,0.25482,0.25083,0.75763,0.76461,0.53837,0.52682,50,50,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,United Kingdom,2019-11-21,Larval,Larval,Blood,Hematopoietic System
55491,SRR10510889,SRX7199560,SRS5705115,SRP231168,PRJNA591000,RNA seq analysis of transcriptomic changes in macrophage lineage cells post acute neural injury in larval zebrafish,GSE140810,Transcriptome Analysis,Both brain resident microglia and peripheral macrophages are important cellular effectors of the inflammatory response to neural injury. They respond to neural injury by secreting a wide range of effector molecules including cytokines  chemokines and neurotrophic factors. To identify additional secreted signalling molecules  we used RNA seq gene expression profiling to detect changes in the transcriptome of macrophage lineage cells post acute neural injury in larval zebrafish. GO term analysis was then used to analyse the list of differentially expressed genes and identify secreted signalling molecules among them. Overall design: The transcriptomes of FACS purified macrophage lineage cells from mpeg1:GFP transgenic zebrafish larvae with or without xxx injury were compared.,,pubmed:32366533,,Sham 4,GSM4186873,,tissue:Macrophage lineage cells|age:4 dpf,Sham 4,Reads were trimmed using Cutadapt version cutadapt 1.9.dev2. Reads were trimmed for quality at the 3’ end using a quality threshold of 30 and for adapter sequences of the TruSeq DNA Nano kit AGATCGGAAGAGC. Reads post trimming were required to have a minimum length of 35. The reference used for mapping was the Danio rerio GRCz10 genome from Ensembl. The annotation used for counting was the standard GTF format annotation for that reference annotation version 84. Reads were aligned to the reference genome using STAR version 2.5.2b specifying paired end reads and the option   outSAMtype BAM Unsorted. All other parameters were left at default. Reads were assigned to features of type ‘exon’ in the input annotation grouped by gene id in the reference genome using featureCounts version 1.5.1. Strandness was set to ‘reverse’ and a minimum alignment quality of 10 was specified. Gene names and other fields were derived from input annotation and added to the count/expression matrices. The raw counts table was filtered to remove genes consisting predominantly of near zero counts  filtering on counts per million CPM to avoid artefacts due to library depth. Specifically  a row of the expression matrix was required to have values greater than 0.1 in at least 3 samples  corresponding to the smallest sample group as defined by Group  once any samples were removed where applicable. Reads were normalised using the weighted trimmed mean of M values method  passing ‘TMM’ as the method to the calcNormFactors method of edgeR. A principal components analysis was undertaken on normalised and filtered expression data to explore observed patterns with respect to experimental factors. The cumulative proportion of variance associated with each factor was used to study the level of structure in the data  while associations between continuous value ranges in principal components and categorical experimental factors was assessed with an ANOVA test. Three samples Injury 3  Injury 5 and Injury 6 were identified as having high duplication rate and low mapping rate during bioinformatics QC. The high levels of variation in these three samples caused signal from the remaining samples to be overwhelmed  and it was clear that inclusion of the poor quality samples would negatively affect the results of the analysis. In summary samples Injury 3  Injury 5 and Injury 6 were removed  and filtering and normalisation re performed  prior to generation of subsequent plots and downstream analysis. Differential analysis was carried out with edgeR version 3.20.1. Fold changes were estimated as per the default behaviour of edgeR  to avoid artefacts which occur with empirical calculation. Statistical assessment of differential expression was carried out with the quasi likelihood QL F test. Genome build: GRCz10 Supplementary files format and content: A comma separated value file of normalised gene wise counts  gene wise differential expression log fold changes and false discovery rates for every sample passed to downstream analysis.,Macrophage lineage cells,Neural injury was induced in mpeg1:GFP transgenic zebrafish larvae at 4 dpf by piercing the optic tectum with a fine metal pin. At 2 xxx post injury hpi  sham and injured larvae were anaesthesised  larval heads were transected  the tissue was homogenised  and GFP+ cells were isolated from the resulting cell suspension using FACS. Sorted cells from about 180 larvae were used per sample. Six samples each were generated for 'Sham' and 'Injury' experimental conditions.,RNA was extracted from sorted cells using a RNeasy Plus Micro kit Qiagen. RNA was reverse transcribed and amplified using an Ovation RNA Seq System V2 NuGEN with an input of at least 500 ng RNA per sample. Libraries were prepared using a manual TruSeq DNA Nano gel free library kit Illumina.,,age:4 dpf,GSM4186873,GSM4186873: Sham 4; Danio rerio; RNA Seq,GSM4186873,,1,RNA was extracted from sorted cells using a RNeasy Plus Micro kit Qiagen. RNA was reverse transcribed and amplified using an Ovation RNA Seq System V2 NuGEN with an input of at least 500 ng RNA per sample. Libraries were prepared using a manual TruSeq DNA Nano gel free library kit Illumina.,GEO Accession:GSM4186873,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP231168,,,180809_A00291_0059_BH3FLKDRXX_2_11398HL0004L01_1.fastq.gz 180809_A00291_0059_BH3FLKDRXX_2_11398HL0004L01_2.fastq.gz,fastq fastq,3157421300.0,31574213.0,GSM4186873 r1,0:50 1:50,A:848052952;C:676336291;G:722614661;T:910199331;N:218065,50,50,,,848052952,676336291,722614661,910199331,218065,SRX7199560,SRS5705115,SRA1000323,GEO,"Centre for Discovery Brain Sciences, University of Edinburgh",2,0.83939,0.81586,0.27396,0.2703,0.75416,0.76096,0.52309,0.53651,50,50,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,United Kingdom,2019-11-21,Larval,Larval,Blood,Hematopoietic System
55492,SRR10510888,SRX7199559,SRS5705114,SRP231168,PRJNA591000,RNA seq analysis of transcriptomic changes in macrophage lineage cells post acute neural injury in larval zebrafish,GSE140810,Transcriptome Analysis,Both brain resident microglia and peripheral macrophages are important cellular effectors of the inflammatory response to neural injury. They respond to neural injury by secreting a wide range of effector molecules including cytokines  chemokines and neurotrophic factors. To identify additional secreted signalling molecules  we used RNA seq gene expression profiling to detect changes in the transcriptome of macrophage lineage cells post acute neural injury in larval zebrafish. GO term analysis was then used to analyse the list of differentially expressed genes and identify secreted signalling molecules among them. Overall design: The transcriptomes of FACS purified macrophage lineage cells from mpeg1:GFP transgenic zebrafish larvae with or without xxx injury were compared.,,pubmed:32366533,,Sham 3,GSM4186872,,tissue:Macrophage lineage cells|age:4 dpf,Sham 3,Reads were trimmed using Cutadapt version cutadapt 1.9.dev2. Reads were trimmed for quality at the 3’ end using a quality threshold of 30 and for adapter sequences of the TruSeq DNA Nano kit AGATCGGAAGAGC. Reads post trimming were required to have a minimum length of 35. The reference used for mapping was the Danio rerio GRCz10 genome from Ensembl. The annotation used for counting was the standard GTF format annotation for that reference annotation version 84. Reads were aligned to the reference genome using STAR version 2.5.2b specifying paired end reads and the option   outSAMtype BAM Unsorted. All other parameters were left at default. Reads were assigned to features of type ‘exon’ in the input annotation grouped by gene id in the reference genome using featureCounts version 1.5.1. Strandness was set to ‘reverse’ and a minimum alignment quality of 10 was specified. Gene names and other fields were derived from input annotation and added to the count/expression matrices. The raw counts table was filtered to remove genes consisting predominantly of near zero counts  filtering on counts per million CPM to avoid artefacts due to library depth. Specifically  a row of the expression matrix was required to have values greater than 0.1 in at least 3 samples  corresponding to the smallest sample group as defined by Group  once any samples were removed where applicable. Reads were normalised using the weighted trimmed mean of M values method  passing ‘TMM’ as the method to the calcNormFactors method of edgeR. A principal components analysis was undertaken on normalised and filtered expression data to explore observed patterns with respect to experimental factors. The cumulative proportion of variance associated with each factor was used to study the level of structure in the data  while associations between continuous value ranges in principal components and categorical experimental factors was assessed with an ANOVA test. Three samples Injury 3  Injury 5 and Injury 6 were identified as having high duplication rate and low mapping rate during bioinformatics QC. The high levels of variation in these three samples caused signal from the remaining samples to be overwhelmed  and it was clear that inclusion of the poor quality samples would negatively affect the results of the analysis. In summary samples Injury 3  Injury 5 and Injury 6 were removed  and filtering and normalisation re performed  prior to generation of subsequent plots and downstream analysis. Differential analysis was carried out with edgeR version 3.20.1. Fold changes were estimated as per the default behaviour of edgeR  to avoid artefacts which occur with empirical calculation. Statistical assessment of differential expression was carried out with the quasi likelihood QL F test. Genome build: GRCz10 Supplementary files format and content: A comma separated value file of normalised gene wise counts  gene wise differential expression log fold changes and false discovery rates for every sample passed to downstream analysis.,Macrophage lineage cells,Neural injury was induced in mpeg1:GFP transgenic zebrafish larvae at 4 dpf by piercing the optic tectum with a fine metal pin. At 2 xxx post injury hpi  sham and injured larvae were anaesthesised  larval heads were transected  the tissue was homogenised  and GFP+ cells were isolated from the resulting cell suspension using FACS. Sorted cells from about 180 larvae were used per sample. Six samples each were generated for 'Sham' and 'Injury' experimental conditions.,RNA was extracted from sorted cells using a RNeasy Plus Micro kit Qiagen. RNA was reverse transcribed and amplified using an Ovation RNA Seq System V2 NuGEN with an input of at least 500 ng RNA per sample. Libraries were prepared using a manual TruSeq DNA Nano gel free library kit Illumina.,,age:4 dpf,GSM4186872,GSM4186872: Sham 3; Danio rerio; RNA Seq,GSM4186872,,1,RNA was extracted from sorted cells using a RNeasy Plus Micro kit Qiagen. RNA was reverse transcribed and amplified using an Ovation RNA Seq System V2 NuGEN with an input of at least 500 ng RNA per sample. Libraries were prepared using a manual TruSeq DNA Nano gel free library kit Illumina.,GEO Accession:GSM4186872,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP231168,,,180809_A00291_0059_BH3FLKDRXX_2_11398HL0003L01_1.fastq.gz 180809_A00291_0059_BH3FLKDRXX_2_11398HL0003L01_2.fastq.gz,fastq fastq,3393847300.0,33938473.0,GSM4186872 r1,0:50 1:50,A:891770304;C:744780247;G:797806720;T:959255404;N:234625,50,50,,,891770304,744780247,797806720,959255404,234625,SRX7199559,SRS5705114,SRA1000323,GEO,"Centre for Discovery Brain Sciences, University of Edinburgh",2,0.84784,0.82366,0.23636,0.23442,0.7651,0.77344,0.52664,0.52603,50,50,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,United Kingdom,2019-11-21,Larval,Larval,Blood,Hematopoietic System
55493,SRR10510887,SRX7199558,SRS5705113,SRP231168,PRJNA591000,RNA seq analysis of transcriptomic changes in macrophage lineage cells post acute neural injury in larval zebrafish,GSE140810,Transcriptome Analysis,Both brain resident microglia and peripheral macrophages are important cellular effectors of the inflammatory response to neural injury. They respond to neural injury by secreting a wide range of effector molecules including cytokines  chemokines and neurotrophic factors. To identify additional secreted signalling molecules  we used RNA seq gene expression profiling to detect changes in the transcriptome of macrophage lineage cells post acute neural injury in larval zebrafish. GO term analysis was then used to analyse the list of differentially expressed genes and identify secreted signalling molecules among them. Overall design: The transcriptomes of FACS purified macrophage lineage cells from mpeg1:GFP transgenic zebrafish larvae with or without xxx injury were compared.,,pubmed:32366533,,Sham 2,GSM4186871,,tissue:Macrophage lineage cells|age:4 dpf,Sham 2,Reads were trimmed using Cutadapt version cutadapt 1.9.dev2. Reads were trimmed for quality at the 3’ end using a quality threshold of 30 and for adapter sequences of the TruSeq DNA Nano kit AGATCGGAAGAGC. Reads post trimming were required to have a minimum length of 35. The reference used for mapping was the Danio rerio GRCz10 genome from Ensembl. The annotation used for counting was the standard GTF format annotation for that reference annotation version 84. Reads were aligned to the reference genome using STAR version 2.5.2b specifying paired end reads and the option   outSAMtype BAM Unsorted. All other parameters were left at default. Reads were assigned to features of type ‘exon’ in the input annotation grouped by gene id in the reference genome using featureCounts version 1.5.1. Strandness was set to ‘reverse’ and a minimum alignment quality of 10 was specified. Gene names and other fields were derived from input annotation and added to the count/expression matrices. The raw counts table was filtered to remove genes consisting predominantly of near zero counts  filtering on counts per million CPM to avoid artefacts due to library depth. Specifically  a row of the expression matrix was required to have values greater than 0.1 in at least 3 samples  corresponding to the smallest sample group as defined by Group  once any samples were removed where applicable. Reads were normalised using the weighted trimmed mean of M values method  passing ‘TMM’ as the method to the calcNormFactors method of edgeR. A principal components analysis was undertaken on normalised and filtered expression data to explore observed patterns with respect to experimental factors. The cumulative proportion of variance associated with each factor was used to study the level of structure in the data  while associations between continuous value ranges in principal components and categorical experimental factors was assessed with an ANOVA test. Three samples Injury 3  Injury 5 and Injury 6 were identified as having high duplication rate and low mapping rate during bioinformatics QC. The high levels of variation in these three samples caused signal from the remaining samples to be overwhelmed  and it was clear that inclusion of the poor quality samples would negatively affect the results of the analysis. In summary samples Injury 3  Injury 5 and Injury 6 were removed  and filtering and normalisation re performed  prior to generation of subsequent plots and downstream analysis. Differential analysis was carried out with edgeR version 3.20.1. Fold changes were estimated as per the default behaviour of edgeR  to avoid artefacts which occur with empirical calculation. Statistical assessment of differential expression was carried out with the quasi likelihood QL F test. Genome build: GRCz10 Supplementary files format and content: A comma separated value file of normalised gene wise counts  gene wise differential expression log fold changes and false discovery rates for every sample passed to downstream analysis.,Macrophage lineage cells,Neural injury was induced in mpeg1:GFP transgenic zebrafish larvae at 4 dpf by piercing the optic tectum with a fine metal pin. At 2 xxx post injury hpi  sham and injured larvae were anaesthesised  larval heads were transected  the tissue was homogenised  and GFP+ cells were isolated from the resulting cell suspension using FACS. Sorted cells from about 180 larvae were used per sample. Six samples each were generated for 'Sham' and 'Injury' experimental conditions.,RNA was extracted from sorted cells using a RNeasy Plus Micro kit Qiagen. RNA was reverse transcribed and amplified using an Ovation RNA Seq System V2 NuGEN with an input of at least 500 ng RNA per sample. Libraries were prepared using a manual TruSeq DNA Nano gel free library kit Illumina.,,age:4 dpf,GSM4186871,GSM4186871: Sham 2; Danio rerio; RNA Seq,GSM4186871,,1,RNA was extracted from sorted cells using a RNeasy Plus Micro kit Qiagen. RNA was reverse transcribed and amplified using an Ovation RNA Seq System V2 NuGEN with an input of at least 500 ng RNA per sample. Libraries were prepared using a manual TruSeq DNA Nano gel free library kit Illumina.,GEO Accession:GSM4186871,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP231168,,,180809_A00291_0059_BH3FLKDRXX_2_11398HL0008L01_1.fastq.gz 180809_A00291_0059_BH3FLKDRXX_2_11398HL0008L01_2.fastq.gz,fastq fastq,3597238000.0,35972380.0,GSM4186871 r1,0:50 1:50,A:971087314;C:774572159;G:820049074;T:1031281870;N:247583,50,50,,,971087314,774572159,820049074,1031281870,247583,SRX7199558,SRS5705113,SRA1000323,GEO,"Centre for Discovery Brain Sciences, University of Edinburgh",2,0.85164,0.83175,0.26819,0.26552,0.75621,0.76378,0.52787,0.53623,50,50,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,United Kingdom,2019-11-21,Larval,Larval,Blood,Hematopoietic System
55494,SRR10510886,SRX7199557,SRS5705112,SRP231168,PRJNA591000,RNA seq analysis of transcriptomic changes in macrophage lineage cells post acute neural injury in larval zebrafish,GSE140810,Transcriptome Analysis,Both brain resident microglia and peripheral macrophages are important cellular effectors of the inflammatory response to neural injury. They respond to neural injury by secreting a wide range of effector molecules including cytokines  chemokines and neurotrophic factors. To identify additional secreted signalling molecules  we used RNA seq gene expression profiling to detect changes in the transcriptome of macrophage lineage cells post acute neural injury in larval zebrafish. GO term analysis was then used to analyse the list of differentially expressed genes and identify secreted signalling molecules among them. Overall design: The transcriptomes of FACS purified macrophage lineage cells from mpeg1:GFP transgenic zebrafish larvae with or without xxx injury were compared.,,pubmed:32366533,,Sham 1,GSM4186870,,tissue:Macrophage lineage cells|age:4 dpf,Sham 1,Reads were trimmed using Cutadapt version cutadapt 1.9.dev2. Reads were trimmed for quality at the 3’ end using a quality threshold of 30 and for adapter sequences of the TruSeq DNA Nano kit AGATCGGAAGAGC. Reads post trimming were required to have a minimum length of 35. The reference used for mapping was the Danio rerio GRCz10 genome from Ensembl. The annotation used for counting was the standard GTF format annotation for that reference annotation version 84. Reads were aligned to the reference genome using STAR version 2.5.2b specifying paired end reads and the option   outSAMtype BAM Unsorted. All other parameters were left at default. Reads were assigned to features of type ‘exon’ in the input annotation grouped by gene id in the reference genome using featureCounts version 1.5.1. Strandness was set to ‘reverse’ and a minimum alignment quality of 10 was specified. Gene names and other fields were derived from input annotation and added to the count/expression matrices. The raw counts table was filtered to remove genes consisting predominantly of near zero counts  filtering on counts per million CPM to avoid artefacts due to library depth. Specifically  a row of the expression matrix was required to have values greater than 0.1 in at least 3 samples  corresponding to the smallest sample group as defined by Group  once any samples were removed where applicable. Reads were normalised using the weighted trimmed mean of M values method  passing ‘TMM’ as the method to the calcNormFactors method of edgeR. A principal components analysis was undertaken on normalised and filtered expression data to explore observed patterns with respect to experimental factors. The cumulative proportion of variance associated with each factor was used to study the level of structure in the data  while associations between continuous value ranges in principal components and categorical experimental factors was assessed with an ANOVA test. Three samples Injury 3  Injury 5 and Injury 6 were identified as having high duplication rate and low mapping rate during bioinformatics QC. The high levels of variation in these three samples caused signal from the remaining samples to be overwhelmed  and it was clear that inclusion of the poor quality samples would negatively affect the results of the analysis. In summary samples Injury 3  Injury 5 and Injury 6 were removed  and filtering and normalisation re performed  prior to generation of subsequent plots and downstream analysis. Differential analysis was carried out with edgeR version 3.20.1. Fold changes were estimated as per the default behaviour of edgeR  to avoid artefacts which occur with empirical calculation. Statistical assessment of differential expression was carried out with the quasi likelihood QL F test. Genome build: GRCz10 Supplementary files format and content: A comma separated value file of normalised gene wise counts  gene wise differential expression log fold changes and false discovery rates for every sample passed to downstream analysis.,Macrophage lineage cells,Neural injury was induced in mpeg1:GFP transgenic zebrafish larvae at 4 dpf by piercing the optic tectum with a fine metal pin. At 2 xxx post injury hpi  sham and injured larvae were anaesthesised  larval heads were transected  the tissue was homogenised  and GFP+ cells were isolated from the resulting cell suspension using FACS. Sorted cells from about 180 larvae were used per sample. Six samples each were generated for 'Sham' and 'Injury' experimental conditions.,RNA was extracted from sorted cells using a RNeasy Plus Micro kit Qiagen. RNA was reverse transcribed and amplified using an Ovation RNA Seq System V2 NuGEN with an input of at least 500 ng RNA per sample. Libraries were prepared using a manual TruSeq DNA Nano gel free library kit Illumina.,,age:4 dpf,GSM4186870,GSM4186870: Sham 1; Danio rerio; RNA Seq,GSM4186870,,1,RNA was extracted from sorted cells using a RNeasy Plus Micro kit Qiagen. RNA was reverse transcribed and amplified using an Ovation RNA Seq System V2 NuGEN with an input of at least 500 ng RNA per sample. Libraries were prepared using a manual TruSeq DNA Nano gel free library kit Illumina.,GEO Accession:GSM4186870,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP231168,,,180809_A00291_0059_BH3FLKDRXX_2_11398HL0001L01_1.fastq.gz 180809_A00291_0059_BH3FLKDRXX_2_11398HL0001L01_2.fastq.gz,fastq fastq,3476774400.0,34767744.0,GSM4186870 r1,0:50 1:50,A:916708367;C:758990814;G:811017343;T:989817555;N:240321,50,50,,,916708367,758990814,811017343,989817555,240321,SRX7199557,SRS5705112,SRA1000323,GEO,"Centre for Discovery Brain Sciences, University of Edinburgh",2,0.84104,0.81935,0.24072,0.23754,0.75515,0.76347,0.52881,0.53924,50,50,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,United Kingdom,2019-11-21,Larval,Larval,Blood,Hematopoietic System
58407,SRR11309042,SRX7913591,SRS6320433,SRP252869,PRJNA612697,RNA seq of hematopoietic stem and progenitor cells from 40 hpf ddx41 mutant and sibling zebrafish,GSE146995,Transcriptome Analysis,The purpose of the experiment was to define the gene expression and splicing alterations occurring when the levels of dead box helicase 41 are lowered in embryonic zebrafish. Results provide insight the role of Ddx41 in hematopoietic development. Overall design: mRNA profiling of cd41 positive hematopoietic stem and progenitor cells isolated from 40 hpf ddx41 mutant and sibling zebrafish using Illumina NovaSeq. Three samples were sequenced for each genotype.,,pubmed:33651979,,cd41gfp WT3,GSM4411870,,tissue:hematopoietic stem and progenitor cells|develpmental stage:40 hpf,cd41gfp WT3,basecalling was done with the Picard module IlluminaBasecallsToFastq Reads were trimmed using TRIM GALORE software to check for quality of 150bp reads. These paired end reads were mapped using STAR aligner version 2.4.2a to the reference genome. Differential expression analysis was done using DESeq2 via DEApp. To calculate FPKM  Cufflinks version 2.2.1 was used. Genome build: GRcz10 Supplementary files format and content: tab delimited text file include gene counts for each sample,hematopoietic stem and progenitor cells,,cd41 positive cells were isolated from zebrafish embryos. RNA was extracted with the quick RNA microprep Zymo. Libraries were made at BGI following their low input RNA protocol.,,develpmental stage:40 hpf,GSM4411870,GSM4411870: cd41gfp WT3; Danio rerio; RNA Seq,GSM4411870,,1,cd41 positive cells were isolated from zebrafish embryos. RNA was extracted with the quick RNA microprep Zymo. Libraries were made at BGI following their low input RNA protocol.,GEO Accession:GSM4411870,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP252869,,,cd41gfp_WT3_2.fq.gz cd41gfp_WT3_1.fq.gz,fastq fastq,11085766500.0,36952555.0,GSM4411870 r1,0:150 1:150,A:2992020230;C:2573519486;G:2581891304;T:2938153427;N:182053,150,150,,,2992020230,2573519486,2581891304,2938153427,182053,SRX7913591,SRS6320433,SRA1055135,GEO,Albert Einstein College of Medicine,2,0.77434,0.77183,0.20553,0.20573,0.77171,0.77922,0.5109,0.495,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2020-03-15,Pharyngula,Embryo,Blood,Hematopoietic System
58408,SRR11309041,SRX7913590,SRS6320432,SRP252869,PRJNA612697,RNA seq of hematopoietic stem and progenitor cells from 40 hpf ddx41 mutant and sibling zebrafish,GSE146995,Transcriptome Analysis,The purpose of the experiment was to define the gene expression and splicing alterations occurring when the levels of dead box helicase 41 are lowered in embryonic zebrafish. Results provide insight the role of Ddx41 in hematopoietic development. Overall design: mRNA profiling of cd41 positive hematopoietic stem and progenitor cells isolated from 40 hpf ddx41 mutant and sibling zebrafish using Illumina NovaSeq. Three samples were sequenced for each genotype.,,pubmed:33651979,,cd41gfp WT2,GSM4411869,,tissue:hematopoietic stem and progenitor cells|develpmental stage:40 hpf,cd41gfp WT2,basecalling was done with the Picard module IlluminaBasecallsToFastq Reads were trimmed using TRIM GALORE software to check for quality of 150bp reads. These paired end reads were mapped using STAR aligner version 2.4.2a to the reference genome. Differential expression analysis was done using DESeq2 via DEApp. To calculate FPKM  Cufflinks version 2.2.1 was used. Genome build: GRcz10 Supplementary files format and content: tab delimited text file include gene counts for each sample,hematopoietic stem and progenitor cells,,cd41 positive cells were isolated from zebrafish embryos. RNA was extracted with the quick RNA microprep Zymo. Libraries were made at BGI following their low input RNA protocol.,,develpmental stage:40 hpf,GSM4411869,GSM4411869: cd41gfp WT2; Danio rerio; RNA Seq,GSM4411869,,1,cd41 positive cells were isolated from zebrafish embryos. RNA was extracted with the quick RNA microprep Zymo. Libraries were made at BGI following their low input RNA protocol.,GEO Accession:GSM4411869,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP252869,,,cd41gfp_WT2_1.fq.gz cd41gfp_WT2_2.fq.gz,fastq fastq,11221423200.0,37404744.0,GSM4411869 r1,0:150 1:150,A:2921284710;C:2714470786;G:2708278380;T:2877145192;N:244132,150,150,,,2921284710,2714470786,2708278380,2877145192,244132,SRX7913590,SRS6320432,SRA1055135,GEO,Albert Einstein College of Medicine,2,0.75116,0.75065,0.18086,0.18146,0.79586,0.80016,0.52492,0.52828,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2020-03-15,Pharyngula,Embryo,Blood,Hematopoietic System
58409,SRR11309040,SRX7913589,SRS6320431,SRP252869,PRJNA612697,RNA seq of hematopoietic stem and progenitor cells from 40 hpf ddx41 mutant and sibling zebrafish,GSE146995,Transcriptome Analysis,The purpose of the experiment was to define the gene expression and splicing alterations occurring when the levels of dead box helicase 41 are lowered in embryonic zebrafish. Results provide insight the role of Ddx41 in hematopoietic development. Overall design: mRNA profiling of cd41 positive hematopoietic stem and progenitor cells isolated from 40 hpf ddx41 mutant and sibling zebrafish using Illumina NovaSeq. Three samples were sequenced for each genotype.,,pubmed:33651979,,cd41gfp WT1,GSM4411868,,tissue:hematopoietic stem and progenitor cells|develpmental stage:40 hpf,cd41gfp WT1,basecalling was done with the Picard module IlluminaBasecallsToFastq Reads were trimmed using TRIM GALORE software to check for quality of 150bp reads. These paired end reads were mapped using STAR aligner version 2.4.2a to the reference genome. Differential expression analysis was done using DESeq2 via DEApp. To calculate FPKM  Cufflinks version 2.2.1 was used. Genome build: GRcz10 Supplementary files format and content: tab delimited text file include gene counts for each sample,hematopoietic stem and progenitor cells,,cd41 positive cells were isolated from zebrafish embryos. RNA was extracted with the quick RNA microprep Zymo. Libraries were made at BGI following their low input RNA protocol.,,develpmental stage:40 hpf,GSM4411868,GSM4411868: cd41gfp WT1; Danio rerio; RNA Seq,GSM4411868,,1,cd41 positive cells were isolated from zebrafish embryos. RNA was extracted with the quick RNA microprep Zymo. Libraries were made at BGI following their low input RNA protocol.,GEO Accession:GSM4411868,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP252869,,,cd41gfp_WT1_1.fq.gz cd41gfp_WT1_2.fq.gz,fastq fastq,11115852900.0,37052843.0,GSM4411868 r1,0:150 1:150,A:3004371197;C:2577587578;G:2575472481;T:2958199318;N:222326,150,150,,,3004371197,2577587578,2575472481,2958199318,222326,SRX7913589,SRS6320431,SRA1055135,GEO,Albert Einstein College of Medicine,2,0.76528,0.76415,0.19581,0.19637,0.77039,0.77579,0.65251,0.64941,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2020-03-15,Pharyngula,Embryo,Blood,Hematopoietic System
58410,SRR11309039,SRX7913588,SRS6320430,SRP252869,PRJNA612697,RNA seq of hematopoietic stem and progenitor cells from 40 hpf ddx41 mutant and sibling zebrafish,GSE146995,Transcriptome Analysis,The purpose of the experiment was to define the gene expression and splicing alterations occurring when the levels of dead box helicase 41 are lowered in embryonic zebrafish. Results provide insight the role of Ddx41 in hematopoietic development. Overall design: mRNA profiling of cd41 positive hematopoietic stem and progenitor cells isolated from 40 hpf ddx41 mutant and sibling zebrafish using Illumina NovaSeq. Three samples were sequenced for each genotype.,,pubmed:33651979,,cd41gfp mut3,GSM4411867,,tissue:hematopoietic stem and progenitor cells|develpmental stage:40 hpf mutant,cd41gfp mut3,basecalling was done with the Picard module IlluminaBasecallsToFastq Reads were trimmed using TRIM GALORE software to check for quality of 150bp reads. These paired end reads were mapped using STAR aligner version 2.4.2a to the reference genome. Differential expression analysis was done using DESeq2 via DEApp. To calculate FPKM  Cufflinks version 2.2.1 was used. Genome build: GRcz10 Supplementary files format and content: tab delimited text file include gene counts for each sample,hematopoietic stem and progenitor cells,,cd41 positive cells were isolated from zebrafish embryos. RNA was extracted with the quick RNA microprep Zymo. Libraries were made at BGI following their low input RNA protocol.,,develpmental stage:40 hpf mutant,GSM4411867,GSM4411867: cd41gfp mut3; Danio rerio; RNA Seq,GSM4411867,,1,cd41 positive cells were isolated from zebrafish embryos. RNA was extracted with the quick RNA microprep Zymo. Libraries were made at BGI following their low input RNA protocol.,GEO Accession:GSM4411867,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP252869,,,cd41gfp_mut3_2.fq.gz cd41gfp_mut3_1.fq.gz,fastq fastq,11157315900.0,37191053.0,GSM4411867 r1,0:150 1:150,A:2980738665;C:2622591667;G:2625477229;T:2928292016;N:216323,150,150,,,2980738665,2622591667,2625477229,2928292016,216323,SRX7913588,SRS6320430,SRA1055135,GEO,Albert Einstein College of Medicine,2,0.77032,0.76857,0.22483,0.22518,0.78685,0.79226,0.64484,0.52439,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2020-03-15,Pharyngula,Embryo,Blood,Hematopoietic System
