E-MTAB-6010 - RNA-Seq of 293T cells depleted of U2AF-related proteins

Submitted on 22 February 2015, last updated on 20 April 2018, released on 25 May 2018
Homo sapiens
Samples (6)
Protocols (7)
Characterization of RNA processing events dependent on U2AF-related proteins PUF60 and RBM39. PUF60 (poly-U-binding factor 60 kDa, also known as FIR, Hfp or Ro-bp1) is a splicing factor homologous to the 65 kD subunit of the auxiliary factor of U2 small nuclear ribonucleoprotein (U2AF65). PUF60 has two central RNA recognition motifs and a C-terminal U2AF homology motif (UHM), but lacks the N terminal arginine/serine-rich (RS) and UHM ligand motif (ULM) domains present in U2AF65. PUF60 activity, in conjunction with U2AF, facilitates the association of U2 snRNP with the pre-mRNA. PUF60 and U2AF65 can bind SF3b155 ULMs simultaneously and noncompetitively. RBM39 (also known as CAPERα, HCC1, FSAP59 or RNPC2) is an RNA processing factor and a hormone-dependent transcriptional coactivator. RBM39 domain structure is similar to PUF60, except for the extra N-terminal RS domain with unknown function. To understand function of the two proteins on a genome-wide scale, each protein was individually depleted from human embryonic kidney cell line 293 using RNAi to systematically characterize the PUF60- and RBM39-dependent exon usage.
Experiment types
RNA-seq of coding RNA, cell component comparison design, validation by real time PCR design
Global exon usage in cells depleted of U2AF-related proteins.
Exp. designProtocolsVariablesProcessedSeq. reads
Investigation descriptionE-MTAB-6010.idf.txt
Sample and data relationshipE-MTAB-6010.sdrf.txt