|
| Status |
Public on Jul 29, 2011 |
| Title |
CSHL_RnaSeq_HepG2_nucleus_longNonPolyA (superseded by GSE90248) |
| Sample type |
SRA |
| |
|
| Source name |
HepG2
|
| Organism |
Homo sapiens |
| Characteristics |
datatype: RnaSeq
datatype description: Sequencing analysis of RNA expression
cell description: hepatocellular carcinoma
rnaextract: longNonPolyA
rnaextract description: Poly(A)- RNA longer than 200 nt
biorep: 013N,013N,014N,014N
labexpid: LID9202,LID9203,LID9203,LID9202
labversion: iIDR
readtype: 2x76D
readtype description: Paired 76 nt directed reads
replicate: 1,2
spikeinpool: Nist14
rnaextract: longNonPolyA
rnaextract description: Poly(A)- RNA longer than 200 nt
biorep: 013N
labexpid: LID9202
readtype: 2x76D
readtype description: Paired 76 n.t. directed reads
replicate: 1
replicate description: tier 1
|
| Biomaterial provider |
ATCC
|
| Growth protocol |
HepG2_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 |
****************************
GSM767850 record metadata submitted on Jul 27 2011 may be obsolete, up to date experimental metadata was resubmitted by ENCODE DCC and is available at GSE90248
****************************
|
| Data processing |
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeCshlLongRnaSeq
|
| |
|
| Submission date |
Jul 27, 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| Superseded by |
GSE90248 |
| SRA |
SRX085300 |
| BioSample |
SAMN00678393 |
| Named Annotation |
GSM767850_wgEncodeCshlLongRnaSeqHepg2NucleusLongnonpolyaMinusRawSigRep1.bigWig |
| Named Annotation |
GSM767850_wgEncodeCshlLongRnaSeqHepg2NucleusLongnonpolyaMinusRawSigRep2.bigWig |
| Named Annotation |
GSM767850_wgEncodeCshlLongRnaSeqHepg2NucleusLongnonpolyaPlusRawSigRep1.bigWig |
| Named Annotation |
GSM767850_wgEncodeCshlLongRnaSeqHepg2NucleusLongnonpolyaPlusRawSigRep2.bigWig |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM767850_hg19_wgEncodeCshlLongRnaSeqHepg2NucleusPamExonsDeNovo.gff.gz |
11.8 Mb |
(ftp)(http) |
GFF |
| GSM767850_hg19_wgEncodeCshlLongRnaSeqHepg2NucleusPamGeneDeNovoV2.gff.gz |
8.1 Mb |
(ftp)(http) |
GFF |
| GSM767850_hg19_wgEncodeCshlLongRnaSeqHepg2NucleusPamTranscriptDeNovoV2.gtf.gz |
8.7 Mb |
(ftp)(http) |
GTF |
| GSM767850_wgEncodeCshlLongRnaSeqHepg2NucleusLongnonpolyaMinusRawSigRep1.bigWig |
365.4 Mb |
(ftp)(http) |
BIGWIG |
| GSM767850_wgEncodeCshlLongRnaSeqHepg2NucleusLongnonpolyaMinusRawSigRep2.bigWig |
399.9 Mb |
(ftp)(http) |
BIGWIG |
| GSM767850_wgEncodeCshlLongRnaSeqHepg2NucleusLongnonpolyaPlusRawSigRep1.bigWig |
368.9 Mb |
(ftp)(http) |
BIGWIG |
| GSM767850_wgEncodeCshlLongRnaSeqHepg2NucleusLongnonpolyaPlusRawSigRep2.bigWig |
402.7 Mb |
(ftp)(http) |
BIGWIG |
| GSM767850_wgEncodeCshlLongRnaSeqHepg2NucleusPamContigs.bedRnaElements.gz |
11.7 Mb |
(ftp)(http) |
BEDRNAELEMENTS |
| GSM767850_wgEncodeCshlLongRnaSeqHepg2NucleusPamExonsGencV7.gtf.gz |
17.8 Mb |
(ftp)(http) |
GTF |
| GSM767850_wgEncodeCshlLongRnaSeqHepg2NucleusPamGeneDeNovo.gtf.gz |
4.1 Mb |
(ftp)(http) |
GTF |
| GSM767850_wgEncodeCshlLongRnaSeqHepg2NucleusPamGeneGencV7.gtf.gz |
2.0 Mb |
(ftp)(http) |
GTF |
| GSM767850_wgEncodeCshlLongRnaSeqHepg2NucleusPamJunctions.bedRnaElements.gz |
6.5 Mb |
(ftp)(http) |
BEDRNAELEMENTS |
| GSM767850_wgEncodeCshlLongRnaSeqHepg2NucleusPamProtocolRep1.pdf.gz |
421.9 Kb |
(ftp)(http) |
PDF |
| GSM767850_wgEncodeCshlLongRnaSeqHepg2NucleusPamProtocolRep2.pdf.gz |
423.5 Kb |
(ftp)(http) |
PDF |
| GSM767850_wgEncodeCshlLongRnaSeqHepg2NucleusPamSpikeinsRep1.spikeins.bam |
226.0 Mb |
(ftp)(http) |
BAM |
| GSM767850_wgEncodeCshlLongRnaSeqHepg2NucleusPamSpikeinsRep2.spikeins.bam |
366.0 Mb |
(ftp)(http) |
BAM |
| GSM767850_wgEncodeCshlLongRnaSeqHepg2NucleusPamTranscriptDeNovo.gtf.gz |
19.9 Mb |
(ftp)(http) |
GTF |
| GSM767850_wgEncodeCshlLongRnaSeqHepg2NucleusPamTranscriptGencV7.gtf.gz |
4.7 Mb |
(ftp)(http) |
GTF |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
