e50020d950428abe91a91dfe3dc1c2655a967682 ccpowell Wed Jun 12 14:26:39 2019 -0700 making edits to newsarch & indexNews for encode 3 tfbs release, refs #21339 diff --git src/hg/htdocs/goldenPath/newsarch.html src/hg/htdocs/goldenPath/newsarch.html index 37ed461..cc84a3b 100755 --- src/hg/htdocs/goldenPath/newsarch.html +++ src/hg/htdocs/goldenPath/newsarch.html @@ -40,80 +40,81 @@

Jun. 13, 2019 New ENCODE 3 transcription factor binding site tracks for human (GRCh37/hg19, GRCh38/hg38)

Jun. 13, 2019 New ENCODE 3 transcription factor binding site track sets for human (GRCh37/hg19, GRCh38/hg38)

-We are pleased to announce two new ENCODE 3 transcription factor binding site tracks for human -(GRCh37/hg19, GRCh38/hg38). These tracks show regions of transcription factor binding +We are pleased to announce two new ENCODE 3 transcription factor binding site track sets for human +(GRCh37/hg19, GRCh38/hg38). These track sets show regions of transcription factor binding derived from a large collection of ChIP-seq experiments performed by the ENCODE project between February 2011 and November 2018.

-The following two sessions express where CTCF binds to the MYC Proto-Oncogene -across more than 100 cell types. CTCF is a transcription factor identified as a repressor of MYC -shown to inhibit cell growth (Qi et al., 2002).
-

The ENCODE TF ChIP-seq data were processed using the ENCODE Transcription Factor ChIP-seq Processing Pipeline to generate peaks of TF binding. Peaks from 1264 experiments (1256 in hg38) representing 338 transcription factors (340 in hg38) in -130 cell types (129 in hg38) were used to generate these two tracks.
+130 cell types (129 in hg38) were used to generate these two track sets.

The ENCODE 3 TF ChIP Clusters tracks are collections of ChIP-seq peaks consolidated into a +
The ENCODE 3 TF ChIP Clusters track sets are collections of ChIP-seq peaks consolidated into a summary display or ‘cluster’ showing occupancy regions for each factor. The cluster - labels now include the count of cell types contributing to the cluster (those with a ChIP-seq peaks - in the region), and the total count of cell types tested for the factor. The new label feature + labels now include the count of cell types contributing to the cluster (those with ChIP-seq peaks + in the region) and the total count of cell types tested for the factor. The new label feature can be disabled via a user option on the track configuration page. You can read more about the - TF ChIP Clusters tracks here: + TF ChIP Clusters track sets here: hg19, hg38.
The ENCODE 3 TF ChIP Peaks tracks are collections of the underlying ChIP-seq peak tracks - which are available collectively or individually. You can read more about the TF ChIP Peaks composite tracks here: +
The ENCODE 3 TF ChIP Peaks track sets are collections of the underlying ChIP-seq peak tracks + which can be viewed individually or collectively by cell type or transcription factor. You can read more about the TF ChIP Peaks track sets here: hg19, hg38.

+An example of these two track sets is shown in the following sessions where CTCF binds to the MYC Proto-Oncogene +across more than 100 cell types. CTCF is a transcription factor identified as a repressor of MYC +shown to inhibit cell growth (Qi et al., 2002).
+

Thanks to the ENCODE Consortium, the ENCODE ChIP-seq production laboratories, and the ENCODE Data Coordination Center for generating -and processing the TF ChIP-seq datasets used here. The ENCODE accession numbers of the constituent -datasets are available from the peak details page. Special thanks to Henry Pratt, Jill Moore, -Michael Purcaro, and Zhiping Weng, PI, at the +and processing the TF ChIP-seq datasets. The ENCODE accession numbers of the constituent +datasets are available on the peak details page as links in the Clusters tracks and in the track +title for the Peaks tracks. Special thanks to Henry Pratt, Jill Moore, Michael Purcaro, and Zhiping +Weng, PI, at the ENCODE Data Analysis Center (ZLab at UMass Medical Center) -for providing the peak datasets, metadata, and guidance developing this track. Thanks to Kate +for providing the peak datasets, metadata, and guidance developing these track sets. Thanks to Kate Rosenbloom and Conner Powell of the UCSC Genome Browser group for their work in creating and -releasing these tracks. +releasing these track sets.

June 6, 2019 New Genome Browser: Chinese Hamster Ovary (CHO) cell line, criGriChoV2 (Cricetulus griseus)

A genome browser is now available for the Chinese Hamster Ovary cell line assembly released in June 2017 by the Eagle Genomics Ltd (CHOK1S_HZDv1).

About the assembly:

UCSC Genome Browser assembly ID: criGriChoV2
Sequencing/Assembly provider ID: Eagle Genomics Ltd
Assembly date: June 2017
Accession ID: GCA_900186095.1
NCBI Genome information: