metadata: run_metadata: 27 rows where experiment.library_layout = "PAIRED", experiment.library_selection = "PolyA" and tissue

27 rows where experiment.library_layout = "PAIRED", experiment.library_selection = "PolyA" and tissue_curation = "Kidney"

descending

Link	rowid ▼	run.accession	experiment.accession	sample.accession	study.accession	bioproject	study.title	study.alias	study.type	study.abstract	study.attributes	sample.description	sample.title	sample.alias	sample.centername	sample.attributes	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.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.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	submission.bioprojectsource.country	earliest_date	devstage_curation	devstage_curation_coarse	tissue_curation	tissue_curation_coarse
10166	10166	ERR5762357	ERX5471113	ERS6291553	ERP128548	PRJEB44492	scRNA seq of kidney marrow cells from Gata2b deficient and wild type zebrafish	E-MTAB-10370	Transcriptome Analysis	GATA2 is a pivotal hematopoietic transcription factor required for generation and maintenance of hematopoietic stem cells HSCs. Due to early embryonic lethality of Gata2 deficiency in mice its role during adult hematopoiesis is incompletely understood. In zebrafish mammalian functions of Gata2 are split between two orthologues: Gata2a and Gata2b. Previous studies have shown that Gata2b is prominently expressed in hematopoietic stem and progenitor cells HSPCs whereas Gata2a is mainly expressed in the vasculature. We found that Gata2b deficient zebrafish have a reduction in embryonic definitive HSPC numbers and have impaired myeloid lineage differentiation but are viable. This allowed us to study the role of Gata2b in adult hematopoiesis. To assess the impact of Gata2b deficiency on the transcriptional profile of HSPCs and differentiated cells we sorted the entire progenitor and HSPC population including the lymphoid population from kidney marrow KM of WT and germline Gata2b deficient zebrafish based on scatter profiles and processed for single cell RNA sequencing. To enrich the scarce HSC population we used pooled KM from two WT and Gata2b deficient TgCD41:GFP zebrafish per sample and included all CD41:GFPlow expressing cells present in the kidney marrow pool as these cells were shown to contain transplantable HSCs.	ENA FIRST PUBLIC:2022 04 09\|ENA LAST UPDATE:2022 04 09	Protocols: Adult zebrafish were euthanized kidney marrow was isolated and dissociated by pipetting in PBS/10% FCS. 7 AAD 7 amino actinomycin D 0.5mg/L BD biosciences was used for live/dead discrimination. Sorting was performed using FACSAriaIII BD. 70.000 single viable cells were sorted from 2 pooled kidney marrow of female TgCD41:GFP zebrafish and supplemented with 114 1607 CD41:GFPlow expressing cells. cDNA was prepared using the manufacturers protocol 10x Chromium V2. Library was prepared using the manufacturers protocol 10x Chromium V2.	wt2 gata2b	SAMEA8606934	Erasmus Medical Center	ENA FIRST PUBLIC:2022 04 09\|ENA LAST UPDATE:2022 04 09\|External Id:SAMEA8606934\|INSDC center alias:Erasmus Medical Center\|INSDC center name:Erasmus Medical Center\|INSDC first public:2022 04 09T00:20:19Z\|INSDC last update:2022 04 09T00:20:19Z\|INSDC status:public\|Submitter Id:E MTAB 10370:wt2 gata2b\|age:5\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:adult\|genotype:wild type genotype\|isolate:not applicable\|organism part:kidney\|sample name:E MTAB 10370:wt2 gata2b\|sampling site:kidney marrow\|sex:female\|strain:AB	Illumina NovaSeq 6000 paired end sequencing; scRNA seq of kidney marrow cells from Gata2b deficient and wild type zebrafish	E MTAB 10370:wt2 gata2b p	wt2 gata2b p	scRNA seq of kidney marrow cells from Gata2b deficient and wild type zebrafish	Adult zebrafish were euthanized kidney marrow was isolated and dissociated by pipetting in PBS/10% FCS. 7 AAD 7 amino actinomycin D 0.5mg/L BD biosciences was used for live/dead discrimination. Sorting was performed using FACSAriaIII BD. 70.000 single viable cells were sorted from 2 pooled kidney marrow of female TgCD41:GFP zebrafish and supplemented with 114 1607 CD41:GFPlow expressing cells. cDNA was prepared using the manufacturers protocol 10x Chromium V2. Library was prepared using the manufacturers protocol 10x Chromium V2.	Experimental Factor: genotype:wild type genotype	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	PolyA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	ERP128548	Illumina NovaSeq 6000 paired end sequencing; scRNA seq of kidney marrow cells from Gata2b deficient and wild type zebrafish	ENA FIRST PUBLIC:2022 04 09\|ENA LAST UPDATE:2022 04 09	wt2_gata2b.bam	bam	25266437196.0	277653156.0	E MTAB 10370:wt2 gata2b	0:91	A:7555470312;C:5144518052;G:5682746714;T:6882396490;N:1305628	91		7555470312	5144518052	5682746714	6882396490	1305628	ERX5471113	ERS6291553	ERA4089475	Erasmus Medical Center\|European Nucleotide Archive	Erasmus Medical Center\|European Nucleotide Archive	1	0.90876		0.18424		0.84017		0.55508		91		B		usable mapping rate	illumina	novaseq_era	unknown	poly_a	unknown	sc	single_cell_droplet	10x	Netherlands	2022-04-09	Adult	Adult	Kidney	Renal System
10167	10167	ERR5762356	ERX5471112	ERS6291552	ERP128548	PRJEB44492	scRNA seq of kidney marrow cells from Gata2b deficient and wild type zebrafish	E-MTAB-10370	Transcriptome Analysis	GATA2 is a pivotal hematopoietic transcription factor required for generation and maintenance of hematopoietic stem cells HSCs. Due to early embryonic lethality of Gata2 deficiency in mice its role during adult hematopoiesis is incompletely understood. In zebrafish mammalian functions of Gata2 are split between two orthologues: Gata2a and Gata2b. Previous studies have shown that Gata2b is prominently expressed in hematopoietic stem and progenitor cells HSPCs whereas Gata2a is mainly expressed in the vasculature. We found that Gata2b deficient zebrafish have a reduction in embryonic definitive HSPC numbers and have impaired myeloid lineage differentiation but are viable. This allowed us to study the role of Gata2b in adult hematopoiesis. To assess the impact of Gata2b deficiency on the transcriptional profile of HSPCs and differentiated cells we sorted the entire progenitor and HSPC population including the lymphoid population from kidney marrow KM of WT and germline Gata2b deficient zebrafish based on scatter profiles and processed for single cell RNA sequencing. To enrich the scarce HSC population we used pooled KM from two WT and Gata2b deficient TgCD41:GFP zebrafish per sample and included all CD41:GFPlow expressing cells present in the kidney marrow pool as these cells were shown to contain transplantable HSCs.	ENA FIRST PUBLIC:2022 04 09\|ENA LAST UPDATE:2022 04 09	Protocols: Adult zebrafish were euthanized kidney marrow was isolated and dissociated by pipetting in PBS/10% FCS. 7 AAD 7 amino actinomycin D 0.5mg/L BD biosciences was used for live/dead discrimination. Sorting was performed using FACSAriaIII BD. 70.000 single viable cells were sorted from 2 pooled kidney marrow of female TgCD41:GFP zebrafish and supplemented with 114 1607 CD41:GFPlow expressing cells. cDNA was prepared using the manufacturers protocol 10x Chromium V2. Library was prepared using the manufacturers protocol 10x Chromium V2.	wt1 gata2b	SAMEA8606933	Erasmus Medical Center	ENA FIRST PUBLIC:2022 04 09\|ENA LAST UPDATE:2022 04 09\|External Id:SAMEA8606933\|INSDC center alias:Erasmus Medical Center\|INSDC center name:Erasmus Medical Center\|INSDC first public:2022 04 09T00:20:19Z\|INSDC last update:2022 04 09T00:20:19Z\|INSDC status:public\|Submitter Id:E MTAB 10370:wt1 gata2b\|age:5\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:adult\|genotype:wild type genotype\|isolate:not applicable\|organism part:kidney\|sample name:E MTAB 10370:wt1 gata2b\|sampling site:kidney marrow\|sex:female\|strain:AB	Illumina NovaSeq 6000 paired end sequencing; scRNA seq of kidney marrow cells from Gata2b deficient and wild type zebrafish	E MTAB 10370:wt1 gata2b p	wt1 gata2b p	scRNA seq of kidney marrow cells from Gata2b deficient and wild type zebrafish	Adult zebrafish were euthanized kidney marrow was isolated and dissociated by pipetting in PBS/10% FCS. 7 AAD 7 amino actinomycin D 0.5mg/L BD biosciences was used for live/dead discrimination. Sorting was performed using FACSAriaIII BD. 70.000 single viable cells were sorted from 2 pooled kidney marrow of female TgCD41:GFP zebrafish and supplemented with 114 1607 CD41:GFPlow expressing cells. cDNA was prepared using the manufacturers protocol 10x Chromium V2. Library was prepared using the manufacturers protocol 10x Chromium V2.	Experimental Factor: genotype:wild type genotype	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	PolyA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	ERP128548	Illumina NovaSeq 6000 paired end sequencing; scRNA seq of kidney marrow cells from Gata2b deficient and wild type zebrafish	ENA FIRST PUBLIC:2022 04 09\|ENA LAST UPDATE:2022 04 09	wt1_gata2b.bam	bam	36376708095.0	399744045.0	E MTAB 10370:wt1 gata2b	0:91	A:10397161431;C:8128518427;G:8799445454;T:9049686061;N:1896722	91		10397161431	8128518427	8799445454	9049686061	1896722	ERX5471112	ERS6291552	ERA4089475	Erasmus Medical Center\|European Nucleotide Archive	Erasmus Medical Center\|European Nucleotide Archive	1	0.94708		0.08938		0.85449		0.52917		91		B		usable mapping rate	illumina	novaseq_era	unknown	poly_a	unknown	sc	single_cell_droplet	10x	Netherlands	2022-04-09	Adult	Adult	Kidney	Renal System
