|
| Status |
Public on Mar 16, 2012 |
| Title |
CSHL_RnaSeq_MCF-7_cell_TAP-Only_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: LID47160,LID47161,LID47161,LID47160
labversion: iIDR
readtype: 1x101
readtype description: Single 101 nt reads
replicate: 1,2
localization: cell
localization description: Whole cell
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: 015WC,016WC
labexpid: LID20743,LID20744
labversion: iIDR
readtype: 1x36
readtype description: Single 36 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 |
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 |
GPL11154 |
| Series (1) |
| GSE24565 |
Small RNA-seq from ENCODE/Cold Spring Harbor Lab |
|
| Relations |
| SRA |
SRX130232 |
| BioSample |
SAMN00829018 |
| Named Annotation |
GSM897081_hg19_wgEncodeCshlShortRnaSeqMcf7CellShorttotalTapMinusRawRep1.bigWig |
| Named Annotation |
GSM897081_hg19_wgEncodeCshlShortRnaSeqMcf7CellShorttotalTapMinusRawRep2.bigWig |
| Named Annotation |
GSM897081_hg19_wgEncodeCshlShortRnaSeqMcf7CellShorttotalTapMinusRawRep3.bigWig |
| Named Annotation |
GSM897081_hg19_wgEncodeCshlShortRnaSeqMcf7CellShorttotalTapMinusRawRep4.bigWig |
| Named Annotation |
GSM897081_hg19_wgEncodeCshlShortRnaSeqMcf7CellShorttotalTapPlusRawRep1.bigWig |
| Named Annotation |
GSM897081_hg19_wgEncodeCshlShortRnaSeqMcf7CellShorttotalTapPlusRawRep2.bigWig |
| Named Annotation |
GSM897081_hg19_wgEncodeCshlShortRnaSeqMcf7CellShorttotalTapPlusRawRep3.bigWig |
| Named Annotation |
GSM897081_hg19_wgEncodeCshlShortRnaSeqMcf7CellShorttotalTapPlusRawRep4.bigWig |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM897081_hg19_wgEncodeCshlShortRnaSeqMcf7CellShorttotalExonsGencV7.gtf.gz |
1.2 Mb |
(ftp)(http) |
GTF |
| GSM897081_hg19_wgEncodeCshlShortRnaSeqMcf7CellShorttotalTapContigs.bedRnaElements.gz |
516.7 Kb |
(ftp)(http) |
BEDRNAELEMENTS |
| GSM897081_hg19_wgEncodeCshlShortRnaSeqMcf7CellShorttotalTapMinusRawRep1.bigWig |
4.9 Mb |
(ftp)(http) |
BIGWIG |
| GSM897081_hg19_wgEncodeCshlShortRnaSeqMcf7CellShorttotalTapMinusRawRep2.bigWig |
4.9 Mb |
(ftp)(http) |
BIGWIG |
| GSM897081_hg19_wgEncodeCshlShortRnaSeqMcf7CellShorttotalTapMinusRawRep3.bigWig |
7.7 Mb |
(ftp)(http) |
BIGWIG |
| GSM897081_hg19_wgEncodeCshlShortRnaSeqMcf7CellShorttotalTapMinusRawRep4.bigWig |
6.5 Mb |
(ftp)(http) |
BIGWIG |
| GSM897081_hg19_wgEncodeCshlShortRnaSeqMcf7CellShorttotalTapPlusRawRep1.bigWig |
4.9 Mb |
(ftp)(http) |
BIGWIG |
| GSM897081_hg19_wgEncodeCshlShortRnaSeqMcf7CellShorttotalTapPlusRawRep2.bigWig |
4.9 Mb |
(ftp)(http) |
BIGWIG |
| GSM897081_hg19_wgEncodeCshlShortRnaSeqMcf7CellShorttotalTapPlusRawRep3.bigWig |
7.6 Mb |
(ftp)(http) |
BIGWIG |
| GSM897081_hg19_wgEncodeCshlShortRnaSeqMcf7CellShorttotalTapPlusRawRep4.bigWig |
6.5 Mb |
(ftp)(http) |
BIGWIG |
| GSM897081_hg19_wgEncodeCshlShortRnaSeqMcf7CellShorttotalTapProtocolRep1.pdf.gz |
300.9 Kb |
(ftp)(http) |
PDF |
| GSM897081_hg19_wgEncodeCshlShortRnaSeqMcf7CellShorttotalTapProtocolRep2.pdf.gz |
303.0 Kb |
(ftp)(http) |
PDF |
| GSM897081_hg19_wgEncodeCshlShortRnaSeqMcf7CellShorttotalTapProtocolRep3.pdf.gz |
138.1 Kb |
(ftp)(http) |
PDF |
| GSM897081_hg19_wgEncodeCshlShortRnaSeqMcf7CellShorttotalTapProtocolRep4.pdf.gz |
138.1 Kb |
(ftp)(http) |
PDF |
| GSM897081_hg19_wgEncodeCshlShortRnaSeqMcf7CellTapContigsV2.bedRnaElements.gz |
910.7 Kb |
(ftp)(http) |
BEDRNAELEMENTS |
| GSM897081_hg19_wgEncodeCshlShortRnaSeqMcf7CellTapExonsGencV10V2.gtf.gz |
1.6 Mb |
(ftp)(http) |
GTF |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
