|
Status |
Public on Jul 26, 2012 |
Title |
CSHL_RnaSeq_MCF-7_cell_CIP-TAP_shortTotal |
Sample type |
SRA |
|
|
Source name |
MCF-7
|
Organism |
Homo sapiens |
Characteristics |
biomaterial_type: immortalized cell line line: MCF-7 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: 089WC,090WC,089WC,090WC labexpid: LID46458,LID46459,LID46458,LID46459 labversion: iIDR readtype: 1x101 readtype description: Single 101 nt reads replicate: 3,4 localization: cell localization description: Whole cell protocol: CIP-TAP protocol description: This kind of library was made from RNA < 200 nucleotides that was pre-treated sequentially with Calf Intestinal Alkaline Phosphatase followed by Tobacco Acid Pyrophosphatase. Hence, it will be enriched for capped RNAs. rnaextract: shortTotal rnaextract description: Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation biorep: 089WC,090WC labexpid: LID46458,LID46459 labversion: iIDR readtype: 1x101 readtype description: Single 101 nt reads
|
Biomaterial provider |
ATCC
|
Extracted molecule |
total 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 HiSeq 2000 |
|
|
Data processing |
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeCshlShortRnaSeq
|
|
|
Submission date |
Jul 25, 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 |
GPL11154 |
Series (1) |
GSE24565 |
Small RNA-seq from ENCODE/Cold Spring Harbor Lab |
|
Relations |
SRA |
SRX171085 |
BioSample |
SAMN01095674 |
Named Annotation |
GSM973676_hg19_wgEncodeCshlShortRnaSeqMcf7CellShorttotalCiptapMinusRep3.bigWig |
Named Annotation |
GSM973676_hg19_wgEncodeCshlShortRnaSeqMcf7CellShorttotalCiptapMinusRep4.bigWig |
Named Annotation |
GSM973676_hg19_wgEncodeCshlShortRnaSeqMcf7CellShorttotalCiptapPlusRep3.bigWig |
Named Annotation |
GSM973676_hg19_wgEncodeCshlShortRnaSeqMcf7CellShorttotalCiptapPlusRep4.bigWig |
Supplementary file |
Size |
Download |
File type/resource |
GSM973676_hg19_wgEncodeCshlShortRnaSeqMcf7CellCiptapContigs.bedRnaElements.gz |
2.1 Mb |
(ftp)(http) |
BEDRNAELEMENTS |
GSM973676_hg19_wgEncodeCshlShortRnaSeqMcf7CellCiptapExonsGencV10.gtf.gz |
1.5 Mb |
(ftp)(http) |
GTF |
GSM973676_hg19_wgEncodeCshlShortRnaSeqMcf7CellCiptapProtocolRep3.pdf.gz |
425.9 Kb |
(ftp)(http) |
PDF |
GSM973676_hg19_wgEncodeCshlShortRnaSeqMcf7CellCiptapProtocolRep4.pdf.gz |
430.3 Kb |
(ftp)(http) |
PDF |
GSM973676_hg19_wgEncodeCshlShortRnaSeqMcf7CellShorttotalCiptapMinusRep3.bigWig |
23.4 Mb |
(ftp)(http) |
BIGWIG |
GSM973676_hg19_wgEncodeCshlShortRnaSeqMcf7CellShorttotalCiptapMinusRep4.bigWig |
17.7 Mb |
(ftp)(http) |
BIGWIG |
GSM973676_hg19_wgEncodeCshlShortRnaSeqMcf7CellShorttotalCiptapPlusRep3.bigWig |
23.4 Mb |
(ftp)(http) |
BIGWIG |
GSM973676_hg19_wgEncodeCshlShortRnaSeqMcf7CellShorttotalCiptapPlusRep4.bigWig |
17.6 Mb |
(ftp)(http) |
BIGWIG |
SRA Run Selector |
Raw data are available in SRA |
Processed data provided as supplementary file |