|
| Status |
Public on Jul 13, 2011 |
| Title |
CSHL_RnaSeq_HepG2_cell_longPolyA (superseded by GSE86659) |
| 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: 014WC,013WC,013WC,014WC
labexpid: LID16635,LID16636,LID16635,LID16636
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: 013WC,014WC
labexpid: LID16635,LID16636
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 |
****************************
GSM758575 record metadata submitted on Jul 11 2011 may be obsolete, up to date experimental metadata was resubmitted by ENCODE DCC and is available at GSE86659
****************************
|
| 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 (3) |
| GSE26284 |
ENCODE Cold Spring Harbor Labs Long RNA-seq |
| GSE30567 |
ENCODE Cold Spring Harbor Labs Long RNA-seq (hg19) |
| GSE49417 |
The conserved organization of the human and mouse transcriptomes |
|
| Relations |
| Superseded by |
GSE86659 |
| SRA |
SRX082581 |
| BioSample |
SAMN00634086 |
| Named Annotation |
GSM758575_wgEncodeCshlLongRnaSeqHepg2CellPapMinusRawSigRep1.bigWig |
| Named Annotation |
GSM758575_wgEncodeCshlLongRnaSeqHepg2CellPapMinusRawSigRep2.bigWig |
| Named Annotation |
GSM758575_wgEncodeCshlLongRnaSeqHepg2CellPapPlusRawSigRep1.bigWig |
| Named Annotation |
GSM758575_wgEncodeCshlLongRnaSeqHepg2CellPapPlusRawSigRep2.bigWig |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM758575_hg19_wgEncodeCshlLongRnaSeqHepg2CellPapExonsDeNovo.gff.gz |
6.5 Mb |
(ftp)(http) |
GFF |
| GSM758575_hg19_wgEncodeCshlLongRnaSeqHepg2CellPapExonsGencV7.gtf.gz |
18.4 Mb |
(ftp)(http) |
GTF |
| GSM758575_hg19_wgEncodeCshlLongRnaSeqHepg2CellPapGeneDeNovoV2.gff.gz |
1.5 Mb |
(ftp)(http) |
GFF |
| GSM758575_hg19_wgEncodeCshlLongRnaSeqHepg2CellPapGeneGencV7.gtf.gz |
2.0 Mb |
(ftp)(http) |
GTF |
| GSM758575_hg19_wgEncodeCshlLongRnaSeqHepg2CellPapTranscriptDeNovoV2.gtf.gz |
1.9 Mb |
(ftp)(http) |
GTF |
| GSM758575_hg19_wgEncodeCshlLongRnaSeqHepg2CellPapTranscriptGencV7.gtf.gz |
4.9 Mb |
(ftp)(http) |
GTF |
| GSM758575_wgEncodeCshlLongRnaSeqHepg2CellPapContigs.bedRnaElements.gz |
12.7 Mb |
(ftp)(http) |
BEDRNAELEMENTS |
| GSM758575_wgEncodeCshlLongRnaSeqHepg2CellPapExonGencV3c.gtf.gz |
14.9 Mb |
(ftp)(http) |
GTF |
| GSM758575_wgEncodeCshlLongRnaSeqHepg2CellPapGeneDeNovo.gtf.gz |
1.4 Mb |
(ftp)(http) |
GTF |
| GSM758575_wgEncodeCshlLongRnaSeqHepg2CellPapGeneGencV3c.gtf.gz |
1.7 Mb |
(ftp)(http) |
GTF |
| GSM758575_wgEncodeCshlLongRnaSeqHepg2CellPapJunctions.bedRnaElements.gz |
8.3 Mb |
(ftp)(http) |
BEDRNAELEMENTS |
| GSM758575_wgEncodeCshlLongRnaSeqHepg2CellPapMinusRawSigRep1.bigWig |
606.4 Mb |
(ftp)(http) |
BIGWIG |
| GSM758575_wgEncodeCshlLongRnaSeqHepg2CellPapMinusRawSigRep2.bigWig |
614.8 Mb |
(ftp)(http) |
BIGWIG |
| GSM758575_wgEncodeCshlLongRnaSeqHepg2CellPapPlusRawSigRep1.bigWig |
616.2 Mb |
(ftp)(http) |
BIGWIG |
| GSM758575_wgEncodeCshlLongRnaSeqHepg2CellPapPlusRawSigRep2.bigWig |
625.0 Mb |
(ftp)(http) |
BIGWIG |
| GSM758575_wgEncodeCshlLongRnaSeqHepg2CellPapProtocolRep1.pdf.gz |
968.2 Kb |
(ftp)(http) |
PDF |
| GSM758575_wgEncodeCshlLongRnaSeqHepg2CellPapProtocolRep2.pdf.gz |
978.8 Kb |
(ftp)(http) |
PDF |
| GSM758575_wgEncodeCshlLongRnaSeqHepg2CellPapSpikeinsRep1.spikeins.bam |
293.1 Mb |
(ftp)(http) |
BAM |
| GSM758575_wgEncodeCshlLongRnaSeqHepg2CellPapSpikeinsRep2.spikeins.bam |
277.9 Mb |
(ftp)(http) |
BAM |
| GSM758575_wgEncodeCshlLongRnaSeqHepg2CellPapTranscriptDeNovo.gtf.gz |
12.4 Mb |
(ftp)(http) |
GTF |
| GSM758575_wgEncodeCshlLongRnaSeqHepg2CellPapTranscriptGencV3c.gtf.gz |
11.4 Mb |
(ftp)(http) |
GTF |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
