|
Status |
Public on Mar 16, 2012 |
Title |
CSHL_RnaSeq_HepG2_nucleus_TAP-Only_shortTotal |
Sample type |
SRA |
|
|
Source name |
HepG2
|
Organism |
Homo sapiens |
Characteristics |
datatype: RnaSeq datatype description: Sequencing analysis of RNA expression cell description: hepatocellular carcinoma rnaextract: shortTotal rnaextract description: Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation biorep: 013N,013N,014N,014N labexpid: LID44463,LID44462,LID44462,LID44463 labversion: 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: 013N labexpid: LID44462 readtype: 1x36 readtype description: Single 36 nt reads replicate: 1
|
Biomaterial provider |
ATCC
|
Growth protocol |
HepG2_protocol.pdf
|
Extracted molecule |
nuclear RNA |
Extraction protocol |
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 |
Mar 16, 2012 |
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 |
SRX130236 |
BioSample |
SAMN00829022 |
Named Annotation |
GSM897085_hg19_wgEncodeCshlShortRnaSeqHepg2NucleusShorttotalTapMinusRawRep1.bigWig |
Named Annotation |
GSM897085_hg19_wgEncodeCshlShortRnaSeqHepg2NucleusShorttotalTapMinusRawRep2.bigWig |
Named Annotation |
GSM897085_hg19_wgEncodeCshlShortRnaSeqHepg2NucleusShorttotalTapPlusRawRep1.bigWig |
Named Annotation |
GSM897085_hg19_wgEncodeCshlShortRnaSeqHepg2NucleusShorttotalTapPlusRawRep2.bigWig |
Supplementary file |
Size |
Download |
File type/resource |
GSM897085_hg19_wgEncodeCshlShortRnaSeqHepg2NucleusShorttotalTapContigs.bedRnaElements.gz |
205.5 Kb |
(ftp)(http) |
BEDRNAELEMENTS |
GSM897085_hg19_wgEncodeCshlShortRnaSeqHepg2NucleusShorttotalTapExonsGencV7.gtf.gz |
610.3 Kb |
(ftp)(http) |
GTF |
GSM897085_hg19_wgEncodeCshlShortRnaSeqHepg2NucleusShorttotalTapMinusRawRep1.bigWig |
1.1 Mb |
(ftp)(http) |
BIGWIG |
GSM897085_hg19_wgEncodeCshlShortRnaSeqHepg2NucleusShorttotalTapMinusRawRep2.bigWig |
1.2 Mb |
(ftp)(http) |
BIGWIG |
GSM897085_hg19_wgEncodeCshlShortRnaSeqHepg2NucleusShorttotalTapPlusRawRep1.bigWig |
1.1 Mb |
(ftp)(http) |
BIGWIG |
GSM897085_hg19_wgEncodeCshlShortRnaSeqHepg2NucleusShorttotalTapPlusRawRep2.bigWig |
1.1 Mb |
(ftp)(http) |
BIGWIG |
GSM897085_hg19_wgEncodeCshlShortRnaSeqHepg2NucleusTapProtocolRep1.pdf.gz |
220.6 Kb |
(ftp)(http) |
PDF |
GSM897085_hg19_wgEncodeCshlShortRnaSeqHepg2NucleusTapProtocolRep2.pdf.gz |
219.6 Kb |
(ftp)(http) |
PDF |
SRA Run Selector |
Raw data are available in SRA |
Processed data provided as supplementary file |