|
Status |
Public on Oct 08, 2010 |
Title |
CSHL_RnaSeq_K562_cytosol_TAP-Only_shortTotal |
Sample type |
SRA |
|
|
Source name |
K562
|
Organism |
Homo sapiens |
Characteristics |
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: gen0142C,001C,002C,001C,002C labexpid: LID10571,crg-36,LID10572,LID10572,LID10571 labversion: Produced by Hannon Lab,iIDR readtype: 1x36 readtype description: Single 36 nt reads replicate: 1,2 localization: cytosol localization description: The fluid between the cells outer membrane and the nucleus 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: 001C labexpid: LID10572 readtype: 1x36 readtype description: Single 36 nt reads replicate: 1
|
Biomaterial provider |
ATCC
|
Growth protocol |
K562_protocol.pdf
|
Extracted molecule |
cytoplasmic RNA |
Extraction protocol |
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeCshlShortRnaSeq hg19: For extraction protocol details see: 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 |
Oct 06, 2010 |
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 |
SRX130247 |
BioSample |
SAMN00829028 |
Named Annotation |
GSM605629_hg19_wgEncodeCshlShortRnaSeqK562CytosolShortMinusRaw.bigWig |
Named Annotation |
GSM605629_hg19_wgEncodeCshlShortRnaSeqK562CytosolShortPlusRaw.bigWig |
Named Annotation |
GSM605629_hg19_wgEncodeCshlShortRnaSeqK562CytosolShorttotalTapMinusRawRep1.bigWig |
Named Annotation |
GSM605629_hg19_wgEncodeCshlShortRnaSeqK562CytosolShorttotalTapMinusRawRep2.bigWig |
Named Annotation |
GSM605629_hg19_wgEncodeCshlShortRnaSeqK562CytosolShorttotalTapPlusRawRep1.bigWig |
Named Annotation |
GSM605629_hg19_wgEncodeCshlShortRnaSeqK562CytosolShorttotalTapPlusRawRep2.bigWig |
Supplementary file |
Size |
Download |
File type/resource |
GSM605629_hg18_wgEncodeCshlShortRnaSeqAlignmentsK562CytosolShort.tagAlign.txt.gz |
22.5 Mb |
(ftp)(http) |
TXT |
GSM605629_hg18_wgEncodeCshlShortRnaSeqTransfragsK562CytosolShort.broadPeak.txt.gz |
12.2 Mb |
(ftp)(http) |
TXT |
GSM605629_hg19_wgEncodeCshlShortRnaSeqK562CytosolShortAln.bam |
62.1 Mb |
(ftp)(http) |
BAM |
GSM605629_hg19_wgEncodeCshlShortRnaSeqK562CytosolShortMinusRaw.bigWig |
21.5 Mb |
(ftp)(http) |
BIGWIG |
GSM605629_hg19_wgEncodeCshlShortRnaSeqK562CytosolShortPlusRaw.bigWig |
21.5 Mb |
(ftp)(http) |
BIGWIG |
GSM605629_hg19_wgEncodeCshlShortRnaSeqK562CytosolShortTransfrags.shortFrags.txt.gz |
1.6 Mb |
(ftp)(http) |
TXT |
GSM605629_hg19_wgEncodeCshlShortRnaSeqK562CytosolShorttotalTapContigs.bedRnaElements.gz |
299.4 Kb |
(ftp)(http) |
BEDRNAELEMENTS |
GSM605629_hg19_wgEncodeCshlShortRnaSeqK562CytosolShorttotalTapExonsGencV7.gtf.gz |
1.0 Mb |
(ftp)(http) |
GTF |
GSM605629_hg19_wgEncodeCshlShortRnaSeqK562CytosolShorttotalTapMinusRawRep1.bigWig |
4.3 Mb |
(ftp)(http) |
BIGWIG |
GSM605629_hg19_wgEncodeCshlShortRnaSeqK562CytosolShorttotalTapMinusRawRep2.bigWig |
3.6 Mb |
(ftp)(http) |
BIGWIG |
GSM605629_hg19_wgEncodeCshlShortRnaSeqK562CytosolShorttotalTapPlusRawRep1.bigWig |
4.2 Mb |
(ftp)(http) |
BIGWIG |
GSM605629_hg19_wgEncodeCshlShortRnaSeqK562CytosolShorttotalTapPlusRawRep2.bigWig |
3.6 Mb |
(ftp)(http) |
BIGWIG |
GSM605629_hg19_wgEncodeCshlShortRnaSeqK562CytosolShorttotalTapProtocolRep1.pdf.gz |
288.9 Kb |
(ftp)(http) |
PDF |
GSM605629_hg19_wgEncodeCshlShortRnaSeqK562CytosolShorttotalTapProtocolRep2.pdf.gz |
287.6 Kb |
(ftp)(http) |
PDF |
SRA Run Selector![Help](/coreweb/images/long_help4.gif) |
Raw data are available in SRA |
Processed data provided as supplementary file |