Trans-NIH Jak-Stat Initiative - Expression Groups

File: ExperimentGroups

GSP Experiment Groups Details

Row Principal Investigator Investigators Experiment Group ID (1) Experiment Group Summary of experiment (2) Purpose of experiment (2) Experimental design (2) Stimulation (6) Mouse (strain) or Human Cell lines / tissue sample Genes WT Genes KO Affy chip(s) platform Dates samples were run Sample Preparation (Lit. ref. is ok) (8) Purification procedure (e.g., FACS, Ab, etc.) (8) Journal ref. if published (ref. PubMed ID) or not yet In mAdb DB (user, project name if yes) (8) In GEO DB (ID if yes) In caArray DB (ID if yes) Data location (mAdb, Geo, DVD, FTP server, Web site, etc.) Additional documentation (file(s), etc.)
1 Lothar Hennighausen Bing-Mei Zhu, Weiping Chen EG001 Ter119+ erythroid cells from mouse fetal liver cells of control and Stat5-null mice 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. Determine Stat5-dependent genes in the Erythropoietic cells in Stat5-KO or WT mice. 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.   mouse Erythroid STAT5 STAT5-null MOE430_2 6/8/2004 B-M Zhu et.al. Blood, 2008 112: 2071-2080 B-M Zhu et.al. Blood, 2008 112: 2071-2081 B-M Zhu et.al. Blood, 2008 112: 2071-2080   GSE11777 No EDGE server  
2 Lothar Hennighausen Peter Klover, Weiping Chen EG003.1 Muscle cells from control and Stat5-null 12-week mice with GH treatment 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). Determine Stat5-dependent genes in the skeletal muscle with and without exogenous GH stimulation. 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. GH mouse Muscle STAT5 STAT5-null MOE430_2 2/9/2007 see Exper. Design see Exper. Design not yet   GSE14710 No EDGE server  
3 Lothar Hennighausen Peter Klover, Weiping Chen EG003.2 Muscle cells from control and Stat5-null 15-week mice without GH treatment Without GH treatment: experiment three Stat5 fl/fl controls (#4035, #4036, and #4042) and three Stat5MKO (#4038, #4060, and #4063) 15 week mice . Determine Stat5-dependent genes in the skeletal muscle with and without exogenous GH stimulation. 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. GH mouse Muscle STAT5 STAT5-null MOE430_2 6/10/2008 see Exper. Design see Exper. Design not yet   GSE14710 No EDGE server  

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