f5bb3841ce07863d41d9a41d99f44546e245c16a
gperez2
  Thu Apr 16 12:23:26 2026 -0700
Adding native mouse developmental timecourse bulk RNA-seq tracks for mm10
and mm39 from the Woldlab public hub using Claude, refs #37001

diff --git src/hg/makeDb/doc/mm10.txt src/hg/makeDb/doc/mm10.txt
index f89d59928be..51cbe526f03 100644
--- src/hg/makeDb/doc/mm10.txt
+++ src/hg/makeDb/doc/mm10.txt
@@ -19776,15 +19776,57 @@
     sed -e 's/^/    # /;' fb.GCF_009873245.2.chainSynMm10Link.txt
     # 809446789 bases of 2374868943 (34.084%) in intersection
 \    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
     \
    -target2bit="/hive/data/genomes/asmHubs/GCF/009/873/245/GCF_009873245.2/GCF_009873245.2.2bit" \
 -targetSizes="/hive/data/genomes/asmHubs/GCF/009/873/245/GCF_009873245.2/GCF_009873245.2.chrom.sizes.txt" \
    GCF_009873245.2 mm10) > rbest.log 2>&1
 
     grep -w real rbest.log | sed -e 's/^/    # /;'
     # real	107m54.409s
 
     sed -e 's/^/    # /;' fb.GCF_009873245.2.chainRBest.Mm10.txt
     # 815513873 bases of 2374868943 (34.339%) in intersection
 
 ##############################################################################
+# Mouse Development Timecourse bulk RNA-seq (2026-04-10 Gerardo)
+# Converting track hub from Wold Lab (Caltech) into native tracks.
+# Hub URL: http://woldlab.caltech.edu/~diane/mouse_development_bulk/mouse_development.hub.txt
+# Publication: https://www.encodeproject.org/publications/e0d01543-9965-4edb-933c-778a40575cd9/
+# 17 tissues, up to 8 timepoints (e10.5-e16.5, P0), two replicates per condition.
+# bigBarChart tracks with FPKM and TPM from RSEM, GENCODE M4 and M21 annotations.
+
+# Download data files from hub to /hive/data/outside/
+mkdir -p /hive/data/outside/woldlab/mouseDevTimecourse/mm10
+cd /hive/data/outside/woldlab/mouseDevTimecourse/mm10
+
+for f in mouse_development_TPM_M4_mm10.bb mouse_development_FPKM_M4_mm10.bb \
+    mouse_development_TPM_M21_mm10.bb mouse_development_FPKM_M21_mm10.bb \
+    mouse_development_M4.categories mouse_development_M4.facets \
+    mouse_development_M21.categories mouse_development_M21.facets; do
+    curl -o "$f" "http://woldlab.caltech.edu/~diane/mouse_development_bulk/$f"
+done
+
+# Create symlinks in /gbdb/mm10/
+mkdir -p /gbdb/mm10/mouseDevTimecourse
+cd /gbdb/mm10/mouseDevTimecourse
+for f in /hive/data/outside/woldlab/mouseDevTimecourse/mm10/*; do
+    ln -s "$f" .
+done
+
+# Add trackDb entry
+cd ~/kent/src/hg/makeDb/trackDb/mouse/mm10
+# Created mouseDevTimecourse.ra (superTrack with 4 bigBarChart subtracks)
+# Created HTML description files:
+#   mouseDevTimecourse.html (supertrack)
+#   developmentTimecourseM4mm10TPM.html
+#   developmentTimecourseM4mm10FPKM.html
+#   developmentTimecourseM21mm10TPM.html
+#   developmentTimecourseM21mm10FPKM.html
+# Added "include mouseDevTimecourse.ra" to trackDb.ra
+
+# Load trackDb
+cd ~/kent/src/hg/makeDb/trackDb
+make DBS=mm10
+##############################################################################
+
+##############################################################################