|
| Status |
Public on Jul 13, 2011 |
| Title |
CSHL_RnaSeq_HepG2_cytosol_longPolyA (superseded by GSE90230) |
| Sample type |
SRA |
| |
|
| Source name |
HepG2
|
| Organism |
Homo sapiens |
| Characteristics |
datatype: RnaSeq
datatype description: Sequencing analysis of RNA expression
cell description: hepatocellular carcinoma
rnaextract: longPolyA
rnaextract description: Poly(A)+ RNA longer than 200 nt
biorep: 013C,014C,014C,013C
labexpid: LID8471,LID8472,LID8471,LID8472
labversion: iIDR
readtype: 2x76D
readtype description: Paired 76 nt directed reads
replicate: 1,2
spikeinpool: Nist14
rnaextract: longPolyA
rnaextract description: Poly(A)+ RNA longer than 200 nt
biorep: 013C,014C
labexpid: LID8471,LID8472
labversion: iIDR
spikeinpool: NIST14
|
| Biomaterial provider |
ATCC
|
| Growth protocol |
HepG2_protocol.pdf
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Instrument model unknown. ("Illumina Genome Analyzer" specified by default). For more information, see 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 |
****************************
GSM758576 record metadata submitted on Jul 11 2011 may be obsolete, up to date experimental metadata was resubmitted by ENCODE DCC and is available at GSE90230
****************************
|
| Data processing |
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeCshlLongRnaSeq
|
| |
|
| Submission date |
Jul 11, 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| Superseded by |
GSE90230 |
| SRA |
SRX082582 |
| BioSample |
SAMN00634087 |
| Named Annotation |
GSM758576_wgEncodeCshlLongRnaSeqHepg2CytosolPapMinusRawSigRep1.bigWig |
| Named Annotation |
GSM758576_wgEncodeCshlLongRnaSeqHepg2CytosolPapMinusRawSigRep2.bigWig |
| Named Annotation |
GSM758576_wgEncodeCshlLongRnaSeqHepg2CytosolPapPlusRawSigRep1.bigWig |
| Named Annotation |
GSM758576_wgEncodeCshlLongRnaSeqHepg2CytosolPapPlusRawSigRep2.bigWig |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM758576_hg19_wgEncodeCshlLongRnaSeqHepg2CytosolPapExonsDeNovo.gff.gz |
5.7 Mb |
(ftp)(http) |
GFF |
| GSM758576_hg19_wgEncodeCshlLongRnaSeqHepg2CytosolPapExonsGencV7.gtf.gz |
18.3 Mb |
(ftp)(http) |
GTF |
| GSM758576_hg19_wgEncodeCshlLongRnaSeqHepg2CytosolPapGeneDeNovoV2.gff.gz |
824.2 Kb |
(ftp)(http) |
GFF |
| GSM758576_hg19_wgEncodeCshlLongRnaSeqHepg2CytosolPapGeneGencV7.gtf.gz |
2.0 Mb |
(ftp)(http) |
GTF |
| GSM758576_hg19_wgEncodeCshlLongRnaSeqHepg2CytosolPapTranscriptDeNovoV2.gtf.gz |
1.2 Mb |
(ftp)(http) |
GTF |
| GSM758576_hg19_wgEncodeCshlLongRnaSeqHepg2CytosolPapTranscriptGencV7.gtf.gz |
4.8 Mb |
(ftp)(http) |
GTF |
| GSM758576_wgEncodeCshlLongRnaSeqHepg2CytosolPapContigs.bedRnaElements.gz |
7.6 Mb |
(ftp)(http) |
BEDRNAELEMENTS |
| GSM758576_wgEncodeCshlLongRnaSeqHepg2CytosolPapExonGencV3c.gtf.gz |
14.9 Mb |
(ftp)(http) |
GTF |
| GSM758576_wgEncodeCshlLongRnaSeqHepg2CytosolPapGeneDeNovo.gtf.gz |
877.4 Kb |
(ftp)(http) |
GTF |
| GSM758576_wgEncodeCshlLongRnaSeqHepg2CytosolPapGeneGencV3c.gtf.gz |
1.7 Mb |
(ftp)(http) |
GTF |
| GSM758576_wgEncodeCshlLongRnaSeqHepg2CytosolPapJunctions.bedRnaElements.gz |
8.0 Mb |
(ftp)(http) |
BEDRNAELEMENTS |
| GSM758576_wgEncodeCshlLongRnaSeqHepg2CytosolPapMinusRawSigRep1.bigWig |
271.3 Mb |
(ftp)(http) |
BIGWIG |
| GSM758576_wgEncodeCshlLongRnaSeqHepg2CytosolPapMinusRawSigRep2.bigWig |
269.7 Mb |
(ftp)(http) |
BIGWIG |
| GSM758576_wgEncodeCshlLongRnaSeqHepg2CytosolPapPlusRawSigRep1.bigWig |
274.8 Mb |
(ftp)(http) |
BIGWIG |
| GSM758576_wgEncodeCshlLongRnaSeqHepg2CytosolPapPlusRawSigRep2.bigWig |
273.2 Mb |
(ftp)(http) |
BIGWIG |
| GSM758576_wgEncodeCshlLongRnaSeqHepg2CytosolPapProtocolRep1.pdf.gz |
964.4 Kb |
(ftp)(http) |
PDF |
| GSM758576_wgEncodeCshlLongRnaSeqHepg2CytosolPapProtocolRep2.pdf.gz |
908.8 Kb |
(ftp)(http) |
PDF |
| GSM758576_wgEncodeCshlLongRnaSeqHepg2CytosolPapSpikeinsRep1.spikeins.bam |
52.6 Mb |
(ftp)(http) |
BAM |
| GSM758576_wgEncodeCshlLongRnaSeqHepg2CytosolPapSpikeinsRep2.spikeins.bam |
49.5 Mb |
(ftp)(http) |
BAM |
| GSM758576_wgEncodeCshlLongRnaSeqHepg2CytosolPapTranscriptDeNovo.gtf.gz |
10.3 Mb |
(ftp)(http) |
GTF |
| GSM758576_wgEncodeCshlLongRnaSeqHepg2CytosolPapTranscriptGencV3c.gtf.gz |
11.3 Mb |
(ftp)(http) |
GTF |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
