Affymetrix GeneChip Murine Genome U74Av2 [MG_U74Av2]

Transcriptional profiling reveals a critical role for Gfi-1 in STAT3-dependent dendritic cell development and –function

rawData

scan

processedDataMatrix

To identify transcription factors that control dendritic cell development, we performed transcriptional profiling analyses of the murine hematopoietic progenitor cell line FDCP-mix that is permissive for DC differentiation in the presence of GMCSF.We reasoned that GM-CSF modulates a defined set of decisive transcription factors governing DC differentiation during the first few days.

Transcription profiling of early dendritic cell DC development in hematopoietic progenitor cell line FDCP-mix that is permissive for DC differentiation in the presence of GMCSF

Transcriptional profiling reveals a critical role for Gfi-1 in STAT3-dependent dendritic cell development and ÃÂfunction

To identify transcription factors that control dendritic cell development, we performed transcriptional profiling analyses of the murine hematopoietic progenitor cell line FDCP-mix that is permissive for DC differentiation in the presence of GMCSF.We reasoned that GM-CSF modulates a defined set of decisive transcription factors governing DC differentiation during the first few days.


Affymetrix:Protocol:ExpressionStat

Title: Affymetrix CHP Analysis (ExpressionStat). Description:

Affymetrix:Protocol:Hybridization-EukGE-WS2v3

Title: Affymetrix EukGE-WS2v3 Hybridization. Description:

Affymetrix:Protocol:Percentile

Title: Affymetrix CEL Analysis (Percentile). Description:

P-MEXP-4880

FDCP-mix cells were cultured in IMDM medium (GIBCO) supplemented with 20 % Horse serum  (GIBCO), 2mM L-glutamine, 1% Penicillin and streptomycin (GIBCO). 

P-MEXP-4881

FDCP-mix cells were not treated with r-mGM-CSF.RNA was isolated directly after starting the culture(0h).  

P-MEXP-4883

FDCP-mix cells were cultured in the presence of r-mGM-CSF (5ng/mL) and 1 % of WEHI supernatant. RNA was isolated 6h after starting the culture(6h).  

P-MEXP-4884

FDCP-mix cells were cultured in the presence of r-mGM-CSF (5ng/mL) and 1 % of WEHI supernatant. RNA was isolated 24h after starting the culture(24h). 

P-MEXP-4885

FDCP-mix cells were cultured in the presence of r-mGM-CSF (5ng/mL) and 1 % of WEHI supernatant. RNA was isolated 48h after starting the culture(48h). 

P-MEXP-4886

FDCP-mix cells were not treated with r-mGM-CSF.RNA was isolated 6h after starting the culture(6h).  

P-MEXP-4887

FDCP-mix cells were not treated with r-mGM-CSF.RNA was isolated 24h after starting the culture(24h).  

P-MEXP-4888

FDCP-mix cells were not treated with r-mGM-CSF.RNA was isolated 48h after starting the culture(48h).  

P-MEXP-4891

Total RNA was isolated  with “Absolutely RNA mini prep kit” (Stratagene, La Jolla, CA).

P-MEXP-4892

For biotin-labeled target synthesis starting from 3 µg of total RNA, reactions were performed using standard protocols supplied by the manufacturer (Affymetrix; Santa Clara, CA). Briefly, 5 µg total RNA were converted to dsDNA using 100 pmol of a T7T23V primer (Eurogentec; Seraing, Belgium) containing a T7 promotor. The cDNA was then used directly in an in-vitro transcription reaction in the presence of biotinylated nucleotides (ENZO BioArray HighYield RNA Transcript Labeling Kit). 

P-MEXP-4893

12.5 µg of each biotinylated cRNA preparation were fragmented and placed in a hybridization cocktail containing four biotinylated hybridization controls (BioB, BioC, BioD, and Cre) as recommended by the manufacturer. After incubation GeneChips were washed, stained with SA-PE and read using an Affymetrix GeneChip scanner (according to manufacturer´s gene chip expression analysis technical manual)  

P-MEXP-4894

For normalization all array experiments were scaled to a target intensity of 150 (for scaling 4% capped median is used), otherwise using the default values of the Microarray suite (MAS5). Quantitation types are described elsewere (Affymetrix Technical Note: “New Statistical Algorithms for Monitoring Gene Expression on GeneChip® Probe Arrays.” (2001))

Transcription profiling of early dendritic cell DC development in hematopoietic progenitor cell line FDCP-mix that is permissive for DC differentiation in the presence of GMCSF

Submitter Supplied Information

Samples