10168	10168	ERR5762355	ERX5471111	ERS6291551	ERP128548	PRJEB44492	scRNA seq of kidney marrow cells from Gata2b deficient and wild type zebrafish	E-MTAB-10370	Transcriptome Analysis	GATA2 is a pivotal hematopoietic transcription factor required for generation and maintenance of hematopoietic stem cells HSCs. Due to early embryonic lethality of Gata2 deficiency in mice its role during adult hematopoiesis is incompletely understood. In zebrafish mammalian functions of Gata2 are split between two orthologues: Gata2a and Gata2b. Previous studies have shown that Gata2b is prominently expressed in hematopoietic stem and progenitor cells HSPCs whereas Gata2a is mainly expressed in the vasculature. We found that Gata2b deficient zebrafish have a reduction in embryonic definitive HSPC numbers and have impaired myeloid lineage differentiation but are viable. This allowed us to study the role of Gata2b in adult hematopoiesis. To assess the impact of Gata2b deficiency on the transcriptional profile of HSPCs and differentiated cells we sorted the entire progenitor and HSPC population including the lymphoid population from kidney marrow KM of WT and germline Gata2b deficient zebrafish based on scatter profiles and processed for single cell RNA sequencing. To enrich the scarce HSC population we used pooled KM from two WT and Gata2b deficient TgCD41:GFP zebrafish per sample and included all CD41:GFPlow expressing cells present in the kidney marrow pool as these cells were shown to contain transplantable HSCs.	ENA FIRST PUBLIC:2022 04 09\|ENA LAST UPDATE:2022 04 09	Protocols: Adult zebrafish were euthanized kidney marrow was isolated and dissociated by pipetting in PBS/10% FCS. 7 AAD 7 amino actinomycin D 0.5mg/L BD biosciences was used for live/dead discrimination. Sorting was performed using FACSAriaIII BD. 70.000 single viable cells were sorted from 2 pooled kidney marrow of female TgCD41:GFP zebrafish and supplemented with 114 1607 CD41:GFPlow expressing cells. cDNA was prepared using the manufacturers protocol 10x Chromium V2. Library was prepared using the manufacturers protocol 10x Chromium V2.	hom2 gata2b	SAMEA8606932	Erasmus Medical Center	ENA FIRST PUBLIC:2022 04 09\|ENA LAST UPDATE:2022 04 09\|External Id:SAMEA8606932\|INSDC center alias:Erasmus Medical Center\|INSDC center name:Erasmus Medical Center\|INSDC first public:2022 04 09T00:20:19Z\|INSDC last update:2022 04 09T00:20:19Z\|INSDC status:public\|Submitter Id:E MTAB 10370:hom2 gata2b\|age:5\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:adult\|genotype:gata2b / \|isolate:not applicable\|organism part:kidney\|sample name:E MTAB 10370:hom2 gata2b\|sampling site:kidney marrow\|sex:female\|strain:AB	Illumina NovaSeq 6000 paired end sequencing; scRNA seq of kidney marrow cells from Gata2b deficient and wild type zebrafish	E MTAB 10370:hom2 gata2b p	hom2 gata2b p	scRNA seq of kidney marrow cells from Gata2b deficient and wild type zebrafish	Adult zebrafish were euthanized kidney marrow was isolated and dissociated by pipetting in PBS/10% FCS. 7 AAD 7 amino actinomycin D 0.5mg/L BD biosciences was used for live/dead discrimination. Sorting was performed using FACSAriaIII BD. 70.000 single viable cells were sorted from 2 pooled kidney marrow of female TgCD41:GFP zebrafish and supplemented with 114 1607 CD41:GFPlow expressing cells. cDNA was prepared using the manufacturers protocol 10x Chromium V2. Library was prepared using the manufacturers protocol 10x Chromium V2.	Experimental Factor: genotype:gata2b /	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	PolyA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	ERP128548	Illumina NovaSeq 6000 paired end sequencing; scRNA seq of kidney marrow cells from Gata2b deficient and wild type zebrafish	ENA FIRST PUBLIC:2022 04 09\|ENA LAST UPDATE:2022 04 09	hom2_gata2b.bam	bam	22416887402.0	246339422.0	E MTAB 10370:hom2 gata2b	0:91	A:6732382430;C:4540586585;G:4933684272;T:6209137814;N:1096301	91		6732382430	4540586585	4933684272	6209137814	1096301	ERX5471111	ERS6291551	ERA4089475	Erasmus Medical Center\|European Nucleotide Archive	Erasmus Medical Center\|European Nucleotide Archive	1	0.91306		0.21566		0.83469		0.53782		91		B		usable mapping rate	illumina	novaseq_era	unknown	poly_a	unknown	sc	single_cell_droplet	10x	Netherlands	2022-04-09	Adult	Adult	Kidney	Renal System
10169	10169	ERR5762354	ERX5471110	ERS6291550	ERP128548	PRJEB44492	scRNA seq of kidney marrow cells from Gata2b deficient and wild type zebrafish	E-MTAB-10370	Transcriptome Analysis	GATA2 is a pivotal hematopoietic transcription factor required for generation and maintenance of hematopoietic stem cells HSCs. Due to early embryonic lethality of Gata2 deficiency in mice its role during adult hematopoiesis is incompletely understood. In zebrafish mammalian functions of Gata2 are split between two orthologues: Gata2a and Gata2b. Previous studies have shown that Gata2b is prominently expressed in hematopoietic stem and progenitor cells HSPCs whereas Gata2a is mainly expressed in the vasculature. We found that Gata2b deficient zebrafish have a reduction in embryonic definitive HSPC numbers and have impaired myeloid lineage differentiation but are viable. This allowed us to study the role of Gata2b in adult hematopoiesis. To assess the impact of Gata2b deficiency on the transcriptional profile of HSPCs and differentiated cells we sorted the entire progenitor and HSPC population including the lymphoid population from kidney marrow KM of WT and germline Gata2b deficient zebrafish based on scatter profiles and processed for single cell RNA sequencing. To enrich the scarce HSC population we used pooled KM from two WT and Gata2b deficient TgCD41:GFP zebrafish per sample and included all CD41:GFPlow expressing cells present in the kidney marrow pool as these cells were shown to contain transplantable HSCs.	ENA FIRST PUBLIC:2022 04 09\|ENA LAST UPDATE:2022 04 09	Protocols: Adult zebrafish were euthanized kidney marrow was isolated and dissociated by pipetting in PBS/10% FCS. 7 AAD 7 amino actinomycin D 0.5mg/L BD biosciences was used for live/dead discrimination. Sorting was performed using FACSAriaIII BD. 70.000 single viable cells were sorted from 2 pooled kidney marrow of female TgCD41:GFP zebrafish and supplemented with 114 1607 CD41:GFPlow expressing cells. cDNA was prepared using the manufacturers protocol 10x Chromium V2. Library was prepared using the manufacturers protocol 10x Chromium V2.	hom1 gata2b	SAMEA8606931	Erasmus Medical Center	ENA FIRST PUBLIC:2022 04 09\|ENA LAST UPDATE:2022 04 09\|External Id:SAMEA8606931\|INSDC center alias:Erasmus Medical Center\|INSDC center name:Erasmus Medical Center\|INSDC first public:2022 04 09T00:20:19Z\|INSDC last update:2022 04 09T00:20:19Z\|INSDC status:public\|Submitter Id:E MTAB 10370:hom1 gata2b\|age:5\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:adult\|genotype:gata2b / \|isolate:not applicable\|organism part:kidney\|sample name:E MTAB 10370:hom1 gata2b\|sampling site:kidney marrow\|sex:female\|strain:AB	Illumina NovaSeq 6000 paired end sequencing; scRNA seq of kidney marrow cells from Gata2b deficient and wild type zebrafish	E MTAB 10370:hom1 gata2b p	hom1 gata2b p	scRNA seq of kidney marrow cells from Gata2b deficient and wild type zebrafish	Adult zebrafish were euthanized kidney marrow was isolated and dissociated by pipetting in PBS/10% FCS. 7 AAD 7 amino actinomycin D 0.5mg/L BD biosciences was used for live/dead discrimination. Sorting was performed using FACSAriaIII BD. 70.000 single viable cells were sorted from 2 pooled kidney marrow of female TgCD41:GFP zebrafish and supplemented with 114 1607 CD41:GFPlow expressing cells. cDNA was prepared using the manufacturers protocol 10x Chromium V2. Library was prepared using the manufacturers protocol 10x Chromium V2.	Experimental Factor: genotype:gata2b /	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	PolyA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	ERP128548	Illumina NovaSeq 6000 paired end sequencing; scRNA seq of kidney marrow cells from Gata2b deficient and wild type zebrafish	ENA FIRST PUBLIC:2022 04 09\|ENA LAST UPDATE:2022 04 09	hom1_gata2b.bam	bam	18004290759.0	197849349.0	E MTAB 10370:hom1 gata2b	0:91	A:5232521408;C:3876317502;G:4287902596;T:4606191653;N:1357600	91		5232521408	3876317502	4287902596	4606191653	1357600	ERX5471110	ERS6291550	ERA4089475	Erasmus Medical Center\|European Nucleotide Archive	Erasmus Medical Center\|European Nucleotide Archive	1	0.94131		0.08871		0.83465		0.52792		91		B		usable mapping rate	illumina	novaseq_era	unknown	poly_a	unknown	sc	single_cell_droplet	10x	Netherlands	2022-04-09	Adult	Adult	Kidney	Renal System