58411,SRR11309038,SRX7913587,SRS6320429,SRP252869,PRJNA612697,RNA seq of hematopoietic stem and progenitor cells from 40 hpf ddx41 mutant and sibling zebrafish,GSE146995,Transcriptome Analysis,The purpose of the experiment was to define the gene expression and splicing alterations occurring when the levels of dead box helicase 41 are lowered in embryonic zebrafish. Results provide insight the role of Ddx41 in hematopoietic development. Overall design: mRNA profiling of cd41 positive hematopoietic stem and progenitor cells isolated from 40 hpf ddx41 mutant and sibling zebrafish using Illumina NovaSeq. Three samples were sequenced for each genotype.,,pubmed:33651979,,cd41gfp mut2,GSM4411866,,tissue:hematopoietic stem and progenitor cells|develpmental stage:40 hpf mutant,cd41gfp mut2,basecalling was done with the Picard module IlluminaBasecallsToFastq Reads were trimmed using TRIM GALORE software to check for quality of 150bp reads. These paired end reads were mapped using STAR aligner version 2.4.2a to the reference genome. Differential expression analysis was done using DESeq2 via DEApp. To calculate FPKM  Cufflinks version 2.2.1 was used. Genome build: GRcz10 Supplementary files format and content: tab delimited text file include gene counts for each sample,hematopoietic stem and progenitor cells,,cd41 positive cells were isolated from zebrafish embryos. RNA was extracted with the quick RNA microprep Zymo. Libraries were made at BGI following their low input RNA protocol.,,develpmental stage:40 hpf mutant,GSM4411866,GSM4411866: cd41gfp mut2; Danio rerio; RNA Seq,GSM4411866,,1,cd41 positive cells were isolated from zebrafish embryos. RNA was extracted with the quick RNA microprep Zymo. Libraries were made at BGI following their low input RNA protocol.,GEO Accession:GSM4411866,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP252869,,,cd41gfp_mut2_1.fq.gz cd41gfp_mut2_2.fq.gz,fastq fastq,10547871900.0,35159573.0,GSM4411866 r1,0:150 1:150,A:2823130170;C:2469329724;G:2474038085;T:2781202013;N:171908,150,150,,,2823130170,2469329724,2474038085,2781202013,171908,SRX7913587,SRS6320429,SRA1055135,GEO,Albert Einstein College of Medicine,2,0.77081,0.76762,0.19951,0.20063,0.78518,0.7905,0.62792,0.62645,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2020-03-15,Pharyngula,Embryo,Blood,Hematopoietic System
58412,SRR11309037,SRX7913586,SRS6320428,SRP252869,PRJNA612697,RNA seq of hematopoietic stem and progenitor cells from 40 hpf ddx41 mutant and sibling zebrafish,GSE146995,Transcriptome Analysis,The purpose of the experiment was to define the gene expression and splicing alterations occurring when the levels of dead box helicase 41 are lowered in embryonic zebrafish. Results provide insight the role of Ddx41 in hematopoietic development. Overall design: mRNA profiling of cd41 positive hematopoietic stem and progenitor cells isolated from 40 hpf ddx41 mutant and sibling zebrafish using Illumina NovaSeq. Three samples were sequenced for each genotype.,,pubmed:33651979,,cd41gfp mut1,GSM4411865,,tissue:hematopoietic stem and progenitor cells|develpmental stage:40 hpf mutant,cd41gfp mut1,basecalling was done with the Picard module IlluminaBasecallsToFastq Reads were trimmed using TRIM GALORE software to check for quality of 150bp reads. These paired end reads were mapped using STAR aligner version 2.4.2a to the reference genome. Differential expression analysis was done using DESeq2 via DEApp. To calculate FPKM  Cufflinks version 2.2.1 was used. Genome build: GRcz10 Supplementary files format and content: tab delimited text file include gene counts for each sample,hematopoietic stem and progenitor cells,,cd41 positive cells were isolated from zebrafish embryos. RNA was extracted with the quick RNA microprep Zymo. Libraries were made at BGI following their low input RNA protocol.,,develpmental stage:40 hpf mutant,GSM4411865,GSM4411865: cd41gfp mut1; Danio rerio; RNA Seq,GSM4411865,,1,cd41 positive cells were isolated from zebrafish embryos. RNA was extracted with the quick RNA microprep Zymo. Libraries were made at BGI following their low input RNA protocol.,GEO Accession:GSM4411865,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP252869,,,cd41gfp_mut1_2.fq.gz cd41gfp_mut1_1.fq.gz,fastq fastq,11189402700.0,37298009.0,GSM4411865 r1,0:150 1:150,A:2871209944;C:2750231891;G:2743649245;T:2824098453;N:213167,150,150,,,2871209944,2750231891,2743649245,2824098453,213167,SRX7913586,SRS6320428,SRA1055135,GEO,Albert Einstein College of Medicine,2,0.74106,0.73935,0.17858,0.18025,0.80574,0.81231,0.60677,0.65263,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2020-03-15,Pharyngula,Embryo,Blood,Hematopoietic System
59146,SRR11700449,SRX8259900,SRS6601868,SRP260213,PRJNA630667,RNAseq expression analysis of FACS sorted macrophages from cxcr3.2 mutant and wt zebrafish larvae,GSE149942,Transcriptome Analysis,The zebrafish Cxcr3.2 is a functional homolog of the human chemokine receptor CXCR3. Zebrafish macrophages lacking this receptor have impaired motility and a rounded shape compared to their wildtype counterparts. To investigate the effects of cxcr3.2 mutation on the transcriptional profile of macrophages  we sorted macrophages from zebrafish larvae lacking a functional cxcr3.2 and compared their transcriptome to that of macrophages from wildtype larvae. Mutant and wildtype macrophages could be clearly distinguished based on the overall differential expression profiles. Classification of genes by compartment showed that peroxisomal  lysosomal and Golgi related genes were most frequently up regulated. Moreover  lysosomal and Golgi related terms were significantly differentially represented in Gene Ontology and KEGG enrichment analysis. Of note  several lysosomal markers  including acidic hydrolases and voltage ATPases were consistently upregulated in cxcr3.2 mutant macrophages  indicating that cxcr3.2 mediated chemokine signaling is tightly connected to the regulation of lysosomal function. Overall design: 3 independent groups of 150 200 5dpf Tg mpeg1: mCherryF cxcr3.2 /  and cxcr3.2+/+ larvae were dissociated and red fluorescent macrophages were FACS sorted. RNA was extracted  retrotranscribed into cDNA and amplified using the SMARTer® Universal Low Input RNA Kit for Sequencing Clontech  prior Illumina sequencing.,,pubmed:33852860,,cxcr3.2wt rep3,GSM4518498,,tissue:FACS mpeg1: mCherryF positive cells|age:6 dpf type:macrophage|strain:mpeg1: mCherryF|genotype:cxcr3.2+/+,cxcr3.2wt rep3,Image analysis and base calling was done by the Illumina HCS version 1.15.1 Quality trimmed reads were aligned to the Ensembl zebrafish genome GRCz10 using Bowtie Reads were mapped to zebrafish transcripts using TopHat Genome build: GRCz10 Supplementary files format and content: tab separated value files of read counts for each sample,FACS mpeg1: mCherryF positive cells,,3 independent groups of 150 200 5dpf Tg mpeg1: mCherryF cxcr3.2 /  and cxcr3.2+/+ larvae were dissociated and red fluorescent macrophages were FACS sorted. RNA was extracted using the miRNeasy mini kit Qiagen according to the manufacturers’ instructions. cDNA synthesis and amplification was done using the SMARTer® Universal Low Input RNA Kit for Sequencing Clontech following the manufacturer’s guidelines. Approximately 10 Mreads were obtained  using Illimuna Single Read runs. Reads were then aligned to GRCz10 Danio rerio genome.,,age:6 dpf type:macrophage|strain:mpeg1: mCherryF|genotype:cxcr3.2+/+,GSM4518498,GSM4518498: cxcr3.2wt rep3; Danio rerio; RNA Seq,GSM4518498,,1,3 independent groups of 150 200 5dpf Tg mpeg1: mCherryF cxcr3.2 /  and cxcr3.2+/+ larvae were dissociated and red fluorescent macrophages were FACS sorted. RNA was extracted using the miRNeasy mini kit Qiagen according to the manufacturers' instructions. cDNA synthesis and amplification was done using the SMARTer® Universal Low Input RNA Kit for Sequencing Clontech following the manufacturer's guidelines. Approximately 10 Mreads were obtained  using Illimuna Single Read runs. Reads were then aligned to GRCz10 Danio rerio genome.,GEO Accession:GSM4518498,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP260213,,,wt3_1.fastq.gz,fastq,173026017.0,3392667.0,GSM4518498 r1,0:51,A:50003437;C:34139662;G:34317418;T:54513188;N:52312,51,,,,50003437,34139662,34317418,54513188,52312,SRX8259900,SRS6601868,SRA1072497,GEO,LSHTM,1,0.80078,,0.22125,,0.78788,,0.53444,,51,,B,,usable mapping rate,illumina,hiseq_era,full_length,cdna_unspecified,smarter,bulk,unknown,unknown,,United Kingdom,2020-05-06,Larval,Larval,Blood,Hematopoietic System
59147,SRR11700450,SRX8259900,SRS6601868,SRP260213,PRJNA630667,RNAseq expression analysis of FACS sorted macrophages from cxcr3.2 mutant and wt zebrafish larvae,GSE149942,Transcriptome Analysis,The zebrafish Cxcr3.2 is a functional homolog of the human chemokine receptor CXCR3. Zebrafish macrophages lacking this receptor have impaired motility and a rounded shape compared to their wildtype counterparts. To investigate the effects of cxcr3.2 mutation on the transcriptional profile of macrophages  we sorted macrophages from zebrafish larvae lacking a functional cxcr3.2 and compared their transcriptome to that of macrophages from wildtype larvae. Mutant and wildtype macrophages could be clearly distinguished based on the overall differential expression profiles. Classification of genes by compartment showed that peroxisomal  lysosomal and Golgi related genes were most frequently up regulated. Moreover  lysosomal and Golgi related terms were significantly differentially represented in Gene Ontology and KEGG enrichment analysis. Of note  several lysosomal markers  including acidic hydrolases and voltage ATPases were consistently upregulated in cxcr3.2 mutant macrophages  indicating that cxcr3.2 mediated chemokine signaling is tightly connected to the regulation of lysosomal function. Overall design: 3 independent groups of 150 200 5dpf Tg mpeg1: mCherryF cxcr3.2 /  and cxcr3.2+/+ larvae were dissociated and red fluorescent macrophages were FACS sorted. RNA was extracted  retrotranscribed into cDNA and amplified using the SMARTer® Universal Low Input RNA Kit for Sequencing Clontech  prior Illumina sequencing.,,pubmed:33852860,,cxcr3.2wt rep3,GSM4518498,,tissue:FACS mpeg1: mCherryF positive cells|age:6 dpf type:macrophage|strain:mpeg1: mCherryF|genotype:cxcr3.2+/+,cxcr3.2wt rep3,Image analysis and base calling was done by the Illumina HCS version 1.15.1 Quality trimmed reads were aligned to the Ensembl zebrafish genome GRCz10 using Bowtie Reads were mapped to zebrafish transcripts using TopHat Genome build: GRCz10 Supplementary files format and content: tab separated value files of read counts for each sample,FACS mpeg1: mCherryF positive cells,,3 independent groups of 150 200 5dpf Tg mpeg1: mCherryF cxcr3.2 /  and cxcr3.2+/+ larvae were dissociated and red fluorescent macrophages were FACS sorted. RNA was extracted using the miRNeasy mini kit Qiagen according to the manufacturers’ instructions. cDNA synthesis and amplification was done using the SMARTer® Universal Low Input RNA Kit for Sequencing Clontech following the manufacturer’s guidelines. Approximately 10 Mreads were obtained  using Illimuna Single Read runs. Reads were then aligned to GRCz10 Danio rerio genome.,,age:6 dpf type:macrophage|strain:mpeg1: mCherryF|genotype:cxcr3.2+/+,GSM4518498,GSM4518498: cxcr3.2wt rep3; Danio rerio; RNA Seq,GSM4518498,,1,3 independent groups of 150 200 5dpf Tg mpeg1: mCherryF cxcr3.2 /  and cxcr3.2+/+ larvae were dissociated and red fluorescent macrophages were FACS sorted. RNA was extracted using the miRNeasy mini kit Qiagen according to the manufacturers' instructions. cDNA synthesis and amplification was done using the SMARTer® Universal Low Input RNA Kit for Sequencing Clontech following the manufacturer's guidelines. Approximately 10 Mreads were obtained  using Illimuna Single Read runs. Reads were then aligned to GRCz10 Danio rerio genome.,GEO Accession:GSM4518498,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP260213,,,wt3_2.fastq.gz,fastq,173719362.0,3406262.0,GSM4518498 r2,0:51,A:50217431;C:34289412;G:34447800;T:54729217;N:35502,51,,,,50217431,34289412,34447800,54729217,35502,SRX8259900,SRS6601868,SRA1072497,GEO,LSHTM,1,0.8033,,0.2226,,0.78498,,0.53485,,51,,B,,usable mapping rate,illumina,hiseq_era,full_length,cdna_unspecified,smarter,bulk,unknown,unknown,,United Kingdom,2020-05-06,Larval,Larval,Blood,Hematopoietic System
