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Degradome sequencing of urine-derived ADO2-iPSCs

ABSTRACT: To identify potential miRNA–mediated targets associated with osteopetrosis at the genome-wide level, two small RNA libraries and a degradome library were constructed from the ADO2-iPSCs and normal control human iPSCs (NC-iPSCs) for deep sequencing.

ORGANISM(S): Homo sapiens

PROVIDER: GSE133938 | GEO | 2022/07/08

REPOSITORIES: GEO

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Small RNA sequencing of urine-derived ADO2-iPSCs

Project description:To identify potential miRNA–mediated targets associated with osteopetrosis at the genome-wide level, two small RNA libraries and a degradome library were constructed from the ADO2-iPSCs and normal control human iPSCs (NC-iPSCs) for deep sequencing.

2021-11-03 | GSE133937 | GEO

Small RNA sequencing of urine-derived PS.

Project description:To identify potential miRNA–mediated targets associated with osteopetrosis at the genome-wide level, two small RNA libraries and a degradome library were constructed from the PS and normal control human iPSCs (NC-iPSCs) for deep sequencing.

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Depleting ribosomal RNA sequencing of urine-derived ADO2-iPSCs.

Project description:To construct comprehensive competing endogenous RNA (ceRNA) networks , depleting ribosomal RNA strand-specific libraries were constructed from the ADO2-iPSCs and normal control human iPSCs (NC-iPSCs) for deep RNA sequencing.

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Degradome sequencing of urine-derived ADO2-iPSCs

Project description:Degradome sequencing of urine-derived ADO2-iPSCs

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Degradome sequencing analysis in developing wheat grains

Project description:We aimed to identify targets of miRNAs during wheat grain development by using degradome sequencing approach. Two degradome libraries were constructed from wheat grains. Verification of miRNA targets from two degradome libraries in developing wheat grains.

2016-07-03 | E-GEOD-65798 | biostudies-arrayexpress

Degradome sequencing analysis in developing wheat grains

Project description:We aimed to identify targets of miRNAs during wheat grain development by using degradome sequencing approach. Two degradome libraries were constructed from wheat grains.

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An improved method of constructing degradome library suitable for Illumina high-throughput sequencing platform

Project description:Post-transcriptional gene regulation is a critical layer of overall gene expression programs and microRNAs (miRNAs) play an indispensable role in this process by guiding cleavage on the messenger RNA targets. The miRNA-guided cleavage on the mRNA targets can be confirmed by analyzing the sequenced degradome or PARE or GMUCT libraries. However, high-throughput sequencing of PARE or degradome libraries is not as straightforward as sequencing small RNA libraries. Moreover, the currently used degradome or PARE methods utilize Mme1 restriction site and the resulting fragments are only 20-nt long, which often poses difficulty in distinguishing between the family members of the same gene family. In this modified degradome protocol, EcoP15I recognition site is introduced to the 3' end of the 5’RNA adaptor of TruSeq small RNA library, the double strand DNA adaptor sequence is modified to suit with the ends generated by the EcoP15I. These modifications allow amplification of the degradome library by primer pairs used for small RNA library preparation. Therefore, degradome library generated using this protocol can be sequenced as easily as small RNA library, and the resulting tag length is ~27-nt, which is longer than previous methods (20-nt). The protocol allows sequencing small RNA and degradome libraries simultaneously.

2019-12-17 | GSE138545 | GEO

degradome sequence data

Project description:To identity the targets of miRNAs, we bundled 12 samples from different developing satages into four mixture samples. These samples were used to cosntruct degradome libraries and preform degradome sequencing on Illumina Hi-seq 2000 analyzer. More than 44.98 millions clean reads were obtained and 33.52 million reads were mapped to the soybean cDNA. The mapped reads were used to identity miRNA targets by CleaveLand4 pipeline. 4 degradome mixed samples, no replicates, but every degradome data consists of two parts data. Please note that every degradome sample has two processed and two raw data files. To have enough data, additional sequencing was performed from each sample library. And each sample raw data was processed separately (tissue_name*degradome.txt) and also combined (all_degradome*.txt).

2017-05-01 | E-GEOD-72903 | biostudies-arrayexpress

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Project description:Five degradome libraries were constructed from three different seed developmental stages. Separate degradome libraries were constructed for seed coat and cotyledons to identify the tissue specific miRNAs and their potential targets. Sequencing and analysis of degradome libraries gives identification of 183 different targets for 80 known soybean miRNAs. We found 30 cotyledon specific, 18 seed coat specific and 32 miRNAs found in both tissues irrespective of the developmental stages. One interesting observation is that we found more miRNA targets in late seed developmental stages than earlier stages. Additionally, we have validated four different auxin response factor genes as targets for gma-miR160 via RNA ligase mediated 5? rapid amplification of cDNA ends (RLM-5?RACE). GO analysis indicated the enrichment of miRNA target genes in seed development. Construction of degradome libraries using cotyledons and seed coats from 3 different developmental stages

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2015-12-24 | E-GEOD-43237 | biostudies-arrayexpress

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