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/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 + 4 files changed, 6 insertions(+) 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/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 @@ +

Retinal ganglion cell mRNA from 4 month (young) and 9 month (pre-glaucomatous) DBA/2J mice and age and sex-matched D2-Gpnmb+ controls

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 @@ +

GPL17021Illumina HiSeq 2500 (Mus musculus)

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 @@ +

RNA-Seq log2 Z-Score

+ +

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).  This removes negative values from the tables.

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 @@ +

RNA-seq analysis from young and pre-glaucomatous DBA/2J retinal ganglion cells and control (age and sex-matched, D2-Gpnmb+) retinal ganglion cells

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