|
Status |
Public on Mar 16, 2012 |
Title |
CSHL_RnaSeq_HUVEC_nucleus_TAP-Only_shortTotal |
Sample type |
SRA |
|
|
Source name |
HUVEC
|
Organism |
Homo sapiens |
Characteristics |
biomaterial_type: primary cell cell_type: endothelial cell of umbilical vein donor_id: ENCDO341AAA datatype: RnaSeq datatype description: Sequencing analysis of RNA expression rnaextract: shortTotal rnaextract description: Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation biorep: 029N,030N,030N,029N labexpid: LID21056,LID21058,LID21058,LID21056 labversion: iIDR readtype: 1x36 readtype description: Single 36 nt reads replicate: 3,4 localization: nucleus 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: 029N labexpid: LID21056 readtype: 1x36 readtype description: Single 36 nt reads replicate: 3
|
Biomaterial provider |
Lonza
|
Growth protocol |
HUVEC_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 |
SRX130226 |
BioSample |
SAMN00829012 |
Named Annotation |
GSM897075_hg19_wgEncodeCshlShortRnaSeqHuvecNucleusShorttotalTapMinusRawRep3.bigWig |
Named Annotation |
GSM897075_hg19_wgEncodeCshlShortRnaSeqHuvecNucleusShorttotalTapMinusRawRep4.bigWig |
Named Annotation |
GSM897075_hg19_wgEncodeCshlShortRnaSeqHuvecNucleusShorttotalTapPlusRawRep3.bigWig |
Named Annotation |
GSM897075_hg19_wgEncodeCshlShortRnaSeqHuvecNucleusShorttotalTapPlusRawRep4.bigWig |
Supplementary file |
Size |
Download |
File type/resource |
GSM897075_hg19_wgEncodeCshlShortRnaSeqHuvecNucleusShorttotalTapContigs.bedRnaElements.gz |
2.3 Mb |
(ftp)(http) |
BEDRNAELEMENTS |
GSM897075_hg19_wgEncodeCshlShortRnaSeqHuvecNucleusShorttotalTapExonsGencV7.gtf.gz |
2.5 Mb |
(ftp)(http) |
GTF |
GSM897075_hg19_wgEncodeCshlShortRnaSeqHuvecNucleusShorttotalTapMinusRawRep3.bigWig |
14.3 Mb |
(ftp)(http) |
BIGWIG |
GSM897075_hg19_wgEncodeCshlShortRnaSeqHuvecNucleusShorttotalTapMinusRawRep4.bigWig |
11.6 Mb |
(ftp)(http) |
BIGWIG |
GSM897075_hg19_wgEncodeCshlShortRnaSeqHuvecNucleusShorttotalTapPlusRawRep3.bigWig |
14.3 Mb |
(ftp)(http) |
BIGWIG |
GSM897075_hg19_wgEncodeCshlShortRnaSeqHuvecNucleusShorttotalTapPlusRawRep4.bigWig |
11.7 Mb |
(ftp)(http) |
BIGWIG |
GSM897075_hg19_wgEncodeCshlShortRnaSeqHuvecNucleusShorttotalTapProtocolRep3.pdf.gz |
325.3 Kb |
(ftp)(http) |
PDF |
GSM897075_hg19_wgEncodeCshlShortRnaSeqHuvecNucleusShorttotalTapProtocolRep4.pdf.gz |
325.4 Kb |
(ftp)(http) |
PDF |
SRA Run Selector |
Raw data are available in SRA |
Processed data provided as supplementary file |