68331	68331	SRR17714674	SRX13877735	SRS11747907	SRP356388	PRJNA799842	RNA seq of CRISPR/Cas9 mediated genome editing zebrafishes; the alligator pipefish spleen and the small white organ of the lined seahorse.	PRJNA799842	Other	To explore the function of the gene in spleen development we generated a knockout zebrafish line. To investigate whether the phenotypic consequences in the seahorses were caused by a missense mutation in this gene we generated a point mutation zebrafish line by CRISPR/Cas9 mediated homologous recombination HR. RNA seq of these samples tissues brain liver kidney and intestine were analyzed. In addition to clarify the splenic phenotype of the Syngnathidaes the transcriptomic profiles of the S. biaculeatus spleens and the H. erectus small white organ were also sampled and sequenced.				KO ki 2		strain:AB type\|isolate:knockout\|breed:KO ki 2\|age:3 month\|dev stage:NA\|sex:NA\|tissue:kidney\|BioSampleModel:Model organism or animal	RNA seq of zebrafish	KO ki 2	KO ki 2	RNA seq			RNA-Seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP356388		loader:fastq load.py	Daniorerio_KO-ki-2_good_1.fq.gz Daniorerio_KO-ki-2_good_2.fq.gz	fastq fastq	6459301738.0	21580856.0	Daniorerio KO ki 2 good 1.fq.gz	0:149.65 1:149.65	A:1784875806;C:1432248891;G:1473557552;T:1768292520;N:326969	149	149	1784875806	1432248891	1473557552	1768292520	326969	SRX13877735	SRS11747907	SRA1360632	South China Sea Institute of Oceanology\|CAS Key Laboratory of Tropical Marine Bio-Resource	South China Sea Institute of Oceanology	2	0.92356	0.92283	0.11927	0.11877	0.69116	0.69286	0.51648	0.51904	122	122	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	China	2022-01-27	Adult	Adult	Kidney	Renal System
68332	68332	SRR17714675	SRX13877734	SRS11747908	SRP356388	PRJNA799842	RNA seq of CRISPR/Cas9 mediated genome editing zebrafishes; the alligator pipefish spleen and the small white organ of the lined seahorse.	PRJNA799842	Other	To explore the function of the gene in spleen development we generated a knockout zebrafish line. To investigate whether the phenotypic consequences in the seahorses were caused by a missense mutation in this gene we generated a point mutation zebrafish line by CRISPR/Cas9 mediated homologous recombination HR. RNA seq of these samples tissues brain liver kidney and intestine were analyzed. In addition to clarify the splenic phenotype of the Syngnathidaes the transcriptomic profiles of the S. biaculeatus spleens and the H. erectus small white organ were also sampled and sequenced.				KO ki 1		strain:AB type\|isolate:knockout\|breed:KO ki 1\|age:3 month\|dev stage:NA\|sex:NA\|tissue:kidney\|BioSampleModel:Model organism or animal	RNA seq of zebrafish	KO ki 1	KO ki 1	RNA seq			RNA-Seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP356388		loader:fastq load.py	Daniorerio_KO-ki-1_good_1.fq.gz Daniorerio_KO-ki-1_good_2.fq.gz	fastq fastq	6099339068.0	20376162.0	Daniorerio KO ki 1 good 1.fq.gz	0:149.67 1:149.67	A:1680007435;C:1355561431;G:1393826814;T:1669638827;N:304561	149	149	1680007435	1355561431	1393826814	1669638827	304561	SRX13877734	SRS11747908	SRA1360632	South China Sea Institute of Oceanology\|CAS Key Laboratory of Tropical Marine Bio-Resource	South China Sea Institute of Oceanology	2	0.92276	0.92011	0.1239	0.12427	0.69353	0.69457	0.52537	0.52715	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	China	2022-01-27	Adult	Adult	Kidney	Renal System
68340	68340	SRR17714683	SRX13877726	SRS11747899	SRP356388	PRJNA799842	RNA seq of CRISPR/Cas9 mediated genome editing zebrafishes; the alligator pipefish spleen and the small white organ of the lined seahorse.	PRJNA799842	Other	To explore the function of the gene in spleen development we generated a knockout zebrafish line. To investigate whether the phenotypic consequences in the seahorses were caused by a missense mutation in this gene we generated a point mutation zebrafish line by CRISPR/Cas9 mediated homologous recombination HR. RNA seq of these samples tissues brain liver kidney and intestine were analyzed. In addition to clarify the splenic phenotype of the Syngnathidaes the transcriptomic profiles of the S. biaculeatus spleens and the H. erectus small white organ were also sampled and sequenced.				WT ki 7		strain:AB type\|isolate:wild type\|breed:WT ki 7\|age:3 month\|dev stage:NA\|sex:NA\|tissue:kidney\|BioSampleModel:Model organism or animal	RNA seq of zebrafish	WT ki 7	WT ki 7	RNA seq			RNA-Seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP356388		loader:fastq load.py	Daniorerio_WT-ki-7_good_1.fq.gz Daniorerio_WT-ki-7_good_2.fq.gz	fastq fastq	5728682916.0	19186928.0	Daniorerio WT ki 7 good 1.fq.gz	0:149.29 1:149.29	A:1579153464;C:1273656952;G:1312180039;T:1563403341;N:289120	149	149	1579153464	1273656952	1312180039	1563403341	289120	SRX13877726	SRS11747899	SRA1360632	South China Sea Institute of Oceanology\|CAS Key Laboratory of Tropical Marine Bio-Resource	South China Sea Institute of Oceanology	2	0.93765	0.9349	0.10683	0.10543	0.71248	0.71313	0.48682	0.50333	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	China	2022-01-27	Adult	Adult	Kidney	Renal System
68341	68341	SRR17714684	SRX13877725	SRS11747898	SRP356388	PRJNA799842	RNA seq of CRISPR/Cas9 mediated genome editing zebrafishes; the alligator pipefish spleen and the small white organ of the lined seahorse.	PRJNA799842	Other	To explore the function of the gene in spleen development we generated a knockout zebrafish line. To investigate whether the phenotypic consequences in the seahorses were caused by a missense mutation in this gene we generated a point mutation zebrafish line by CRISPR/Cas9 mediated homologous recombination HR. RNA seq of these samples tissues brain liver kidney and intestine were analyzed. In addition to clarify the splenic phenotype of the Syngnathidaes the transcriptomic profiles of the S. biaculeatus spleens and the H. erectus small white organ were also sampled and sequenced.				WT ki 4		strain:AB type\|isolate:wild type\|breed:WT ki 4\|age:3 month\|dev stage:NA\|sex:NA\|tissue:kidney\|BioSampleModel:Model organism or animal	RNA seq of zebrafish	WT ki 4	WT ki 4	RNA seq			RNA-Seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP356388		loader:fastq load.py	Daniorerio_WT-ki-4_good_1.fq.gz Daniorerio_WT-ki-4_good_2.fq.gz	fastq fastq	6538230102.0	21840569.0	Daniorerio WT ki 4 good 1.fq.gz	0:149.68 1:149.68	A:1712166805;C:1543306905;G:1570047290;T:1712688420;N:20682	149	149	1712166805	1543306905	1570047290	1712688420	20682	SRX13877725	SRS11747898	SRA1360632	South China Sea Institute of Oceanology\|CAS Key Laboratory of Tropical Marine Bio-Resource	South China Sea Institute of Oceanology	2	0.93239	0.93289	0.03511	0.03508	0.71285	0.71313	0.4785	0.48034	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	China	2022-01-27	Adult	Adult	Kidney	Renal System
68342	68342	SRR17714685	SRX13877724	SRS11747897	SRP356388	PRJNA799842	RNA seq of CRISPR/Cas9 mediated genome editing zebrafishes; the alligator pipefish spleen and the small white organ of the lined seahorse.	PRJNA799842	Other	To explore the function of the gene in spleen development we generated a knockout zebrafish line. To investigate whether the phenotypic consequences in the seahorses were caused by a missense mutation in this gene we generated a point mutation zebrafish line by CRISPR/Cas9 mediated homologous recombination HR. RNA seq of these samples tissues brain liver kidney and intestine were analyzed. In addition to clarify the splenic phenotype of the Syngnathidaes the transcriptomic profiles of the S. biaculeatus spleens and the H. erectus small white organ were also sampled and sequenced.				WT ki 3		strain:AB type\|isolate:wild type\|breed:WT ki 3\|age:3 month\|dev stage:NA\|sex:NA\|tissue:kidney\|BioSampleModel:Model organism or animal	RNA seq of zebrafish	WT ki 3	WT ki 3	RNA seq			RNA-Seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP356388		loader:fastq load.py	Daniorerio_WT-ki-3_good_1.fq.gz Daniorerio_WT-ki-3_good_2.fq.gz	fastq fastq	6535179260.0	21823644.0	Daniorerio WT ki 3 good 1.fq.gz	0:149.73 1:149.73	A:1783453491;C:1473349126;G:1511499971;T:1766854951;N:21721	149	149	1783453491	1473349126	1511499971	1766854951	21721	SRX13877724	SRS11747897	SRA1360632	South China Sea Institute of Oceanology\|CAS Key Laboratory of Tropical Marine Bio-Resource	South China Sea Institute of Oceanology	2	0.93369	0.93255	0.097	0.09643	0.67848	0.6788	0.51146	0.50793	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	China	2022-01-27	Adult	Adult	Kidney	Renal System
68343	68343	SRR17714686	SRX13877723	SRS11747896	SRP356388	PRJNA799842	RNA seq of CRISPR/Cas9 mediated genome editing zebrafishes; the alligator pipefish spleen and the small white organ of the lined seahorse.	PRJNA799842	Other	To explore the function of the gene in spleen development we generated a knockout zebrafish line. To investigate whether the phenotypic consequences in the seahorses were caused by a missense mutation in this gene we generated a point mutation zebrafish line by CRISPR/Cas9 mediated homologous recombination HR. RNA seq of these samples tissues brain liver kidney and intestine were analyzed. In addition to clarify the splenic phenotype of the Syngnathidaes the transcriptomic profiles of the S. biaculeatus spleens and the H. erectus small white organ were also sampled and sequenced.				WT ki 2		strain:AB type\|isolate:wild type\|breed:WT ki 2\|age:3 month\|dev stage:NA\|sex:NA\|tissue:kidney\|BioSampleModel:Model organism or animal	RNA seq of zebrafish	WT ki 2	WT ki 2	RNA seq			RNA-Seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP356388		loader:fastq load.py	Daniorerio_WT-ki-2_good_1.fq.gz Daniorerio_WT-ki-2_good_2.fq.gz	fastq fastq	7459816636.0	24952918.0	Daniorerio WT ki 2 good 1.fq.gz	0:149.48 1:149.48	A:2038726076;C:1677988595;G:1720392114;T:2022686081;N:23770	149	149	2038726076	1677988595	1720392114	2022686081	23770	SRX13877723	SRS11747896	SRA1360632	South China Sea Institute of Oceanology\|CAS Key Laboratory of Tropical Marine Bio-Resource	South China Sea Institute of Oceanology	2	0.92812	0.92786	0.12105	0.12019	0.69347	0.69463	0.51823	0.51342	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	China	2022-01-27	Adult	Adult	Kidney	Renal System