59148,SRR11700451,SRX8259900,SRS6601868,SRP260213,PRJNA630667,RNAseq expression analysis of FACS sorted macrophages from cxcr3.2 mutant and wt zebrafish larvae,GSE149942,Transcriptome Analysis,The zebrafish Cxcr3.2 is a functional homolog of the human chemokine receptor CXCR3. Zebrafish macrophages lacking this receptor have impaired motility and a rounded shape compared to their wildtype counterparts. To investigate the effects of cxcr3.2 mutation on the transcriptional profile of macrophages  we sorted macrophages from zebrafish larvae lacking a functional cxcr3.2 and compared their transcriptome to that of macrophages from wildtype larvae. Mutant and wildtype macrophages could be clearly distinguished based on the overall differential expression profiles. Classification of genes by compartment showed that peroxisomal  lysosomal and Golgi related genes were most frequently up regulated. Moreover  lysosomal and Golgi related terms were significantly differentially represented in Gene Ontology and KEGG enrichment analysis. Of note  several lysosomal markers  including acidic hydrolases and voltage ATPases were consistently upregulated in cxcr3.2 mutant macrophages  indicating that cxcr3.2 mediated chemokine signaling is tightly connected to the regulation of lysosomal function. Overall design: 3 independent groups of 150 200 5dpf Tg mpeg1: mCherryF cxcr3.2 /  and cxcr3.2+/+ larvae were dissociated and red fluorescent macrophages were FACS sorted. RNA was extracted  retrotranscribed into cDNA and amplified using the SMARTer® Universal Low Input RNA Kit for Sequencing Clontech  prior Illumina sequencing.,,pubmed:33852860,,cxcr3.2wt rep3,GSM4518498,,tissue:FACS mpeg1: mCherryF positive cells|age:6 dpf type:macrophage|strain:mpeg1: mCherryF|genotype:cxcr3.2+/+,cxcr3.2wt rep3,Image analysis and base calling was done by the Illumina HCS version 1.15.1 Quality trimmed reads were aligned to the Ensembl zebrafish genome GRCz10 using Bowtie Reads were mapped to zebrafish transcripts using TopHat Genome build: GRCz10 Supplementary files format and content: tab separated value files of read counts for each sample,FACS mpeg1: mCherryF positive cells,,3 independent groups of 150 200 5dpf Tg mpeg1: mCherryF cxcr3.2 /  and cxcr3.2+/+ larvae were dissociated and red fluorescent macrophages were FACS sorted. RNA was extracted using the miRNeasy mini kit Qiagen according to the manufacturers’ instructions. cDNA synthesis and amplification was done using the SMARTer® Universal Low Input RNA Kit for Sequencing Clontech following the manufacturer’s guidelines. Approximately 10 Mreads were obtained  using Illimuna Single Read runs. Reads were then aligned to GRCz10 Danio rerio genome.,,age:6 dpf type:macrophage|strain:mpeg1: mCherryF|genotype:cxcr3.2+/+,GSM4518498,GSM4518498: cxcr3.2wt rep3; Danio rerio; RNA Seq,GSM4518498,,1,3 independent groups of 150 200 5dpf Tg mpeg1: mCherryF cxcr3.2 /  and cxcr3.2+/+ larvae were dissociated and red fluorescent macrophages were FACS sorted. RNA was extracted using the miRNeasy mini kit Qiagen according to the manufacturers' instructions. cDNA synthesis and amplification was done using the SMARTer® Universal Low Input RNA Kit for Sequencing Clontech following the manufacturer's guidelines. Approximately 10 Mreads were obtained  using Illimuna Single Read runs. Reads were then aligned to GRCz10 Danio rerio genome.,GEO Accession:GSM4518498,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP260213,,,wt3_3.fastq.gz,fastq,117503031.0,2303981.0,GSM4518498 r3,0:51,A:33926847;C:22984117;G:23302421;T:37279310;N:10336,51,,,,33926847,22984117,23302421,37279310,10336,SRX8259900,SRS6601868,SRA1072497,GEO,LSHTM,1,0.76501,,0.22042,,0.79912,,0.54263,,51,,B,,usable mapping rate,illumina,hiseq_era,full_length,cdna_unspecified,smarter,bulk,unknown,unknown,,United Kingdom,2020-05-06,Larval,Larval,Blood,Hematopoietic System
59149,SRR11700452,SRX8259900,SRS6601868,SRP260213,PRJNA630667,RNAseq expression analysis of FACS sorted macrophages from cxcr3.2 mutant and wt zebrafish larvae,GSE149942,Transcriptome Analysis,The zebrafish Cxcr3.2 is a functional homolog of the human chemokine receptor CXCR3. Zebrafish macrophages lacking this receptor have impaired motility and a rounded shape compared to their wildtype counterparts. To investigate the effects of cxcr3.2 mutation on the transcriptional profile of macrophages  we sorted macrophages from zebrafish larvae lacking a functional cxcr3.2 and compared their transcriptome to that of macrophages from wildtype larvae. Mutant and wildtype macrophages could be clearly distinguished based on the overall differential expression profiles. Classification of genes by compartment showed that peroxisomal  lysosomal and Golgi related genes were most frequently up regulated. Moreover  lysosomal and Golgi related terms were significantly differentially represented in Gene Ontology and KEGG enrichment analysis. Of note  several lysosomal markers  including acidic hydrolases and voltage ATPases were consistently upregulated in cxcr3.2 mutant macrophages  indicating that cxcr3.2 mediated chemokine signaling is tightly connected to the regulation of lysosomal function. Overall design: 3 independent groups of 150 200 5dpf Tg mpeg1: mCherryF cxcr3.2 /  and cxcr3.2+/+ larvae were dissociated and red fluorescent macrophages were FACS sorted. RNA was extracted  retrotranscribed into cDNA and amplified using the SMARTer® Universal Low Input RNA Kit for Sequencing Clontech  prior Illumina sequencing.,,pubmed:33852860,,cxcr3.2wt rep3,GSM4518498,,tissue:FACS mpeg1: mCherryF positive cells|age:6 dpf type:macrophage|strain:mpeg1: mCherryF|genotype:cxcr3.2+/+,cxcr3.2wt rep3,Image analysis and base calling was done by the Illumina HCS version 1.15.1 Quality trimmed reads were aligned to the Ensembl zebrafish genome GRCz10 using Bowtie Reads were mapped to zebrafish transcripts using TopHat Genome build: GRCz10 Supplementary files format and content: tab separated value files of read counts for each sample,FACS mpeg1: mCherryF positive cells,,3 independent groups of 150 200 5dpf Tg mpeg1: mCherryF cxcr3.2 /  and cxcr3.2+/+ larvae were dissociated and red fluorescent macrophages were FACS sorted. RNA was extracted using the miRNeasy mini kit Qiagen according to the manufacturers’ instructions. cDNA synthesis and amplification was done using the SMARTer® Universal Low Input RNA Kit for Sequencing Clontech following the manufacturer’s guidelines. Approximately 10 Mreads were obtained  using Illimuna Single Read runs. Reads were then aligned to GRCz10 Danio rerio genome.,,age:6 dpf type:macrophage|strain:mpeg1: mCherryF|genotype:cxcr3.2+/+,GSM4518498,GSM4518498: cxcr3.2wt rep3; Danio rerio; RNA Seq,GSM4518498,,1,3 independent groups of 150 200 5dpf Tg mpeg1: mCherryF cxcr3.2 /  and cxcr3.2+/+ larvae were dissociated and red fluorescent macrophages were FACS sorted. RNA was extracted using the miRNeasy mini kit Qiagen according to the manufacturers' instructions. cDNA synthesis and amplification was done using the SMARTer® Universal Low Input RNA Kit for Sequencing Clontech following the manufacturer's guidelines. Approximately 10 Mreads were obtained  using Illimuna Single Read runs. Reads were then aligned to GRCz10 Danio rerio genome.,GEO Accession:GSM4518498,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP260213,,,wt3_4.fastq.gz,fastq,114086745.0,2236995.0,GSM4518498 r4,0:51,A:32945373;C:22224999;G:22487321;T:36409257;N:19795,51,,,,32945373,22224999,22487321,36409257,19795,SRX8259900,SRS6601868,SRA1072497,GEO,LSHTM,1,0.74509,,0.21675,,0.80653,,0.54624,,51,,B,,usable mapping rate,illumina,hiseq_era,full_length,cdna_unspecified,smarter,bulk,unknown,unknown,,United Kingdom,2020-05-06,Larval,Larval,Blood,Hematopoietic System
59150,SRR11700447,SRX8259899,SRS6601867,SRP260213,PRJNA630667,RNAseq expression analysis of FACS sorted macrophages from cxcr3.2 mutant and wt zebrafish larvae,GSE149942,Transcriptome Analysis,The zebrafish Cxcr3.2 is a functional homolog of the human chemokine receptor CXCR3. Zebrafish macrophages lacking this receptor have impaired motility and a rounded shape compared to their wildtype counterparts. To investigate the effects of cxcr3.2 mutation on the transcriptional profile of macrophages  we sorted macrophages from zebrafish larvae lacking a functional cxcr3.2 and compared their transcriptome to that of macrophages from wildtype larvae. Mutant and wildtype macrophages could be clearly distinguished based on the overall differential expression profiles. Classification of genes by compartment showed that peroxisomal  lysosomal and Golgi related genes were most frequently up regulated. Moreover  lysosomal and Golgi related terms were significantly differentially represented in Gene Ontology and KEGG enrichment analysis. Of note  several lysosomal markers  including acidic hydrolases and voltage ATPases were consistently upregulated in cxcr3.2 mutant macrophages  indicating that cxcr3.2 mediated chemokine signaling is tightly connected to the regulation of lysosomal function. Overall design: 3 independent groups of 150 200 5dpf Tg mpeg1: mCherryF cxcr3.2 /  and cxcr3.2+/+ larvae were dissociated and red fluorescent macrophages were FACS sorted. RNA was extracted  retrotranscribed into cDNA and amplified using the SMARTer® Universal Low Input RNA Kit for Sequencing Clontech  prior Illumina sequencing.,,pubmed:33852860,,cxcr3.2mu rep3,GSM4518497,,tissue:FACS mpeg1: mCherryF positive cells|age:6 dpf type:macrophage|strain:mpeg1: mCherryF|genotype:cxcr3.2 / ,cxcr3.2mu rep3,Image analysis and base calling was done by the