|
| Status |
Public on Jul 13, 2011 |
| Title |
CSHL_RnaSeq_HSMM_cell_longPolyA (superseded by GSE78587) |
| Sample type |
SRA |
| |
|
| Source name |
HSMM
|
| Organism |
Homo sapiens |
| Characteristics |
datatype: RnaSeq
datatype description: Sequencing analysis of RNA expression
rnaextract: longPolyA
rnaextract description: Poly(A)+ RNA longer than 200 nt
biorep: 023WC,024WC,024WC,023WC
labexpid: LID8710,LID8711,LID8710,LID8711
labversion: iIDR
readtype: 2x76D
readtype description: Paired 76 nt directed reads
replicate: 1,2
spikeinpool: Nist14
localization description: Whole cell
rnaextract: longPolyA
rnaextract description: Poly(A)+ RNA longer than 200 nt
biorep: 023WC,024WC
labexpid: LID8710,LID8711
labversion: iIDR
spikeinpool: NIST14
|
| Biomaterial provider |
Refer to the protocol documents for differing sources
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Instrument model unknown. ("Illumina Genome Analyzer" specified by default). For more information, see 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 |
****************************
GSM758578 record metadata submitted on July 11, 2011 may be obsolete, up to date experimental metadata was resubmitted by ENCODE DCC and is available at GSE78587
****************************
|
| Data processing |
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeCshlLongRnaSeq
|
| |
|
| Submission date |
Jul 11, 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| Superseded by |
GSE78587 |
| SRA |
SRX082584 |
| BioSample |
SAMN00634089 |
| Named Annotation |
GSM758578_wgEncodeCshlLongRnaSeqHsmmCellPapMinusRawSigRep1.bigWig |
| Named Annotation |
GSM758578_wgEncodeCshlLongRnaSeqHsmmCellPapMinusRawSigRep2.bigWig |
| Named Annotation |
GSM758578_wgEncodeCshlLongRnaSeqHsmmCellPapPlusRawSigRep1.bigWig |
| Named Annotation |
GSM758578_wgEncodeCshlLongRnaSeqHsmmCellPapPlusRawSigRep2.bigWig |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM758578_hg19_wgEncodeCshlLongRnaSeqHsmmCellPapExonsDeNovo.gff.gz |
6.0 Mb |
(ftp)(http) |
GFF |
| GSM758578_hg19_wgEncodeCshlLongRnaSeqHsmmCellPapExonsGencV7.gtf.gz |
18.7 Mb |
(ftp)(http) |
GTF |
| GSM758578_hg19_wgEncodeCshlLongRnaSeqHsmmCellPapGeneDeNovoV2.gff.gz |
841.8 Kb |
(ftp)(http) |
GFF |
| GSM758578_hg19_wgEncodeCshlLongRnaSeqHsmmCellPapGeneGencV7.gtf.gz |
2.0 Mb |
(ftp)(http) |
GTF |
| GSM758578_hg19_wgEncodeCshlLongRnaSeqHsmmCellPapTranscriptDeNovoV2.gtf.gz |
1.2 Mb |
(ftp)(http) |
GTF |
| GSM758578_hg19_wgEncodeCshlLongRnaSeqHsmmCellPapTranscriptGencV7.gtf.gz |
5.0 Mb |
(ftp)(http) |
GTF |
| GSM758578_wgEncodeCshlLongRnaSeqHsmmCellPapContigs.bedRnaElements.gz |
10.2 Mb |
(ftp)(http) |
BEDRNAELEMENTS |
| GSM758578_wgEncodeCshlLongRnaSeqHsmmCellPapExonGencV3c.gtf.gz |
15.2 Mb |
(ftp)(http) |
GTF |
| GSM758578_wgEncodeCshlLongRnaSeqHsmmCellPapGeneDeNovo.gtf.gz |
957.0 Kb |
(ftp)(http) |
GTF |
| GSM758578_wgEncodeCshlLongRnaSeqHsmmCellPapGeneGencV3c.gtf.gz |
1.7 Mb |
(ftp)(http) |
GTF |
| GSM758578_wgEncodeCshlLongRnaSeqHsmmCellPapJunctions.bedRnaElements.gz |
8.2 Mb |
(ftp)(http) |
BEDRNAELEMENTS |
| GSM758578_wgEncodeCshlLongRnaSeqHsmmCellPapMinusRawSigRep1.bigWig |
330.8 Mb |
(ftp)(http) |
BIGWIG |
| GSM758578_wgEncodeCshlLongRnaSeqHsmmCellPapMinusRawSigRep2.bigWig |
496.2 Mb |
(ftp)(http) |
BIGWIG |
| GSM758578_wgEncodeCshlLongRnaSeqHsmmCellPapPlusRawSigRep1.bigWig |
341.2 Mb |
(ftp)(http) |
BIGWIG |
| GSM758578_wgEncodeCshlLongRnaSeqHsmmCellPapPlusRawSigRep2.bigWig |
513.2 Mb |
(ftp)(http) |
BIGWIG |
| GSM758578_wgEncodeCshlLongRnaSeqHsmmCellPapProtocolRep1.pdf.gz |
580.4 Kb |
(ftp)(http) |
PDF |
| GSM758578_wgEncodeCshlLongRnaSeqHsmmCellPapProtocolRep2.pdf.gz |
575.6 Kb |
(ftp)(http) |
PDF |
| GSM758578_wgEncodeCshlLongRnaSeqHsmmCellPapSpikeinsRep1.spikeins.bam |
130.0 Mb |
(ftp)(http) |
BAM |
| GSM758578_wgEncodeCshlLongRnaSeqHsmmCellPapSpikeinsRep2.spikeins.bam |
178.1 Mb |
(ftp)(http) |
BAM |
| GSM758578_wgEncodeCshlLongRnaSeqHsmmCellPapTranscriptDeNovo.gtf.gz |
11.1 Mb |
(ftp)(http) |
GTF |
| GSM758578_wgEncodeCshlLongRnaSeqHsmmCellPapTranscriptGencV3c.gtf.gz |
11.5 Mb |
(ftp)(http) |
GTF |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
