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Series GSE38842 Query DataSets for GSE38842
Status Public on Sep 08, 2013
Title Selective Functions of Individual Zinc Fingers Within the DNA-Binding Domain of Ikaros (RNA-seq: sorted proB cell Hardy Fractions B and C+C')
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 sorted primary proB cell Hardy Fractions B and C+C', comparing wt, Ikaros-ZnF1-/- mutant and Ikaros-ZnF4-/- mutant.
Contributor(s) Schjerven H, Smale ST
Citation(s) 24013668
Submission date Jun 21, 2012
Last update date May 15, 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 (1)
GPL13112 Illumina HiSeq 2000 (Mus musculus)
Samples (6)
GSM950636 sorted_Hardy_fraction_B_wt
GSM950637 sorted_Hardy_fraction_B_Ikaros_ZnF1-/-
GSM950638 sorted_Hardy_fraction_B_Ikaros_ZnF4-/-
This SubSeries is part of SuperSeries:
GSE33693 Selective Functions of Individual Zinc Fingers Within the DNA-Binding Domain of Ikaros
BioProject PRJNA169093
SRA SRP013847

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
GSE38842_RAW.tar 491.5 Mb (http)(custom) TAR (of BEDGRAPH)
GSE38842_RPKM_sorted_fraction_B_and_C.txt.gz 439.0 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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