|
| Status |
Public on Jul 22, 2011 |
| Title |
CSHL_RnaSeq_HSMM_cell_longNonPolyA (superseded by GSE78597) |
| Sample type |
SRA |
| |
|
| Source name |
HSMM
|
| Organism |
Homo sapiens |
| Characteristics |
datatype: RnaSeq
datatype description: Sequencing analysis of RNA expression
cell description: skeletal muscle myoblasts
rnaextract: longNonPolyA
rnaextract description: Poly(A)- RNA longer than 200 nt
biorep: 023WC,024WC,024WC,023WC
labexpid: LID8826,LID8827,LID8826,LID8827
labversion: iIDR
readtype: 2x76D
readtype description: Paired 76 nt directed reads
replicate: 1,2
spikeinpool: Nist14
rnaextract: longNonPolyA
rnaextract description: Poly(A)- RNA longer than 200 nt
biorep: 023WC
labexpid: LID8826
readtype: 2x76D
readtype description: Paired 76 n.t. directed reads
replicate: 1
replicate description: tier 1
|
| Biomaterial provider |
Refer to the protocol documents for differing sources
|
| 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 |
****************************
GSM765391 record metadata submitted on Jul 21 2011 may be obsolete, up to date experimental metadata was resubmitted by ENCODE DCC and is available at GSE78597
****************************
|
| 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| Superseded by |
GSE78597 |
| SRA |
SRX084669 |
| BioSample |
SAMN00672624 |
| Named Annotation |
GSM765391_wgEncodeCshlLongRnaSeqHsmmCellLongnonpolyaMinusRawSigRep1.bigWig |
| Named Annotation |
GSM765391_wgEncodeCshlLongRnaSeqHsmmCellLongnonpolyaMinusRawSigRep2.bigWig |
| Named Annotation |
GSM765391_wgEncodeCshlLongRnaSeqHsmmCellLongnonpolyaPlusRawSigRep1.bigWig |
| Named Annotation |
GSM765391_wgEncodeCshlLongRnaSeqHsmmCellLongnonpolyaPlusRawSigRep2.bigWig |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM765391_hg19_wgEncodeCshlLongRnaSeqHsmmCellPamExonsDeNovo.gff.gz |
3.8 Mb |
(ftp)(http) |
GFF |
| GSM765391_hg19_wgEncodeCshlLongRnaSeqHsmmCellPamGeneDeNovoV2.gff.gz |
825.6 Kb |
(ftp)(http) |
GFF |
| GSM765391_hg19_wgEncodeCshlLongRnaSeqHsmmCellPamTranscriptDeNovoV2.gtf.gz |
1.0 Mb |
(ftp)(http) |
GTF |
| GSM765391_wgEncodeCshlLongRnaSeqHsmmCellLongnonpolyaMinusRawSigRep1.bigWig |
133.2 Mb |
(ftp)(http) |
BIGWIG |
| GSM765391_wgEncodeCshlLongRnaSeqHsmmCellLongnonpolyaMinusRawSigRep2.bigWig |
154.4 Mb |
(ftp)(http) |
BIGWIG |
| GSM765391_wgEncodeCshlLongRnaSeqHsmmCellLongnonpolyaPlusRawSigRep1.bigWig |
137.3 Mb |
(ftp)(http) |
BIGWIG |
| GSM765391_wgEncodeCshlLongRnaSeqHsmmCellLongnonpolyaPlusRawSigRep2.bigWig |
159.9 Mb |
(ftp)(http) |
BIGWIG |
| GSM765391_wgEncodeCshlLongRnaSeqHsmmCellPamContigs.bedRnaElements.gz |
5.4 Mb |
(ftp)(http) |
BEDRNAELEMENTS |
| GSM765391_wgEncodeCshlLongRnaSeqHsmmCellPamExonGencV3c.gtf.gz |
14.0 Mb |
(ftp)(http) |
GTF |
| GSM765391_wgEncodeCshlLongRnaSeqHsmmCellPamGeneDeNovo.gtf.gz |
548.6 Kb |
(ftp)(http) |
GTF |
| GSM765391_wgEncodeCshlLongRnaSeqHsmmCellPamGeneGencV3c.gtf.gz |
1.6 Mb |
(ftp)(http) |
GTF |
| GSM765391_wgEncodeCshlLongRnaSeqHsmmCellPamJunctions.bedRnaElements.gz |
3.7 Mb |
(ftp)(http) |
BEDRNAELEMENTS |
| GSM765391_wgEncodeCshlLongRnaSeqHsmmCellPamProtocolRep1.pdf.gz |
432.0 Kb |
(ftp)(http) |
PDF |
| GSM765391_wgEncodeCshlLongRnaSeqHsmmCellPamProtocolRep2.pdf.gz |
431.5 Kb |
(ftp)(http) |
PDF |
| GSM765391_wgEncodeCshlLongRnaSeqHsmmCellPamSpikeinsRep1.spikeins.bam |
960.0 Mb |
(ftp)(http) |
BAM |
| GSM765391_wgEncodeCshlLongRnaSeqHsmmCellPamSpikeinsRep2.spikeins.bam |
852.3 Mb |
(ftp)(http) |
BAM |
| GSM765391_wgEncodeCshlLongRnaSeqHsmmCellPamTranscriptDeNovo.gtf.gz |
3.2 Mb |
(ftp)(http) |
GTF |
| GSM765391_wgEncodeCshlLongRnaSeqHsmmCellPamTranscriptGencV3c.gtf.gz |
10.6 Mb |
(ftp)(http) |
GTF |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