68358	68358	SRR17714701	SRX13877708	SRS11747880	SRP356388	PRJNA799842	RNA seq of CRISPR/Cas9 mediated genome editing zebrafishes; the alligator pipefish spleen and the small white organ of the lined seahorse.	PRJNA799842	Other	To explore the function of the gene in spleen development we generated a knockout zebrafish line. To investigate whether the phenotypic consequences in the seahorses were caused by a missense mutation in this gene we generated a point mutation zebrafish line by CRISPR/Cas9 mediated homologous recombination HR. RNA seq of these samples tissues brain liver kidney and intestine were analyzed. In addition to clarify the splenic phenotype of the Syngnathidaes the transcriptomic profiles of the S. biaculeatus spleens and the H. erectus small white organ were also sampled and sequenced.				MU ki 4		strain:AB type\|isolate:point mutation\|breed:MU ki 4\|age:3 month\|dev stage:NA\|sex:NA\|tissue:kidney\|BioSampleModel:Model organism or animal	RNA seq of zebrafish	MU ki 4	MU ki 4	RNA seq			RNA-Seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP356388		loader:fastq load.py	Daniorerio_MU-ki-4_good_1.fq.gz Daniorerio_MU-ki-4_good_2.fq.gz	fastq fastq	6642468464.0	22227277.0	Daniorerio MU ki 4 good 1.fq.gz	0:149.42 1:149.42	A:1806510861;C:1499915463;G:1544497199;T:1791210925;N:334016	149	149	1806510861	1499915463	1544497199	1791210925	334016	SRX13877708	SRS11747880	SRA1360632	South China Sea Institute of Oceanology\|CAS Key Laboratory of Tropical Marine Bio-Resource	South China Sea Institute of Oceanology	2	0.93502	0.93305	0.0993	0.09919	0.68519	0.68617	0.50471	0.502	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	China	2022-01-27	Adult	Adult	Kidney	Renal System
68359	68359	SRR17714702	SRX13877707	SRS11747881	SRP356388	PRJNA799842	RNA seq of CRISPR/Cas9 mediated genome editing zebrafishes; the alligator pipefish spleen and the small white organ of the lined seahorse.	PRJNA799842	Other	To explore the function of the gene in spleen development we generated a knockout zebrafish line. To investigate whether the phenotypic consequences in the seahorses were caused by a missense mutation in this gene we generated a point mutation zebrafish line by CRISPR/Cas9 mediated homologous recombination HR. RNA seq of these samples tissues brain liver kidney and intestine were analyzed. In addition to clarify the splenic phenotype of the Syngnathidaes the transcriptomic profiles of the S. biaculeatus spleens and the H. erectus small white organ were also sampled and sequenced.				MU ki 3		strain:AB type\|isolate:point mutation\|breed:MU ki 3\|age:3 month\|dev stage:NA\|sex:NA\|tissue:kidney\|BioSampleModel:Model organism or animal	RNA seq of zebrafish	MU ki 3	MU ki 3	RNA seq			RNA-Seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP356388		loader:fastq load.py	Daniorerio_MU-ki-3_good_1.fq.gz Daniorerio_MU-ki-3_good_2.fq.gz	fastq fastq	8129697250.0	27275691.0	Daniorerio MU ki 3 good 1.fq.gz	0:149.03 1:149.03	A:2186818686;C:1865874012;G:1906801031;T:2169800472;N:403049	149	149	2186818686	1865874012	1906801031	2169800472	403049	SRX13877707	SRS11747881	SRA1360632	South China Sea Institute of Oceanology\|CAS Key Laboratory of Tropical Marine Bio-Resource	South China Sea Institute of Oceanology	2	0.93373	0.93291	0.09256	0.09199	0.68363	0.68582	0.50121	0.49901	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	China	2022-01-27	Adult	Adult	Kidney	Renal System
68360	68360	SRR17714703	SRX13877706	SRS11747879	SRP356388	PRJNA799842	RNA seq of CRISPR/Cas9 mediated genome editing zebrafishes; the alligator pipefish spleen and the small white organ of the lined seahorse.	PRJNA799842	Other	To explore the function of the gene in spleen development we generated a knockout zebrafish line. To investigate whether the phenotypic consequences in the seahorses were caused by a missense mutation in this gene we generated a point mutation zebrafish line by CRISPR/Cas9 mediated homologous recombination HR. RNA seq of these samples tissues brain liver kidney and intestine were analyzed. In addition to clarify the splenic phenotype of the Syngnathidaes the transcriptomic profiles of the S. biaculeatus spleens and the H. erectus small white organ were also sampled and sequenced.				MU ki 2		strain:AB type\|isolate:point mutation\|breed:MU ki 2\|age:3 month\|dev stage:NA\|sex:NA\|tissue:kidney\|BioSampleModel:Model organism or animal	RNA seq of zebrafish	MU ki 2	MU ki 2	RNA seq			RNA-Seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP356388		loader:fastq load.py	Daniorerio_MU-ki-2_good_1.fq.gz Daniorerio_MU-ki-2_good_2.fq.gz	fastq fastq	8613479966.0	28864538.0	Daniorerio MU ki 2 good 1.fq.gz	0:149.21 1:149.21	A:2341268944;C:1952093439;G:1997306668;T:2322383690;N:427225	149	149	2341268944	1952093439	1997306668	2322383690	427225	SRX13877706	SRS11747879	SRA1360632	South China Sea Institute of Oceanology\|CAS Key Laboratory of Tropical Marine Bio-Resource	South China Sea Institute of Oceanology	2	0.92686	0.92514	0.10387	0.10349	0.68278	0.68465	0.5126	0.51299	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	China	2022-01-27	Adult	Adult	Kidney	Renal System
68361	68361	SRR17714704	SRX13877705	SRS11747878	SRP356388	PRJNA799842	RNA seq of CRISPR/Cas9 mediated genome editing zebrafishes; the alligator pipefish spleen and the small white organ of the lined seahorse.	PRJNA799842	Other	To explore the function of the gene in spleen development we generated a knockout zebrafish line. To investigate whether the phenotypic consequences in the seahorses were caused by a missense mutation in this gene we generated a point mutation zebrafish line by CRISPR/Cas9 mediated homologous recombination HR. RNA seq of these samples tissues brain liver kidney and intestine were analyzed. In addition to clarify the splenic phenotype of the Syngnathidaes the transcriptomic profiles of the S. biaculeatus spleens and the H. erectus small white organ were also sampled and sequenced.				MU ki 1		strain:AB type\|isolate:point mutation\|breed:MU ki 1\|age:3 month\|dev stage:NA\|sex:NA\|tissue:kidney\|BioSampleModel:Model organism or animal	RNA seq of zebrafish	MU ki 1	MU ki 1	RNA seq			RNA-Seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP356388		loader:fastq load.py	Daniorerio_MU-ki-1_good_1.fq.gz Daniorerio_MU-ki-1_good_2.fq.gz	fastq fastq	6361721340.0	21272731.0	Daniorerio MU ki 1 good 1.fq.gz	0:149.53 1:149.53	A:1764729780;C:1403968855;G:1444221125;T:1748483646;N:317934	149	149	1764729780	1403968855	1444221125	1748483646	317934	SRX13877705	SRS11747878	SRA1360632	South China Sea Institute of Oceanology\|CAS Key Laboratory of Tropical Marine Bio-Resource	South China Sea Institute of Oceanology	2	0.91983	0.91698	0.11213	0.11	0.69603	0.69816	0.51786	0.51691	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	China	2022-01-27	Adult	Adult	Kidney	Renal System
68375	68375	SRR17714718	SRX13877691	SRS11747864	SRP356388	PRJNA799842	RNA seq of CRISPR/Cas9 mediated genome editing zebrafishes; the alligator pipefish spleen and the small white organ of the lined seahorse.	PRJNA799842	Other	To explore the function of the gene in spleen development we generated a knockout zebrafish line. To investigate whether the phenotypic consequences in the seahorses were caused by a missense mutation in this gene we generated a point mutation zebrafish line by CRISPR/Cas9 mediated homologous recombination HR. RNA seq of these samples tissues brain liver kidney and intestine were analyzed. In addition to clarify the splenic phenotype of the Syngnathidaes the transcriptomic profiles of the S. biaculeatus spleens and the H. erectus small white organ were also sampled and sequenced.				KO ki 4		strain:AB type\|isolate:knockout\|breed:KO ki 4\|age:3 month\|dev stage:NA\|sex:NA\|tissue:kidney\|BioSampleModel:Model organism or animal	RNA seq of zebrafish	KO ki 4	KO ki 4	RNA seq			RNA-Seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP356388		loader:fastq load.py	Daniorerio_KO-ki-4_good_1.fq.gz Daniorerio_KO-ki-4_good_2.fq.gz	fastq fastq	7271417184.0	24262326.0	Daniorerio KO ki 4 good 1.fq.gz	0:149.85 1:149.85	A:1942212311;C:1672440540;G:1729389358;T:1927007172;N:367803	149	149	1942212311	1672440540	1729389358	1927007172	367803	SRX13877691	SRS11747864	SRA1360632	South China Sea Institute of Oceanology\|CAS Key Laboratory of Tropical Marine Bio-Resource	South China Sea Institute of Oceanology	2	0.93084	0.92784	0.10122	0.10007	0.70496	0.70648	0.52353	0.51998	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	China	2022-01-27	Adult	Adult	Kidney	Renal System
68376	68376	SRR17714719	SRX13877690	SRS11747863	SRP356388	PRJNA799842	RNA seq of CRISPR/Cas9 mediated genome editing zebrafishes; the alligator pipefish spleen and the small white organ of the lined seahorse.	PRJNA799842	Other	To explore the function of the gene in spleen development we generated a knockout zebrafish line. To investigate whether the phenotypic consequences in the seahorses were caused by a missense mutation in this gene we generated a point mutation zebrafish line by CRISPR/Cas9 mediated homologous recombination HR. RNA seq of these samples tissues brain liver kidney and intestine were analyzed. In addition to clarify the splenic phenotype of the Syngnathidaes the transcriptomic profiles of the S. biaculeatus spleens and the H. erectus small white organ were also sampled and sequenced.				KO ki 3		strain:AB type\|isolate:knockout\|breed:KO ki 3\|age:3 month\|dev stage:NA\|sex:NA\|tissue:kidney\|BioSampleModel:Model organism or animal	RNA seq of zebrafish	KO ki 3	KO ki 3	RNA seq			RNA-Seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP356388		loader:fastq load.py	Daniorerio_KO-ki-3_good_1.fq.gz Daniorerio_KO-ki-3_good_2.fq.gz	fastq fastq	7380278536.0	24738542.0	Daniorerio KO ki 3 good 1.fq.gz	0:149.17 1:149.17	A:1960997842;C:1716280740;G:1751732155;T:1950894353;N:373446	149	149	1960997842	1716280740	1751732155	1950894353	373446	SRX13877690	SRS11747863	SRA1360632	South China Sea Institute of Oceanology\|CAS Key Laboratory of Tropical Marine Bio-Resource	South China Sea Institute of Oceanology	2	0.92496	0.9235	0.12088	0.11977	0.69923	0.69968	0.53733	0.53696	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	China	2022-01-27	Adult	Adult	Kidney	Renal System
68886	68886	SRR18218068	SRX14364510	SRS12177805	SRP362416	PRJNA812715	Mutant IL7R collaborates with MYC to induce T cell Acute Lymphoblastic Leukemia	PRJNA812715	Other	T cell acute lymphoblastic leukemia T ALL is an aggressive pediatric cancer. Amongst the wide array of driver mutations 10% of T ALL patients display gain of function mutations in the IL 7 receptor alpha chain IL 7Ralpha encoded by IL7R which occur in different molecular subtypes of this disease. However it is still unclear whether IL 7R mutational activation is sufficient to transform T cell precursors. Also which genes cooperate with IL7R to drive leukemogenesis remain poorly defined. Here we demonstrate that mutant IL7R alone is capable of inducing T ALL with long latency in stable transgenic zebrafish and transformation is associated with MYC transcriptional activation. Additionally we find that mutant IL7R collaborates with Myc to induce early onset T ALL in transgenic zebrafish. T ALLs co expressing mutant IL7R and Myc show activation of STAT5 and AKT pathways harbor reduced numbers of apoptotic cells and remake tumors in transplanted zebrafish faster than T ALLs expressing Myc alone. Moreover limiting dilution cell transplantation experiments reveal that activated IL 7R signaling increases the overall frequency of leukemia propagating cells. Our work highlights a synergy between mutant IL7R and Myc in inducing T ALL and demonstrates that mutant IL7R enriches for leukemia propagating potential.				WKM CG1 1		strain:CG1\|age:not collected\|sex:not collected\|tissue:whole kidney marrow\|birth date: \|death date:16 07 2019\|genotype:Wild type\|biological replicate:WKM CG1 biological replicate 1\|BioSampleModel:Model organism or animal	RNA seq of Danio rerio whole kidney marrow CG1	WKM CG1 1	WKM CG1 1	CG1 WT zebrafish were sacrificed to harvest the whole kidney marrow WKM for further analysis. The RNA was extracted from WKM cells using the RNeasy Mini Kit according to the manufacturers instructions Qiagen. mRNA was enriched using magnetic beads with Oligo dT fragmented and converted to cDNA size selected and PCR amplified generating paired end 100 bp sequences using a Illumina NovaSeq 6000.			RNA-Seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP362416			FCHT5GHDSXX_L1_HKRDZEBmfpEAAARAAPEI-P1A1_1.fq.gz FCHT5GHDSXX_L1_HKRDZEBmfpEAAARAAPEI-P1A1_2.fq.gz	fastq fastq	18015161100.0	60050537.0	FCHT5GHDSXX L1 HKRDZEBmfpEAAARAAPEI P1A1 1.fq.gz	0:150 1:150	A:4626900295;C:4400273225;G:4421661364;T:4566300408;N:25808	150	150	4626900295	4400273225	4421661364	4566300408	25808	SRX14364510	SRS12177805	SRA1380603	Instituto de Medicina Molecular Joao Lobo Antunes\|JBarata lab	Instituto de Medicina Molecular Joao Lobo Antunes	2	0.94715	0.94844	0.03897	0.03893	0.72176	0.72182	0.51658	0.50581	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	Portugal	2022-03-04	Undetermined	Undetermined	Kidney	Renal System
68901	68901	SRR18218080	SRX14364495	SRS12177790	SRP362416	PRJNA812715	Mutant IL7R collaborates with MYC to induce T cell Acute Lymphoblastic Leukemia	PRJNA812715	Other	T cell acute lymphoblastic leukemia T ALL is an aggressive pediatric cancer. Amongst the wide array of driver mutations 10% of T ALL patients display gain of function mutations in the IL 7 receptor alpha chain IL 7Ralpha encoded by IL7R which occur in different molecular subtypes of this disease. However it is still unclear whether IL 7R mutational activation is sufficient to transform T cell precursors. Also which genes cooperate with IL7R to drive leukemogenesis remain poorly defined. Here we demonstrate that mutant IL7R alone is capable of inducing T ALL with long latency in stable transgenic zebrafish and transformation is associated with MYC transcriptional activation. Additionally we find that mutant IL7R collaborates with Myc to induce early onset T ALL in transgenic zebrafish. T ALLs co expressing mutant IL7R and Myc show activation of STAT5 and AKT pathways harbor reduced numbers of apoptotic cells and remake tumors in transplanted zebrafish faster than T ALLs expressing Myc alone. Moreover limiting dilution cell transplantation experiments reveal that activated IL 7R signaling increases the overall frequency of leukemia propagating cells. Our work highlights a synergy between mutant IL7R and Myc in inducing T ALL and demonstrates that mutant IL7R enriches for leukemia propagating potential.				WKM CG1 P2mut 7		strain:CG1\|age:8 month\|sex:not collected\|tissue:whole kidney marrow\|birth date:17 11 2018\|death date:17 07 2019\|genotype:rag2:hIL7R mut2 tdTomato\|biological replicate:WKM CG1 P2mut biological replicate 6\|BioSampleModel:Model organism or animal	RNA seq of Danio rerio whole kidney marrow stably expressing human mutant IL7R CG1	WKM CG1 P2mut 7	WKM CG1 P2mut 7	CG1 zebrafish stably expressing human mutant IL7R were sacrificed without xxx of overt leukemia and whole kidney marrow WKM was harvested for further analysis. The RNA was extracted from WKM cells using the RNeasy Mini Kit according to the manufacturers instructions Qiagen. mRNA was enriched using magnetic beads with Oligo dT fragmented and converted to cDNA size selected and PCR amplified generating paired end 100 bp sequences using a Illumina NovaSeq 6000.			RNA-Seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP362416			FCHT5GHDSXX_L1_HKRDZEBmfpEAAKRAAPEI-P26C2_1.fq.gz FCHT5GHDSXX_L1_HKRDZEBmfpEAAKRAAPEI-P26C2_2.fq.gz	fastq fastq	16762989900.0	55876633.0	FCHT5GHDSXX L1 HKRDZEBmfpEAAKRAAPEI P26C2 1.fq.gz	0:150 1:150	A:4442983154;C:3951385839;G:4007817362;T:4360778933;N:24612	150	150	4442983154	3951385839	4007817362	4360778933	24612	SRX14364495	SRS12177790	SRA1380603	Instituto de Medicina Molecular Joao Lobo Antunes\|JBarata lab	Instituto de Medicina Molecular Joao Lobo Antunes	2	0.94363	0.94514	0.04876	0.04869	0.73369	0.73379	0.53344	0.5343	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	Portugal	2022-03-04	Adult	Adult	Kidney	Renal System
68902	68902	SRR18218081	SRX14364494	SRS12177789	SRP362416	PRJNA812715	Mutant IL7R collaborates with MYC to induce T cell Acute Lymphoblastic Leukemia	PRJNA812715	Other	T cell acute lymphoblastic leukemia T ALL is an aggressive pediatric cancer. Amongst the wide array of driver mutations 10% of T ALL patients display gain of function mutations in the IL 7 receptor alpha chain IL 7Ralpha encoded by IL7R which occur in different molecular subtypes of this disease. However it is still unclear whether IL 7R mutational activation is sufficient to transform T cell precursors. Also which genes cooperate with IL7R to drive leukemogenesis remain poorly defined. Here we demonstrate that mutant IL7R alone is capable of inducing T ALL with long latency in stable transgenic zebrafish and transformation is associated with MYC transcriptional activation. Additionally we find that mutant IL7R collaborates with Myc to induce early onset T ALL in transgenic zebrafish. T ALLs co expressing mutant IL7R and Myc show activation of STAT5 and AKT pathways harbor reduced numbers of apoptotic cells and remake tumors in transplanted zebrafish faster than T ALLs expressing Myc alone. Moreover limiting dilution cell transplantation experiments reveal that activated IL 7R signaling increases the overall frequency of leukemia propagating cells. Our work highlights a synergy between mutant IL7R and Myc in inducing T ALL and demonstrates that mutant IL7R enriches for leukemia propagating potential.				WKM CG1 P2mut 6		strain:CG1\|age:8 month\|sex:not collected\|tissue:whole kidney marrow\|birth date:17 11 2018\|death date:17 07 2019\|genotype:rag2:hIL7R mut2 tdTomato\|biological replicate:WKM CG1 P2mut biological replicate 5\|BioSampleModel:Model organism or animal	RNA seq of Danio rerio whole kidney marrow stably expressing human mutant IL7R CG1	WKM CG1 P2mut 6	WKM CG1 P2mut 6	CG1 zebrafish stably expressing human mutant IL7R were sacrificed without xxx of overt leukemia and whole kidney marrow WKM was harvested for further analysis. The RNA was extracted from WKM cells using the RNeasy Mini Kit according to the manufacturers instructions Qiagen. mRNA was enriched using magnetic beads with Oligo dT fragmented and converted to cDNA size selected and PCR amplified generating paired end 100 bp sequences using a Illumina NovaSeq 6000.			RNA-Seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP362416			FCHT5GHDSXX_L1_HKRDZEBmfpEAAJRABPEI-P14B2_1.fq.gz FCHT5GHDSXX_L1_HKRDZEBmfpEAAJRABPEI-P14B2_2.fq.gz	fastq fastq	18194856000.0	60649520.0	FCHT5GHDSXX L1 HKRDZEBmfpEAAJRABPEI P14B2 1.fq.gz	0:150 1:150	A:4776137612;C:4328521118;G:4394651128;T:4695520357;N:25785	150	150	4776137612	4328521118	4394651128	4695520357	25785	SRX14364494	SRS12177789	SRA1380603	Instituto de Medicina Molecular Joao Lobo Antunes\|JBarata lab	Instituto de Medicina Molecular Joao Lobo Antunes	2	0.94185	0.94348	0.05607	0.05578	0.73332	0.73281	0.5284	0.52266	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	Portugal	2022-03-04	Adult	Adult	Kidney	Renal System
