run_metadata: 30011

This data as json

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
30011	SRR27663963	SRX23331817	SRS20194270	SRP484810	PRJNA1066877	p65 signaling dynamics drive the developmental progression of hematopoietic stem and progenitor cells through cell cycle regulation	GSE253758	Transcriptome Analysis	While hematopoietic stem and progenitor cells HSPCs and the signaling pathways that specify them have been well defined in vivo deriving functional HSPCs from human pluripotent stem cells hPSCs is still an outstanding challenge in the stem cell field. This has impaired efforts to use patient specific HSPCs and their derivatives to treat leukemia lymphoma anemia and solid cancers. Identifying the missing element to derive functional human HSPCs will be critical to advance these therapies. Here we found that in contrast to in vitro protocols where signaling pathways are typically manipulated statically the natural developmental progression of HSPC fate in the embryo requires a precise and temporally controlled oscillatory signaling dynamics. Particularly our work reveals that NF kB signaling works as an oscillatory clock that controls the developmental progression of HSPCs by driving phases of quiescence and proliferation precisely during embryonic development. This was revealed by live imaging of a custom NF kB zebrafish reporter line in conjunction with transcriptomic profiling and precise temporal manipulations of the NF kB family member p65 the driver of these signaling events. We also show that in vitro protocols of human hematopoietic differentiation from iPSCs depend on initial pro inflammatory signaling activation. In summary our results uncover the functional role of pro inflammatory signaling during HSPC specification revealed their oscillatory dynamics and define this signaling pathway as the main driver of HSPC fate progression. The integration of these dynamics in vitro will be fundamental to achieve the long standing goal of generating and expanding patient derived functional HSPCs. Overall design: To gain insights into how NF kB in endothelium was contributing to HSPC specification NFKB+ or NFKB endothelial cells kdrl+ were sorted and collected from 22hpf zebrafish embryos in triplicate and subject to RNA seq.		pubmed:39242546		NFKB+ biol rep 1	GSM8027547		tissue:endothelial cells\|cell type:endothelial cells\|genotype:NFKB:d2eGFP x kdrl:mCherry\|treatment:kdrl+/NFKB+ sorted\|geo loc name:missing\|collection date:missing	NFKB+ biol rep 1	Data was analyzed by ROSALIND® https://rosalind.bio/ with a HyperScale architecture developed by ROSALIND Inc. San Diego CA. Reads were trimmed using cutadapt. Reads were aligned to the Danio rerio genome build danRer10 using STAR. Individual sample reads were quantified using HTseq and normalized via Relative Log Expression RLE using DESeq2. Assembly: danRer10 Supplementary files format and content: comma delimited text files include fold change p values adjusted p values and normalized abundance values per sample for each gene	endothelial cells	22hpf NFKB:d2eGFP x kdrl:mCherry zebrafish embryos were screened with Leica M165FC stereomicroscope dechorionated with pronase Millipore Sigma; 11459643001 anesthetized in 1% tricaine Pentair; TRS5 and dissociated. Specifically the trunk region of each embryo was surgically isolated posterior to the yolk ball and anterior to the urogenital canal using a scalpel. The collected tissue was then gently vortexed at 28C for 5 20 mins with 50 µg/ml Liberase TM Millipore Sigma: 5401127001 in Dulbecco′s Phosphate Buffered Saline solution with Ca2+ and Mg2+ Millipore Sigma D8662. The resulting cell suspension was filtered through 30 µm nylon mesh Fisher Scientific; NC9084441 using a 21 gauge syringe Fisher Scientific; BD 309624 and stained with SYTOX™ Red Life Technologies; S34859 to exclude dead cells. Kdrl+/NFKB and kdrl+/NFKB+ cells were each sorted and collected with BD FACS Aria III. 7 000 cells per sample were collected by FACS in Eppendorf tubes containing 250 µl of RLT buffer.	RNA was then isolated and purified with RNeasy® Micro Kit Qiagen. DNase I treatment was performed as specified by the manufacturer. Total RNA was assessed for quality and quantity using an Agilent 2100 Bioanalyzer with RNA 6000 Pico Kit. Triplicate RNA samples of each condition were processed following manufacturer’s instructions. Samples were then used to generate RNA sequencing libraries using NEBNext Single Cell/Low Input RNA Library Prep Kit NEB #E6420S/L for Illumina and NEB's Unique Dual Index primers for Illumina E6440.	Zebrafish Danio rerio embryos and adults were mated staged raised and processed in a circulating aquarium system maintained at 26 °C on a 14 hr light/10 hr dark cycle.	cell type:endothelial cells\|genotype:NFKB:d2eGFP x kdrl:mCherry\|treatment:kdrl+/NFKB+ sorted	GSM8027547	GSM8027547: NFKB+ biol rep 1; Danio rerio; RNA Seq	GSM8027547 r1	GSM8027547	1	RNA was then isolated and purified with RNeasy® Micro Kit Qiagen. DNase I treatment was performed as specified by the manufacturer. Total RNA was assessed for quality and quantity using an Agilent 2100 Bioanalyzer with RNA 6000 Pico Kit. Triplicate RNA samples of each condition were processed following manufacturer's instructions. Samples were then used to generate RNA sequencing libraries using NEBNext Single Cell/Low Input RNA Library Prep Kit NEB #E6420S/L for Illumina and NEB's Unique Dual Index primers for Illumina E6440.		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000		SRP484810		loader:fastq load.py	1-RNA-0917_S1_L001_R1_001.fastq.gz	fastq	6201542500.0	62015425.0	GSM8027547 r1	0:100	A:1696049302;C:1431941155;G:1441395671;T:1632027072;N:129300	100				1696049302	1431941155	1441395671	1632027072	129300	SRX23331817	SRS20194270	SRA1788753	Iowa State University	Iowa State University												B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	nebnext	bulk	unknown	unknown		United States	2024-01-19	Multi-stage	Multi-stage	Endothelium	Cardiovascular System