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Identification of long non-protein coding RNAs in chicken skeletal muscle by Solexa sequencing

ABSTRACT: Deep sequencing as a high-throughput technology has been widely used in the transcriptome profiling in mammals. In the present study, we aimed to identify chicken lncRNAs ranging from 300-1600 nt long. Total RNAs from chicken skeletal muscle at the embryonic stage were fractionated by 6% urea PAGE. Selected RNA fractions (300-1600 nt) were sequenced by Solexa technology.

ORGANISM(S): Gallus gallus

PROVIDER: GSE28080 | GEO | 2012/02/20

SECONDARY ACCESSION(S): PRJNA139729

REPOSITORIES: GEO

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Identification of long non-protein coding RNAs in chicken skeletal muscle by Solexa sequencing

Project description:Deep sequencing as a high-throughput technology has been widely used in the transcriptome profiling in mammals. In the present study, we aimed to identify chicken lncRNAs ranging from 300-1600 nt long. Total RNAs from chicken skeletal muscle at the embryonic stage were fractionated by 6% urea PAGE. Selected RNA fractions (300-1600 nt) were sequenced by Solexa technology. Chicken eggs (White Leghorn) were incubated at 37.5°C for 10 days (E10), 12 days (E12), 14 days (E14), 18 days (E18). Skeletal muscles (pectoralis) were collected from chicken embryo incubated at above four stages. All muscle samples were immediately frozen in liquid nitrogen and stored at -80°C until RNA isolation. All embryonic manipulations were conducted in accordance with the protocols of the Chinese Academy of Medical Sciences and the Institutional Animal Care and Use Committee of Peking Union Medical College. The single 'Chicken_muscle' Sample represents muscle pooled from all four stages.

2012-02-20 | E-GEOD-28080 | biostudies-arrayexpress

Qualitative proteomics analysis of the chicken amniotic fluid

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chicken liver cells under mycotoxin treatment with iTRAQ sequencing

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Small RNA seq in ALKBH3 stable over expresion and control HeLa cells

Project description:Total RNA (100 μg) were denatured at 70 °C for 5 min and separated by a 15% TBE-Urea gel with 20/100 or 10/60 oligo length standard ladder (Integrated DNA Technologies, Coralville, IA). After visualized by SYBR Gold (Ref. S11494 from Life Technologies), tRFs (15~50 nt) in gels were cut according to sizes and recovered by small RNA PAGE recovery kit (Zymo Research, Irvine, CA, USA). The recovered tRFs was used to establish the library by NEB small RNA library preparation kit (E7330S).

2021-04-21 | GSE113490 | GEO

Small RNA-Seq in ALKBH3 stable over expression and control HeLa cells

2021-04-09 | GSE112870 | GEO

The small RNA profile in wildtype, R2D2 and loquacious mutant Drosophila

Project description:We used SOLiD technology to deep sequence libraries prepared from 18-35 nt PAGE purfied small RNAs derived from female Drosophila. The objective of our study was to compare the impact of R2D2 or loquacious mutantions on different small RNA populations in the fruit fly.

2009-11-04 | GSE18871 | GEO

Transcription profiling of chicken histone H1 variant deletion DT40 mutant cell

Project description:There are six histone H1 variant in chicken. 01H1/02H1/03H1/.10H1/H1L and H1R. In those variant we forcused on H1L and H1R those molecule were most similar H1 among six H1 variants. we established linker histone H1L and H1R deleted mutant in chicken B-cell derived DT40 cell and assay gene expression in normal condition in those mutant cells. The detail charactalization of those mutant cell was published in Takami et al., BBRC 268, 501-508 (2000) and Hashimoto et al., DNA repair (in press) Experiment Overall Design: There are six linker histone H1 variant in chicken. Linker histone was thought to be general gene supplesser. We established linker histone H1 variant mutant in chicken B-cell derived DT40 cell, and analyze total protein by 2D-PAGE to find up- or down- regulatd protein. In these mutant, there are some up regulated protein expression and down regulated protein expression (Takami et al., BBRC 268, 501-508 (2000), PubMedID 10679234). Experiment Overall Design: These 2D-PAGE experiment were limited at low density protein region, we use Affymetrix array to search the gene that were regulated specific linker histone H1 variant mutant. Experiment Overall Design: We assayed total gene expression profile in H1L and H1R deleted mutant cells. Experiment Overall Design: all mutant cells were cultured in normal culture condition in RPMI 1640 medium supplemented with 10 ÂµM 2-mercaptoethanol, 10% FCS (Biowest) and 1% chicken serum (Gibco) at 39.5ËC. Total RNA were isolated from exponently growing DT40 cells.

2008-11-08 | E-GEOD-5114 | biostudies-arrayexpress

Transcriptome analysis reveals differentially expressed genes associated with high rates of egg production in chicken hypothalamic-pituitary-ovarian axis

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2019-12-07 | GSE141588 | GEO

Gene expression during chicken myogenesis

Project description:Chick is an ideal model system for myogenesis study. Lots of genes would change their expression during myogenesis, however, is there any difference about gene expression between chick and mice? Our study represents the detailed analysis of the transcriptomes of chicken primary myoblasts, growing myoblasts, and myotubes, with biologic replicates, generated by RNA-seq technology. The data reported here may provide an important understanding of the genes involved in the regulation of chicken myogenesis.

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High-throughput sequencing of small RNAs in chicken somite embryos

Project description:High-throughput sequencing of small RNAs in chicken somite embryos Dissected tissue white leghorn chicken embryos was disaggregated and RNA extracted using the miRVana kit (Ambion). Small RNA fraction between 19 and 24 nt was isolated from 15% denaturing polyacrylamide gel and 15 micro gram was ligated to Solexa adaptors (Illumina) without de-phosphorylating and re-phosphorylating. The short RNAs were converted to DNA by RT-PCR following the Illumina protocol.

2009-04-27 | E-GEOD-15513 | biostudies-arrayexpress

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