|
| Status |
Public on Jul 22, 2011 |
| Title |
CSHL_RnaSeq_K562_nucleoplasm_total (superseded by GSE90240) |
| Sample type |
SRA |
| |
|
| Source name |
K562
|
| Organism |
Homo sapiens |
| Characteristics |
datatype: RnaSeq
datatype description: Sequencing analysis of RNA expression
rnaextract: total
rnaextract description: Total RNA extract (longer than 200 nt)
biorep: 025NP,026NP,025NP,026NP
labexpid: LID9190,LID9189,LID9190,LID9189
labversion: iIDR
readtype: 2x76D
readtype description: Paired 76 nt directed reads
replicate: 3,4
spikeinpool: Nist14
localization description: That part of the nuclear content other than the chromosomes or the nucleolus
rnaextract: total
rnaextract description: Total RNA extract (longer than 200 nt)
biorep: 025NP
labexpid: LID9189
readtype: 2x76D
readtype description: Paired 76 n.t. directed reads
replicate: 3
replicate description: tier 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=wgEncodeCshlLongRnaSeq
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Description |
****************************
GSM765390 record metadata submitted on Jul 21 2011 may be obsolete, up to date experimental metadata was resubmitted by ENCODE DCC and is available at GSE90240
****************************
|
| Data processing |
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeCshlLongRnaSeq
|
| |
|
| Submission date |
Jul 21, 2011 |
| 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 (2) |
| GSE26284 |
ENCODE Cold Spring Harbor Labs Long RNA-seq |
| GSE30567 |
ENCODE Cold Spring Harbor Labs Long RNA-seq (hg19) |
|
| Relations |
| Superseded by |
GSE90240 |
| SRA |
SRX084668 |
| BioSample |
SAMN00672623 |
| Named Annotation |
GSM765390_wgEncodeCshlLongRnaSeqK562NucleoplasmTotalMinusRawSigRep3.bigWig |
| Named Annotation |
GSM765390_wgEncodeCshlLongRnaSeqK562NucleoplasmTotalMinusRawSigRep4.bigWig |
| Named Annotation |
GSM765390_wgEncodeCshlLongRnaSeqK562NucleoplasmTotalPlusRawSigRep3.bigWig |
| Named Annotation |
GSM765390_wgEncodeCshlLongRnaSeqK562NucleoplasmTotalPlusRawSigRep4.bigWig |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM765390_hg19_wgEncodeCshlLongRnaSeqK562NucleoplasmTotalExonsDeNovo.gff.gz |
9.5 Mb |
(ftp)(http) |
GFF |
| GSM765390_hg19_wgEncodeCshlLongRnaSeqK562NucleoplasmTotalGeneDeNovoV2.gff.gz |
6.5 Mb |
(ftp)(http) |
GFF |
| GSM765390_hg19_wgEncodeCshlLongRnaSeqK562NucleoplasmTotalProtocolRep3V2.pdf.gz |
336.0 Kb |
(ftp)(http) |
PDF |
| GSM765390_hg19_wgEncodeCshlLongRnaSeqK562NucleoplasmTotalProtocolRep4V2.pdf.gz |
338.2 Kb |
(ftp)(http) |
PDF |
| GSM765390_hg19_wgEncodeCshlLongRnaSeqK562NucleoplasmTotalTranscriptDeNovoV2.gtf.gz |
7.1 Mb |
(ftp)(http) |
GTF |
| GSM765390_wgEncodeCshlLongRnaSeqK562NucleoplasmTotalContigs.bedRnaElements.gz |
11.6 Mb |
(ftp)(http) |
BEDRNAELEMENTS |
| GSM765390_wgEncodeCshlLongRnaSeqK562NucleoplasmTotalExonGencV3c.gtf.gz |
14.3 Mb |
(ftp)(http) |
GTF |
| GSM765390_wgEncodeCshlLongRnaSeqK562NucleoplasmTotalGeneDeNovo.gtf.gz |
5.5 Mb |
(ftp)(http) |
GTF |
| GSM765390_wgEncodeCshlLongRnaSeqK562NucleoplasmTotalGeneGencV3c.gtf.gz |
1.7 Mb |
(ftp)(http) |
GTF |
| GSM765390_wgEncodeCshlLongRnaSeqK562NucleoplasmTotalJunctions.bedRnaElements.gz |
8.8 Mb |
(ftp)(http) |
BEDRNAELEMENTS |
| GSM765390_wgEncodeCshlLongRnaSeqK562NucleoplasmTotalMinusRawSigRep3.bigWig |
1.2 Gb |
(ftp)(http) |
BIGWIG |
| GSM765390_wgEncodeCshlLongRnaSeqK562NucleoplasmTotalMinusRawSigRep4.bigWig |
1.3 Gb |
(ftp)(http) |
BIGWIG |
| GSM765390_wgEncodeCshlLongRnaSeqK562NucleoplasmTotalPlusRawSigRep3.bigWig |
1.3 Gb |
(ftp)(http) |
BIGWIG |
| GSM765390_wgEncodeCshlLongRnaSeqK562NucleoplasmTotalPlusRawSigRep4.bigWig |
1.3 Gb |
(ftp)(http) |
BIGWIG |
| GSM765390_wgEncodeCshlLongRnaSeqK562NucleoplasmTotalSpikeinsRep3.spikeins.bam |
442.6 Mb |
(ftp)(http) |
BAM |
| GSM765390_wgEncodeCshlLongRnaSeqK562NucleoplasmTotalSpikeinsRep4.spikeins.bam |
447.0 Mb |
(ftp)(http) |
BAM |
| GSM765390_wgEncodeCshlLongRnaSeqK562NucleoplasmTotalTranscriptDeNovo.gtf.gz |
29.0 Mb |
(ftp)(http) |
GTF |
| GSM765390_wgEncodeCshlLongRnaSeqK562NucleoplasmTotalTranscriptGencV3c.gtf.gz |
11.0 Mb |
(ftp)(http) |
GTF |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
