From b2feda451ccfbeaed02dce9088d6dd228cf15861 Mon Sep 17 00:00:00 2001
From: Bonface
Date: Tue, 13 Feb 2024 23:52:26 -0600
Subject: Update dataset RTF Files.

---
 general/datasets/Jax_d2gm_rseq_log2z_0418/citation.rtf          | 3 +++
 general/datasets/Jax_d2gm_rseq_log2z_0418/experiment-design.rtf | 1 +
 general/datasets/Jax_d2gm_rseq_log2z_0418/platform.rtf          | 1 +
 general/datasets/Jax_d2gm_rseq_log2z_0418/specifics.rtf         | 3 +++
 general/datasets/Jax_d2gm_rseq_log2z_0418/summary.rtf           | 1 +
 5 files changed, 9 insertions(+)
 create mode 100644 general/datasets/Jax_d2gm_rseq_log2z_0418/citation.rtf
 create mode 100644 general/datasets/Jax_d2gm_rseq_log2z_0418/experiment-design.rtf
 create mode 100644 general/datasets/Jax_d2gm_rseq_log2z_0418/platform.rtf
 create mode 100644 general/datasets/Jax_d2gm_rseq_log2z_0418/specifics.rtf
 create mode 100644 general/datasets/Jax_d2gm_rseq_log2z_0418/summary.rtf

(limited to 'general/datasets/Jax_d2gm_rseq_log2z_0418')

diff --git a/general/datasets/Jax_d2gm_rseq_log2z_0418/citation.rtf b/general/datasets/Jax_d2gm_rseq_log2z_0418/citation.rtf
new file mode 100644
index 0000000..fe14fa7
--- /dev/null
+++ b/general/datasets/Jax_d2gm_rseq_log2z_0418/citation.rtf
@@ -0,0 +1,3 @@
+<ul>
+	<li>Williams PA, Harder JM, Foxworth NE, Cochran KE et al.&nbsp;Vitamin B3&nbsp;modulates mitochondrial vulnerability and prevents glaucoma in aged mice.&nbsp;Science&nbsp;2017 Feb 17;355(6326):756-760. PMID:&nbsp;<a href="https://www.ncbi.nlm.nih.gov/pubmed/28209901" title="Link to PubMed record">28209901</a></li>
+</ul>
diff --git a/general/datasets/Jax_d2gm_rseq_log2z_0418/experiment-design.rtf b/general/datasets/Jax_d2gm_rseq_log2z_0418/experiment-design.rtf
new file mode 100644
index 0000000..5b2f4c9
--- /dev/null
+++ b/general/datasets/Jax_d2gm_rseq_log2z_0418/experiment-design.rtf
@@ -0,0 +1 @@
+<p>Retinal ganglion cell mRNA from 4 month (young) and 9 month (pre-glaucomatous) DBA/2J mice and age and sex-matched D2-Gpnmb+ controls</p>
diff --git a/general/datasets/Jax_d2gm_rseq_log2z_0418/platform.rtf b/general/datasets/Jax_d2gm_rseq_log2z_0418/platform.rtf
new file mode 100644
index 0000000..c967d36
--- /dev/null
+++ b/general/datasets/Jax_d2gm_rseq_log2z_0418/platform.rtf
@@ -0,0 +1 @@
+<p><a href="https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL17021">GPL17021</a>Illumina HiSeq 2500 (Mus musculus)</p>
diff --git a/general/datasets/Jax_d2gm_rseq_log2z_0418/specifics.rtf b/general/datasets/Jax_d2gm_rseq_log2z_0418/specifics.rtf
new file mode 100644
index 0000000..f57a155
--- /dev/null
+++ b/general/datasets/Jax_d2gm_rseq_log2z_0418/specifics.rtf
@@ -0,0 +1,3 @@
+<p>RNA-Seq log2 Z-Score</p>
+
+<p>In general, the array data that we put in GeneNetwork has been 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). &nbsp;This removes negative values from the tables.</p>
diff --git a/general/datasets/Jax_d2gm_rseq_log2z_0418/summary.rtf b/general/datasets/Jax_d2gm_rseq_log2z_0418/summary.rtf
new file mode 100644
index 0000000..1cf2292
--- /dev/null
+++ b/general/datasets/Jax_d2gm_rseq_log2z_0418/summary.rtf
@@ -0,0 +1 @@
+<p>RNA-seq analysis from young and pre-glaucomatous DBA/2J retinal ganglion cells and control (age and sex-matched, D2-Gpnmb+) retinal ganglion cells</p>
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