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Series GSE39123 Query DataSets for GSE39123
Status Public on Nov 23, 2019
Title Role of Ikaros in Early B-cell Development: Studies of IkZnF1-/- and IkZnF4-/- mutant mice
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Summary Ikaros is a zinc finger (ZnF) transcription factor critical for B-cell development. 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 (Schjerven et al., Nat Immunol, 2013; PMID: 24013668). Each mutant strain exhibited a specific subset of the phenotypes observed with Ikaros null mice, and revealed that different subsets of fingers within multi-finger transcription factors can regulate distinct target genes and biological functions. We here study the effect of these mutants on early B-cell development in the bone marrow (BM) with transcriptome profiling of sorted proB-cells (Hardy fractions B+C+C') from BM of wt and the two ZnF mutants (this GEO submission: RNA-Seq).
Overall design RNA-Seq from sorted primary proB cells of combined Hardy Fractions B+C+C' (BC), comparing wt, Ikaros-ZnF1-/- mutant and Ikaros-ZnF4-/- mutant (B220+, CD19+, IgM-, CD24+, BP1+/-).
Contributor(s) Schjerven H, Smale ST
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Submission date Jul 05, 2012
Last update date Nov 24, 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 (3)
GSM956442 sorted_Hardy_fraction_BC_wt
GSM956443 sorted_Hardy_fraction_BC_Ikaros_ZnF1-/-
GSM956444 sorted_Hardy_fraction_BC_Ikaros_ZnF4-/-
BioProject PRJNA170057
SRA SRP014028

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Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE39123_RAW.tar 346.5 Mb (http)(custom) TAR (of BEDGRAPH)
GSE39123_RPKM_sorted_fraction_BC.txt.gz 343.2 Kb (ftp)(http) TXT
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Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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