|
| Status |
Public on Jul 26, 2012 |
| Title |
CSHL_RnaSeq_SK-N-SH_cell_CIP-TAP_shortTotal |
| Sample type |
SRA |
| |
|
| Source name |
SK-N-SH
|
| Organism |
Homo sapiens |
| Characteristics |
biomaterial_type: immortalized cell line
line: SK-N-SH
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: 086WC,085WC,086WC,085WC
labexpid: LID46270,LID46270,LID46271,LID46271
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: 085WC,086WC
labexpid: LID46270,LID46271
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 |
SRX171086 |
| BioSample |
SAMN01095675 |
| Named Annotation |
GSM973677_hg19_wgEncodeCshlShortRnaSeqSknshCellShorttotalCiptapMinusRep3.bigWig |
| Named Annotation |
GSM973677_hg19_wgEncodeCshlShortRnaSeqSknshCellShorttotalCiptapMinusRep4.bigWig |
| Named Annotation |
GSM973677_hg19_wgEncodeCshlShortRnaSeqSknshCellShorttotalCiptapPlusRep3.bigWig |
| Named Annotation |
GSM973677_hg19_wgEncodeCshlShortRnaSeqSknshCellShorttotalCiptapPlusRep4.bigWig |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM973677_hg19_wgEncodeCshlShortRnaSeqSknshCellCiptapContigs.bedRnaElements.gz |
2.2 Mb |
(ftp)(http) |
BEDRNAELEMENTS |
| GSM973677_hg19_wgEncodeCshlShortRnaSeqSknshCellCiptapExonsGencV10.gtf.gz |
1.4 Mb |
(ftp)(http) |
GTF |
| GSM973677_hg19_wgEncodeCshlShortRnaSeqSknshCellCiptapProtocolRep3.pdf.gz |
544.9 Kb |
(ftp)(http) |
PDF |
| GSM973677_hg19_wgEncodeCshlShortRnaSeqSknshCellCiptapProtocolRep4.pdf.gz |
560.4 Kb |
(ftp)(http) |
PDF |
| GSM973677_hg19_wgEncodeCshlShortRnaSeqSknshCellShorttotalCiptapMinusRep3.bigWig |
20.8 Mb |
(ftp)(http) |
BIGWIG |
| GSM973677_hg19_wgEncodeCshlShortRnaSeqSknshCellShorttotalCiptapMinusRep4.bigWig |
19.0 Mb |
(ftp)(http) |
BIGWIG |
| GSM973677_hg19_wgEncodeCshlShortRnaSeqSknshCellShorttotalCiptapPlusRep3.bigWig |
20.8 Mb |
(ftp)(http) |
BIGWIG |
| GSM973677_hg19_wgEncodeCshlShortRnaSeqSknshCellShorttotalCiptapPlusRep4.bigWig |
18.9 Mb |
(ftp)(http) |
BIGWIG |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
