|
| Status |
Public on Jul 22, 2011 |
| Title |
CSHL_RnaSeq_NHEK_cell_longPolyA (superseded by GSE78594) |
| 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: 007WC,008WC,007WC,008WC,035WC
labexpid: LID8694,LID16631,LID16631,LID16632,LID16632
labversion: iIDR
readtype: 2x76D
readtype description: Paired 76 nt directed reads
replicate: 1,2,5
spikeinpool: Nist14
rnaextract: longPolyA
rnaextract description: Poly(A)+ RNA longer than 200 nt
biorep: 007WC
labexpid: LID16631
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 |
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 |
****************************
GSM765401 record metadata submitted on July 11, 2011 may be obsolete, up to date experimental metadata was resubmitted by ENCODE DCC and is available at GSE78594
****************************
|
| 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 (3) |
| GSE26284 |
ENCODE Cold Spring Harbor Labs Long RNA-seq |
| GSE30567 |
ENCODE Cold Spring Harbor Labs Long RNA-seq (hg19) |
| GSE49417 |
The conserved organization of the human and mouse transcriptomes |
|
| Relations |
| Superseded by |
GSE78594 |
| SRA |
SRX084679 |
| BioSample |
SAMN00672634 |
| Named Annotation |
GSM765401_wgEncodeCshlLongRnaSeqNhekCellPapMinusRawSigRep1.bigWig |
| Named Annotation |
GSM765401_wgEncodeCshlLongRnaSeqNhekCellPapMinusRawSigRep2.bigWig |
| Named Annotation |
GSM765401_wgEncodeCshlLongRnaSeqNhekCellPapMinusRawSigRep5.bigWig |
| Named Annotation |
GSM765401_wgEncodeCshlLongRnaSeqNhekCellPapPlusRawSigRep1.bigWig |
| Named Annotation |
GSM765401_wgEncodeCshlLongRnaSeqNhekCellPapPlusRawSigRep2.bigWig |
| Named Annotation |
GSM765401_wgEncodeCshlLongRnaSeqNhekCellPapPlusRawSigRep5.bigWig |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM765401_hg19_wgEncodeCshlLongRnaSeqNhekCellPapContigsV2.bedRnaElements.gz |
12.2 Mb |
(ftp)(http) |
BEDRNAELEMENTS |
| GSM765401_hg19_wgEncodeCshlLongRnaSeqNhekCellPapExonsDeNovo.gff.gz |
7.0 Mb |
(ftp)(http) |
GFF |
| GSM765401_hg19_wgEncodeCshlLongRnaSeqNhekCellPapExonsDeNovoRep5.gff.gz |
4.9 Mb |
(ftp)(http) |
GFF |
| GSM765401_hg19_wgEncodeCshlLongRnaSeqNhekCellPapGeneDeNovoRep5V2.gff.gz |
558.8 Kb |
(ftp)(http) |
GFF |
| GSM765401_hg19_wgEncodeCshlLongRnaSeqNhekCellPapGeneDeNovoV2.gff.gz |
1.5 Mb |
(ftp)(http) |
GFF |
| GSM765401_hg19_wgEncodeCshlLongRnaSeqNhekCellPapTranscriptDeNovoRep5V2.gtf.gz |
904.7 Kb |
(ftp)(http) |
GTF |
| GSM765401_hg19_wgEncodeCshlLongRnaSeqNhekCellPapTranscriptDeNovoV2.gtf.gz |
1.9 Mb |
(ftp)(http) |
GTF |
| GSM765401_wgEncodeCshlLongRnaSeqNhekCellPapContigs.bedRnaElements.gz |
12.2 Mb |
(ftp)(http) |
BEDRNAELEMENTS |
| GSM765401_wgEncodeCshlLongRnaSeqNhekCellPapExonGencV3c.gtf.gz |
13.1 Mb |
(ftp)(http) |
GTF |
| GSM765401_wgEncodeCshlLongRnaSeqNhekCellPapGeneDeNovo.gtf.gz |
585.3 Kb |
(ftp)(http) |
GTF |
| GSM765401_wgEncodeCshlLongRnaSeqNhekCellPapGeneGencV3c.gtf.gz |
1.5 Mb |
(ftp)(http) |
GTF |
| GSM765401_wgEncodeCshlLongRnaSeqNhekCellPapJunctions.bedRnaElements.gz |
5.4 Mb |
(ftp)(http) |
BEDRNAELEMENTS |
| GSM765401_wgEncodeCshlLongRnaSeqNhekCellPapMinusRawSigRep1.bigWig |
640.2 Mb |
(ftp)(http) |
BIGWIG |
| GSM765401_wgEncodeCshlLongRnaSeqNhekCellPapMinusRawSigRep2.bigWig |
524.3 Mb |
(ftp)(http) |
BIGWIG |
| GSM765401_wgEncodeCshlLongRnaSeqNhekCellPapMinusRawSigRep5.bigWig |
373.4 Mb |
(ftp)(http) |
BIGWIG |
| GSM765401_wgEncodeCshlLongRnaSeqNhekCellPapPlusRawSigRep1.bigWig |
664.2 Mb |
(ftp)(http) |
BIGWIG |
| GSM765401_wgEncodeCshlLongRnaSeqNhekCellPapPlusRawSigRep2.bigWig |
542.9 Mb |
(ftp)(http) |
BIGWIG |
| GSM765401_wgEncodeCshlLongRnaSeqNhekCellPapPlusRawSigRep5.bigWig |
383.9 Mb |
(ftp)(http) |
BIGWIG |
| GSM765401_wgEncodeCshlLongRnaSeqNhekCellPapProtocolRep1.pdf.gz |
1.4 Mb |
(ftp)(http) |
PDF |
| GSM765401_wgEncodeCshlLongRnaSeqNhekCellPapProtocolRep2.pdf.gz |
1.4 Mb |
(ftp)(http) |
PDF |
| GSM765401_wgEncodeCshlLongRnaSeqNhekCellPapProtocolRep5.pdf.gz |
552.7 Kb |
(ftp)(http) |
PDF |
| GSM765401_wgEncodeCshlLongRnaSeqNhekCellPapSpikeinsRep1.spikeins.bam |
433.5 Mb |
(ftp)(http) |
BAM |
| GSM765401_wgEncodeCshlLongRnaSeqNhekCellPapSpikeinsRep2.spikeins.bam |
397.0 Mb |
(ftp)(http) |
BAM |
| GSM765401_wgEncodeCshlLongRnaSeqNhekCellPapSpikeinsRep5.spikeins.bam |
262.7 Mb |
(ftp)(http) |
BAM |
| GSM765401_wgEncodeCshlLongRnaSeqNhekCellPapTranscriptDeNovo.gtf.gz |
8.1 Mb |
(ftp)(http) |
GTF |
| GSM765401_wgEncodeCshlLongRnaSeqNhekCellPapTranscriptGencV3c.gtf.gz |
10.3 Mb |
(ftp)(http) |
GTF |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
