From 72b4b29047c52333e6d0a97e0a6a74c7b281bc6d Mon Sep 17 00:00:00 2001
From: Ethan Moyer <57536747+ethanmoyer@users.noreply.github.com>
Date: Mon, 19 Apr 2021 17:56:53 -0400
Subject: [PATCH 1/2] Update README.md

When I have HPC access, I'll work on transferring the data files we have on this array to the webserver so they can be included on this page.

I'm not sure how much we have (compared to mouse), but I wanted to include the same sections as Mouse for the time being for sake of continuity.
---
 Mammal40/README.md | 63 +++++++++++++++++++++++++++++++++++++++++++++-
 1 file changed, 62 insertions(+), 1 deletion(-)

diff --git a/Mammal40/README.md b/Mammal40/README.md
index 9f94681..42c63ae 100644
--- a/Mammal40/README.md
+++ b/Mammal40/README.md
@@ -1 +1,62 @@
-# Mammal40 Array
\ No newline at end of file
+# Mammal40 Array
+
+see also [other infinium arrays](../README.md)
+
+## [Manifest (based on xxx assembly)]()
+
+[Column Header Specification]().
+
+#### [Mammal Array ID system]()
+
+## [Gene Association]()
+
+Gene association of probes based on (GENCODE vM25)? transcript definition. This file includes annotation of probes if they fall from 1.5kbp upstream Transcription Start Site (TSS/Promoter), to Transcription Termination Site. A probe can be considered promoter associated if it is located from 1.5kbps upstream TSS to 1.5kbps dwonstream TSS. This information is given in the distToTSS column. Otherwise, the probe is considered associated with gene body. All isoforms are considered for each gene.
+
+## Epigenomic Feature Annotation
+
+### [ChromHMM]()
+
+### Histone Modification 
+
+Histone modification data was obtained through the ENCODE database. Each tsv.gz file is identified by its GSM ID corresponding to the sample from the Gene Expression Omnibus (GEO).
+ 
+#### Column Description
+- 1: Mammal40 Illumina probe ID
+- 2: Histone ChIP-seq signal peaks
+
+### Transcription Factor Binding Site 
+
+Transcription Factor Binding Site (TFBS) data was obtained through the ENCODE database. Each tsv.gz file is identified by its GSM ID corresponding to the sample from GEO.
+
+#### Column Description
+- 1: Mammal40 Illumina probe ID
+- 2: TF ChIP-seq signal peaks
+
+## Using SeSAMe for preprocessing Infinium Mouse Array
+
+Please note that you need sesame (Bioconductor link: [stable release](https://bioconductor.org/packages/release/bioc/html/sesame.html), [development](https://bioconductor.org/packages/devel/bioc/html/sesame.html)) version 1.9+ (currently on development branch, which needs [R-4.1](https://cran.r-project.org/bin/windows/base/rdevel.html)) for native mouse array support. You can simply call the openSesame pipeline
+
+```R
+library(sesame)
+betas = openSesame("IDAT_folder")
+```
+
+More information can be found at the sesame [mouse array vignette](https://bioconductor.org/packages/devel/bioc/vignettes/sesame/inst/doc/mammal.html).
+
+For previous versions, you need to supply the custom sesame order file for mouse array. Here is an example of using custom order file.
+
+```R
+library(sesame)
+mft <- readRDS(url(""))
+ssets <- lapply(searchIDATprefixes('path_to_IDAT_folder'), readIDATpair, manifest=mft$ordering, controls=mft$controls, platform='Mammal40')
+```
+
+## Illumina manifest
+
+#### [Support Document Download Page]()
+
+#### [Manifest File]()
+
+## Reference
+
+_in submission_

From a188c785a9ea1be9469401d92bfaf472b53f2a8c Mon Sep 17 00:00:00 2001
From: Ethan Moyer <57536747+ethanmoyer@users.noreply.github.com>
Date: Wed, 21 Apr 2021 20:15:00 -0400
Subject: [PATCH 2/2] Update README.md

---
 Mammal40/README.md | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/Mammal40/README.md b/Mammal40/README.md
index 42c63ae..2c2109a 100644
--- a/Mammal40/README.md
+++ b/Mammal40/README.md
@@ -2,7 +2,7 @@
 
 see also [other infinium arrays](../README.md)
 
-## [Manifest (based on xxx assembly)]()
+## [Manifest (based on xxx assembly)](https://zhouserver.research.chop.edu/moyerej/InfiniumAnnotation/HorvathMammal40.CanonicalManifest.3.2019.manifest.csv)
 
 [Column Header Specification]().
 
@@ -53,7 +53,7 @@ ssets <- lapply(searchIDATprefixes('path_to_IDAT_folder'), readIDATpair, manifes
 
 ## Illumina manifest
 
-#### [Support Document Download Page]()
+<!-- #### [Support Document Download Page]() --->
 
 #### [Manifest File]()