NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM605627 Query DataSets for GSM605627
Status Public on Oct 08, 2010
Title CSHL_RnaSeq_GM12878_cytosol_TAP-Only_shortTotal
Sample type SRA
 
Source name GM12878
Organism Homo sapiens
Characteristics datatype: RnaSeq
datatype description: Sequencing analysis of RNA expression
cell description: B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus
rnaextract: shortTotal
rnaextract description: Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation
biorep: 004C,003C,004C,003C,gen0108C
labexpid: LID20901,LID20904,LID20901,crg-4,LID20904
labversion: Produced by Hannon Lab,iIDR
readtype: 1x36
readtype description: Single 36 nt reads
replicate: 1,2
localization description: The fluid between the cells outer membrane and the nucleus
protocol: TAP-Only
protocol description: This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned.
rnaextract: shortTotal
rnaextract description: Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation
biorep: 003C
labexpid: LID20901
readtype: 1x36
readtype description: Single 36 nt reads
replicate: 1
Biomaterial provider Coriell
Growth protocol GM12878_protocol.pdf
Extracted molecule cytoplasmic RNA
Extraction protocol http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeCshlShortRnaSeq
hg19: For extraction protocol details see: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeCshlShortRnaSeq
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina Genome Analyzer IIx
 
Data processing http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeCshlShortRnaSeq
 
Submission date Oct 06, 2010
Last update date May 15, 2019
Contact name ENCODE DCC
E-mail(s) encode-help@lists.stanford.edu
Organization name ENCODE DCC
Street address 300 Pasteur Dr
City Stanford
State/province CA
ZIP/Postal code 94305-5120
Country USA
 
Platform ID GPL10999
Series (1)
GSE24565 Small RNA-seq from ENCODE/Cold Spring Harbor Lab
Relations
SRA SRX028002
BioSample SAMN00115097
Named Annotation GSM605627_hg19_wgEncodeCshlShortRnaSeqGm12878CytosolShortMinusRaw.bigWig
Named Annotation GSM605627_hg19_wgEncodeCshlShortRnaSeqGm12878CytosolShortPlusRaw.bigWig
Named Annotation GSM605627_hg19_wgEncodeCshlShortRnaSeqGm12878CytosolShorttotalTapMinusRawRep1.bigWig
Named Annotation GSM605627_hg19_wgEncodeCshlShortRnaSeqGm12878CytosolShorttotalTapMinusRawRep2.bigWig
Named Annotation GSM605627_hg19_wgEncodeCshlShortRnaSeqGm12878CytosolShorttotalTapPlusRawRep1.bigWig
Named Annotation GSM605627_hg19_wgEncodeCshlShortRnaSeqGm12878CytosolShorttotalTapPlusRawRep2.bigWig

Supplementary file Size Download File type/resource
GSM605627_hg18_wgEncodeCshlShortRnaSeqAlignmentsGm12878CytosolShort.tagAlign.txt.gz 23.6 Mb (ftp)(http) TXT
GSM605627_hg18_wgEncodeCshlShortRnaSeqTransfragsGm12878CytosolShort.broadPeak.txt.gz 13.5 Mb (ftp)(http) TXT
GSM605627_hg19_wgEncodeCshlShortRnaSeqGm12878CytosolShortAln.bam 27.7 Mb (ftp)(http) BAM
GSM605627_hg19_wgEncodeCshlShortRnaSeqGm12878CytosolShortMinusRaw.bigWig 8.7 Mb (ftp)(http) BIGWIG
GSM605627_hg19_wgEncodeCshlShortRnaSeqGm12878CytosolShortPlusRaw.bigWig 8.7 Mb (ftp)(http) BIGWIG
GSM605627_hg19_wgEncodeCshlShortRnaSeqGm12878CytosolShortTransfrags.shortFrags.txt.gz 876.0 Kb (ftp)(http) TXT
GSM605627_hg19_wgEncodeCshlShortRnaSeqGm12878CytosolShorttotalTapContigs.bedRnaElements.gz 437.2 Kb (ftp)(http) BEDRNAELEMENTS
GSM605627_hg19_wgEncodeCshlShortRnaSeqGm12878CytosolShorttotalTapExonsGencV7.gtf.gz 1.2 Mb (ftp)(http) GTF
GSM605627_hg19_wgEncodeCshlShortRnaSeqGm12878CytosolShorttotalTapMinusRawRep1.bigWig 3.8 Mb (ftp)(http) BIGWIG
GSM605627_hg19_wgEncodeCshlShortRnaSeqGm12878CytosolShorttotalTapMinusRawRep2.bigWig 4.9 Mb (ftp)(http) BIGWIG
GSM605627_hg19_wgEncodeCshlShortRnaSeqGm12878CytosolShorttotalTapPlusRawRep1.bigWig 3.8 Mb (ftp)(http) BIGWIG
GSM605627_hg19_wgEncodeCshlShortRnaSeqGm12878CytosolShorttotalTapPlusRawRep2.bigWig 4.9 Mb (ftp)(http) BIGWIG
GSM605627_hg19_wgEncodeCshlShortRnaSeqGm12878CytosolShorttotalTapProtocolRep1.pdf.gz 303.7 Kb (ftp)(http) PDF
GSM605627_hg19_wgEncodeCshlShortRnaSeqGm12878CytosolShorttotalTapProtocolRep2.pdf.gz 314.7 Kb (ftp)(http) PDF
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap