|
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 |
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 |
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 Selector |
Raw data are available in SRA |
Processed data provided as supplementary file |