Expression Group Detailed Data

$$EXTRACT_ROW$$

Spreadsheet Notes

(1) The Experiment Group consists of one or more file folders of .CEL files (and possibly additional analysis data). This means that several sets of .CEL files may be part of the same experiment group. Each experiment group is assigned an identifier with a EG prefix such as EG003. If a group of related experiments should be split into several subgroups, then it is split into EG003.1, EG003.2, etc.
(2) The following annotation fields are entered once per experiment group of data:
Summary of experiment, Purpose of the experiment, and Experimental design.
(3) The Sample identifier is entered if it is different from the .CEL file name.
(4) Some sample names have a date inconsistent with the directory it is in. The sample date is the one used.
(5) We list all of stimulation agents in the Experiment Group.
(6) ---
(7) For details on each of the following Experiment Groups below, see the Experiment Groups sheet for the particular Experiment Group.
(8) If a paper reference is available then list it. Can be modified by in-press or in-prep or not-yet.
((9) Each sample gets a unique sample GSP ID using the following rule:
{Simple GSP ID}-{Tissue}.{GeneWT/KO}.{opt. Sample ID or 'br#' or "tr#"}.{Stimulation}.{opt. A or B}
Where: the {Simple GSP ID} is defined below in (10).
If there is no Sample ID, then the ".{Sample ID}" is just left off.
If there is no Sample ID and the sample is a replicate, to identify it we add "br1", "br2", etc. for biological replicates and "tr1", "tr2" etc. for technical replicates.
If a multichip platform is used, then the optional .A and .B are added.
Example: EG003.1-05.Muscle.Stat5MKO.48.GH
(10) Each sample gets a unique sample Simple GSP ID using the following rule:
EGx.y-n where x.y is the Experiment group and n is the index of the sample starting at 1 in the experiment group
Examples: EG006-03, EG003.1-01, EG003.1-02, etc.
(11) "Stim." is the stimulation if any.
(12) "Dur. Stim" is the duration of the stimulation
(13) "Rep." means is it a replicate. Put nothing, "biological", or "technical".
(14) "AffyPlat" is the Affy chip(s) platform, E.g., MOE430_2
(15) "Date" is the date the sample was run.
(16) "Affy .CEL file" nameis required with the ".CEL" file extension.
(17) "Folder" is the project or file folder source of the .CEL files from the Investigator.


This Web page was derived in collaboration with GSP consortium members.

Home: jak-stat.nih.gov
Home: Jak-Stat Prospector

Revised: $$DATE$$