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Series GSE32190 Query DataSets for GSE32190
Status Public on Sep 08, 2013
Title Selective Functions of Individual Zinc Fingers Within the DNA-Binding Domain of Ikaros (RNA-seq: Thymocytes)
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Summary The C2H2 zinc finger is the most prevalent DNA-binding motif in the mammalian proteome, with DNA-binding domains usually containing more tandem fingers than are needed for stable sequence-specific DNA recognition. To examine the reason for the frequent presence of multiple zinc fingers, we generated mice lacking finger 1 or finger 4 of the 4-finger DNA-binding domain of Ikaros, a critical regulator of lymphopoiesis and leukemogenesis. Each mutant strain exhibited a specific subset of the phenotypes observed with Ikaros null mice. Of particular relevance, fingers 1 and 4 contributed to distinct stages of B- and T-cell development and finger 4 was selectively required for tumor suppression in thymocytes and in a new model of BCR-ABL+ acute lymphoblastic leukemia. These results, combined with transcriptome profiling (this GEO submission: RNA-Seg of whole thymus from wt and the two ZnF mutants), reveal that different subsets of fingers within multi-finger transcription factors can regulate distinct target genes and biological functions, and they demonstrate that selective mutagenesis can facilitate efforts to elucidate the functions and mechanisms of action of this prevalent class of factors.
 
Overall design RNA-Seq from Whole Thymus comparing wt (3 replicates), Ikaros-ZnF1-/- mutant (2 replicates) and Ikaros-ZnF4-/- mutant (2 replicates)
RPKM_Thymocytes.txt (linked below as a supplementary file) reports the relative mRNA expression levels (RPKM)values for all annotated Refseq genes that had at least one read in at least one of the samples, with duplicates for the same gene (different transcripts for same gene) filtered out. RPKM (Mortazavi et al., 2008) were calculated based on exonic reads obtained by using the software SeqMonk (Babraham Bioinformatics) and reference genome annotations from NCBI (mm9).
 
Contributor(s) Schjerven H, Smale ST
Citation(s) 24013668
Submission date Sep 16, 2011
Last update date Mar 19, 2019
Contact name Hilde Schjerven
Organization name UCSF
Department Laboratory Medicine
Street address 513 Parnassus Ave
City San Francisco
State/province CA
ZIP/Postal code 94143
Country USA
 
Platforms (2)
GPL9250 Illumina Genome Analyzer II (Mus musculus)
GPL13112 Illumina HiSeq 2000 (Mus musculus)
Samples (7)
GSM797702 wt Thymus rep1
GSM797703 Ikaros ZnF1-/- Thymus rep1
GSM797704 Ikaros ZnF4-/- Thymus rep1
This SubSeries is part of SuperSeries:
GSE33693 Selective Functions of Individual Zinc Fingers Within the DNA-Binding Domain of Ikaros
Relations
SRA SRP008272
BioProject PRJNA154865

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE32190_RAW.tar 16.4 Gb (http)(custom) TAR (of BAM, BEDGRAPH, BIGWIG, SAM)
GSE32190_RPKM_Thymocytes.txt.gz 377.8 Kb (ftp)(http) TXT
Raw data are available in SRA
Processed data provided as supplementary file
Processed data is available on Series record

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