|
| Status |
Public on Jul 29, 2011 |
| Title |
CSHL_RnaSeq_NHEK_nucleus_longNonPolyA (superseded by GSE78603) |
| Sample type |
SRA |
| |
|
| Source name |
NHEK
|
| Organism |
Homo sapiens |
| Characteristics |
datatype: RnaSeq
datatype description: Sequencing analysis of RNA expression
cell sex: F
rnaextract: longNonPolyA
rnaextract description: Poly(A)- RNA longer than 200 nt
biorep: 028N,027N,027N,028N
labexpid: LID9205,LID9204,LID9204,LID9205
labversion: iIDR
readtype: 2x76D
readtype description: Paired 76 nt directed reads
replicate: 3,4
spikeinpool: Nist14
rnaextract: longNonPolyA
rnaextract description: Poly(A)- RNA longer than 200 nt
biorep: 027N
labexpid: LID9204
readtype: 2x76D
readtype description: Paired 76 n.t. directed reads
replicate: 3
replicate description: tier 3
|
| Biomaterial provider |
Lonza
|
| Growth protocol |
Keratinocyte_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 |
****************************
GSM767846 record metadata submitted on Jul 27 2011 may be obsolete, up to date experimental metadata was resubmitted by ENCODE DCC and is available at GSE78603
****************************
|
| 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| Superseded by |
GSE78603 |
| SRA |
SRX085296 |
| BioSample |
SAMN00678389 |
| Named Annotation |
GSM767846_wgEncodeCshlLongRnaSeqNhekNucleusLongnonpolyaMinusRawSigRep3.bigWig |
| Named Annotation |
GSM767846_wgEncodeCshlLongRnaSeqNhekNucleusLongnonpolyaMinusRawSigRep4.bigWig |
| Named Annotation |
GSM767846_wgEncodeCshlLongRnaSeqNhekNucleusLongnonpolyaPlusRawSigRep3.bigWig |
| Named Annotation |
GSM767846_wgEncodeCshlLongRnaSeqNhekNucleusLongnonpolyaPlusRawSigRep4.bigWig |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM767846_hg19_wgEncodeCshlLongRnaSeqNhekNucleusPamExonsDeNovo.gff.gz |
10.1 Mb |
(ftp)(http) |
GFF |
| GSM767846_hg19_wgEncodeCshlLongRnaSeqNhekNucleusPamGeneDeNovoV2.gff.gz |
5.1 Mb |
(ftp)(http) |
GFF |
| GSM767846_hg19_wgEncodeCshlLongRnaSeqNhekNucleusPamTranscriptDeNovoV2.gtf.gz |
5.6 Mb |
(ftp)(http) |
GTF |
| GSM767846_wgEncodeCshlLongRnaSeqNhekNucleusLongnonpolyaMinusRawSigRep3.bigWig |
203.5 Mb |
(ftp)(http) |
BIGWIG |
| GSM767846_wgEncodeCshlLongRnaSeqNhekNucleusLongnonpolyaMinusRawSigRep4.bigWig |
162.6 Mb |
(ftp)(http) |
BIGWIG |
| GSM767846_wgEncodeCshlLongRnaSeqNhekNucleusLongnonpolyaPlusRawSigRep3.bigWig |
213.1 Mb |
(ftp)(http) |
BIGWIG |
| GSM767846_wgEncodeCshlLongRnaSeqNhekNucleusLongnonpolyaPlusRawSigRep4.bigWig |
169.2 Mb |
(ftp)(http) |
BIGWIG |
| GSM767846_wgEncodeCshlLongRnaSeqNhekNucleusPamContigs.bedRnaElements.gz |
14.5 Mb |
(ftp)(http) |
BEDRNAELEMENTS |
| GSM767846_wgEncodeCshlLongRnaSeqNhekNucleusPamExonsGencV7.gtf.gz |
17.8 Mb |
(ftp)(http) |
GTF |
| GSM767846_wgEncodeCshlLongRnaSeqNhekNucleusPamGeneDeNovo.gtf.gz |
4.0 Mb |
(ftp)(http) |
GTF |
| GSM767846_wgEncodeCshlLongRnaSeqNhekNucleusPamGeneGencV7.gtf.gz |
2.0 Mb |
(ftp)(http) |
GTF |
| GSM767846_wgEncodeCshlLongRnaSeqNhekNucleusPamJunctions.bedRnaElements.gz |
5.1 Mb |
(ftp)(http) |
BEDRNAELEMENTS |
| GSM767846_wgEncodeCshlLongRnaSeqNhekNucleusPamProtocolRep3.pdf.gz |
424.0 Kb |
(ftp)(http) |
PDF |
| GSM767846_wgEncodeCshlLongRnaSeqNhekNucleusPamProtocolRep4.pdf.gz |
426.9 Kb |
(ftp)(http) |
PDF |
| GSM767846_wgEncodeCshlLongRnaSeqNhekNucleusPamSpikeinsRep3.spikeins.bam |
293.6 Mb |
(ftp)(http) |
BAM |
| GSM767846_wgEncodeCshlLongRnaSeqNhekNucleusPamSpikeinsRep4.spikeins.bam |
218.4 Mb |
(ftp)(http) |
BAM |
| GSM767846_wgEncodeCshlLongRnaSeqNhekNucleusPamTranscriptDeNovo.gtf.gz |
19.8 Mb |
(ftp)(http) |
GTF |
| GSM767846_wgEncodeCshlLongRnaSeqNhekNucleusPamTranscriptGencV7.gtf.gz |
4.7 Mb |
(ftp)(http) |
GTF |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
