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Sample GSM605633 Query DataSets for GSM605633
Status Public on Oct 08, 2010
Title CSHL_RnaSeq_GM12878_nucleus_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: 003N,004N,003N,gen0112N,004N
labexpid: LID20903,LID20900,LID20903,LID20900,crg-6
labversion: Produced by Hannon Lab,iIDR
readtype: 1x36
readtype description: Single 36 nt reads
replicate: 1,2
localization description: Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA
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: 003N
labexpid: LID20900
readtype: 1x36
readtype description: Single 36 nt reads
replicate: 1
Biomaterial provider Coriell
Growth protocol GM12878_protocol.pdf
Extracted molecule nuclear RNA
Extraction protocol
hg19: For extraction protocol details see:
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina Genome Analyzer IIx
Data processing
Submission date Oct 06, 2010
Last update date May 15, 2019
Contact name ENCODE DCC
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
SRA SRX028006
BioSample SAMN00115101
Named Annotation GSM605633_hg19_wgEncodeCshlShortRnaSeqGm12878NucleusShortMinusRaw.bigWig
Named Annotation GSM605633_hg19_wgEncodeCshlShortRnaSeqGm12878NucleusShortPlusRaw.bigWig
Named Annotation GSM605633_hg19_wgEncodeCshlShortRnaSeqGm12878NucleusShorttotalTapMinusRawRep1.bigWig
Named Annotation GSM605633_hg19_wgEncodeCshlShortRnaSeqGm12878NucleusShorttotalTapMinusRawRep2.bigWig
Named Annotation GSM605633_hg19_wgEncodeCshlShortRnaSeqGm12878NucleusShorttotalTapPlusRawRep1.bigWig
Named Annotation GSM605633_hg19_wgEncodeCshlShortRnaSeqGm12878NucleusShorttotalTapPlusRawRep2.bigWig

Supplementary file Size Download File type/resource
GSM605633_hg18_wgEncodeCshlShortRnaSeqAlignmentsGm12878NucleusShort.tagAlign.txt.gz 16.4 Mb (ftp)(http) TXT
GSM605633_hg18_wgEncodeCshlShortRnaSeqTransfragsGm12878NucleusShort.broadPeak.txt.gz 5.3 Mb (ftp)(http) TXT
GSM605633_hg19_wgEncodeCshlShortRnaSeqGm12878NucleusShortAln.bam 50.2 Mb (ftp)(http) BAM
GSM605633_hg19_wgEncodeCshlShortRnaSeqGm12878NucleusShortMinusRaw.bigWig 8.1 Mb (ftp)(http) BIGWIG
GSM605633_hg19_wgEncodeCshlShortRnaSeqGm12878NucleusShortPlusRaw.bigWig 8.2 Mb (ftp)(http) BIGWIG
GSM605633_hg19_wgEncodeCshlShortRnaSeqGm12878NucleusShortTransfrags.shortFrags.txt.gz 1.2 Mb (ftp)(http) TXT
GSM605633_hg19_wgEncodeCshlShortRnaSeqGm12878NucleusShorttotalTapContigs.bedRnaElements.gz 721.2 Kb (ftp)(http) BEDRNAELEMENTS
GSM605633_hg19_wgEncodeCshlShortRnaSeqGm12878NucleusShorttotalTapExonsGencV7.gtf.gz 1.5 Mb (ftp)(http) GTF
GSM605633_hg19_wgEncodeCshlShortRnaSeqGm12878NucleusShorttotalTapMinusRawRep1.bigWig 4.4 Mb (ftp)(http) BIGWIG
GSM605633_hg19_wgEncodeCshlShortRnaSeqGm12878NucleusShorttotalTapMinusRawRep2.bigWig 3.8 Mb (ftp)(http) BIGWIG
GSM605633_hg19_wgEncodeCshlShortRnaSeqGm12878NucleusShorttotalTapPlusRawRep1.bigWig 4.3 Mb (ftp)(http) BIGWIG
GSM605633_hg19_wgEncodeCshlShortRnaSeqGm12878NucleusShorttotalTapPlusRawRep2.bigWig 3.8 Mb (ftp)(http) BIGWIG
GSM605633_hg19_wgEncodeCshlShortRnaSeqGm12878NucleusShorttotalTapProtocolRep1.pdf.gz 307.5 Kb (ftp)(http) PDF
GSM605633_hg19_wgEncodeCshlShortRnaSeqGm12878NucleusShorttotalTapProtocolRep2.pdf.gz 337.9 Kb (ftp)(http) PDF
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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