Trans-NIH Jak-Stat Initiative - Expression Groups

File: EG003.1

GSP Experiment Group Samples

Row	Principal Investigator	Investigators	Cell type	Simple GSP ID (10)	GSP ID (9)	Genes WT/KO	Stim. (11)	Rep. (13)	Experiment Group ID (1)	Sample ID (3)	AffyPlat (14)	Date (15)	Affy .CEL file (16)	Folder (17)
1	Lothar Hennighausen	Peter Klover	mouse muscle	EG003.1-01	EG003.1-01.Muscle.Stat5MKO.42.GH	Stat5MKO	GH	biological	EG003.1	42	MOE430_2	2/9/2007	02-09-07_Hennighausen_PK_Mouse430_2_M42	02-08-07_Hennighausen_PK
2	Lothar Hennighausen	Peter Klover	mouse muscle	EG003.1-02	EG003.1-02.Muscle.Stat5MKO.43.GH	Stat5MKO	GH	biological	EG003.1	43	MOE430_2	2/9/2007	02-09-07_Hennighausen_PK_Mouse430_2_M43	02-08-07_Hennighausen_PK
3	Lothar Hennighausen	Peter Klover	mouse muscle	EG003.1-03	EG003.1-03.Muscle.WT.44.GH	WT	GH	biological	EG003.1	44	MOE430_2	2/9/2007	02-09-07_Hennighausen_PK_Mouse430_2_M44	02-08-07_Hennighausen_PK
4	Lothar Hennighausen	Peter Klover	mouse muscle	EG003.1-04	EG003.1-04.Muscle.WT.47.GH	WT	GH	biological	EG003.1	47	MOE430_2	2/9/2007	02-09-07_Hennighausen_PK_Mouse430_2_M47	02-08-07_Hennighausen_PK
5	Lothar Hennighausen	Peter Klover	mouse muscle	EG003.1-05	EG003.1-05.Muscle.Stat5MKO.48.GH	Stat5MKO	GH	biological	EG003.1	48	MOE430_2	2/9/2007	02-09-07_Hennighausen_PK_Mouse430_2_M48	02-08-07_Hennighausen_PK
6	Lothar Hennighausen	Peter Klover	mouse muscle	EG003.1-06	EG003.1-06.Muscle.WT.50.GH	WT	GH	biological	EG003.1	50	MOE430_2	2/9/2007	02-09-07_Hennighausen_PK_Mouse430_2_M50	02-08-07_Hennighausen_PK

EG003.1

Principal Investigator: Lothar Hennighausen
Investigators: Peter Klover, Weiping Chen
Experiment Group ID (1): EG003.1
Experiment Group: Muscle cells from control and Stat5-null 12-week mice with GH treatment
Summary of experiment (2): With GT treatment: three Stat5 fl/fl controls (#44, #47, and #50) and three Stat5 muscle-ko 12-week mice (Stat5MKO, #42, #43, and #48).
Purpose of experiment (2): Determine Stat5-dependent genes in the skeletal muscle with and without exogenous GH stimulation.
Experimental design (2): The treated mice were given growth hormone (GH) midday for 3 hours and quadriceps muscle was isolated RNA and frozen in dry ice. RNA was isolated using TriZol reagent (Invitrogen) followed by RNeasy column purification(Qiagen). The untreated mice quadriceps muscle was isolated midday and frozen in dry ice. RNA was prepared as before.
Stimulation (6): GH
Mouse (strain) or Human: mouse
Cell lines / tissue sample: Muscle
Genes WT: STAT5
Genes KO: STAT5-null
Affy chip(s) platform: MOE430_2
Dates samples were run: 2/9/2007
Sample Preparation (Lit. ref. is ok) (8): see Exper. Design
Purification procedure (e.g., FACS, Ab, etc.) (8): see Exper. Design
Journal ref. if published (ref. PubMed ID) or not yet: not yet
In mAdb DB (user, project name if yes) (8): (N.A.)
In GEO DB (ID if yes): GSE14710
In caArray DB (ID if yes): No
Data location (mAdb, Geo, DVD, FTP server, Web site, etc.): EDGE server
Additional documentation (file(s), etc.): (N.A.)

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.

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Home: Jak-Stat Prospector Revised: Mon Sep 28 15:09:36 EDT 2009