68903	68903	SRR18218082	SRX14364493	SRS12177788	SRP362416	PRJNA812715	Mutant IL7R collaborates with MYC to induce T cell Acute Lymphoblastic Leukemia	PRJNA812715	Other	T cell acute lymphoblastic leukemia T ALL is an aggressive pediatric cancer. Amongst the wide array of driver mutations 10% of T ALL patients display gain of function mutations in the IL 7 receptor alpha chain IL 7Ralpha encoded by IL7R which occur in different molecular subtypes of this disease. However it is still unclear whether IL 7R mutational activation is sufficient to transform T cell precursors. Also which genes cooperate with IL7R to drive leukemogenesis remain poorly defined. Here we demonstrate that mutant IL7R alone is capable of inducing T ALL with long latency in stable transgenic zebrafish and transformation is associated with MYC transcriptional activation. Additionally we find that mutant IL7R collaborates with Myc to induce early onset T ALL in transgenic zebrafish. T ALLs co expressing mutant IL7R and Myc show activation of STAT5 and AKT pathways harbor reduced numbers of apoptotic cells and remake tumors in transplanted zebrafish faster than T ALLs expressing Myc alone. Moreover limiting dilution cell transplantation experiments reveal that activated IL 7R signaling increases the overall frequency of leukemia propagating cells. Our work highlights a synergy between mutant IL7R and Myc in inducing T ALL and demonstrates that mutant IL7R enriches for leukemia propagating potential.				WKM CG1 P2mut 5		strain:CG1\|age:8 month\|sex:not collected\|tissue:whole kidney marrow\|birth date:17 11 2018\|death date:17 07 2019\|genotype:rag2:hIL7R mut2 tdTomato\|biological replicate:WKM CG1 P2mut biological replicate 4\|BioSampleModel:Model organism or animal	RNA seq of Danio rerio whole kidney marrow stably expressing human mutant IL7R CG1	WKM CG1 P2mut 5	WKM CG1 P2mut 5	CG1 zebrafish stably expressing human mutant IL7R were sacrificed without xxx of overt leukemia and whole kidney marrow WKM was harvested for further analysis. The RNA was extracted from WKM cells using the RNeasy Mini Kit according to the manufacturers instructions Qiagen. mRNA was enriched using magnetic beads with Oligo dT fragmented and converted to cDNA size selected and PCR amplified generating paired end 100 bp sequences using a Illumina NovaSeq 6000.			RNA-Seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP362416			FCHT5GHDSXX_L1_HKRDZEBmfpEAAIRAAPEI-P2A2_1.fq.gz FCHT5GHDSXX_L1_HKRDZEBmfpEAAIRAAPEI-P2A2_2.fq.gz	fastq fastq	18218380200.0	60727934.0	FCHT5GHDSXX L1 HKRDZEBmfpEAAIRAAPEI P2A2 1.fq.gz	0:150 1:150	A:4769839227;C:4349260666;G:4417289893;T:4681963719;N:26695	150	150	4769839227	4349260666	4417289893	4681963719	26695	SRX14364493	SRS12177788	SRA1380603	Instituto de Medicina Molecular Joao Lobo Antunes\|JBarata lab	Instituto de Medicina Molecular Joao Lobo Antunes	2	0.94341	0.94473	0.04954	0.04988	0.71192	0.7121	0.52338	0.52876	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	Portugal	2022-03-04	Adult	Adult	Kidney	Renal System
68904	68904	SRR18218083	SRX14364492	SRS12177787	SRP362416	PRJNA812715	Mutant IL7R collaborates with MYC to induce T cell Acute Lymphoblastic Leukemia	PRJNA812715	Other	T cell acute lymphoblastic leukemia T ALL is an aggressive pediatric cancer. Amongst the wide array of driver mutations 10% of T ALL patients display gain of function mutations in the IL 7 receptor alpha chain IL 7Ralpha encoded by IL7R which occur in different molecular subtypes of this disease. However it is still unclear whether IL 7R mutational activation is sufficient to transform T cell precursors. Also which genes cooperate with IL7R to drive leukemogenesis remain poorly defined. Here we demonstrate that mutant IL7R alone is capable of inducing T ALL with long latency in stable transgenic zebrafish and transformation is associated with MYC transcriptional activation. Additionally we find that mutant IL7R collaborates with Myc to induce early onset T ALL in transgenic zebrafish. T ALLs co expressing mutant IL7R and Myc show activation of STAT5 and AKT pathways harbor reduced numbers of apoptotic cells and remake tumors in transplanted zebrafish faster than T ALLs expressing Myc alone. Moreover limiting dilution cell transplantation experiments reveal that activated IL 7R signaling increases the overall frequency of leukemia propagating cells. Our work highlights a synergy between mutant IL7R and Myc in inducing T ALL and demonstrates that mutant IL7R enriches for leukemia propagating potential.				WKM CG1 P2mut 4		strain:CG1\|age:8 month\|sex:not collected\|tissue:whole kidney marrow\|birth date:17 11 2018\|death date:17 07 2019\|genotype:rag2:hIL7R mut2 tdTomato\|biological replicate:WKM CG1 P2mut biological replicate 3\|BioSampleModel:Model organism or animal	RNA seq of Danio rerio whole kidney marrow stably expressing human mutant IL7R CG1	WKM CG1 P2mut 4	WKM CG1 P2mut 4	CG1 zebrafish stably expressing human mutant IL7R were sacrificed without xxx of overt leukemia and whole kidney marrow WKM was harvested for further analysis. The RNA was extracted from WKM cells using the RNeasy Mini Kit according to the manufacturers instructions Qiagen. mRNA was enriched using magnetic beads with Oligo dT fragmented and converted to cDNA size selected and PCR amplified generating paired end 100 bp sequences using a Illumina NovaSeq 6000.			RNA-Seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP362416			FCHT5GHDSXX_L1_HKRDZEBmfpEAAHRABPEI-P85H1_1.fq.gz FCHT5GHDSXX_L1_HKRDZEBmfpEAAHRABPEI-P85H1_2.fq.gz	fastq fastq	18205310400.0	60684368.0	FCHT5GHDSXX L1 HKRDZEBmfpEAAHRABPEI P85H1 1.fq.gz	0:150 1:150	A:4801894426;C:4309153266;G:4380582553;T:4713653706;N:26449	150	150	4801894426	4309153266	4380582553	4713653706	26449	SRX14364492	SRS12177787	SRA1380603	Instituto de Medicina Molecular Joao Lobo Antunes\|JBarata lab	Instituto de Medicina Molecular Joao Lobo Antunes	2	0.94333	0.94441	0.04893	0.04829	0.73026	0.73101	0.52749	0.52823	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	Portugal	2022-03-04	Adult	Adult	Kidney	Renal System
68905	68905	SRR18218084	SRX14364491	SRS12177786	SRP362416	PRJNA812715	Mutant IL7R collaborates with MYC to induce T cell Acute Lymphoblastic Leukemia	PRJNA812715	Other	T cell acute lymphoblastic leukemia T ALL is an aggressive pediatric cancer. Amongst the wide array of driver mutations 10% of T ALL patients display gain of function mutations in the IL 7 receptor alpha chain IL 7Ralpha encoded by IL7R which occur in different molecular subtypes of this disease. However it is still unclear whether IL 7R mutational activation is sufficient to transform T cell precursors. Also which genes cooperate with IL7R to drive leukemogenesis remain poorly defined. Here we demonstrate that mutant IL7R alone is capable of inducing T ALL with long latency in stable transgenic zebrafish and transformation is associated with MYC transcriptional activation. Additionally we find that mutant IL7R collaborates with Myc to induce early onset T ALL in transgenic zebrafish. T ALLs co expressing mutant IL7R and Myc show activation of STAT5 and AKT pathways harbor reduced numbers of apoptotic cells and remake tumors in transplanted zebrafish faster than T ALLs expressing Myc alone. Moreover limiting dilution cell transplantation experiments reveal that activated IL 7R signaling increases the overall frequency of leukemia propagating cells. Our work highlights a synergy between mutant IL7R and Myc in inducing T ALL and demonstrates that mutant IL7R enriches for leukemia propagating potential.				WKM CG1 P2mut 3		strain:CG1\|age:8 month\|sex:not collected\|tissue:whole kidney marrow\|birth date:17 11 2018\|death date:17 07 2019\|genotype:rag2:hIL7R mut2 tdTomato\|biological replicate:WKM CG1 P2mut biological replicate 2\|BioSampleModel:Model organism or animal	RNA seq of Danio rerio whole kidney marrow stably expressing human mutant IL7R CG1	WKM CG1 P2mut 3	WKM CG1 P2mut 3	CG1 zebrafish stably expressing human mutant IL7R were sacrificed without xxx of overt leukemia and whole kidney marrow WKM was harvested for further analysis. The RNA was extracted from WKM cells using the RNeasy Mini Kit according to the manufacturers instructions Qiagen. mRNA was enriched using magnetic beads with Oligo dT fragmented and converted to cDNA size selected and PCR amplified generating paired end 100 bp sequences using a Illumina NovaSeq 6000.			RNA-Seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP362416			FCHT5GHDSXX_L1_HKRDZEBmfpEAAGRAAPEI-P73G1_1.fq.gz FCHT5GHDSXX_L1_HKRDZEBmfpEAAGRAAPEI-P73G1_2.fq.gz	fastq fastq	18143381100.0	60477937.0	FCHT5GHDSXX L1 HKRDZEBmfpEAAGRAAPEI P73G1 1.fq.gz	0:150 1:150	A:4669037373;C:4411451517;G:4473720090;T:4589145705;N:26415	150	150	4669037373	4411451517	4473720090	4589145705	26415	SRX14364491	SRS12177786	SRA1380603	Instituto de Medicina Molecular Joao Lobo Antunes\|JBarata lab	Instituto de Medicina Molecular Joao Lobo Antunes	2	0.94105	0.94205	0.0448	0.04442	0.71553	0.71581	0.5171	0.51695	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	Portugal	2022-03-04	Adult	Adult	Kidney	Renal System