Illumina HCS version 1.15.1 Quality trimmed reads were aligned to the Ensembl zebrafish genome GRCz10 using Bowtie Reads were mapped to zebrafish transcripts using TopHat Genome build: GRCz10 Supplementary files format and content: tab separated value files of read counts for each sample,FACS mpeg1: mCherryF positive cells,,3 independent groups of 150 200 5dpf Tg mpeg1: mCherryF cxcr3.2 /  and cxcr3.2+/+ larvae were dissociated and red fluorescent macrophages were FACS sorted. RNA was extracted using the miRNeasy mini kit Qiagen according to the manufacturers’ instructions. cDNA synthesis and amplification was done using the SMARTer® Universal Low Input RNA Kit for Sequencing Clontech following the manufacturer’s guidelines. Approximately 10 Mreads were obtained  using Illimuna Single Read runs. Reads were then aligned to GRCz10 Danio rerio genome.,,age:6 dpf type:macrophage|strain:mpeg1: mCherryF|genotype:cxcr3.2 / ,GSM4518497,GSM4518497: cxcr3.2mu rep3; Danio rerio; RNA Seq,GSM4518497,,1,3 independent groups of 150 200 5dpf Tg mpeg1: mCherryF cxcr3.2 /  and cxcr3.2+/+ larvae were dissociated and red fluorescent macrophages were FACS sorted. RNA was extracted using the miRNeasy mini kit Qiagen according to the manufacturers' instructions. cDNA synthesis and amplification was done using the SMARTer® Universal Low Input RNA Kit for Sequencing Clontech following the manufacturer's guidelines. Approximately 10 Mreads were obtained  using Illimuna Single Read runs. Reads were then aligned to GRCz10 Danio rerio genome.,GEO Accession:GSM4518497,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP260213,,,mu3_1.fastq.gz,fastq,425713881.0,8347331.0,GSM4518497 r1,0:51,A:122037955;C:83276458;G:83884392;T:136385789;N:129287,51,,,,122037955,83276458,83884392,136385789,129287,SRX8259899,SRS6601867,SRA1072497,GEO,LSHTM,1,0.79761,,0.24807,,0.78031,,0.55233,,51,,B,,usable mapping rate,illumina,hiseq_era,full_length,cdna_unspecified,smarter,bulk,unknown,unknown,,United Kingdom,2020-05-06,Larval,Larval,Blood,Hematopoietic System
59151,SRR11700448,SRX8259899,SRS6601867,SRP260213,PRJNA630667,RNAseq expression analysis of FACS sorted macrophages from cxcr3.2 mutant and wt zebrafish larvae,GSE149942,Transcriptome Analysis,The zebrafish Cxcr3.2 is a functional homolog of the human chemokine receptor CXCR3. Zebrafish macrophages lacking this receptor have impaired motility and a rounded shape compared to their wildtype counterparts. To investigate the effects of cxcr3.2 mutation on the transcriptional profile of macrophages  we sorted macrophages from zebrafish larvae lacking a functional cxcr3.2 and compared their transcriptome to that of macrophages from wildtype larvae. Mutant and wildtype macrophages could be clearly distinguished based on the overall differential expression profiles. Classification of genes by compartment showed that peroxisomal  lysosomal and Golgi related genes were most frequently up regulated. Moreover  lysosomal and Golgi related terms were significantly differentially represented in Gene Ontology and KEGG enrichment analysis. Of note  several lysosomal markers  including acidic hydrolases and voltage ATPases were consistently upregulated in cxcr3.2 mutant macrophages  indicating that cxcr3.2 mediated chemokine signaling is tightly connected to the regulation of lysosomal function. Overall design: 3 independent groups of 150 200 5dpf Tg mpeg1: mCherryF cxcr3.2 /  and cxcr3.2+/+ larvae were dissociated and red fluorescent macrophages were FACS sorted. RNA was extracted  retrotranscribed into cDNA and amplified using the SMARTer® Universal Low Input RNA Kit for Sequencing Clontech  prior Illumina sequencing.,,pubmed:33852860,,cxcr3.2mu rep3,GSM4518497,,tissue:FACS mpeg1: mCherryF positive cells|age:6 dpf type:macrophage|strain:mpeg1: mCherryF|genotype:cxcr3.2 / ,cxcr3.2mu rep3,Image analysis and base calling was done by the Illumina HCS version 1.15.1 Quality trimmed reads were aligned to the Ensembl zebrafish genome GRCz10 using Bowtie Reads were mapped to zebrafish transcripts using TopHat Genome build: GRCz10 Supplementary files format and content: tab separated value files of read counts for each sample,FACS mpeg1: mCherryF positive cells,,3 independent groups of 150 200 5dpf Tg mpeg1: mCherryF cxcr3.2 /  and cxcr3.2+/+ larvae were dissociated and red fluorescent macrophages were FACS sorted. RNA was extracted using the miRNeasy mini kit Qiagen according to the manufacturers’ instructions. cDNA synthesis and amplification was done using the SMARTer® Universal Low Input RNA Kit for Sequencing Clontech following the manufacturer’s guidelines. Approximately 10 Mreads were obtained  using Illimuna Single Read runs. Reads were then aligned to GRCz10 Danio rerio genome.,,age:6 dpf type:macrophage|strain:mpeg1: mCherryF|genotype:cxcr3.2 / ,GSM4518497,GSM4518497: cxcr3.2mu rep3; Danio rerio; RNA Seq,GSM4518497,,1,3 independent groups of 150 200 5dpf Tg mpeg1: mCherryF cxcr3.2 /  and cxcr3.2+/+ larvae were dissociated and red fluorescent macrophages were FACS sorted. RNA was extracted using the miRNeasy mini kit Qiagen according to the manufacturers' instructions. cDNA synthesis and amplification was done using the SMARTer® Universal Low Input RNA Kit for Sequencing Clontech following the manufacturer's guidelines. Approximately 10 Mreads were obtained  using Illimuna Single Read runs. Reads were then aligned to GRCz10 Danio rerio genome.,GEO Accession:GSM4518497,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP260213,,,mu3_2.fastq.gz,fastq,432332151.0,8477101.0,GSM4518497 r2,0:51,A:124004077;C:84578395;G:85238663;T:138421813;N:89203,51,,,,124004077,84578395,85238663,138421813,89203,SRX8259899,SRS6601867,SRA1072497,GEO,LSHTM,1,0.79871,,0.25156,,0.77962,,0.54833,,51,,B,,usable mapping rate,illumina,hiseq_era,full_length,cdna_unspecified,smarter,bulk,unknown,unknown,,United Kingdom,2020-05-06,Larval,Larval,Blood,Hematopoietic System
59152,SRR11700445,SRX8259898,SRS6601866,SRP260213,PRJNA630667,RNAseq expression analysis of FACS sorted macrophages from cxcr3.2 mutant and wt zebrafish larvae,GSE149942,Transcriptome Analysis,The zebrafish Cxcr3.2 is a functional homolog of the human chemokine receptor CXCR3. Zebrafish macrophages lacking this receptor have impaired motility and a rounded shape compared to their wildtype counterparts. To investigate the effects of cxcr3.2 mutation on the transcriptional profile of macrophages  we sorted macrophages from zebrafish larvae lacking a functional cxcr3.2 and compared their transcriptome to that of macrophages from wildtype larvae. Mutant and wildtype macrophages could be clearly distinguished based on the overall differential expression profiles. Classification of genes by compartment showed that peroxisomal  lysosomal and Golgi related genes were most frequently up regulated. Moreover  lysosomal and Golgi related terms were significantly differentially represented in Gene Ontology and KEGG enrichment analysis. Of note  several lysosomal markers  including acidic hydrolases and voltage ATPases were consistently upregulated in cxcr3.2 mutant macrophages  indicating that cxcr3.2 mediated chemokine signaling is tightly connected to the regulation of lysosomal function. Overall design: 3 independent groups of 150 200 5dpf Tg mpeg1: mCherryF cxcr3.2 /  and cxcr3.2+/+ larvae were dissociated and red fluorescent macrophages were FACS sorted. RNA was extracted  retrotranscribed into cDNA and amplified using the SMARTer® Universal Low Input RNA Kit for Sequencing Clontech  prior Illumina sequencing.,,pubmed:33852860,,cxcr3.2wt rep2,GSM4518496,,tissue:FACS mpeg1: mCherryF positive cells|age:6 dpf type:macrophage|strain:mpeg1: mCherryF|genotype:cxcr3.2+/+,cxcr3.2wt rep2,Image analysis and base calling was done by the Illumina HCS version 1.15.1 Quality trimmed reads were aligned to the Ensembl zebrafish genome GRCz10 using Bowtie Reads were mapped to zebrafish transcripts using TopHat Genome build: GRCz10 Supplementary files format and content: tab separated value files of read counts for each sample,FACS mpeg1: mCherryF positive cells,,3 independent groups of 150 200 5dpf Tg mpeg1: mCherryF cxcr3.2 /  and cxcr3.2+/+ larvae were dissociated and red fluorescent macrophages were FACS sorted. RNA was extracted using the miRNeasy mini kit Qiagen according to the manufacturers’ instructions. cDNA synthesis and amplification was done using the SMARTer® Universal Low Input RNA Kit for Sequencing Clontech following the manufacturer’s guidelines. Approximately 10 Mreads were obtained  using Illimuna Single Read runs. Reads were then aligned to GRCz10 Danio rerio genome.,,age:6 dpf type:macrophage|strain:mpeg1: mCherryF|genotype:cxcr3.2+/+,GSM4518496,GSM4518496: cxcr3.2wt rep2; Danio rerio; RNA Seq,GSM4518496,,1,3 independent groups of 150 200 5dpf Tg mpeg1: mCherryF cxcr3.2 /  and cxcr3.2+/+ larvae were dissociated and red fluorescent macrophages were FACS sorted. RNA was extracted using the miRNeasy mini kit Qiagen according to the manufacturers' instructions. cDNA synthesis and amplification was done using the SMARTer® Universal Low Input RNA Kit for Sequencing Clontech following the manufacturer's guidelines. Approximately 10 Mreads were obtained  using Illimuna Single Read runs. Reads were then aligned to GRCz10 Danio rerio genome.,GEO Accession:GSM4518496,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP260213,,,wt2_1.fastq.gz,fastq,338884596.0,6644796.0,GSM4518496 r1,0:51,A:95060797;C:69418429;G:69712092;T:104594793;N:98485,51,,,,95060797,69418429,69712092,104594793,98485,SRX8259898,SRS6601866,SRA1072497,GEO,LSHTM,1,0.82037,,0.19262,,0.78573,,0.50787,,51,,B,,usable mapping rate,illumina,hiseq_era,full_length,cdna_unspecified,smarter,bulk,unknown,unknown,,United Kingdom,2020-05-06,Larval,Larval,Blood,Hematopoietic System
