|
| Status |
Public on Jul 29, 2011 |
| Title |
CSHL_RnaSeq_HepG2_cytosol_longNonPolyA (superseded by GSE90256) |
| 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: 014C,013C,014C,013C
labexpid: LID18552,LID18553,LID18552,LID18553
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: 013C
labexpid: LID18552
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 |
cytoplasmic 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 |
****************************
GSM767840 record metadata submitted on Jul 27 2011 may be obsolete, up to date experimental metadata was resubmitted by ENCODE DCC and is available at GSE90256
****************************
|
| 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| Superseded by |
GSE90256 |
| SRA |
SRX085290 |
| BioSample |
SAMN00678383 |
| Named Annotation |
GSM767840_wgEncodeCshlLongRnaSeqHepg2CytosolLongnonpolyaMinusRawSigRep1.bigWig |
| Named Annotation |
GSM767840_wgEncodeCshlLongRnaSeqHepg2CytosolLongnonpolyaMinusRawSigRep2.bigWig |
| Named Annotation |
GSM767840_wgEncodeCshlLongRnaSeqHepg2CytosolLongnonpolyaPlusRawSigRep1.bigWig |
| Named Annotation |
GSM767840_wgEncodeCshlLongRnaSeqHepg2CytosolLongnonpolyaPlusRawSigRep2.bigWig |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM767840_hg19_wgEncodeCshlLongRnaSeqHepg2CytosolPamExonsDeNovo.gff.gz |
5.6 Mb |
(ftp)(http) |
GFF |
| GSM767840_hg19_wgEncodeCshlLongRnaSeqHepg2CytosolPamGeneDeNovoV2.gff.gz |
779.2 Kb |
(ftp)(http) |
GFF |
| GSM767840_hg19_wgEncodeCshlLongRnaSeqHepg2CytosolPamTranscriptDeNovoV2.gtf.gz |
1.1 Mb |
(ftp)(http) |
GTF |
| GSM767840_wgEncodeCshlLongRnaSeqHepg2CytosolLongnonpolyaMinusRawSigRep1.bigWig |
40.1 Mb |
(ftp)(http) |
BIGWIG |
| GSM767840_wgEncodeCshlLongRnaSeqHepg2CytosolLongnonpolyaMinusRawSigRep2.bigWig |
41.0 Mb |
(ftp)(http) |
BIGWIG |
| GSM767840_wgEncodeCshlLongRnaSeqHepg2CytosolLongnonpolyaPlusRawSigRep1.bigWig |
40.2 Mb |
(ftp)(http) |
BIGWIG |
| GSM767840_wgEncodeCshlLongRnaSeqHepg2CytosolLongnonpolyaPlusRawSigRep2.bigWig |
41.2 Mb |
(ftp)(http) |
BIGWIG |
| GSM767840_wgEncodeCshlLongRnaSeqHepg2CytosolPamContigs.bedRnaElements.gz |
4.9 Mb |
(ftp)(http) |
BEDRNAELEMENTS |
| GSM767840_wgEncodeCshlLongRnaSeqHepg2CytosolPamExonsGencV7.gtf.gz |
17.1 Mb |
(ftp)(http) |
GTF |
| GSM767840_wgEncodeCshlLongRnaSeqHepg2CytosolPamGeneDeNovo.gtf.gz |
572.6 Kb |
(ftp)(http) |
GTF |
| GSM767840_wgEncodeCshlLongRnaSeqHepg2CytosolPamGeneGencV7.gtf.gz |
1.9 Mb |
(ftp)(http) |
GTF |
| GSM767840_wgEncodeCshlLongRnaSeqHepg2CytosolPamJunctions.bedRnaElements.gz |
3.0 Mb |
(ftp)(http) |
BEDRNAELEMENTS |
| GSM767840_wgEncodeCshlLongRnaSeqHepg2CytosolPamProtocolRep1.pdf.gz |
498.3 Kb |
(ftp)(http) |
PDF |
| GSM767840_wgEncodeCshlLongRnaSeqHepg2CytosolPamProtocolRep2.pdf.gz |
492.7 Kb |
(ftp)(http) |
PDF |
| GSM767840_wgEncodeCshlLongRnaSeqHepg2CytosolPamSpikeinsRep1.spikeins.bam |
256.2 Mb |
(ftp)(http) |
BAM |
| GSM767840_wgEncodeCshlLongRnaSeqHepg2CytosolPamSpikeinsRep2.spikeins.bam |
218.0 Mb |
(ftp)(http) |
BAM |
| GSM767840_wgEncodeCshlLongRnaSeqHepg2CytosolPamTranscriptDeNovo.gtf.gz |
5.3 Mb |
(ftp)(http) |
GTF |
| GSM767840_wgEncodeCshlLongRnaSeqHepg2CytosolPamTranscriptGencV7.gtf.gz |
4.5 Mb |
(ftp)(http) |
GTF |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
