Trans-NIH Jak-Stat Initiative - Expression Groups

File: EG001

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)	AffyPlat (14)	Date (15)	Affy .CEL file (16)	Folder (17)
1	Lothar Hennighausen	Bing-Mei Zhu	fetal mouse liver Ter119+ erythroid	EG001-01	EG001-01.Erythroid.Stat5KO.br1.noStim	Stat5-null	no-stimulation	biological	EG001	MOE430_2	6/8/2004	06-08-04_Hennighausen_Mouse430_2_KO1	06-08-04_Hennighausen.Celfiles
2	Lothar Hennighausen	Bing-Mei Zhu	fetal mouse liver Ter119+ erythroid	EG001-02	EG001-02.Erythroid.Stat5KO.br2.noStim	Stat5-null	no-stimulation	biological	EG001	MOE430_2	6/8/2004	06-08-04_Hennighausen_Mouse430_2_KO2	06-08-04_Hennighausen.Celfiles
3	Lothar Hennighausen	Bing-Mei Zhu	fetal mouse liver Ter119+ erythroid	EG001-03	EG001-03.Erythroid.Stat5KO.br3.noStim	Stat5-null	no-stimulation	biological	EG001	MOE430_2	6/8/2004	06-08-04_Hennighausen_Mouse430_2_KO3	06-08-04_Hennighausen.Celfiles
4	Lothar Hennighausen	Bing-Mei Zhu	fetal mouse liver Ter119+ erythroid	EG001-04	EG001-04.Erythroid.WT.br1.noStim	WT	no-stimulation	biological	EG001	MOE430_2	6/8/2004	06-08-04_Hennighausen_Mouse430_2_WT1	06-08-04_Hennighausen.Celfiles
5	Lothar Hennighausen	Bing-Mei Zhu	fetal mouse liver Ter119+ erythroid	EG001-05	EG001-05.Erythroid.WT.br2.noStim	WT	no-stimulation	biological	EG001	MOE430_2	6/8/2004	06-08-04_Hennighausen_Mouse430_2_WT2	06-08-04_Hennighausen.Celfiles
6	Lothar Hennighausen	Bing-Mei Zhu	fetal mouse liver Ter119+ erythroid	EG001-06	EG001-06.Erythroid.WT.br3.noStim	WT	no-stimulation	biological	EG001	MOE430_2	6/8/2004	06-08-04_Hennighausen_Mouse430_2_WT3	06-08-04_Hennighausen.Celfiles

EG001

Principal Investigator: Lothar Hennighausen
Investigators: Bing-Mei Zhu, Weiping Chen
Experiment Group ID (1): EG001
Experiment Group: Ter119+ erythroid cells from mouse fetal liver cells of control and Stat5-null mice
Summary of experiment (2): Determine some of the major up and down regulated genes dependent on Stat5. Especially iron metabolism-related genes were down regulated and resulted in impaired iron uptake into erythropoietic cells and then microcytic anemia.
Purpose of experiment (2): Determine Stat5-dependent genes in the Erythropoietic cells in Stat5-KO or WT mice.
Experimental design (2): Isolated Ter119-positive fetal liver cells from three to five E14.5 embryos of the same genotype were combined, and total RNA was extracted using TRIzol reagent (Life Technologies) with two additional ethanol precipitations. Microarray analyses were performed using Affymetrix Mouse Genome 430 2.0 array GeneChips (Affymetrix). Up- and down-regulated genes were selected based on P values of <0.05 and fold changes of >1.5 or -1.5 as assessed by ANOVA using Partek Pro software (Partek). To determine specific pathways, gene pathway analysis was obtained using the statistically significant gene list (P<0.05) represented on the chip.
Stimulation (6): (N.A.)
Mouse (strain) or Human: mouse
Cell lines / tissue sample: Erythroid
Genes WT: STAT5
Genes KO: STAT5-null
Affy chip(s) platform: MOE430_2
Dates samples were run: 6/8/2004
Sample Preparation (Lit. ref. is ok) (8): B-M Zhu et.al. Blood, 2008 112: 2071-2080
Purification procedure (e.g., FACS, Ab, etc.) (8): B-M Zhu et.al. Blood, 2008 112: 2071-2081
Journal ref. if published (ref. PubMed ID) or not yet: B-M Zhu et.al. Blood, 2008 112: 2071-2080
In mAdb DB (user, project name if yes) (8): (N.A.)
In GEO DB (ID if yes): GSE11777
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