68906	68906	SRR18218085	SRX14364490	SRS12177785	SRP362416	PRJNA812715	Mutant IL7R collaborates with MYC to induce T cell Acute Lymphoblastic Leukemia	PRJNA812715	Other	T cell acute lymphoblastic leukemia T ALL is an aggressive pediatric cancer. Amongst the wide array of driver mutations 10% of T ALL patients display gain of function mutations in the IL 7 receptor alpha chain IL 7Ralpha encoded by IL7R which occur in different molecular subtypes of this disease. However it is still unclear whether IL 7R mutational activation is sufficient to transform T cell precursors. Also which genes cooperate with IL7R to drive leukemogenesis remain poorly defined. Here we demonstrate that mutant IL7R alone is capable of inducing T ALL with long latency in stable transgenic zebrafish and transformation is associated with MYC transcriptional activation. Additionally we find that mutant IL7R collaborates with Myc to induce early onset T ALL in transgenic zebrafish. T ALLs co expressing mutant IL7R and Myc show activation of STAT5 and AKT pathways harbor reduced numbers of apoptotic cells and remake tumors in transplanted zebrafish faster than T ALLs expressing Myc alone. Moreover limiting dilution cell transplantation experiments reveal that activated IL 7R signaling increases the overall frequency of leukemia propagating cells. Our work highlights a synergy between mutant IL7R and Myc in inducing T ALL and demonstrates that mutant IL7R enriches for leukemia propagating potential.				WKM CG1 5		strain:CG1\|age:not collected\|sex:not collected\|tissue:whole kidney marrow\|birth date: \|death date:16 07 2019\|genotype:Wild type\|biological replicate:WKM CG1 biological replicate 5\|BioSampleModel:Model organism or animal	RNA seq of Danio rerio whole kidney marrow CG1	WKM CG1 5	WKM CG1 5	CG1 WT zebrafish were sacrificed to harvest the whole kidney marrow WKM for further analysis. The RNA was extracted from WKM cells using the RNeasy Mini Kit according to the manufacturers instructions Qiagen. mRNA was enriched using magnetic beads with Oligo dT fragmented and converted to cDNA size selected and PCR amplified generating paired end 100 bp sequences using a Illumina NovaSeq 6000.			RNA-Seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP362416			FCHT5GHDSXX_L1_HKRDZEBmfpEAAERABPEI-P49E1_1.fq.gz FCHT5GHDSXX_L1_HKRDZEBmfpEAAERABPEI-P49E1_2.fq.gz	fastq fastq	18184234500.0	60614115.0	FCHT5GHDSXX L1 HKRDZEBmfpEAAERABPEI P49E1 1.fq.gz	0:150 1:150	A:4903189861;C:4188361342;G:4259034739;T:4833623925;N:24633	150	150	4903189861	4188361342	4259034739	4833623925	24633	SRX14364490	SRS12177785	SRA1380603	Instituto de Medicina Molecular Joao Lobo Antunes\|JBarata lab	Instituto de Medicina Molecular Joao Lobo Antunes	2	0.93501	0.93633	0.05446	0.05438	0.71583	0.71368	0.5862	0.56886	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	Portugal	2022-03-04	Undetermined	Undetermined	Kidney	Renal System
68907	68907	SRR18218087	SRX14364489	SRS12177784	SRP362416	PRJNA812715	Mutant IL7R collaborates with MYC to induce T cell Acute Lymphoblastic Leukemia	PRJNA812715	Other	T cell acute lymphoblastic leukemia T ALL is an aggressive pediatric cancer. Amongst the wide array of driver mutations 10% of T ALL patients display gain of function mutations in the IL 7 receptor alpha chain IL 7Ralpha encoded by IL7R which occur in different molecular subtypes of this disease. However it is still unclear whether IL 7R mutational activation is sufficient to transform T cell precursors. Also which genes cooperate with IL7R to drive leukemogenesis remain poorly defined. Here we demonstrate that mutant IL7R alone is capable of inducing T ALL with long latency in stable transgenic zebrafish and transformation is associated with MYC transcriptional activation. Additionally we find that mutant IL7R collaborates with Myc to induce early onset T ALL in transgenic zebrafish. T ALLs co expressing mutant IL7R and Myc show activation of STAT5 and AKT pathways harbor reduced numbers of apoptotic cells and remake tumors in transplanted zebrafish faster than T ALLs expressing Myc alone. Moreover limiting dilution cell transplantation experiments reveal that activated IL 7R signaling increases the overall frequency of leukemia propagating cells. Our work highlights a synergy between mutant IL7R and Myc in inducing T ALL and demonstrates that mutant IL7R enriches for leukemia propagating potential.				WKM CG1 4		strain:CG1\|age:not collected\|sex:not collected\|tissue:whole kidney marrow\|birth date: \|death date:16 07 2019\|genotype:Wild type\|biological replicate:WKM CG1 biological replicate 4\|BioSampleModel:Model organism or animal	RNA seq of Danio rerio whole kidney marrow CG1	WKM CG1 4	WKM CG1 4	CG1 WT zebrafish were sacrificed to harvest the whole kidney marrow WKM for further analysis. The RNA was extracted from WKM cells using the RNeasy Mini Kit according to the manufacturers instructions Qiagen. mRNA was enriched using magnetic beads with Oligo dT fragmented and converted to cDNA size selected and PCR amplified generating paired end 100 bp sequences using a Illumina NovaSeq 6000.			RNA-Seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP362416			FCHT5GHDSXX_L1_HKRDZEBmfpEAADRAAPEI-P37D1_1.fq.gz FCHT5GHDSXX_L1_HKRDZEBmfpEAADRAAPEI-P37D1_2.fq.gz	fastq fastq	18145210500.0	60484035.0	FCHT5GHDSXX L1 HKRDZEBmfpEAADRAAPEI P37D1 1.fq.gz	0:150 1:150	A:4734947807;C:4358845691;G:4370947434;T:4680443888;N:25680	150	150	4734947807	4358845691	4370947434	4680443888	25680	SRX14364489	SRS12177784	SRA1380603	Instituto de Medicina Molecular Joao Lobo Antunes\|JBarata lab	Instituto de Medicina Molecular Joao Lobo Antunes	2	0.93212	0.93296	0.05289	0.05244	0.71433	0.71465	0.5085	0.49253	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	Portugal	2022-03-04	Undetermined	Undetermined	Kidney	Renal System
68908	68908	SRR18218088	SRX14364488	SRS12177783	SRP362416	PRJNA812715	Mutant IL7R collaborates with MYC to induce T cell Acute Lymphoblastic Leukemia	PRJNA812715	Other	T cell acute lymphoblastic leukemia T ALL is an aggressive pediatric cancer. Amongst the wide array of driver mutations 10% of T ALL patients display gain of function mutations in the IL 7 receptor alpha chain IL 7Ralpha encoded by IL7R which occur in different molecular subtypes of this disease. However it is still unclear whether IL 7R mutational activation is sufficient to transform T cell precursors. Also which genes cooperate with IL7R to drive leukemogenesis remain poorly defined. Here we demonstrate that mutant IL7R alone is capable of inducing T ALL with long latency in stable transgenic zebrafish and transformation is associated with MYC transcriptional activation. Additionally we find that mutant IL7R collaborates with Myc to induce early onset T ALL in transgenic zebrafish. T ALLs co expressing mutant IL7R and Myc show activation of STAT5 and AKT pathways harbor reduced numbers of apoptotic cells and remake tumors in transplanted zebrafish faster than T ALLs expressing Myc alone. Moreover limiting dilution cell transplantation experiments reveal that activated IL 7R signaling increases the overall frequency of leukemia propagating cells. Our work highlights a synergy between mutant IL7R and Myc in inducing T ALL and demonstrates that mutant IL7R enriches for leukemia propagating potential.				WKM CG1 3		strain:CG1\|age:not collected\|sex:not collected\|tissue:whole kidney marrow\|birth date: \|death date:16 07 2019\|genotype:Wild type\|biological replicate:WKM CG1 biological replicate 3\|BioSampleModel:Model organism or animal	RNA seq of Danio rerio whole kidney marrow CG1	WKM CG1 3	WKM CG1 3	CG1 WT zebrafish were sacrificed to harvest the whole kidney marrow WKM for further analysis. The RNA was extracted from WKM cells using the RNeasy Mini Kit according to the manufacturers instructions Qiagen. mRNA was enriched using magnetic beads with Oligo dT fragmented and converted to cDNA size selected and PCR amplified generating paired end 100 bp sequences using a Illumina NovaSeq 6000.			RNA-Seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP362416			FCHT5GHDSXX_L1_HKRDZEBmfpEAACRAAPEI-P25C1_1.fq.gz FCHT5GHDSXX_L1_HKRDZEBmfpEAACRAAPEI-P25C1_2.fq.gz	fastq fastq	18002689500.0	60008965.0	FCHT5GHDSXX L1 HKRDZEBmfpEAACRAAPEI P25C1 1.fq.gz	0:150 1:150	A:4624819223;C:4407791489;G:4420933608;T:4549119250;N:25930	150	150	4624819223	4407791489	4420933608	4549119250	25930	SRX14364488	SRS12177783	SRA1380603	Instituto de Medicina Molecular Joao Lobo Antunes\|JBarata lab	Instituto de Medicina Molecular Joao Lobo Antunes	2	0.94795	0.94827	0.03817	0.03816	0.72991	0.72987	0.49707	0.49202	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	Portugal	2022-03-04	Undetermined	Undetermined	Kidney	Renal System
