|
| Status |
Public on Jul 29, 2011 |
| Title |
CSHL_RnaSeq_HeLa-S3_nucleus_longNonPolyA (superseded by GSE90246) |
| Sample type |
SRA |
| |
|
| Source name |
HeLa-S3
|
| Organism |
Homo sapiens |
| Characteristics |
datatype: RnaSeq
datatype description: Sequencing analysis of RNA expression
cell lineage: ectoderm
rnaextract: longNonPolyA
rnaextract description: Poly(A)- RNA longer than 200 nt
biorep: 011N,012N,012N,011N
labexpid: LID9200,LID9201,LID9201,LID9200
labversion: iIDR
readtype: 2x76D
readtype description: Paired 76 nt directed reads
replicate: 1,2
spikeinpool: Nist14
rnaextract description: Poly(A)- RNA longer than 200 nt
biorep: 011N
labexpid: LID9200
readtype: 2x76D
readtype description: Paired 76 n.t. directed reads
replicate: 1
replicate description: tier 1
|
| Biomaterial provider |
ATCC
|
| Growth protocol |
HeLa-S3_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 |
****************************
GSM767848 record metadata submitted on Jul 27 2011 may be obsolete, up to date experimental metadata was resubmitted by ENCODE DCC and is available at GSE90246
****************************
|
| 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| Superseded by |
GSE90246 |
| SRA |
SRX085298 |
| BioSample |
SAMN00678391 |
| Named Annotation |
GSM767848_wgEncodeCshlLongRnaSeqHelas3NucleusLongnonpolyaMinusRawSigRep1.bigWig |
| Named Annotation |
GSM767848_wgEncodeCshlLongRnaSeqHelas3NucleusLongnonpolyaMinusRawSigRep2.bigWig |
| Named Annotation |
GSM767848_wgEncodeCshlLongRnaSeqHelas3NucleusLongnonpolyaPlusRawSigRep1.bigWig |
| Named Annotation |
GSM767848_wgEncodeCshlLongRnaSeqHelas3NucleusLongnonpolyaPlusRawSigRep2.bigWig |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM767848_hg19_wgEncodeCshlLongRnaSeqHelas3NucleusPamExonsDeNovo.gff.gz |
11.5 Mb |
(ftp)(http) |
GFF |
| GSM767848_hg19_wgEncodeCshlLongRnaSeqHelas3NucleusPamGeneDeNovoV2.gff.gz |
7.9 Mb |
(ftp)(http) |
GFF |
| GSM767848_hg19_wgEncodeCshlLongRnaSeqHelas3NucleusPamTranscriptDeNovoV2.gtf.gz |
8.5 Mb |
(ftp)(http) |
GTF |
| GSM767848_wgEncodeCshlLongRnaSeqHelas3NucleusLongnonpolyaMinusRawSigRep1.bigWig |
263.0 Mb |
(ftp)(http) |
BIGWIG |
| GSM767848_wgEncodeCshlLongRnaSeqHelas3NucleusLongnonpolyaMinusRawSigRep2.bigWig |
237.7 Mb |
(ftp)(http) |
BIGWIG |
| GSM767848_wgEncodeCshlLongRnaSeqHelas3NucleusLongnonpolyaPlusRawSigRep1.bigWig |
271.3 Mb |
(ftp)(http) |
BIGWIG |
| GSM767848_wgEncodeCshlLongRnaSeqHelas3NucleusLongnonpolyaPlusRawSigRep2.bigWig |
246.8 Mb |
(ftp)(http) |
BIGWIG |
| GSM767848_wgEncodeCshlLongRnaSeqHelas3NucleusPamContigs.bedRnaElements.gz |
14.2 Mb |
(ftp)(http) |
BEDRNAELEMENTS |
| GSM767848_wgEncodeCshlLongRnaSeqHelas3NucleusPamExonsGencV7.gtf.gz |
17.8 Mb |
(ftp)(http) |
GTF |
| GSM767848_wgEncodeCshlLongRnaSeqHelas3NucleusPamGeneDeNovo.gtf.gz |
6.3 Mb |
(ftp)(http) |
GTF |
| GSM767848_wgEncodeCshlLongRnaSeqHelas3NucleusPamGeneGencV7.gtf.gz |
2.0 Mb |
(ftp)(http) |
GTF |
| GSM767848_wgEncodeCshlLongRnaSeqHelas3NucleusPamJunctions.bedRnaElements.gz |
5.7 Mb |
(ftp)(http) |
BEDRNAELEMENTS |
| GSM767848_wgEncodeCshlLongRnaSeqHelas3NucleusPamProtocolRep1.pdf.gz |
424.1 Kb |
(ftp)(http) |
PDF |
| GSM767848_wgEncodeCshlLongRnaSeqHelas3NucleusPamProtocolRep2.pdf.gz |
421.6 Kb |
(ftp)(http) |
PDF |
| GSM767848_wgEncodeCshlLongRnaSeqHelas3NucleusPamSpikeinsRep1.spikeins.bam |
175.0 Mb |
(ftp)(http) |
BAM |
| GSM767848_wgEncodeCshlLongRnaSeqHelas3NucleusPamSpikeinsRep2.spikeins.bam |
213.4 Mb |
(ftp)(http) |
BAM |
| GSM767848_wgEncodeCshlLongRnaSeqHelas3NucleusPamTranscriptDeNovo.gtf.gz |
29.8 Mb |
(ftp)(http) |
GTF |
| GSM767848_wgEncodeCshlLongRnaSeqHelas3NucleusPamTranscriptGencV7.gtf.gz |
4.7 Mb |
(ftp)(http) |
GTF |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
