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Bulk RNA sequencing on sorted blood cells from Drosophila lymph glands [MZ IZ bulk RNA-seq]

ABSTRACT: Bulk RNA sequencing on sorted blood cells from Drosophila lymph glands [MZ IZ bulk RNA-seq]

PROVIDER: PRJNA714094 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR13953621_1.fastq.gz	Fastqsanger.gz
	SRR13953621_2.fastq.gz	Fastqsanger.gz
	SRR13953622_1.fastq.gz	Fastqsanger.gz
	SRR13953622_2.fastq.gz	Fastqsanger.gz
	SRR13953623_1.fastq.gz	Fastqsanger.gz

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Bulk RNA sequencing on sorted blood cells from Drosophila lymph glands [MZ IZ bulk RNA-seq]

Project description:Bulk RNA sequencing on sorted blood cells from Drosophila lymph glands [MZ IZ bulk RNA-seq]

| PRJNA714094 | ENA

Bulk RNA sequencing on sorted blood cells from Drosophila lymph glands [MZ IZ bulk RNA-seq]

Project description:We report the use of bulk mRNA sequencing on FACS-sorted blood cells to identify new and unique genetic markers for each major zone of the Drosophila lymph gland. We used flow cytomotery in a wild-type genetic background whihc contains two fluorescent reporters that allow for the separation of 4 distinct populations. Progenitors of the medullary zone (MZ) are marked by dome-meso-EGFP expression. Differentitating cels of the cortical zone (CZ) are marked by Hml-DsRed. These two sorted populations (MZ and CZ) are positive for the expected zone-specific markers (i.e. Tep4, dome, and shg for MZ and Hml, Pxn, vkg, Col4a1, and NimC1 for plasmatocytes of the CZ), however, the CZ population also expresses crystal cell markers (hnt, lz, ProPO), indicating that it is a mix of plasmatocytes and crystal cells. Intermediate progenitors of the intermediate zone (IZ), which are not well understood and do not have specific markers, but are characterized by simultaneous expression of EGFP and DsRed (double positives) were also sorted. In addtiion, there is a population of lymph gland cells that is double negative for both EGFP and DsRed fluorescence. This double negative population contains a mix of cell types including posterior signaling center (PSC) cells, MZ and CZ cells that have lost fluorescence, late crystal cells that do not express Hml (early CCs do express), and non-blood cells (i.e. dorsal vessel and pericardial cells). These double negatives were excluded from the analysis for these reasons. We analyzed transcript data of these 4 sorted populations in the early third instart larvae (90-96 hours after eggs lay at 25 degrees C). We identified novel markers that are differentially expressed in each of the three major blood cell populations (MZ, IZ, CZ) that have been useful to definetely identify populations in scRNA-Seq and give information about transcript isoforms in each of the distinct populations.

2021-11-03 | GSE168821 | GEO

Single cell RNA-sequencing on blood cells from Drosophila lymph glands [scRNA-seq]

Project description:We report the use of single cell mRNA sequencing to identify new blood cell types, subtypes, genetic markers, and important developmental pathways in the Drosophila lymph gland. We analyzed transcript data for 21,157 cells from wild-type early third instar larvae (90-93 hours after eggs lay at 25 degrees C) which contain reporter constructs that mark progenitors and differentiated cells. We find that lymph gland blood cells can be catorgorized into 9 major clusters. One cluster corrresponds to the niche cells of the posterior signaling center (PSC) that expressed the PSC markers Antennopedia and Collier. Progenitors of the medullary zone (MZ) are found in two distinct clusters (MZ1 and MZ2), both of which express the MZ markers domeless and Tep4. One cluster contains intermediate progenitors of the intermediate zone (IZ), and these express markers such as CG30090, lectin-24A, and MFS3 that we found to be IZ-specific in previous bulk RNA-seq experiments with sorted lymph gland cells. Another cluster (PL) contains plasmatocytes that express NimC1, as well as Hml, Pxn, vkg, and Col4a1. Crystal cells are found in one major population that subclusters into two distinct subclusters (CC1 and CC2) that express the markers lz, Hnt, and proPO.. Another transitory population that we dub proplasmatocytes expresses Hml, Pxn, vkg, and Col4a1, but not PL marker Nimc1 or IZ-markers. One cluster is not well understood, butis highly enriched for cell cycle- and replication stress genes. Pseudotime and Trajectory analysis results in fruther sub-division of these zones based on pseudotime states and aids in building a model of lymph gland development that will be the basis for future studies.

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Bulk RNA sequencing on sorted blood cells from Drosophila lymph glands [PL iCC mCC bulk RNA-Seq]

Project description:Bulk RNA sequencing on sorted blood cells from Drosophila lymph glands [PL iCC mCC bulk RNA-Seq]

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Project description:We report the use of bulk mRNA sequencing on FACS-sorted blood cells to identify new and unique genetic markers for each major differentiated cell type of the Drosophila lymph gland. We used flow cytomotery in a wild-type genetic background whihc contains two fluorescent reporters that allow for the separation of 3 distinct populations. Plasmatcytes express the markers Hml, Pxn, vkg, Col4a1, and NimC1 , while crystal cells are markered by expression of hnt, lz, ProPO. mCC has higher expression of ProPO relitive to iCC, but lower expression of Hml and DsRed. We identified novel markers that are differentially expressed in each of the three major differentiated blood cell populations (PL, iCC, and mCC) that have been useful to definetely identify populations in scRNA-Seq and give information about transcript isoforms in each of the distinct populations.

2021-11-03 | GSE168820 | GEO

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Project description:Our single-cell and bulk transcriptome analyses revealed striking molecular heterogeneity in the mesenchymal cells of embryonic submandibular and parotid salivary glands during bud initiation, including distinct mesodermal and neural crest-derived molecular signatures that foreshadow later functions.

2019-10-25 | GSE127260 | GEO

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2024-05-15 | E-MTAB-14073 | biostudies-arrayexpress

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Investigation of somatic copy number variation in MZ twins

Project description:There is growing evidence that genomic DNA sequence changes occur in individual somatic cells during the lifetime of an individual and accumulation of these changes may influence aging and disease. In light of this, and contradicting reports regarding discordant copy number profiles between MZ twins(BARANZINI et al. 2010; BRUDER et al. 2008), we set out to identify de novo somatic copy number mutations in DNA from blood for MZ twin pairs of Mexican American descent who were participants of the San Antonio Family Heart Study (SAFHS) or San Antonio Family Diabetes/Gallbladder study (SAFDGS). By applying circular binary segmentation (CBS) to B-allele ratio differences we determined that the 3 MZ twin pairs in this study had concordant copy number profiles. We also detected 2 de novo germ-line CNVs in 2 MZ twin pairs from the SAFHS. This study includes data for 4 monozygotic (MZ) twin pairs, and both parents of 2 of these MZ twin pairs. The purpose of this study was to compare concordance of copy number profiles between MZ twins.

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