25 July 2012 - Mouse ENCODE data releases: UW RNA-seq, FSU Repli-chip, CSHL Long RNA-seq (Release 2)
Replication Timing by Repli-chip from ENCODE/FSU:
shows genome-wide assessment of DNA replication timing using NimbleGen tiling CGH microarrays. Each experiment represents the relative enrichment of early vs. late S-phase nascent strands in a given cell line, with data represented as a loess-smoothed function of individual timing values at probes spaced at even intervals across the genome. Regions with high values indicate domains of early replication where initiation occurs earlier in S-phase or early in a higher proportion of cells.
RNA-seq from ENCODE/UW:
shows RNA-seq measured genome-wide in 25 mouse tissues and cell lines. Poly-A selected mRNA was used as the source for transcriptome profiling of tissues and cell types that also had corresponding DNase I hypersensitive profiles.
Long RNA-seq from ENCODE/Cold Spring Harbor Lab (Release 2):
includes a new browser view (Splice Junctions) and 6 new analysis files per experiment (de novo exons, genes and transcripts with expression levels defined by Cufflinks and Flux Capacitor, and expression levels for Ensembl and Cufflinks models at each level).
16 July 2012 - Human ENCODE data releases: CSHL Small RNA-seq (Release 3), UCSC Regulation Transcription Track (Release 2), UW Affy Exon (Release 3), UMass 5C (Release 2)
Small RNA-seq from ENCODE/Cold Spring Harbor Lab (Release 3) :
adds 53 additional experiments, with twenty-two new cell lines represented: CD20+, CD34+_Mobilized, HAoAF, HAoEC, HCH, HFDPC, HMEpC, hMSC-AT, hMSC-UC, HOB, HPC-PL, HPIEpC, HSaVEC, HVMF, HWP, IMR90, Monocytes-CD14+, NHDF, NHEM.f_M2, NHEM_M2, SkMC, SK-N-SH. There are also two new variations in protocol (CIP-TAP and untreated) used to create different RNA populations.
UCSC Integrated Regulation: Transcription Levels Assayed by RNA-seq on 9 Cell Lines from ENCODE:
includes transcription levels for 2 additional cell lines: HeLa-S3 and HepG2.
Affymetrix Exon Array from ENCODE/University of Washington (Release 3):
revokes previously released K562 zinc-finger experiments due to a data merging issue.
Chromatin Interactions by 5C from ENCODE/Dekker Univ. Mass. (Release 2):
contains reanalyzed peak files and more complete raw data.
02 July 2012 - Quality metrics for human ENCODE data
The ENCODE Consortium analysis working group has analyzed the quality of the data produced using a variety of metrics. The ENCODE portal
Quality Metrics page provides
spreadsheets showing quality metrics for human ENCODE datasets, along with descriptions of what the metrics are and what they appear to measure. Spreadsheets are provided for DNase-seq, FAIRE-seq, Transcription Factor ChIP-seq, Histone ChIP-seq, and ChIP Controls. This page is linked from the related
Data Standards page.
Many of the software tools used for quality metrics, along with their citations, can be found on the portal
Software Tools page.
26 Jun 2012 - Human ENCODE data releases: GENCODE Genes V12, CSHL Long RNA-seq (Release 2), SYDH Histone (Rel 3), UW DNaseI HS (Rel 5)
Four track updates were released on the hg19 genome browser: