From d029d5d7f8ead1f1de8d318045004a4a6f68f5fb Mon Sep 17 00:00:00 2001 From: Bonface Date: Fri, 9 Feb 2024 09:41:28 -0600 Subject: Update dataset RTF Files. --- general/datasets/CMS_Hipp_ZScr_1115/cases.rtf | 992 +++++++++++++++++++++ .../CMS_Hipp_ZScr_1115/experiment-design.rtf | 9 + general/datasets/CMS_Hipp_ZScr_1115/processing.rtf | 3 + general/datasets/CMS_Hipp_ZScr_1115/specifics.rtf | 1 + general/datasets/CMS_Hipp_ZScr_1115/summary.rtf | 1 + general/datasets/CMS_Hipp_ZScr_1115/tissue.rtf | 1 + 6 files changed, 1007 insertions(+) create mode 100644 general/datasets/CMS_Hipp_ZScr_1115/cases.rtf create mode 100644 general/datasets/CMS_Hipp_ZScr_1115/experiment-design.rtf create mode 100644 general/datasets/CMS_Hipp_ZScr_1115/processing.rtf create mode 100644 general/datasets/CMS_Hipp_ZScr_1115/specifics.rtf create mode 100644 general/datasets/CMS_Hipp_ZScr_1115/summary.rtf create mode 100644 general/datasets/CMS_Hipp_ZScr_1115/tissue.rtf (limited to 'general/datasets/CMS_Hipp_ZScr_1115') diff --git a/general/datasets/CMS_Hipp_ZScr_1115/cases.rtf b/general/datasets/CMS_Hipp_ZScr_1115/cases.rtf new file mode 100644 index 0000000..c201f08 --- /dev/null +++ b/general/datasets/CMS_Hipp_ZScr_1115/cases.rtf @@ -0,0 +1,992 @@ +

The original data set included four individuals of each strain under baseline (B) conditions and eight individuals from each strain for each of the treatment groups, chronic mild stress (C), acute restraint (R), and chronic mild stress followed by acute retraint (CR). However, some samples have been removed due to technical problems with tissue collection or microarray performance.

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MTA_IDMTA prefixGN_IDFM_IDMouse_IDCaseIdStrainStrain_CodeTreatment codeNanoDrop, ng/ulNanoDrop, 260/280NanoDrop, 260/230Agilent, ng/µlRINNotes
1BCJ 1.CMS_D-B-215-1CMS_000215215020615.01DBA/2JDB163.611.92.311308.6 
2BCJ 2.CMS_D-C-86-1CMS_00008686012115.23DBA/2JDC98.511.792.43298.8 
3BCJ 3.CMS_D-CR-94-1CMS_00009494012115.16DBA/2JDCR162.781.872.381669.2 
4BCJ 4.CMS_D-R-133-1CMS_000133133012115.14DBA/2JDR88.951.822.45908.2 
5BCJ 5.CMS_B-B-208-1CMS_000208208012215.04C57BL/6JBB129.241.862.412238.1 
6BCJ 6.CMS_B-C-101-1CMS_000101101012115.25C57BL/6JBC72.291.862.261359.2 
7BCJ 7.CMS_B-CR-109-1CMS_000109109012115.21C57BL/6JBCR158.561.72.463058.8Microarray outlier; sample removed.
8BCJ 8.CMS_B-R-143-1CMS_000143143012215.08C57BL/6JBR161.571.862.382179.3 
9BCJ 9.CMS_N-B-210-1CMS_000210210012115.04C57BL/6NJNB132.391.892.31928.5 
10BCJ 10.CMS_N-C-117-1CMS_000117117012115.30C57BL/6NJNC151.431.912.381878.8 
11BCJ 11.CMS_N-CR-126-1CMS_000126126012115.33C57BL/6NJNCR137.871.882.29769 
12BCJ 12.CMS_N-R-152-1CMS_000152152012215.29C57BL/6NJNR197.951.882.351509.1 
13BCJ 13.CMS_D-B-216-1CMS_000216216020615.02DBA/2JDB98.641.912.03608.6 
15BCJ 15.CMS_D-CR-93-1CMS_00009393012115.11DBA/2JDCR71.361.832.251098.5 
16BCJ 16.CMS_D-R-134-1CMS_000134134012115.17DBA/2JDR73.491.852.431498.2 
17BCJ 17.CMS_B-B-205-1CMS_000205205012015.02C57BL/6JBB174.782.022.212668.9 
18BCJ 18.CMS_B-C-104-1CMS_000104104012215.30C57BL/6JBC84.72.642.011689.2 
19BCJ 19.CMS_B-CR-110-1CMS_000110110012115.26C57BL/6JBCR136.71.962.161789.5 
20BCJ 20.CMS_B-R-141-1CMS_000141141012115.22C57BL/6JBR86.0420.22.532088.9 
21BCJ 21.CMS_N-B-209-1CMS_000209209012015.04C57BL/6NJNB98.31.992.351698.8 
22BCJ 22.CMS_N-C-119-1CMS_000119119012215.18C57BL/6NJNC94.631.962.361798.5 
24BCJ 24.CMS_N-R-150-1CMS_000150150012115.29C57BL/6NJNR407.341.982.244257.5Microarray outlier; sample removed.
25BCJ 25.CMS_D-B-217-1CMS_000217217020615.03DBA/2JDB84.611.822.181777.9 
26BCJ 26.CMS_D-C-85-1CMS_00008585012115.20DBA/2JDC172.861.982.272888.9 
27BCJ 27.CMS_D-CR-95-1CMS_00009595012215.16DBA/2JDCR109.81.982.471578.9 
28BCJ 28.CMS_D-R-132-1CMS_000132132012015.29DBA/2JDR140.821.912.473189 
29BCJ 29.CMS_B-B-207-1CMS_000207207012215.02C57BL/6JBB96.251.892.671768.5 
30BCJ 30.CMS_B-C-102-1CMS_000102102012115.28C57BL/6JBC129.691.892.321058.7 
31BCJ 31.CMS_B-CR-111-1CMS_000111111012215.26C57BL/6JBCR165.671.842.311769.5 
32BCJ 32.CMS_B-R-142-1CMS_000142142012115.24C57BL/6JBR116.931.842.22969.4 
33BCJ 33.CMS_N-B-211-1CMS_000211211012315.02C57BL/6NJNB1062.092.291567.4 
34BCJ 34.CMS_N-C-118-1CMS_000118118012115.32C57BL/6NJNC219.21.912.341979.2 
35BCJ 35.CMS_N-CR-127-1CMS_000127127012215.33C57BL/6NJNCR8922.561579.4 
36BCJ 36.CMS_N-R-149-1CMS_000149149012115.27C57BL/6NJNR72.911.842.141078.6 
37BCJ 37.CMS_D-B-218-1CMS_000218218020615.04DBA/2JDB154.341.991.991199.3 
38BCJ 38.CMS_D-C-87-1CMS_00008787012215.13DBA/2JDC105.31.982.211097.4 
39BCJ 39.CMS_D-CR-97-1CMS_00009797012315.05DBA/2JDCR55.851.892.41858.3 
40BCJ 40.CMS_D-R-137-1CMS_000137137012315.06DBA/2JDR128.972.012.241598.1Microarray outlier; sample removed.
41BCJ 41.CMS_B-B-206-1CMS_000206206012115.02C57BL/6JBB159.892.032.12737.8 
42BCJ 42.CMS_B-C-103-1CMS_000103103012215.15C57BL/6JBC111.791.872.451608.9 
43BCJ 43.CMS_B-CR-112-1CMS_000112112012215.31C57BL/6JBCR172.141.862.221809.4 
44BCJ 44.CMS_B-R-145-1CMS_000145145012315.12C57BL/6JBR103.742.062.17998.9 
45BCJ 45.CMS_N-B-212-1CMS_000212212012315.04C57BL/6NJNB189.51.92.42488.5 
47BCJ 47.CMS_N-CR-128-1CMS_000128128012215.34C57BL/6NJNCR90.652.072.251899.3 
48BCJ 48.CMS_N-R-154-1CMS_000154154012315.29C57BL/6NJNR114.731.942.341678.8 
49BCJ 49.CMS_D-C-88-1CMS_00008888012215.28DBA/2JDC961.762.551588.5 
50BCJ 50.CMS_D-CR-96-1CMS_00009696012215.21DBA/2JDCR133.661.782.362038.3 
51BCJ 51.CMS_D-R-138-1CMS_000138138012315.22DBA/2JDR127.131.762.24819.3 
52BCJ 52.CMS_B-C-105-1CMS_000105105012315.13C57BL/6JBC203.241.922.353107 
53BCJ 53.CMS_B-CR-113-1CMS_000113113012315.09C57BL/6JBCR168.671.822.412409.1 
55BCJ 55.CMS_N-C-120-1CMS_000120120012215.32C57BL/6NJNC73.671.932.313718.4 
56BCJ 56.CMS_N-CR-125-1CMS_000125125012115.31C57BL/6NJNCR121.931.922.26738.3 
59BCJ 59.CMS_N-C-122-1CMS_000122122012315.30C57BL/6NJNC131.741.852.421869.4 
60BCJ 60.CMS_D-C-89-1CMS_00008989012315.10DBA/2JDC781.772.32748.9 
62BCJ 62.CMS_N-CR-130-1CMS_000130130012315.34C57BL/6NJNCR100.741.712.361138.8 
65BCJ 65.CMS_B-R-144-1CMS_000144144012215.27C57BL/6JBR80.11.812.3958.9 
66BCJ 66.CMS_N-R-151-1CMS_000151151012215.12C57BL/6NJNR80.221.772.21168.6 
diff --git a/general/datasets/CMS_Hipp_ZScr_1115/experiment-design.rtf b/general/datasets/CMS_Hipp_ZScr_1115/experiment-design.rtf new file mode 100644 index 0000000..f2d6c93 --- /dev/null +++ b/general/datasets/CMS_Hipp_ZScr_1115/experiment-design.rtf @@ -0,0 +1,9 @@ +

