|
| Status |
Public on Oct 08, 2010 |
| Title |
CSHL_RnaSeq_K562_nucleoplasm_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: 025NP,026NP,025NP,gen0146NP,026NP
labexpid: LID8929,LID8929,LID18559,crg-39,LID18559
labversion: Produced by Hannon Lab,iIDR
readtype: 1x36
readtype description: Single 36 nt reads
replicate: 3,4
localization: nucleoplasm
localization description: That part of the nuclear content other than the chromosomes or the nucleolus
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: 025NP
labexpid: LID8929
readtype: 1x36
readtype description: Single 36 nt reads
replicate: 3
|
| Biomaterial provider |
ATCC
|
| Growth protocol |
K562_protocol.pdf
|
| Extracted molecule |
nuclear 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 |
SRX028007 |
| BioSample |
SAMN00115102 |
| Named Annotation |
GSM605634_hg19_wgEncodeCshlShortRnaSeqK562NucleoplasmShortMinusRaw.bigWig |
| Named Annotation |
GSM605634_hg19_wgEncodeCshlShortRnaSeqK562NucleoplasmShortPlusRaw.bigWig |
| Named Annotation |
GSM605634_hg19_wgEncodeCshlShortRnaSeqK562NucleoplasmShorttotalTapMinusRawRep3.bigWig |
| Named Annotation |
GSM605634_hg19_wgEncodeCshlShortRnaSeqK562NucleoplasmShorttotalTapMinusRawRep4.bigWig |
| Named Annotation |
GSM605634_hg19_wgEncodeCshlShortRnaSeqK562NucleoplasmShorttotalTapPlusRawRep3.bigWig |
| Named Annotation |
GSM605634_hg19_wgEncodeCshlShortRnaSeqK562NucleoplasmShorttotalTapPlusRawRep4.bigWig |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM605634_hg18_wgEncodeCshlShortRnaSeqAlignmentsK562NucleoplasmShort.tagAlign.txt.gz |
336.7 Mb |
(ftp)(http) |
TXT |
| GSM605634_hg18_wgEncodeCshlShortRnaSeqTransfragsK562NucleoplasmShort.broadPeak.txt.gz |
213.6 Mb |
(ftp)(http) |
TXT |
| GSM605634_hg19_wgEncodeCshlShortRnaSeqK562NucleoplasmShortAln.bam |
553.3 Mb |
(ftp)(http) |
BAM |
| GSM605634_hg19_wgEncodeCshlShortRnaSeqK562NucleoplasmShortMinusRaw.bigWig |
435.8 Mb |
(ftp)(http) |
BIGWIG |
| GSM605634_hg19_wgEncodeCshlShortRnaSeqK562NucleoplasmShortPlusRaw.bigWig |
445.7 Mb |
(ftp)(http) |
BIGWIG |
| GSM605634_hg19_wgEncodeCshlShortRnaSeqK562NucleoplasmShortTransfrags.shortFrags.txt.gz |
150.4 Mb |
(ftp)(http) |
TXT |
| GSM605634_hg19_wgEncodeCshlShortRnaSeqK562NucleoplasmShorttotalTapContigs.bedRnaElements.gz |
12.7 Mb |
(ftp)(http) |
BEDRNAELEMENTS |
| GSM605634_hg19_wgEncodeCshlShortRnaSeqK562NucleoplasmShorttotalTapExonsGencV7.gtf.gz |
3.7 Mb |
(ftp)(http) |
GTF |
| GSM605634_hg19_wgEncodeCshlShortRnaSeqK562NucleoplasmShorttotalTapMinusRawRep3.bigWig |
33.8 Mb |
(ftp)(http) |
BIGWIG |
| GSM605634_hg19_wgEncodeCshlShortRnaSeqK562NucleoplasmShorttotalTapMinusRawRep4.bigWig |
33.1 Mb |
(ftp)(http) |
BIGWIG |
| GSM605634_hg19_wgEncodeCshlShortRnaSeqK562NucleoplasmShorttotalTapPlusRawRep3.bigWig |
33.7 Mb |
(ftp)(http) |
BIGWIG |
| GSM605634_hg19_wgEncodeCshlShortRnaSeqK562NucleoplasmShorttotalTapPlusRawRep4.bigWig |
33.1 Mb |
(ftp)(http) |
BIGWIG |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
