Fixes in SMD


The cgap plates 29, 30, 35 and 36 were mistracked such that plate 29
and 30 had been switched, and 35 and 36 had been switched, when they
had been repippetted into 384 well plates.  These plates had been used
in the following MAST plates, from the Stanford Functional Genomic
Facility:

MAST:1957
MAST:1958
MAST:1959
MAST:1961
MAST:1962
MAST:1963

These plates, in turn, had been printed in the following positions, in
the following prints:

MAST:1957 and MAST:1961

Print              Positions

SHAG               56 + 57
SHAH               54 + 53
SHAI               54 + 53
SHAJ               54 + 53
SHAK               54 + 53
SHAM               54 + 53
SHAN               54 + 53
SHAO               54 + 53
SHAP               54 + 53

MAST:1958 and MAST:1962

Print              Positions

SHP               33 + 34 
SHQ               48 + 49
SHR                7 +  9
SHS               54 + 53 
SHT               54 + 53
SHU               54 + 53
SHV               54 + 53
SHW               54 + 53

MAST:1959 and MAST:1963

Print              Positions

SHX                54 + 53
SHY                54 + 53
SHZ                54 + 53
SHAA               54 + 53
SHAB               52 + 51
SHAC               56 + 57
SHAD               54 + 53
SHAE               54 + 53
SHAE-DCT	   54 + 53

Thus each of the above prints had 384 clones that were incorrectly identified (4 x 96). A list of these clones, and their current annotation, is available here.

Targeted Fixes:


Plate 10 in print SHCB was found to be rotated - this affects the
identity of 384 clones.  A list of these clones is available here.

Plate 25 in print SHV was found to be rotated - this affects the
identity of 384 clones.  A list of these clones is available here.

Fixes : Part II - March 5th 2002

A 96 well plate, tracked as gf207sv413, was found to be inverted in all the 384 well plates it had been used in. It affects prints SHAQ through SHBT. The clones in the 96 well plate are available here. The affected plate was used in 384 well plates that appeared in the following positions in the following prints:


Print              Position

SHAQ               104 
SHAS               104 
SHAT               104 
SHAU               99 
SHAV               99 
SHAW               99 
SHAX               99 
SHAY               99 
SHAZ               99 
SHBA               99 
SHBB               99 
SHBC               99 
SHBD               99 
SHBE               101 
SHBF               101 
SHBG               101 
SHBH               101 
SHBI               101 
SHBJ               101 
SHBK               104 
SHBL               100 
SHBM               101 
SHBN               99 
SHBO               99 
SHBP               99 
SHBQ               101 
SHBR               99 
SHBS               101 
SHBT               101

Targeted fixes

The following 384 well plate flips were discovered, each of which is linked to a list of the affected clones.


SHBE : print plate 5                                            
SHBL : print plate 21                                           
SHBK : print plate 34

Fixes : Part III - March 26th 2002

Targeted Fixes:


Plate 22 in print SVC was found to be rotated - this affects the
identity of 384 clones.  A list of these clones is available here.

Plate 57 in print SHAX was found to be printed twice, and plate 58 was
not printed - this affects the identity of 384 clones.  A list of
these clones is available here.

Please send comments or questions to: array@genome.stanford.edu