Helmholtz Center Treg CD4+CD25+ M430v2 (Nov06) RMA modify this page

    Summary:


This is the first regulatory T cell (CD4+CD25+) data set generated by Prof. Dr. Klaus Schughart and colleagues at the Helmholtz Centre for Infection Research. Samples were processed using a total of 35 Affymetrix Mouse Expression 430 2.0 short oligomer microarrays (MOE430 2.0), of which 33 passed stringent quality control and error checking.

 

This is the first data freeze and the set is still private. Please contact Dr. Klaus Schughart for access.

 

About the material used to generate this set of data:

BXD spleen sample pools (from 2-3 mice) were obtained from a pathogen-free mice of the Dutch Mouse Phenomics Consortium (MPC) in Amsterdam. The mice were imported into the central animal facility at the HZI and kept at a pathogen-free status. The mice were euthanized using CO2 and spleenocytes prepared. At the age of preparation, most mice were between 17 and 22 weeks of age.

FACS sorting was applied to select the CD4 positive T-cells. These cells were further separated into CD4+CD25+ and CD4+CD25- pools.

 

The BXD genetic reference population of recombinant inbred strains consists of approximately 80 strains. Approximately 800 classical phenotypes from sets of 10 to 70 of these strains been integrated in the GeneNetwork. These data set includes expression values for 18 of the BXD strains made by Benjamin Taylor at the Jackson Laboratoryin the 1970s and 1990s (BXD1 through BXD40, as well as the two parental strains, C57BL/6J and DBA/2J. All of these strains are fully inbred, many well beyond the 100th filial (F) generation of inbreeding.

 

Strain

Sex

Age

Date of preparation

BXD6

f

17

31.01.2006

BXD6

m

18

31.01.2006

BXD14

m

17

31.01.2006

BXD34

f

17

01.02.2006

BXD40

f

17

01.02.2006

BXD40

m

17

02.02.2006

BXD12

f

17

14.02.2006

BXD2

f

17

14.02.2006

BXD33

m

17

14.02.2006

BXD11

m

18

14.02.2006

BXD18

f

17

15.02.2006

BXD18

m

18

15.02.2006

BXD23

m

18

15.02.2006

BXD9

f

21

05.04.2006

BXD9

m

21

05.04.2006

BXD32

f

21

06.04.2006

BXD32

m

22

06.04.2006

BXD2

m

21

06.04.2006

BXD39

f

18

11.04.2006

BXD33

f

19

11.04.2006

DBA2/J

m

21

11.04.2006

BXD21

f

19

12.04.2006

BXD16

f

18

12.04.2006

BXD21

m

18

12.04.2006

DBA/2J

f

16

10.05.2006

C57BL/6J

f

16

10.05.2006

BXD39

m

17

10.05.2006

BXD11

f

17

11.05.2006

BXD1

f

18

06.07.2006

BXD36

f

16

06.07.2006

BXD1

m

18

06.07.2006

BXD31

f

16

07.07.2006

BXD9

m

15

07.07.2006

 

About the array platform:

Affymetrix Mouse Genome 430 2.0 array: The 430v2 array consists of 992,936 useful 25-nucleotide probes that estimate the expression of approximately 39,000 transcripts and the majority of known genes and expressed sequence tags. The array sequences were selected late in 2002 using Unigene Build 107 by Affymetrix. The UTHSC group has recently reannotated all probe sets on this array, producing more accurate data on probe and probe set targets. All probes were aligned to the most recent assembly of the Mouse Genome (Build 34, mm6) using Jim Kent's BLAT program. Many of the probe sets have been manually curated by Jing Gu and Rob Williams.

 

About the array set:

Probe Set ID

probe_id:

sample_desc:

HZI1008 MOE430 2.0

HZI1008

BXD-06f (f1)

HZI1009 MOE430 2.0

HZI1009

BXD-06m (m2)

HZI1010 MOE430 2.0

HZI1010

BXD-14m (m3)

HZI1011 MOE430 2.0

HZI1011

BXD-34f (f4)

HZI1013 MOE430 2.0

HZI1013

BXD-40f (f6)

HZI1014 MOE430 2.0

HZI1014

BXD-40m (m7)

HZI1019 MOE430 2.0

HZI1019

BXD-12f (f10)

HZI1015 MOE430 2.0

HZI1015

BXD-02f (f8)

HZI1021 MOE430 2.0

HZI1021

BXD-33m (m11)

HZI1018 MOE430 2.0

HZI1018

BXD-11m (m9)

HZI1022 MOE430 2.0

HZI1022

BXD-18f (f14)

HZI1023 MOE430 2.0

HZI1023

BXD-18m (m13)

HZI1024 MOE430 2.0

HZI1024

BXD-23m (m15)

HZI1026 MOE430 2.0

HZI1026

BXD-09f (f17)

HZI1027 MOE430 2.0

HZI1027

BXD-09m (m16)

HZI1029 MOE430 2.0

HZI1029

BXD-32f (f18)

HZI1030 MOE430 2.0

HZI1030

BXD-32m (m19)

HZI1016 MOE430 2.0

HZI1016

BXD-02m (m20)

HZI1031 MOE430 2.0

HZI1031

BXD-39f (f22)

HZI1020 MOE430 2.0

HZI1020

BXD-33f (f23)

HZI1042 MOE430 2.0

HZI1042

DBA/2Jm (m21)

HZI1036 MOE430 2.0

HZI1036

BXD-21f (f25)

HZI1035 MOE430 2.0

HZI1035

BXD-16f (f26)

HZI1037 MOE430 2.0

HZI1037

BXD-21m (m24)

HZI1041 MOE430 2.0

HZI1041

DBA/2Jf (f27)

HZI1040 MOE430 2.0

HZI1040

C57BL/6Jf (f28)

HZI1032 MOE430 2.0

HZI1032

BXD-39m (m29)

HZI1017 MOE430 2.0

HZI1017

BXD-11f (f30)

HZI1033 MOE430 2.0

HZI1033

BXD-01f (f32)

HZI1038 MOE430 2.0

HZI1038

BXD-36f (f33)

HZI1034 MOE430 2.0

HZI1034

BXD-01m (m31)

HZI1039 MOE430 2.0

HZI1039

BXD-31f (f34)

HZI1028 MOE430 2.0

HZI1028

BXD-09m (m35)

 

 

About the data processing:

This data set was processed using the RMA protocol. We then calculated the log base 2 of the intensity signal and subsequently computed the Z scores for each value. We multiplied all Z scores by 2 and added 8. The consequence of this simple set of transformations is to produce a set of Z scores that have a mean of 8, a variance of 4, and a standard deviation of 2. The advantage of this modified Z score is that a two-fold difference in expression level (probe brightness level) corresponds approximately to a 1 unit difference.

 

DataDesk was then used to examine the statistical quality of the data. All except two fulfilled the stringency criteria, except for two arrays BXD27f and BXD34m which were subsequently excluded from the set.

 

DataDesk allows a rapid detection of subsets of probes that are particular sensitive to still unknown factors in array processing. Arrays can then be categorized at the probe level into "reaction classes." A reaction class is a group of arrays for which the expression of essentially all probes are colinear over the full range of log2 values. A single but large group of arrays (n = 32) processed in essentially the identical manner by a single operator can produce arrays belonging to as many as four different reaction classes. Reaction classes are NOT related to strain, age, sex, treatment, or any known biological parameter (technical replicates can belong to different reaction classes).

 

Acknowledgment:

These Data were generated by Prof. Dr. Klaus Schughart (Department of Experimental Mouse Genetics) and Dr. Dunja Bruder (Research Group Immune Regulation) at the Helmholtz Center for Infection research with the help of Dr. Lothar Gröbe (FACS sorting, Research Group Mucosal Immunity).

Funding was provided by the Helmholtz-Association and publicly funded research projects awarded to Klaus Schughart and Dunja Bruder.

 

 

This text file was generated by KS on November 18, 2006.