59153,SRR11700446,SRX8259898,SRS6601866,SRP260213,PRJNA630667,RNAseq expression analysis of FACS sorted macrophages from cxcr3.2 mutant and wt zebrafish larvae,GSE149942,Transcriptome Analysis,The zebrafish Cxcr3.2 is a functional homolog of the human chemokine receptor CXCR3. Zebrafish macrophages lacking this receptor have impaired motility and a rounded shape compared to their wildtype counterparts. To investigate the effects of cxcr3.2 mutation on the transcriptional profile of macrophages  we sorted macrophages from zebrafish larvae lacking a functional cxcr3.2 and compared their transcriptome to that of macrophages from wildtype larvae. Mutant and wildtype macrophages could be clearly distinguished based on the overall differential expression profiles. Classification of genes by compartment showed that peroxisomal  lysosomal and Golgi related genes were most frequently up regulated. Moreover  lysosomal and Golgi related terms were significantly differentially represented in Gene Ontology and KEGG enrichment analysis. Of note  several lysosomal markers  including acidic hydrolases and voltage ATPases were consistently upregulated in cxcr3.2 mutant macrophages  indicating that cxcr3.2 mediated chemokine signaling is tightly connected to the regulation of lysosomal function. Overall design: 3 independent groups of 150 200 5dpf Tg mpeg1: mCherryF cxcr3.2 /  and cxcr3.2+/+ larvae were dissociated and red fluorescent macrophages were FACS sorted. RNA was extracted  retrotranscribed into cDNA and amplified using the SMARTer® Universal Low Input RNA Kit for Sequencing Clontech  prior Illumina sequencing.,,pubmed:33852860,,cxcr3.2wt rep2,GSM4518496,,tissue:FACS mpeg1: mCherryF positive cells|age:6 dpf type:macrophage|strain:mpeg1: mCherryF|genotype:cxcr3.2+/+,cxcr3.2wt rep2,Image analysis and base calling was done by the Illumina HCS version 1.15.1 Quality trimmed reads were aligned to the Ensembl zebrafish genome GRCz10 using Bowtie Reads were mapped to zebrafish transcripts using TopHat Genome build: GRCz10 Supplementary files format and content: tab separated value files of read counts for each sample,FACS mpeg1: mCherryF positive cells,,3 independent groups of 150 200 5dpf Tg mpeg1: mCherryF cxcr3.2 /  and cxcr3.2+/+ larvae were dissociated and red fluorescent macrophages were FACS sorted. RNA was extracted using the miRNeasy mini kit Qiagen according to the manufacturers’ instructions. cDNA synthesis and amplification was done using the SMARTer® Universal Low Input RNA Kit for Sequencing Clontech following the manufacturer’s guidelines. Approximately 10 Mreads were obtained  using Illimuna Single Read runs. Reads were then aligned to GRCz10 Danio rerio genome.,,age:6 dpf type:macrophage|strain:mpeg1: mCherryF|genotype:cxcr3.2+/+,GSM4518496,GSM4518496: cxcr3.2wt rep2; Danio rerio; RNA Seq,GSM4518496,,1,3 independent groups of 150 200 5dpf Tg mpeg1: mCherryF cxcr3.2 /  and cxcr3.2+/+ larvae were dissociated and red fluorescent macrophages were FACS sorted. RNA was extracted using the miRNeasy mini kit Qiagen according to the manufacturers' instructions. cDNA synthesis and amplification was done using the SMARTer® Universal Low Input RNA Kit for Sequencing Clontech following the manufacturer's guidelines. Approximately 10 Mreads were obtained  using Illimuna Single Read runs. Reads were then aligned to GRCz10 Danio rerio genome.,GEO Accession:GSM4518496,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP260213,,,wt2_2.fastq.gz,fastq,340274448.0,6672048.0,GSM4518496 r2,0:51,A:95520411;C:69702700;G:69990821;T:104992786;N:67730,51,,,,95520411,69702700,69990821,104992786,67730,SRX8259898,SRS6601866,SRA1072497,GEO,LSHTM,1,0.8231,,0.19334,,0.78644,,0.5196,,51,,B,,usable mapping rate,illumina,hiseq_era,full_length,cdna_unspecified,smarter,bulk,unknown,unknown,,United Kingdom,2020-05-06,Larval,Larval,Blood,Hematopoietic System
59154,SRR11700443,SRX8259897,SRS6601865,SRP260213,PRJNA630667,RNAseq expression analysis of FACS sorted macrophages from cxcr3.2 mutant and wt zebrafish larvae,GSE149942,Transcriptome Analysis,The zebrafish Cxcr3.2 is a functional homolog of the human chemokine receptor CXCR3. Zebrafish macrophages lacking this receptor have impaired motility and a rounded shape compared to their wildtype counterparts. To investigate the effects of cxcr3.2 mutation on the transcriptional profile of macrophages  we sorted macrophages from zebrafish larvae lacking a functional cxcr3.2 and compared their transcriptome to that of macrophages from wildtype larvae. Mutant and wildtype macrophages could be clearly distinguished based on the overall differential expression profiles. Classification of genes by compartment showed that peroxisomal  lysosomal and Golgi related genes were most frequently up regulated. Moreover  lysosomal and Golgi related terms were significantly differentially represented in Gene Ontology and KEGG enrichment analysis. Of note  several lysosomal markers  including acidic hydrolases and voltage ATPases were consistently upregulated in cxcr3.2 mutant macrophages  indicating that cxcr3.2 mediated chemokine signaling is tightly connected to the regulation of lysosomal function. Overall design: 3 independent groups of 150 200 5dpf Tg mpeg1: mCherryF cxcr3.2 /  and cxcr3.2+/+ larvae were dissociated and red fluorescent macrophages were FACS sorted. RNA was extracted  retrotranscribed into cDNA and amplified using the SMARTer® Universal Low Input RNA Kit for Sequencing Clontech  prior Illumina sequencing.,,pubmed:33852860,,cxcr3.2mu rep2,GSM4518495,,tissue:FACS mpeg1: mCherryF positive cells|age:6 dpf type:macrophage|strain:mpeg1: mCherryF|genotype:cxcr3.2 / ,cxcr3.2mu rep2,Image analysis and base calling was done by the Illumina HCS version 1.15.1 Quality trimmed reads were aligned to the Ensembl zebrafish genome GRCz10 using Bowtie Reads were mapped to zebrafish transcripts using TopHat Genome build: GRCz10 Supplementary files format and content: tab separated value files of read counts for each sample,FACS mpeg1: mCherryF positive cells,,3 independent groups of 150 200 5dpf Tg mpeg1: mCherryF cxcr3.2 /  and cxcr3.2+/+ larvae were dissociated and red fluorescent macrophages were FACS sorted. RNA was extracted using the miRNeasy mini kit Qiagen according to the manufacturers’ instructions. cDNA synthesis and amplification was done using the SMARTer® Universal Low Input RNA Kit for Sequencing Clontech following the manufacturer’s guidelines. Approximately 10 Mreads were obtained  using Illimuna Single Read runs. Reads were then aligned to GRCz10 Danio rerio genome.,,age:6 dpf type:macrophage|strain:mpeg1: mCherryF|genotype:cxcr3.2 / ,GSM4518495,GSM4518495: cxcr3.2mu rep2; Danio rerio; RNA Seq,GSM4518495,,1,3 independent groups of 150 200 5dpf Tg mpeg1: mCherryF cxcr3.2 /  and cxcr3.2+/+ larvae were dissociated and red fluorescent macrophages were FACS sorted. RNA was extracted using the miRNeasy mini kit Qiagen according to the manufacturers' instructions. cDNA synthesis and amplification was done using the SMARTer® Universal Low Input RNA Kit for Sequencing Clontech following the manufacturer's guidelines. Approximately 10 Mreads were obtained  using Illimuna Single Read runs. Reads were then aligned to GRCz10 Danio rerio genome.,GEO Accession:GSM4518495,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP260213,,,mu2_1.fastq.gz,fastq,289744005.0,5681255.0,GSM4518495 r1,0:51,A:83941467;C:56685263;G:57155798;T:91875606;N:85871,51,,,,83941467,56685263,57155798,91875606,85871,SRX8259897,SRS6601865,SRA1072497,GEO,LSHTM,1,0.797,,0.19874,,0.77948,,0.54924,,51,,B,,usable mapping rate,illumina,hiseq_era,full_length,cdna_unspecified,smarter,bulk,unknown,unknown,,United Kingdom,2020-05-06,Larval,Larval,Blood,Hematopoietic System
59155,SRR11700444,SRX8259897,SRS6601865,SRP260213,PRJNA630667,RNAseq expression analysis of FACS sorted macrophages from cxcr3.2 mutant and wt zebrafish larvae,GSE149942,Transcriptome Analysis,The zebrafish Cxcr3.2 is a functional homolog of the human chemokine receptor CXCR3. Zebrafish macrophages lacking this receptor have impaired motility and a rounded shape compared to their wildtype counterparts. To investigate the effects of cxcr3.2 mutation on the transcriptional profile of macrophages  we sorted macrophages from zebrafish larvae lacking a functional cxcr3.2 and compared their transcriptome to that of macrophages from wildtype larvae. Mutant and wildtype macrophages could be clearly distinguished based on the overall differential expression profiles. Classification of genes by compartment showed that peroxisomal  lysosomal and Golgi related genes were most frequently up regulated. Moreover  lysosomal and Golgi related terms were significantly differentially represented in Gene Ontology and KEGG enrichment analysis. Of note  several lysosomal markers  including acidic hydrolases and voltage ATPases were consistently upregulated in cxcr3.2 mutant macrophages  indicating that cxcr3.2 mediated chemokine signaling is tightly connected to the regulation of lysosomal function. Overall design: 3 independent groups of 150 200 5dpf Tg mpeg1: mCherryF cxcr3.2 /  and cxcr3.2+/+ larvae were dissociated and red fluorescent macrophages were FACS sorted. RNA was extracted  retrotranscribed into cDNA and amplified using the SMARTer® Universal Low Input RNA Kit for Sequencing Clontech  prior Illumina sequencing.,,pubmed:33852860,,cxcr3.2mu rep2,GSM4518495,,tissue:FACS mpeg1: mCherryF positive cells|age:6 dpf type:macrophage|strain:mpeg1: mCherryF|genotype:cxcr3.2 / ,cxcr3.2mu rep2,Image analysis and base calling was done by the Illumina HCS version 1.15.1 Quality trimmed reads were aligned to the Ensembl zebrafish genome GRCz10 using Bowtie Reads were mapped to zebrafish transcripts using TopHat Genome build: GRCz10 Supplementary files format and content: tab separated value files of read counts for each sample,FACS mpeg1: mCherryF positive cells,,3 independent groups of 150 200 5dpf Tg mpeg1: mCherryF cxcr3.2 /  and cxcr3.2+/+ larvae were dissociated and red fluorescent macrophages were FACS sorted. RNA was extracted using the miRNeasy mini kit Qiagen according to the manufacturers’ instructions. cDNA synthesis and amplification was done using the SMARTer® Universal Low Input RNA Kit for Sequencing Clontech following the manufacturer’s guidelines. Approximately 10 Mreads were obtained  using Illimuna Single Read runs. Reads were then aligned to GRCz10 Danio rerio genome.,,age:6 dpf type:macrophage|strain:mpeg1: mCherryF|genotype:cxcr3.2 / ,GSM4518495,GSM4518495: cxcr3.2mu rep2; Danio rerio; RNA Seq,GSM4518495,,1,3 independent groups of 150 200 5dpf Tg mpeg1: mCherryF cxcr3.2 /  and cxcr3.2+/+ larvae were dissociated and red fluorescent macrophages were FACS sorted. RNA was extracted using the miRNeasy mini kit Qiagen according to the manufacturers' instructions. cDNA synthesis and amplification was done using the SMARTer® Universal Low Input RNA Kit for Sequencing Clontech following the manufacturer's guidelines. Approximately 10 Mreads were obtained  using Illimuna Single Read runs. Reads were then aligned to GRCz10 Danio rerio genome.,GEO Accession:GSM4518495,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP260213,,,mu2_2.fastq.gz,fastq,292004937.0,5725587.0,GSM4518495 r2,0:51,A:84614504;C:57133336;G:57626820;T:92570322;N:59955,51,,,,84614504,57133336,57626820,92570322,59955,SRX8259897,SRS6601865,SRA1072497,GEO,LSHTM,1,0.79923,,0.19835,,0.77855,,0.53966,,51,,B,,usable mapping rate,illumina,hiseq_era,full_length,cdna_unspecified,smarter,bulk,unknown,unknown,,United Kingdom,2020-05-06,Larval,Larval,Blood,Hematopoietic System
