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Gain of chromatin loops marks the exit from naïve pluripotency – in-situ Hi-C data

ABSTRACT: In-situ Hi-C data for mouse embryonic stem cells (ES cells, grown in the presence of FBS and LIF) and for NS cells.

INSTRUMENT(S): NextSeq 500

ORGANISM(S): Mus musculus

SUBMITTER: Bernd Klaus

PROVIDER: E-MTAB-6591 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Genome-wide Chromatin Maps Derived from Limited Numbers of Hematopoietic Progenitors

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Cap analysis of gene expression (CAGE) of polysome-associated RNA against total RNA from human HEK293 cell line

Project description:In this study, we used CAGE followed by deep sequencing to globally profile the transcript 5’ isoforms in the translatome (i.e., polysome-associated RNA) and transcriptome (i.e., total RNA) of human HEK293 cells at single-nucleotide resolution. After removing low-quality sequencing reads, we obtained approximately 18 million and 14 million CAGE tags respectively for the translatome and transcriptome of HEK293 cells. These tags were then mapped to the human genome (assembly GRCh37) using bowtie with two mismatches allowed. Tags mapped to rRNA were less than 17.9% for translatome and 7.5% for transcriptome, indicating high quality of the two CAGE libraries. By comparing CAGE tags between HEK293's translatome and transcriptome, we revealed selective usage of the TSS-derived 5’ ends by polysome.

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Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

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