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RNA sequencing of chicken limb distal mesenchyme cells to compare gene expression over time and in heterochronic grafted cells

ABSTRACT: RNA sequencing of chicken limb distal mesenchyme cells to compare gene expression over time and in heterochronic grafted cells

PROVIDER: PRJEB24716 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR2275580_1.fastq.gz	Fastqsanger.gz
	ERR2275580_2.fastq.gz	Fastqsanger.gz
	ERR2275581_1.fastq.gz	Fastqsanger.gz
	ERR2275581_2.fastq.gz	Fastqsanger.gz
	ERR2275582_1.fastq.gz	Fastqsanger.gz

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RNA sequencing of chicken limb distal mesenchyme to compare gene expression over time and in heterochronic grafted cells.

Project description:Distal limb mesenchyme cells were collected from embryonic chickens at Hamburger Hamilton (HH) stages HH24 and HH27, and from samples that had been grafted from HH20 to HH24 and left to develop for 24 hours. Bioinformatics and clustering analyses were then performed to determine whether grafted cells are more similar to HH24 (graft stage) or HH27 (host stage).

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RNA sequencing of chicken limb distal mesenchyme cells to compare gene expression over time and in heterochronic grafted cells

Project description:Distal limb mesenchyme cells were collected from embryonic chickens at Hamburger Hamilton (HH) stages HH24, HH27, and HH29, and also from samples that had been grafted from HH27 to HH20 and left to develop for 24 hours (equivalent to HH24). Samples were collected in triplicate (with 10 distal tips pooled per replicate), the RNA extracted, and sequenced on a HiSeq 2000 (Instrument: ST300). Bioinformatic and clustering analyses were performed to determine whether grafted cells are more similar to HH29 or HH24 samples, ie. which genes can be reset to expression levels observed in an earlier developmental stage.

2018-04-20 | E-MTAB-6437 | biostudies-arrayexpress

RNA sequencing of chicken limb distal mesenchyme to compare gene expression over time and in heterochronic grafted cells.

Project description:RNA sequencing of chicken limb distal mesenchyme to compare gene expression over time and in heterochronic grafted cells.

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Identification and characterization of novel and conserved microRNAs in self-grafted and grafted watermelon by high-throughput sequencing

Project description:In this study, Solexa sequencing technology has been used to discover small RNA populations of self-grafted watermelon and grafted watermelon (bottle gourd and squash were used as rootstocks). A total of 11,458,476, 11,614,094 and 9,339,089 raw reads representing 2,957,751, 2,880,328 and 2,964,990 unique sequences were obtained from the scions of self-grafted watermelon and watermelon grafted on-to bottle gourd and squash at two true-leaf stage, respectively. 39 known miRNAs belonging to 30 miRNA families and 80 novel miRNAs were identified in our small RNA dataset. Compared with self-grafted watermelon, 20 (5 known and 15 novel miRNAs) and 51 (21 known miRNAs and 30 novel miRNAs) miRNAs were expressed significantly different with higher abundance or lower abundance in watermelon grafted on to bottle gourd and squash, respectively. The differentially expressed miRNA target various transcriptional factors and other genes which involved in a wide range of biological processes. This study was firstly conducted to identify and compare miRNAs on genome-wide scale in watermelon grafting system. The miRNAs expressed differentially when watermelon was grafted onto different rootstocks suggesting that miRNAs might play an important role in diverse biological and metabolic processes in watermelon and grafting may possibly by changing miRNAs expression to regulate plant growth and response to stresses. The small RNA transcriptomes obtained in this study provided insights into molecular basis of miRNA regulation of genes expressed in self-grafted and grafted watermelon.

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