Dataset: Effects of HMGN variants on cellular transcription profile
HMGN (high mobility group N) is a family of intrinsically disordered nuclear proteins that binds to nucleosomes, alters the structure of...
HMGN (high mobility group N) is a family of intrinsically disordered nuclear proteins that binds to nucleosomes, alters the structure of chromatin and affects transcription. A major unresolved question is the extent of functional specificity, or redundancy, between the various members of the HMGN protein family. Here we analyze the transcriptional profile of cells in which the expression of various HMGN proteins has been either deleted or doubled. The results reveal an HMGN-variant specific effect on the fidelity of the cellular transcription profile, indicating that functionally, the various HMGN subtypes are not fully redundant. RNA was collected from either primary knock-out MEFs or SV40-transformed MEFs and MIN6 cells over expressing various HMGN proteins and mutants and hybridized to Affymetrix arrays. We obtained a double ammount of HMGN proteins in MEFs and MIN6 cells by retroviral infection and subsequent selection procedure. We collected all infected cells (pools, not clones) in order to eliminate the effect of viral integration in the genome.
- Species:
- mouse
- Samples:
- 51
- Source:
- E-GEOD-27546
- PubMed:
- 21278158
- Updated:
- Dec.12, 2014
- Registered:
- Nov.11, 2014
| Sample | GENOTYPE/VARIATION | CELL TYPE |
|---|---|---|
| GSM680215 | HMGN1 knock out | primary MEFs |
| GSM680215 | HMGN1 knock out | primary MEFs |
| GSM680215 | HMGN1 knock out | primary MEFs |
| GSM680218 | HMGN1 WT | primary MEFs |
| GSM680218 | HMGN1 WT | primary MEFs |
| GSM680218 | HMGN1 WT | primary MEFs |
| GSM68022 | HMGN3 knock out | primary MEFs |
| GSM68022 | HMGN3 knock out | primary MEFs |
| GSM68022 | HMGN3 knock out | primary MEFs |
| GSM680224 | HMGN3 WT | primary MEFs |
| GSM680224 | HMGN3 WT | primary MEFs |
| GSM680224 | HMGN3 WT | primary MEFs |
| GSM680227 | HMGN5 knock out | primary MEFs |
| GSM680227 | HMGN5 knock out | primary MEFs |
| GSM680227 | HMGN5 knock out | primary MEFs |
| GSM680230 | HMGN5 WT | primary MEFs |
| GSM680230 | HMGN5 WT | primary MEFs |
| GSM680230 | HMGN5 WT | primary MEFs |
| GSM680233 | empty vector OE | SV40 transformed MEFs |
| GSM680233 | empty vector OE | SV40 transformed MEFs |
| GSM680233 | empty vector OE | SV40 transformed MEFs |
| GSM680236 | HMGN1 OE | SV40 transformed MEFs |
| GSM680236 | HMGN1 OE | SV40 transformed MEFs |
| GSM680236 | HMGN1 OE | SV40 transformed MEFs |
| GSM680239 | HMGN2 OE | SV40 transformed MEFs |
| GSM680239 | HMGN2 OE | SV40 transformed MEFs |
| GSM680239 | HMGN2 OE | SV40 transformed MEFs |
| GSM680242 | HMGN3a OE | SV40 transformed MEFs |
| GSM680242 | HMGN3a OE | SV40 transformed MEFs |
| GSM680242 | HMGN3a OE | SV40 transformed MEFs |
| GSM680245 | HMGN5 OE | SV40 transformed MEFs |
| GSM680245 | HMGN5 OE | SV40 transformed MEFs |
| GSM680245 | HMGN5 OE | SV40 transformed MEFs |
| GSM680248 | HMGN5SE OE | SV40 transformed MEFs |
| GSM680248 | HMGN5SE OE | SV40 transformed MEFs |
| GSM680248 | HMGN5SE OE | SV40 transformed MEFs |
| GSM68025 | HMGN1_N2swap | SV40 transformed MEFs |
| GSM68025 | HMGN1_N2swap | SV40 transformed MEFs |
| GSM68025 | HMGN1_N2swap | SV40 transformed MEFs |
| GSM680254 | HMGN1_N3swap | SV40 transformed MEFs |
| GSM680254 | HMGN1_N3swap | SV40 transformed MEFs |
| GSM680254 | HMGN1_N3swap | SV40 transformed MEFs |
| GSM680257 | empty vector OE | MIN6 cells |
| GSM680257 | empty vector OE | MIN6 cells |
| GSM680257 | empty vector OE | MIN6 cells |
| GSM680260 | HMGN1 OE | MIN6 cells |
| GSM680260 | HMGN1 OE | MIN6 cells |
| GSM680260 | HMGN1 OE | MIN6 cells |
| GSM680263 | HMGN3a OE | MIN6 cells |
| GSM680263 | HMGN3a OE | MIN6 cells |
| GSM680263 | HMGN3a OE | MIN6 cells |