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| Status |
Public on Jun 14, 2012 |
| Title |
The B cell identity factor Pax5 regulates distinct transcriptional programs in early and late B lymphopoiesis |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
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| Summary |
Pax5 controls the identity and development of B cells by repressing lineage-inappropriate genes and activating B-cell-specific genes. Here, we used genome-wide approaches to identify Pax5 target genes in pro-B and mature B cells. In these cell types, Pax5 bound to 40% of the cis- regulatory elements defined by mapping Dnase I hypersensitive (DHS) sites, transcription start sites and histone modifications. Although Pax5 bound to 8,000 target genes, it regulated only 4% of them in pro-B and mature B cells by inducing enhancers at activated genes and eliminating DHS sites at repressed genes. Pax5-regulated genes in pro-B cells account for 23% of all expression changes occurring between common lymphoid progenitors and committed pro-B cells, which identifies Pax5 as an important regulator of this developmental transition. Regulated Pax5 target genes minimally overlap in pro-B and mature B cells, which reflects massive expression changes between these cell types. Hence, Pax5 controls B cell identity and function by regulating distinct target genes in early and late B lymphopoiesis.
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| Overall design |
44 samples (16 RNA-seq, 15 ChIP-seq, 6 DHS-seq, 5 Bio-ChIP-seq, 2 CAGE-seq). All but four samples in in 2 biological replicates (8819, 8275, 8095, 8666). WT and experimental samples are provided.
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| Contributor(s) |
Revilla-i-Domingo R, Bilic I, Vilagos B, Tagoh H, Ebert A, Tamir I, Smeenk L, Sommer A, Jaritz M, Trupke J |
| Citation(s) |
22669466 |
| Submission date |
May 18, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Meinrad Busslinger |
| E-mail(s) |
busslinger@imp.ac.at
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| Phone |
00431-79730
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| Organization name |
Instutute of Molecular Pathology
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| Street address |
Dr. Bohrgasse 7
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| City |
Vienna |
| ZIP/Postal code |
1030 |
| Country |
Austria |
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| Platforms (1) |
| GPL11002 |
Illumina Genome Analyzer IIx (Mus musculus) |
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| Samples (76)
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| GSM932902 |
RNA-seq BLP [8559] |
| GSM932903 |
RNA-seq pro-B [8817] |
| GSM932904 |
RNA-seq pro-B [8818] |
| GSM932905 |
RNA-seq pro-B [8819] |
| GSM932906 |
RNA-seq mature B [8276], 1 |
| GSM932907 |
RNA-seq mature B [8276], 2 |
| GSM932908 |
RNA-seq mature B [8159], 1 |
| GSM932909 |
RNA-seq mature B [8159], 2 |
| GSM932910 |
RNA-seq pro-B [8275], 1 |
| GSM932911 |
RNA-seq pro-B [8275], 2 |
| GSM932912 |
RNA-seq pro-B [8275], 3 |
| GSM932913 |
RNA-seq pro-B [8275], 4 |
| GSM932914 |
RNA-seq pro-B [8403] |
| GSM932915 |
RNA-seq pro-B [8404] |
| GSM932916 |
RNA-seq Pax5-deleted pro-B [8402] |