This data set includes four experimental conditions, B (baseline, untreated), C (chronic mild stress), CR (chronic mild stress followed by acute restraint), and R (acute restraint only). 

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B = untreated

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C = 7 weeks of chronic unpredictable stress

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R = 30 minutes of restraint

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CR = 7 weeks of chronic unpredictable stress followed by 30 minutes of restraint

diff --git a/general/datasets/CMS_Hipp_ZScr_1115/processing.rtf b/general/datasets/CMS_Hipp_ZScr_1115/processing.rtf new file mode 100644 index 0000000..1b6ca30 --- /dev/null +++ b/general/datasets/CMS_Hipp_ZScr_1115/processing.rtf @@ -0,0 +1,3 @@ +

Outlier Detection. Samples 7 (J-CR-21), 24 (N-R-29), and 40 (D-R-6) were detected as outliers and have abnormal expression profiles (i.e. they do not cluster with other samples and have abnormal median and quartile ranges after normalization. These samples have been removed from the analysis.

+ +

RMA Algorithm. The Robust Multichip Analysis (RMA) algorithm fits a robust linear model at the probe level to minimize the effect of probe-specific affinity differences. This approach: n Increases sensitivity to small changes between experiment and control samples. n Minimizes variance across the dynamic range, but does compress calculated fold change values. RMA consists of three steps: 1. Background adjustment 2. Quantile normalization 3. Summarization This is a multi-chip analysis approach. Therefore, all arrays intended for comparison should be included together in the summarization step. For a more detailed description of the RMA algorithm, see the publication, Exploration, Normalization, and Summaries of High Density Oligonucleotide Array Probe Level Data, Biostatistics, April 2003; Vol. 4; Number 2: 249–264.

diff --git a/general/datasets/CMS_Hipp_ZScr_1115/specifics.rtf b/general/datasets/CMS_Hipp_ZScr_1115/specifics.rtf new file mode 100644 index 0000000..5d45792 --- /dev/null +++ b/general/datasets/CMS_Hipp_ZScr_1115/specifics.rtf @@ -0,0 +1 @@ +

Z-Score. In general, the array data that we put in GeneNetwork has be logged and then z normalized, but instead of leaving the mean at 0 and the standard deviation of 1 unit, we shift up to a mean of 8 units and increase the spread by having an standard deviation of 2 units (what we call 2Z + 8 normalized data).  This removes negative values from the tables.

diff --git a/general/datasets/CMS_Hipp_ZScr_1115/summary.rtf b/general/datasets/CMS_Hipp_ZScr_1115/summary.rtf new file mode 100644 index 0000000..1fededf --- /dev/null +++ b/general/datasets/CMS_Hipp_ZScr_1115/summary.rtf @@ -0,0 +1 @@ +

This data set was generated to study the effects of strain and stress on hippocampal gene expression in female mice. The data set includes three inbred strains of mice and four treatment groups.

diff --git a/general/datasets/CMS_Hipp_ZScr_1115/tissue.rtf b/general/datasets/CMS_Hipp_ZScr_1115/tissue.rtf new file mode 100644 index 0000000..25b50be --- /dev/null +++ b/general/datasets/CMS_Hipp_ZScr_1115/tissue.rtf @@ -0,0 +1 @@ +

This data set includes expression data from mouse hippocampus.

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