|
| Status |
Public on Jul 13, 2011 |
| Title |
CSHL_RnaSeq_GM12878_cell_longPolyA (superseded by GSE86658) |
| Sample type |
SRA |
| |
|
| Source name |
GM12878
|
| Organism |
Homo sapiens |
| Characteristics |
datatype: RnaSeq
datatype description: Sequencing analysis of RNA expression
cell description: B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus
rnaextract: longPolyA
rnaextract description: Poly(A)+ RNA longer than 200 nt
biorep: 003WC,003WC,004WC,004WC
labexpid: LID16629,LID16629,LID16630,LID16630
labversion: iIDR
readtype: 2x76D
readtype description: Paired 76 nt directed reads
replicate: 1,2
spikeinpool: Nist14
rnaextract: longPolyA
rnaextract description: Poly(A)+ RNA longer than 200 nt
biorep: 003WC,004WC
labexpid: LID16629,LID16630
labversion: iIDR
spikeinpool: NIST14
|
| Biomaterial provider |
Coriell; http://ccr.coriell.org/Sections/Search/Search.aspx?PgId=165&q=GM12878
|
| Growth protocol |
GM12878_protocol.pdf
|
| 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 |
****************************
GSM758559 record metadata submitted on Jul 11 2011 may be obsolete, up to date experimental metadata was resubmitted by ENCODE DCC and is available at GSE86658
****************************
|
| 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| Superseded by |
GSE86658 |
| SRA |
SRX082565 |
| BioSample |
SAMN00634070 |
| Named Annotation |
GSM758559_wgEncodeCshlLongRnaSeqGm12878CellPapMinusRawSigRep1.bigWig |
| Named Annotation |
GSM758559_wgEncodeCshlLongRnaSeqGm12878CellPapMinusRawSigRep2.bigWig |
| Named Annotation |
GSM758559_wgEncodeCshlLongRnaSeqGm12878CellPapPlusRawSigRep1.bigWig |
| Named Annotation |
GSM758559_wgEncodeCshlLongRnaSeqGm12878CellPapPlusRawSigRep2.bigWig |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM758559_hg19_wgEncodeCshlLongRnaSeqGm12878CellPapExonsDeNovo.gff.gz |
7.5 Mb |
(ftp)(http) |
GFF |
| GSM758559_hg19_wgEncodeCshlLongRnaSeqGm12878CellPapExonsGencV7.gtf.gz |
18.5 Mb |
(ftp)(http) |
GTF |
| GSM758559_hg19_wgEncodeCshlLongRnaSeqGm12878CellPapGeneDeNovoV2.gff.gz |
2.4 Mb |
(ftp)(http) |
GFF |
| GSM758559_hg19_wgEncodeCshlLongRnaSeqGm12878CellPapGeneGencV7.gtf.gz |
2.0 Mb |
(ftp)(http) |
GTF |
| GSM758559_hg19_wgEncodeCshlLongRnaSeqGm12878CellPapTranscriptDeNovoV2.gtf.gz |
2.8 Mb |
(ftp)(http) |
GTF |
| GSM758559_hg19_wgEncodeCshlLongRnaSeqGm12878CellPapTranscriptGencV7.gtf.gz |
5.0 Mb |
(ftp)(http) |
GTF |
| GSM758559_wgEncodeCshlLongRnaSeqGm12878CellPapContigs.bedRnaElements.gz |
12.9 Mb |
(ftp)(http) |
BEDRNAELEMENTS |
| GSM758559_wgEncodeCshlLongRnaSeqGm12878CellPapExonGencV3c.gtf.gz |
15.0 Mb |
(ftp)(http) |
GTF |
| GSM758559_wgEncodeCshlLongRnaSeqGm12878CellPapGeneDeNovo.gtf.gz |
2.0 Mb |
(ftp)(http) |
GTF |
| GSM758559_wgEncodeCshlLongRnaSeqGm12878CellPapGeneGencV3c.gtf.gz |
1.7 Mb |
(ftp)(http) |
GTF |
| GSM758559_wgEncodeCshlLongRnaSeqGm12878CellPapJunctions.bedRnaElements.gz |
9.1 Mb |
(ftp)(http) |
BEDRNAELEMENTS |
| GSM758559_wgEncodeCshlLongRnaSeqGm12878CellPapMinusRawSigRep1.bigWig |
806.6 Mb |
(ftp)(http) |
BIGWIG |
| GSM758559_wgEncodeCshlLongRnaSeqGm12878CellPapMinusRawSigRep2.bigWig |
825.4 Mb |
(ftp)(http) |
BIGWIG |
| GSM758559_wgEncodeCshlLongRnaSeqGm12878CellPapPlusRawSigRep1.bigWig |
843.1 Mb |
(ftp)(http) |
BIGWIG |
| GSM758559_wgEncodeCshlLongRnaSeqGm12878CellPapPlusRawSigRep2.bigWig |
860.1 Mb |
(ftp)(http) |
BIGWIG |
| GSM758559_wgEncodeCshlLongRnaSeqGm12878CellPapProtocolRep1.pdf.gz |
1.4 Mb |
(ftp)(http) |
PDF |
| GSM758559_wgEncodeCshlLongRnaSeqGm12878CellPapProtocolRep2.pdf.gz |
1.4 Mb |
(ftp)(http) |
PDF |
| GSM758559_wgEncodeCshlLongRnaSeqGm12878CellPapSpikeinsRep1.spikeins.bam |
595.3 Mb |
(ftp)(http) |
BAM |
| GSM758559_wgEncodeCshlLongRnaSeqGm12878CellPapSpikeinsRep2.spikeins.bam |
379.2 Mb |
(ftp)(http) |
BAM |
| GSM758559_wgEncodeCshlLongRnaSeqGm12878CellPapTranscriptDeNovo.gtf.gz |
15.6 Mb |
(ftp)(http) |
GTF |
| GSM758559_wgEncodeCshlLongRnaSeqGm12878CellPapTranscriptGencV3c.gtf.gz |
11.4 Mb |
(ftp)(http) |
GTF |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