| GSM932917 |
RNA-seq Pax5-deleted pro-B [8405] |
| GSM932918 |
RNA-seq Pax5-deleted mature B [8743] |
| GSM932919 |
RNA-seq Pax5-deleted mature B [8742],1 |
| GSM932920 |
RNA-seq Pax5-deleted mature B [8742],2 |
| GSM932921 |
Pax5 Bio-ChIP-seq pro-B [8093], 1 |
| GSM932922 |
Pax5 Bio-ChIP-seq pro-B [8093], 2 |
| GSM932923 |
Pax5 Bio-ChIP-seq pro-B [8093], 3 |
| GSM932924 |
Pax5 Bio-ChIP-seq pro-B [8417] |
| GSM932925 |
Pax5 Bio-ChIP-seq mature B [8097], 1 |
| GSM932926 |
Pax5 Bio-ChIP-seq mature B [8097], 2 |
| GSM932927 |
Pax5 Bio-ChIP-seq mature B [8097], 3 |
| GSM932928 |
Pax5 Bio-ChIP-seq mature B [8097], 4 |
| GSM932929 |
Pax5 Bio-ChIP-seq mature B [8097], 5 |
| GSM932930 |
Pax5 Bio-ChIP-seq mature B [8090], 1 |
| GSM932931 |
Pax5 Bio-ChIP-seq mature B [8090], 2 |
| GSM932932 |
Control Bio-ChIP-seq mature B input [8095], 1 |
| GSM932933 |
Control Bio-ChIP-seq mature B input [8095], 2 |
| GSM932934 |
H3K4me1 ChIP-seq pro-B [8666] |
| GSM932935 |
H3K4me2 ChIP-seq pro-B [8114], 1 |
| GSM932936 |
H3K4me2 ChIP-seq pro-B [8114], 2 |
| GSM932937 |
H3K4me2 ChIP-seq pro-B [8109], 1 |
| GSM932938 |
H3K4me2 ChIP-seq pro-B [8109], 2 |
| GSM932939 |
H3K4me3 ChIP-seq pro-B [8115], 1 |
| GSM932940 |
H3K4me3 ChIP-seq pro-B [8115], 2 |
| GSM932941 |
H3K4me3 ChIP-seq pro-B [8110], 1 |
| GSM932942 |
H3K4me3 ChIP-seq pro-B [8110], 2 |
| GSM932943 |
H3K9ac ChIP-seq pro-B [8113], 1 |
| GSM932944 |
H3K9ac ChIP-seq pro-B [8113], 2 |
| GSM932945 |
H3K9ac ChIP-seq pro-B [8108], 1 |
| GSM932946 |
H3K9ac ChIP-seq pro-B [8108], 2 |
| GSM932947 |
H3K27me3 ChIP-seq pro-B [8111], 1 |
| GSM932948 |
H3K27me3 ChIP-seq pro-B [8111], 2 |
| GSM932949 |
H3K27me3 ChIP-seq pro-B [8111], 3 |
| GSM932950 |
H3K27me3 ChIP-seq pro-B [8116], 1 |
| GSM932951 |
H3K27me3 ChIP-seq pro-B [8116], 2 |
| GSM932952 |
H3K4me2 ChIP-seq mature B [8069], 1 |
| GSM932953 |
H3K4me2 ChIP-seq mature B [8069], 2 |
| GSM932954 |
H3K4me3 ChIP-seq mature B [8088], 1 |
| GSM932955 |
H3K4me3 ChIP-seq mature B [8088], 2 |
| GSM932956 |
H3K4me3 ChIP-seq mature B [8088], 3 |
| GSM932957 |
H3K4me3 ChIP-seq mature B [8070], 1 |
| GSM932958 |
H3K4me3 ChIP-seq mature B [8070], 2 |
| GSM932959 |
H3K9ac ChIP-seq mature B [8059], 1 |
| GSM932960 |
H3K9ac ChIP-seq mature B [8059], 2 |
| GSM932961 |
H3K9ac ChIP-seq mature B [8059], 3 |
| GSM932962 |
H3K9ac ChIP-seq mature B [8059], 4 |
| GSM932963 |
H3K9ac ChIP-seq mature B [8086] |
| GSM932964 |
H3K27me3 ChIP-seq mature B [8080], 1 |
| GSM932965 |
H3K27me3 ChIP-seq mature B [8080], 2 |
| GSM932966 |
CAGE-seq pro-B [8300] |
| GSM932967 |
CAGE-seq mature B [8300] |
| GSM932968 |
DHS-seq pro-B [8439], 1 |
| GSM932969 |
DHS-seq pro-B [8439], 2 |
| GSM932970 |
DHS-seq pro-B [8335] |
| GSM932971 |
DHS-seq Pax5-deleted pro-B [8953] |
| GSM932972 |
DHS-seq Pax5-deleted pro-B [8438] |
| GSM932973 |
DHS-seq mature B [8440] |
| GSM932974 |
DHS-seq mature B [8630] |
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| Relations |
| BioProject |
PRJNA167176 |
| SRA |
SRP013275 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE38046_RAW.tar |
3.2 Gb |
(http)(custom) |
TAR (of BED) |
SRA Run Selector |
| Processed data provided as supplementary file |
| Raw data are available in SRA |
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