|
| Status |
Public on Jul 22, 2011 |
| Title |
CSHL_RnaSeq_NHEK_cytosol_longPolyA (superseded by GSE78593) |
| Sample type |
SRA |
| |
|
| Source name |
NHEK
|
| Organism |
Homo sapiens |
| Characteristics |
datatype: RnaSeq
datatype description: Sequencing analysis of RNA expression
cell sex: F
rnaextract: longPolyA
rnaextract description: Poly(A)+ RNA longer than 200 nt
biorep: 027C,027C,028C,028C
labexpid: LID8795,LID8796,LID8795,LID8796
labversion: iIDR
readtype: 2x76D
readtype description: Paired 76 nt directed reads
replicate: 3,4
spikeinpool: Nist14
rnaextract: longPolyA
rnaextract description: Poly(A)+ RNA longer than 200 nt
biorep: 027C
labexpid: LID8795
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 |
polyA 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 |
****************************
GSM765400 record metadata submitted on Jul 21 2011 may be obsolete, up to date experimental metadata was resubmitted by ENCODE DCC and is available at GSE78593
****************************
|
| Data processing |
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeCshlLongRnaSeq
|
| |
|
| Submission date |
Jul 21, 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| Superseded by |
GSE78593 |
| SRA |
SRX084678 |
| BioSample |
SAMN00672633 |
| Named Annotation |
GSM765400_wgEncodeCshlLongRnaSeqNhekCytosolPapMinusRawSigRep3.bigWig |
| Named Annotation |
GSM765400_wgEncodeCshlLongRnaSeqNhekCytosolPapMinusRawSigRep4.bigWig |
| Named Annotation |
GSM765400_wgEncodeCshlLongRnaSeqNhekCytosolPapPlusRawSigRep3.bigWig |
| Named Annotation |
GSM765400_wgEncodeCshlLongRnaSeqNhekCytosolPapPlusRawSigRep4.bigWig |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM765400_hg19_wgEncodeCshlLongRnaSeqNhekCytosolPapExonsDeNovo.gff.gz |
6.4 Mb |
(ftp)(http) |
GFF |
| GSM765400_hg19_wgEncodeCshlLongRnaSeqNhekCytosolPapGeneDeNovoV2.gff.gz |
748.3 Kb |
(ftp)(http) |
GFF |
| GSM765400_hg19_wgEncodeCshlLongRnaSeqNhekCytosolPapTranscriptDeNovoV2.gtf.gz |
1.1 Mb |
(ftp)(http) |
GTF |
| GSM765400_wgEncodeCshlLongRnaSeqNhekCytosolPapContigs.bedRnaElements.gz |
5.5 Mb |
(ftp)(http) |
BEDRNAELEMENTS |
| GSM765400_wgEncodeCshlLongRnaSeqNhekCytosolPapExonGencV3c.gtf.gz |
14.9 Mb |
(ftp)(http) |
GTF |
| GSM765400_wgEncodeCshlLongRnaSeqNhekCytosolPapGeneDeNovo.gtf.gz |
775.5 Kb |
(ftp)(http) |
GTF |
| GSM765400_wgEncodeCshlLongRnaSeqNhekCytosolPapGeneGencV3c.gtf.gz |
1.7 Mb |
(ftp)(http) |
GTF |
| GSM765400_wgEncodeCshlLongRnaSeqNhekCytosolPapJunctions.bedRnaElements.gz |
8.4 Mb |
(ftp)(http) |
BEDRNAELEMENTS |
| GSM765400_wgEncodeCshlLongRnaSeqNhekCytosolPapMinusRawSigRep3.bigWig |
191.4 Mb |
(ftp)(http) |
BIGWIG |
| GSM765400_wgEncodeCshlLongRnaSeqNhekCytosolPapMinusRawSigRep4.bigWig |
213.1 Mb |
(ftp)(http) |
BIGWIG |
| GSM765400_wgEncodeCshlLongRnaSeqNhekCytosolPapPlusRawSigRep3.bigWig |
195.5 Mb |
(ftp)(http) |
BIGWIG |
| GSM765400_wgEncodeCshlLongRnaSeqNhekCytosolPapPlusRawSigRep4.bigWig |
217.5 Mb |
(ftp)(http) |
BIGWIG |
| GSM765400_wgEncodeCshlLongRnaSeqNhekCytosolPapProtocolRep3.pdf.gz |
564.2 Kb |
(ftp)(http) |
PDF |
| GSM765400_wgEncodeCshlLongRnaSeqNhekCytosolPapProtocolRep4.pdf.gz |
559.9 Kb |
(ftp)(http) |
PDF |
| GSM765400_wgEncodeCshlLongRnaSeqNhekCytosolPapSpikeinsRep3.spikeins.bam |
118.4 Mb |
(ftp)(http) |
BAM |
| GSM765400_wgEncodeCshlLongRnaSeqNhekCytosolPapSpikeinsRep4.spikeins.bam |
62.9 Mb |
(ftp)(http) |
BAM |
| GSM765400_wgEncodeCshlLongRnaSeqNhekCytosolPapTranscriptDeNovo.gtf.gz |
11.5 Mb |
(ftp)(http) |
GTF |
| GSM765400_wgEncodeCshlLongRnaSeqNhekCytosolPapTranscriptGencV3c.gtf.gz |
11.3 Mb |
(ftp)(http) |
GTF |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
