|
| Status |
Public on Jul 22, 2011 |
| Title |
CSHL_RnaSeq_NHEK_cell_longNonPolyA (superseded by GSE78591) |
| 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: 007WC,008WC,007WC,008WC,035WC
labexpid: LID8665,LID8666,LID8665,LID8666,LID8830
labversion: iIDR
readtype: 2x76D
readtype description: Paired 76 nt directed reads
replicate: 1,2,5
spikeinpool: Nist14
rnaextract: longNonPolyA
rnaextract description: Poly(A)- RNA longer than 200 nt
biorep: 007WC
labexpid: LID8665
readtype: 2x76D
readtype description: Paired 76 n.t. directed reads
replicate: 1
replicate description: tier 1
|
| Biomaterial provider |
Lonza
|
| Growth protocol |
Keratinocyte_protocol.pdf
|
| Extracted molecule |
total 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 |
****************************
GSM765398 record metadata submitted on Jul 21 2011 may be obsolete, up to date experimental metadata was resubmitted by ENCODE DCC and is available at GSE78591
****************************
|
| 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| Superseded by |
GSE78591 |
| SRA |
SRX084676 |
| BioSample |
SAMN00672631 |
| Named Annotation |
GSM765398_wgEncodeCshlLongRnaSeqNhekCellLongnonpolyaMinusRawSigRep1.bigWig |
| Named Annotation |
GSM765398_wgEncodeCshlLongRnaSeqNhekCellLongnonpolyaMinusRawSigRep2.bigWig |
| Named Annotation |
GSM765398_wgEncodeCshlLongRnaSeqNhekCellLongnonpolyaMinusRawSigRep5.bigWig |
| Named Annotation |
GSM765398_wgEncodeCshlLongRnaSeqNhekCellLongnonpolyaPlusRawSigRep1.bigWig |
| Named Annotation |
GSM765398_wgEncodeCshlLongRnaSeqNhekCellLongnonpolyaPlusRawSigRep2.bigWig |
| Named Annotation |
GSM765398_wgEncodeCshlLongRnaSeqNhekCellLongnonpolyaPlusRawSigRep5.bigWig |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM765398_hg19_wgEncodeCshlLongRnaSeqNhekCellPamContigsV2.bedRnaElements.gz |
10.7 Mb |
(ftp)(http) |
BEDRNAELEMENTS |
| GSM765398_hg19_wgEncodeCshlLongRnaSeqNhekCellPamExonsDeNovo.gff.gz |
8.6 Mb |
(ftp)(http) |
GFF |
| GSM765398_hg19_wgEncodeCshlLongRnaSeqNhekCellPamExonsDeNovoRep5.gff.gz |
2.6 Mb |
(ftp)(http) |
GFF |
| GSM765398_hg19_wgEncodeCshlLongRnaSeqNhekCellPamGeneDeNovoRep5V2.gff.gz |
502.3 Kb |
(ftp)(http) |
GFF |
| GSM765398_hg19_wgEncodeCshlLongRnaSeqNhekCellPamGeneDeNovoV2.gff.gz |
3.7 Mb |
(ftp)(http) |
GFF |
| GSM765398_hg19_wgEncodeCshlLongRnaSeqNhekCellPamTranscriptDeNovoRep5V2.gtf.gz |
680.0 Kb |
(ftp)(http) |
GTF |
| GSM765398_hg19_wgEncodeCshlLongRnaSeqNhekCellPamTranscriptDeNovoV2.gtf.gz |
4.2 Mb |
(ftp)(http) |
GTF |
| GSM765398_wgEncodeCshlLongRnaSeqNhekCellLongnonpolyaMinusRawSigRep1.bigWig |
803.4 Mb |
(ftp)(http) |
BIGWIG |
| GSM765398_wgEncodeCshlLongRnaSeqNhekCellLongnonpolyaMinusRawSigRep2.bigWig |
563.1 Mb |
(ftp)(http) |
BIGWIG |
| GSM765398_wgEncodeCshlLongRnaSeqNhekCellLongnonpolyaMinusRawSigRep5.bigWig |
161.8 Mb |
(ftp)(http) |
BIGWIG |
| GSM765398_wgEncodeCshlLongRnaSeqNhekCellLongnonpolyaPlusRawSigRep1.bigWig |
834.6 Mb |
(ftp)(http) |
BIGWIG |
| GSM765398_wgEncodeCshlLongRnaSeqNhekCellLongnonpolyaPlusRawSigRep2.bigWig |
585.8 Mb |
(ftp)(http) |
BIGWIG |
| GSM765398_wgEncodeCshlLongRnaSeqNhekCellLongnonpolyaPlusRawSigRep5.bigWig |
166.5 Mb |
(ftp)(http) |
BIGWIG |
| GSM765398_wgEncodeCshlLongRnaSeqNhekCellPamContigs.bedRnaElements.gz |
10.6 Mb |
(ftp)(http) |
BEDRNAELEMENTS |
| GSM765398_wgEncodeCshlLongRnaSeqNhekCellPamExonGencV3c.gtf.gz |
12.4 Mb |
(ftp)(http) |
GTF |
| GSM765398_wgEncodeCshlLongRnaSeqNhekCellPamGeneDeNovo.gtf.gz |
460.3 Kb |
(ftp)(http) |
GTF |
| GSM765398_wgEncodeCshlLongRnaSeqNhekCellPamGeneGencV3c.gtf.gz |
1.5 Mb |
(ftp)(http) |
GTF |
| GSM765398_wgEncodeCshlLongRnaSeqNhekCellPamJunctions.bedRnaElements.gz |
2.2 Mb |
(ftp)(http) |
BEDRNAELEMENTS |
| GSM765398_wgEncodeCshlLongRnaSeqNhekCellPamProtocolRep1.pdf.gz |
433.7 Kb |
(ftp)(http) |
PDF |
| GSM765398_wgEncodeCshlLongRnaSeqNhekCellPamProtocolRep2.pdf.gz |
431.7 Kb |
(ftp)(http) |
PDF |
| GSM765398_wgEncodeCshlLongRnaSeqNhekCellPamProtocolRep5.pdf.gz |
431.5 Kb |
(ftp)(http) |
PDF |
| GSM765398_wgEncodeCshlLongRnaSeqNhekCellPamSpikeinsRep1.spikeins.bam |
289.1 Mb |
(ftp)(http) |
BAM |
| GSM765398_wgEncodeCshlLongRnaSeqNhekCellPamSpikeinsRep2.spikeins.bam |
288.1 Mb |
(ftp)(http) |
BAM |
| GSM765398_wgEncodeCshlLongRnaSeqNhekCellPamSpikeinsRep5.spikeins.bam |
553.2 Mb |
(ftp)(http) |
BAM |
| GSM765398_wgEncodeCshlLongRnaSeqNhekCellPamTranscriptDeNovo.gtf.gz |
2.9 Mb |
(ftp)(http) |
GTF |
| GSM765398_wgEncodeCshlLongRnaSeqNhekCellPamTranscriptGencV3c.gtf.gz |
9.9 Mb |
(ftp)(http) |
GTF |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