59156,SRR11700441,SRX8259896,SRS6601864,SRP260213,PRJNA630667,RNAseq expression analysis of FACS sorted macrophages from cxcr3.2 mutant and wt zebrafish larvae,GSE149942,Transcriptome Analysis,The zebrafish Cxcr3.2 is a functional homolog of the human chemokine receptor CXCR3. Zebrafish macrophages lacking this receptor have impaired motility and a rounded shape compared to their wildtype counterparts. To investigate the effects of cxcr3.2 mutation on the transcriptional profile of macrophages  we sorted macrophages from zebrafish larvae lacking a functional cxcr3.2 and compared their transcriptome to that of macrophages from wildtype larvae. Mutant and wildtype macrophages could be clearly distinguished based on the overall differential expression profiles. Classification of genes by compartment showed that peroxisomal  lysosomal and Golgi related genes were most frequently up regulated. Moreover  lysosomal and Golgi related terms were significantly differentially represented in Gene Ontology and KEGG enrichment analysis. Of note  several lysosomal markers  including acidic hydrolases and voltage ATPases were consistently upregulated in cxcr3.2 mutant macrophages  indicating that cxcr3.2 mediated chemokine signaling is tightly connected to the regulation of lysosomal function. Overall design: 3 independent groups of 150 200 5dpf Tg mpeg1: mCherryF cxcr3.2 /  and cxcr3.2+/+ larvae were dissociated and red fluorescent macrophages were FACS sorted. RNA was extracted  retrotranscribed into cDNA and amplified using the SMARTer® Universal Low Input RNA Kit for Sequencing Clontech  prior Illumina sequencing.,,pubmed:33852860,,cxcr3.2wt rep1,GSM4518494,,tissue:FACS mpeg1: mCherryF positive cells|age:6 dpf type:macrophage|strain:mpeg1: mCherryF|genotype:cxcr3.2+/+,cxcr3.2wt rep1,Image analysis and base calling was done by the Illumina HCS version 1.15.1 Quality trimmed reads were aligned to the Ensembl zebrafish genome GRCz10 using Bowtie Reads were mapped to zebrafish transcripts using TopHat Genome build: GRCz10 Supplementary files format and content: tab separated value files of read counts for each sample,FACS mpeg1: mCherryF positive cells,,3 independent groups of 150 200 5dpf Tg mpeg1: mCherryF cxcr3.2 /  and cxcr3.2+/+ larvae were dissociated and red fluorescent macrophages were FACS sorted. RNA was extracted using the miRNeasy mini kit Qiagen according to the manufacturers’ instructions. cDNA synthesis and amplification was done using the SMARTer® Universal Low Input RNA Kit for Sequencing Clontech following the manufacturer’s guidelines. Approximately 10 Mreads were obtained  using Illimuna Single Read runs. Reads were then aligned to GRCz10 Danio rerio genome.,,age:6 dpf type:macrophage|strain:mpeg1: mCherryF|genotype:cxcr3.2+/+,GSM4518494,GSM4518494: cxcr3.2wt rep1; Danio rerio; RNA Seq,GSM4518494,,1,3 independent groups of 150 200 5dpf Tg mpeg1: mCherryF cxcr3.2 /  and cxcr3.2+/+ larvae were dissociated and red fluorescent macrophages were FACS sorted. RNA was extracted using the miRNeasy mini kit Qiagen according to the manufacturers' instructions. cDNA synthesis and amplification was done using the SMARTer® Universal Low Input RNA Kit for Sequencing Clontech following the manufacturer's guidelines. Approximately 10 Mreads were obtained  using Illimuna Single Read runs. Reads were then aligned to GRCz10 Danio rerio genome.,GEO Accession:GSM4518494,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP260213,,,wt1_1.fastq.gz,fastq,365558718.0,7167818.0,GSM4518494 r1,0:51,A:106749458;C:71670361;G:72075682;T:114952902;N:110315,51,,,,106749458,71670361,72075682,114952902,110315,SRX8259896,SRS6601864,SRA1072497,GEO,LSHTM,1,0.80168,,0.20934,,0.78336,,0.55284,,51,,B,,usable mapping rate,illumina,hiseq_era,full_length,cdna_unspecified,smarter,bulk,unknown,unknown,,United Kingdom,2020-05-06,Larval,Larval,Blood,Hematopoietic System
59157,SRR11700442,SRX8259896,SRS6601864,SRP260213,PRJNA630667,RNAseq expression analysis of FACS sorted macrophages from cxcr3.2 mutant and wt zebrafish larvae,GSE149942,Transcriptome Analysis,The zebrafish Cxcr3.2 is a functional homolog of the human chemokine receptor CXCR3. Zebrafish macrophages lacking this receptor have impaired motility and a rounded shape compared to their wildtype counterparts. To investigate the effects of cxcr3.2 mutation on the transcriptional profile of macrophages  we sorted macrophages from zebrafish larvae lacking a functional cxcr3.2 and compared their transcriptome to that of macrophages from wildtype larvae. Mutant and wildtype macrophages could be clearly distinguished based on the overall differential expression profiles. Classification of genes by compartment showed that peroxisomal  lysosomal and Golgi related genes were most frequently up regulated. Moreover  lysosomal and Golgi related terms were significantly differentially represented in Gene Ontology and KEGG enrichment analysis. Of note  several lysosomal markers  including acidic hydrolases and voltage ATPases were consistently upregulated in cxcr3.2 mutant macrophages  indicating that cxcr3.2 mediated chemokine signaling is tightly connected to the regulation of lysosomal function. Overall design: 3 independent groups of 150 200 5dpf Tg mpeg1: mCherryF cxcr3.2 /  and cxcr3.2+/+ larvae were dissociated and red fluorescent macrophages were FACS sorted. RNA was extracted  retrotranscribed into cDNA and amplified using the SMARTer® Universal Low Input RNA Kit for Sequencing Clontech  prior Illumina sequencing.,,pubmed:33852860,,cxcr3.2wt rep1,GSM4518494,,tissue:FACS mpeg1: mCherryF positive cells|age:6 dpf type:macrophage|strain:mpeg1: mCherryF|genotype:cxcr3.2+/+,cxcr3.2wt rep1,Image analysis and base calling was done by the Illumina HCS version 1.15.1 Quality trimmed reads were aligned to the Ensembl zebrafish genome GRCz10 using Bowtie Reads were mapped to zebrafish transcripts using TopHat Genome build: GRCz10 Supplementary files format and content: tab separated value files of read counts for each sample,FACS mpeg1: mCherryF positive cells,,3 independent groups of 150 200 5dpf Tg mpeg1: mCherryF cxcr3.2 /  and cxcr3.2+/+ larvae were dissociated and red fluorescent macrophages were FACS sorted. RNA was extracted using the miRNeasy mini kit Qiagen according to the manufacturers’ instructions. cDNA synthesis and amplification was done using the SMARTer® Universal Low Input RNA Kit for Sequencing Clontech following the manufacturer’s guidelines. Approximately 10 Mreads were obtained  using Illimuna Single Read runs. Reads were then aligned to GRCz10 Danio rerio genome.,,age:6 dpf type:macrophage|strain:mpeg1: mCherryF|genotype:cxcr3.2+/+,GSM4518494,GSM4518494: cxcr3.2wt rep1; Danio rerio; RNA Seq,GSM4518494,,1,3 independent groups of 150 200 5dpf Tg mpeg1: mCherryF cxcr3.2 /  and cxcr3.2+/+ larvae were dissociated and red fluorescent macrophages were FACS sorted. RNA was extracted using the miRNeasy mini kit Qiagen according to the manufacturers' instructions. cDNA synthesis and amplification was done using the SMARTer® Universal Low Input RNA Kit for Sequencing Clontech following the manufacturer's guidelines. Approximately 10 Mreads were obtained  using Illimuna Single Read runs. Reads were then aligned to GRCz10 Danio rerio genome.,GEO Accession:GSM4518494,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP260213,,,wt1_2.fastq.gz,fastq,369956805.0,7254055.0,GSM4518494 r2,0:51,A:108102133;C:72565792;G:72967269;T:116246235;N:75376,51,,,,108102133,72565792,72967269,116246235,75376,SRX8259896,SRS6601864,SRA1072497,GEO,LSHTM,1,0.80058,,0.21005,,0.78303,,0.54972,,51,,B,,usable mapping rate,illumina,hiseq_era,full_length,cdna_unspecified,smarter,bulk,unknown,unknown,,United Kingdom,2020-05-06,Larval,Larval,Blood,Hematopoietic System
59158,SRR11700439,SRX8259895,SRS6601863,SRP260213,PRJNA630667,RNAseq expression analysis of FACS sorted macrophages from cxcr3.2 mutant and wt zebrafish larvae,GSE149942,Transcriptome Analysis,The zebrafish Cxcr3.2 is a functional homolog of the human chemokine receptor CXCR3. Zebrafish macrophages lacking this receptor have impaired motility and a rounded shape compared to their wildtype counterparts. To investigate the effects of cxcr3.2 mutation on the transcriptional profile of macrophages  we sorted macrophages from zebrafish larvae lacking a functional cxcr3.2 and compared their transcriptome to that of macrophages from wildtype larvae. Mutant and wildtype macrophages could be clearly distinguished based on the overall differential expression profiles. Classification of genes by compartment showed that peroxisomal  lysosomal and Golgi related genes were most frequently up regulated. Moreover  lysosomal and Golgi related terms were significantly differentially represented in Gene Ontology and KEGG enrichment analysis. Of note  several lysosomal markers  including acidic hydrolases and voltage ATPases were consistently upregulated in cxcr3.2 mutant macrophages  indicating that cxcr3.2 mediated chemokine signaling is tightly connected to the regulation of lysosomal function. Overall design: 3 independent groups of 150 200 5dpf Tg mpeg1: mCherryF cxcr3.2 /  and cxcr3.2+/+ larvae were dissociated and red fluorescent macrophages were FACS sorted. RNA was extracted  retrotranscribed into cDNA and amplified using the SMARTer® Universal Low Input RNA Kit for Sequencing Clontech  prior Illumina sequencing.,,pubmed:33852860,,cxcr3.2mu rep1,GSM4518493,,tissue:FACS mpeg1: mCherryF positive cells|age:6 dpf type:macrophage|strain:mpeg1: mCherryF|genotype:cxcr3.2 / ,cxcr3.2mu rep1,Image analysis and base calling was done by the Illumina HCS version 1.15.1 Quality trimmed reads were aligned to the Ensembl zebrafish genome GRCz10 using Bowtie Reads were mapped to zebrafish transcripts using TopHat Genome build: GRCz10 Supplementary files format and content: tab separated value files of read counts for each sample,FACS mpeg1: mCherryF positive cells,,3 independent groups of 150 200 5dpf Tg mpeg1: mCherryF cxcr3.2 /  and cxcr3.2+/+ larvae were dissociated and red fluorescent macrophages were FACS sorted. RNA was extracted using the miRNeasy mini kit Qiagen according to the manufacturers’ instructions. cDNA synthesis and amplification was done using the SMARTer® Universal Low Input RNA Kit for Sequencing Clontech following the manufacturer’s guidelines. Approximately 10 Mreads were obtained  using Illimuna Single Read runs. Reads were then aligned to GRCz10 Danio rerio genome.,,age:6 dpf type:macrophage|strain:mpeg1: mCherryF|genotype:cxcr3.2 / ,GSM4518493,GSM4518493: cxcr3.2mu rep1; Danio rerio; RNA Seq,GSM4518493,,1,3 independent groups of 150 200 5dpf Tg mpeg1: mCherryF cxcr3.2 /  and cxcr3.2+/+ larvae were dissociated and red fluorescent macrophages were FACS sorted. RNA was extracted using the miRNeasy mini kit Qiagen according to the manufacturers' instructions. cDNA synthesis and amplification was done using the SMARTer® Universal Low Input RNA Kit for Sequencing Clontech following the manufacturer's guidelines. Approximately 10 Mreads were obtained  using Illimuna Single Read runs. Reads were then aligned to GRCz10 Danio rerio genome.,GEO Accession:GSM4518493,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP260213,,,mu1_1.fastq.gz,fastq,413105049.0,8100099.0,GSM4518493 r1,0:51,A:117770136;C:83069765;G:83597140;T:128544513;N:123495,51,,,,117770136,83069765,83597140,128544513,123495,SRX8259895,SRS6601863,SRA1072497,GEO,LSHTM,1,0.74703,,0.18405,,0.79072,,0.52251,,51,,B,,usable mapping rate,illumina,hiseq_era,full_length,cdna_unspecified,smarter,bulk,unknown,unknown,,United Kingdom,2020-05-06,Larval,Larval,Blood,Hematopoietic System