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TranscriptomicsMating of the stichotrichous ciliate Oxytricha trifallax induces production of a class of 27nt small RNAs derived from the parental macronucleus
Here we report that soon after mating of Oxytricha trifallax, abundant 27nt small RNAs are produced that are not present prior to mating. We performed next generation sequencing of these 27nt RNAs from various times after mating. Using sequence comparisons between macronuclear and micronuclear versi...
ORGANISM(S): Oxytricha trifallax 
2012-04-19 | E-GEOD-37390 | biostudies-arrayexpress
TranscriptomicsChromatin Conformation Capture in two biological replicates of K562 cells to identify interactions between tRNA genes in human cells.
tRNA genes are believed to form clusters in three-dimensional space in smaller eukaryotes (yeasts). In the course of investigating a cluster of tRNA genes for insulator activity in humans, we addressed whether these tRNA genes clustered with other tRNA genes. We used an anchor point to generate 4C m...
ORGANISM(S): Homo sapiens 
2011-10-10 | E-GEOD-31105 | biostudies-arrayexpress
TranscriptomicsRNA-seq of postnatal day 0 (P0) wild-type and Satb2-/- cortices
The goal of the study was to compare gene expression of P0 wild-type and P0 Satb2-/- cortices. Total RNAs were isolated from P0 cortices dissected from wild-type and Satb2-/- mice (n=3 for each genotype), following Qiagen RNAeasy kit instruction.Sequence libraries were made following Illumina RNA Tr...
ORGANISM(S): Mus musculus 
2015-09-08 | E-GEOD-68911 | biostudies-arrayexpress
GenomicsChIP-seq for Satb2 in E15 cortex
The goal of the study was to identify the binding site of SATB2 in wild-ype cortex by performing ChIP-seq using SATB2 antibody. E15 cortical tissues were dissected, lysed and fixed. Chromatin was prepared by sonication. Sequences bound by SATB2 protein was precipitated using a SATB2 antibody. Sequen...
ORGANISM(S): Mus musculus 
2015-09-08 | E-GEOD-68910 | biostudies-arrayexpress
TranscriptomicsThe polyA+ transcriptomes of mouse embryonic stem cells and their derived neural precursors from strand-specific RNA-Seq
We have examined the nuclear (nuc) and cytoplasmic (cyt) polyA+ transcriptomes of undifferentiated mouse embryonic stem cells (un) and cells differentiated to neural precursors (d5) using strand-specific RNA-Seq. The 46C mouse embryonic stem cell line was used for this study. Two cell types were exa...
ORGANISM(S): Mus musculus 
2012-08-01 | E-GEOD-38990 | biostudies-arrayexpress
TranscriptomicsFragSeq: transcriptome-wide RNA structure probing using high-throughput sequencing.
To accelerate previous RNA structure probing approaches, which focus on analyzing one RNA sequence at a time, we have developed FragSeq, a high-throughput RNA structure probing method that uses high-throughput RNA sequencing to identify single-stranded RNA (ssRNA) regions from fragments generated by...
ORGANISM(S): Mus musculus 
2010-11-07 | E-GEOD-24622 | biostudies-arrayexpress
TranscriptomicsTranscription profiling of Pairwise comparisons of purified mouse LT-HSC, ST-HSC and MPP
Pairwise comparisons of purified mouse LT-HSC, ST-HSC and MPP.
ORGANISM(S): Mus musculus 
2005-09-09 | E-SMDB-3457 | biostudies-arrayexpress
TranscriptomicsIGF2BP3 controls cancer cell invasiveness by modulation RISC function
The goal of this study was to determine IGF2BP3 regulation of RNA targets in human pacreatic ductal adenocarcinoma cell lines Included are iCLIP-seq libraries for IGF2BP3 from PL45 and Panc1 PDAC cell samples, RIP-seq samples from PL45 and Panc1 PDAC cells, RNA-seq data sets from control and IGF2BP3...
ORGANISM(S): Homo sapiens 
2016-03-12 | E-GEOD-79147 | biostudies-arrayexpress
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