|
| Status |
Public on Jul 29, 2011 |
| Title |
CSHL_RnaSeq_NHEK_cytosol_longNonPolyA (superseded by GSE78602) |
| 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: 027C
labexpid: LID18554
labversion: iIDR
readtype: 2x76D
readtype description: Paired 76 nt directed reads
spikeinpool: Nist14
localization description: The fluid between the cells outer membrane and the nucleus
rnaextract: longNonPolyA
rnaextract description: Poly(A)- RNA longer than 200 nt
biorep: 027C
labexpid: LID18554
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 |
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 |
****************************
GSM767843 record metadata submitted on Jul 27 2011 may be obsolete, up to date experimental metadata was resubmitted by ENCODE DCC and is available at GSE78602
****************************
|
| 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| Superseded by |
GSE78602 |
| SRA |
SRX085293 |
| BioSample |
SAMN00678386 |
| Named Annotation |
GSM767843_wgEncodeCshlLongRnaSeqNhekCytosolLongnonpolyaMinusRawSigRep3.bigWig |
| Named Annotation |
GSM767843_wgEncodeCshlLongRnaSeqNhekCytosolLongnonpolyaPlusRawSigRep3.bigWig |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM767843_hg19_wgEncodeCshlLongRnaSeqNhekCytosolPamContigsV2.bedRnaElements.gz |
3.5 Mb |
(ftp)(http) |
BEDRNAELEMENTS |
| GSM767843_hg19_wgEncodeCshlLongRnaSeqNhekCytosolPamExonsDeNovo.gff.gz |
2.6 Mb |
(ftp)(http) |
GFF |
| GSM767843_hg19_wgEncodeCshlLongRnaSeqNhekCytosolPamGeneDeNovoV2.gff.gz |
387.4 Kb |
(ftp)(http) |
GFF |
| GSM767843_hg19_wgEncodeCshlLongRnaSeqNhekCytosolPamTranscriptDeNovoV2.gtf.gz |
563.5 Kb |
(ftp)(http) |
GTF |
| GSM767843_wgEncodeCshlLongRnaSeqNhekCytosolLongnonpolyaMinusRawSigRep3.bigWig |
19.8 Mb |
(ftp)(http) |
BIGWIG |
| GSM767843_wgEncodeCshlLongRnaSeqNhekCytosolLongnonpolyaPlusRawSigRep3.bigWig |
20.0 Mb |
(ftp)(http) |
BIGWIG |
| GSM767843_wgEncodeCshlLongRnaSeqNhekCytosolPamContigs.bedRnaElements.gz |
3.5 Mb |
(ftp)(http) |
BEDRNAELEMENTS |
| GSM767843_wgEncodeCshlLongRnaSeqNhekCytosolPamExonsGencV7.gtf.gz |
15.1 Mb |
(ftp)(http) |
GTF |
| GSM767843_wgEncodeCshlLongRnaSeqNhekCytosolPamGeneDeNovo.gtf.gz |
325.1 Kb |
(ftp)(http) |
GTF |
| GSM767843_wgEncodeCshlLongRnaSeqNhekCytosolPamGeneGencV7.gtf.gz |
1.3 Mb |
(ftp)(http) |
GTF |
| GSM767843_wgEncodeCshlLongRnaSeqNhekCytosolPamJunctions.bedRnaElements.gz |
1.7 Mb |
(ftp)(http) |
BEDRNAELEMENTS |
| GSM767843_wgEncodeCshlLongRnaSeqNhekCytosolPamProtocolRep4.pdf.gz |
490.8 Kb |
(ftp)(http) |
PDF |
| GSM767843_wgEncodeCshlLongRnaSeqNhekCytosolPamSpikeinsRep3.spikeins.bam |
64.7 Mb |
(ftp)(http) |
BAM |
| GSM767843_wgEncodeCshlLongRnaSeqNhekCytosolPamTranscriptDeNovo.gtf.gz |
2.3 Mb |
(ftp)(http) |
GTF |
| GSM767843_wgEncodeCshlLongRnaSeqNhekCytosolPamTranscriptGencV7.gtf.gz |
3.9 Mb |
(ftp)(http) |
GTF |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