68909	68909	SRR18218089	SRX14364487	SRS12177782	SRP362416	PRJNA812715	Mutant IL7R collaborates with MYC to induce T cell Acute Lymphoblastic Leukemia	PRJNA812715	Other	T cell acute lymphoblastic leukemia T ALL is an aggressive pediatric cancer. Amongst the wide array of driver mutations 10% of T ALL patients display gain of function mutations in the IL 7 receptor alpha chain IL 7Ralpha encoded by IL7R which occur in different molecular subtypes of this disease. However it is still unclear whether IL 7R mutational activation is sufficient to transform T cell precursors. Also which genes cooperate with IL7R to drive leukemogenesis remain poorly defined. Here we demonstrate that mutant IL7R alone is capable of inducing T ALL with long latency in stable transgenic zebrafish and transformation is associated with MYC transcriptional activation. Additionally we find that mutant IL7R collaborates with Myc to induce early onset T ALL in transgenic zebrafish. T ALLs co expressing mutant IL7R and Myc show activation of STAT5 and AKT pathways harbor reduced numbers of apoptotic cells and remake tumors in transplanted zebrafish faster than T ALLs expressing Myc alone. Moreover limiting dilution cell transplantation experiments reveal that activated IL 7R signaling increases the overall frequency of leukemia propagating cells. Our work highlights a synergy between mutant IL7R and Myc in inducing T ALL and demonstrates that mutant IL7R enriches for leukemia propagating potential.				WKM CG1 2		strain:CG1\|age:not collected\|sex:not collected\|tissue:whole kidney marrow\|birth date: \|death date:16 07 2019\|genotype:Wild type\|biological replicate:WKM CG1 biological replicate 2\|BioSampleModel:Model organism or animal	RNA seq of Danio rerio whole kidney marrow CG1	WKM CG1 2	WKM CG1 2	CG1 WT zebrafish were sacrificed to harvest the whole kidney marrow WKM for further analysis. The RNA was extracted from WKM cells using the RNeasy Mini Kit according to the manufacturers instructions Qiagen. mRNA was enriched using magnetic beads with Oligo dT fragmented and converted to cDNA size selected and PCR amplified generating paired end 100 bp sequences using a Illumina NovaSeq 6000.			RNA-Seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP362416			FCHT5GHDSXX_L1_HKRDZEBmfpEAABRAAPEI-P13B1_1.fq.gz FCHT5GHDSXX_L1_HKRDZEBmfpEAABRAAPEI-P13B1_2.fq.gz	fastq fastq	18005451300.0	60018171.0	FCHT5GHDSXX L1 HKRDZEBmfpEAABRAAPEI P13B1 1.fq.gz	0:150 1:150	A:4630108478;C:4397001180;G:4413434449;T:4564880633;N:26560	150	150	4630108478	4397001180	4413434449	4564880633	26560	SRX14364487	SRS12177782	SRA1380603	Instituto de Medicina Molecular Joao Lobo Antunes\|JBarata lab	Instituto de Medicina Molecular Joao Lobo Antunes	2	0.95098	0.95069	0.0373	0.03685	0.72312	0.72301	0.51708	0.51873	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	Portugal	2022-03-04	Undetermined	Undetermined	Kidney	Renal System
68910	68910	SRR18218086	SRX14364486	SRS12177781	SRP362416	PRJNA812715	Mutant IL7R collaborates with MYC to induce T cell Acute Lymphoblastic Leukemia	PRJNA812715	Other	T cell acute lymphoblastic leukemia T ALL is an aggressive pediatric cancer. Amongst the wide array of driver mutations 10% of T ALL patients display gain of function mutations in the IL 7 receptor alpha chain IL 7Ralpha encoded by IL7R which occur in different molecular subtypes of this disease. However it is still unclear whether IL 7R mutational activation is sufficient to transform T cell precursors. Also which genes cooperate with IL7R to drive leukemogenesis remain poorly defined. Here we demonstrate that mutant IL7R alone is capable of inducing T ALL with long latency in stable transgenic zebrafish and transformation is associated with MYC transcriptional activation. Additionally we find that mutant IL7R collaborates with Myc to induce early onset T ALL in transgenic zebrafish. T ALLs co expressing mutant IL7R and Myc show activation of STAT5 and AKT pathways harbor reduced numbers of apoptotic cells and remake tumors in transplanted zebrafish faster than T ALLs expressing Myc alone. Moreover limiting dilution cell transplantation experiments reveal that activated IL 7R signaling increases the overall frequency of leukemia propagating cells. Our work highlights a synergy between mutant IL7R and Myc in inducing T ALL and demonstrates that mutant IL7R enriches for leukemia propagating potential.				WKM CG1 P2mut 2		strain:CG1\|age:16 month\|sex:not collected\|tissue:whole kidney marrow\|birth date:17 03 2018\|death date:17 07 2019\|genotype:rag2:hIL7R mut2 tdTomato\|biological replicate:WKM CG1 P2mut biological replicate 1\|BioSampleModel:Model organism or animal	RNA seq of Danio rerio whole kidney marrow stably expressing human mutant IL7R CG1	WKM CG1 P2mut 2	WKM CG1 P2mut 2	CG1 zebrafish stably expressing human mutant IL7R were sacrificed without xxx of overt leukemia and whole kidney marrow WKM was harvested for further analysis. The RNA was extracted from WKM cells using the RNeasy Mini Kit according to the manufacturers instructions Qiagen. mRNA was enriched using magnetic beads with Oligo dT fragmented and converted to cDNA size selected and PCR amplified generating paired end 100 bp sequences using a Illumina NovaSeq 6000.			RNA-Seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP362416			FCHT5GHDSXX_L1_HKRDZEBmfpEAAFRAAPEI-P61F1_1.fq.gz FCHT5GHDSXX_L1_HKRDZEBmfpEAAFRAAPEI-P61F1_2.fq.gz	fastq fastq	18210767700.0	60702559.0	FCHT5GHDSXX L1 HKRDZEBmfpEAAFRAAPEI P61F1 1.fq.gz	0:150 1:150	A:4648945418;C:4475968423;G:4497341113;T:4588486811;N:25935	150	150	4648945418	4475968423	4497341113	4588486811	25935	SRX14364486	SRS12177781	SRA1380603	Instituto de Medicina Molecular Joao Lobo Antunes\|JBarata lab	Instituto de Medicina Molecular Joao Lobo Antunes	2	0.94563	0.94587	0.03836	0.03819	0.73148	0.73042	0.49281	0.49845	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	Portugal	2022-03-04	Adult	Adult	Kidney	Renal System

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CREATE TABLE run_metadata("run.accession" VARCHAR, "experiment.accession" VARCHAR, "sample.accession" VARCHAR, "study.accession" VARCHAR, bioproject VARCHAR, "study.title" VARCHAR, "study.alias" VARCHAR, "study.type" VARCHAR, "study.abstract" VARCHAR, "study.attributes" VARCHAR, "study.PMIDs" VARCHAR, "sample.description" VARCHAR, "sample.title" VARCHAR, "sample.alias" VARCHAR, "sample.centername" VARCHAR, "sample.attributes" VARCHAR, "GEOsample.title" VARCHAR, "GEOsample.dataprocessing" VARCHAR, "GEOsample.source" VARCHAR, "GEOsample.treatmentprotocol" VARCHAR, "GEOsample.extractprotocol" VARCHAR, "GEOsample.growthprotocol" VARCHAR, "GEOsample.characteristics" VARCHAR, "GEOsample.accession" VARCHAR, "experiment.title" VARCHAR, "experiment.alias" VARCHAR, "experiment.library_name" VARCHAR, "experiment.design_description" VARCHAR, "experiment.library_construction_protocol" VARCHAR, "experiment.attributes" VARCHAR, "experiment.library_strategy" VARCHAR, "experiment.library_source" VARCHAR, "experiment.library_selection" VARCHAR, "experiment.library_layout" VARCHAR, "experiment.platform" VARCHAR, "experiment.instrument_model" VARCHAR, "experiment.spot_descriptor" VARCHAR, "experiment.study_ref" VARCHAR, "run.title" VARCHAR, "run.attributes" VARCHAR, "run.filename" VARCHAR, "run.semantic_name" VARCHAR, "run.total_bases" DOUBLE, "run.total_spots" DOUBLE, "run.alias" VARCHAR, "run.read_lengths" VARCHAR, "run.base_counts" VARCHAR, "run.r1_length" BIGINT, "run.r2_length" BIGINT, "run.r3_length" BIGINT, "run.r4_length" BIGINT, "run.Acount" BIGINT, "run.Ccount" BIGINT, "run.Gcount" BIGINT, "run.Tcount" BIGINT, "run.Ncount" BIGINT, "run.experiment" VARCHAR, "run.pool_member" VARCHAR, "submission.accession" VARCHAR, "submission.srasource" VARCHAR, "submission.bioprojectsource" VARCHAR, "seqdetective.n_mates" BIGINT, "seqdetective.mapping_rate.mate1" DOUBLE, "seqdetective.mapping_rate.mate2" DOUBLE, "seqdetective.nofeature_rate.mate1" DOUBLE, "seqdetective.nofeature_rate.mate2" DOUBLE, "seqdetective.sparsity.mate1" DOUBLE, "seqdetective.sparsity.mate2" DOUBLE, "seqdetective.pos_strand_rate.mate1" DOUBLE, "seqdetective.pos_strand_rate.mate2" DOUBLE, "seqdetective.readlen.mate1" BIGINT, "seqdetective.readlen.mate2" BIGINT, "seqdetective.judgement.mate1" VARCHAR, "seqdetective.judgement.mate2" VARCHAR, "seqdetective.judgement.reason" VARCHAR, platform_family VARCHAR, instrument_generation VARCHAR, read_bias VARCHAR, selection_class VARCHAR, prep_kit VARCHAR, sc_or_bulk VARCHAR, tech_class VARCHAR, technology VARCHAR, tech_variant VARCHAR, "submission.bioprojectsource.country" VARCHAR, earliest_date DATE, devstage_curation VARCHAR, devstage_curation_coarse VARCHAR, tissue_curation VARCHAR, tissue_curation_coarse VARCHAR);;
CREATE INDEX idx_run_bioproject ON run_metadata(bioproject);;
CREATE INDEX idx_run_run_accession ON run_metadata("run.accession");;