|
| Status |
Public on Jul 13, 2011 |
| Title |
CSHL_RnaSeq_GM12878_cytosol_longPolyA (superseded by GSE90222) |
| 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: 004C,003C,004C,003C
labexpid: LID8467,LID8468,LID8467,LID8468
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: 003C,004C
labexpid: LID8467,LID8468
labversion: iIDR
spikeinpool: NIST14
|
| Biomaterial provider |
Coriell
|
| 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 |
****************************
GSM758560 record metadata submitted on Jul 11 2011 may be obsolete, up to date experimental metadata was resubmitted by ENCODE DCC and is available at GSE90222
****************************
|
| 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 (2) |
| GSE26284 |
ENCODE Cold Spring Harbor Labs Long RNA-seq |
| GSE30567 |
ENCODE Cold Spring Harbor Labs Long RNA-seq (hg19) |
|
| Relations |
| Superseded by |
GSE90222 |
| SRA |
SRX082566 |
| BioSample |
SAMN00634071 |
| Named Annotation |
GSM758560_wgEncodeCshlLongRnaSeqGm12878CytosolPapMinusRawSigRep1.bigWig |
| Named Annotation |
GSM758560_wgEncodeCshlLongRnaSeqGm12878CytosolPapMinusRawSigRep2.bigWig |
| Named Annotation |
GSM758560_wgEncodeCshlLongRnaSeqGm12878CytosolPapPlusRawSigRep1.bigWig |
| Named Annotation |
GSM758560_wgEncodeCshlLongRnaSeqGm12878CytosolPapPlusRawSigRep2.bigWig |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM758560_hg19_wgEncodeCshlLongRnaSeqGm12878CytosolPapExonsDeNovo.gff.gz |
6.1 Mb |
(ftp)(http) |
GFF |
| GSM758560_hg19_wgEncodeCshlLongRnaSeqGm12878CytosolPapExonsGencV7.gtf.gz |
18.5 Mb |
(ftp)(http) |
GTF |
| GSM758560_hg19_wgEncodeCshlLongRnaSeqGm12878CytosolPapGeneDeNovoV2.gff.gz |
1.1 Mb |
(ftp)(http) |
GFF |
| GSM758560_hg19_wgEncodeCshlLongRnaSeqGm12878CytosolPapGeneGencV7.gtf.gz |
2.0 Mb |
(ftp)(http) |
GTF |
| GSM758560_hg19_wgEncodeCshlLongRnaSeqGm12878CytosolPapTranscriptDeNovoV2.gtf.gz |
1.5 Mb |
(ftp)(http) |
GTF |
| GSM758560_hg19_wgEncodeCshlLongRnaSeqGm12878CytosolPapTranscriptGencV7.gtf.gz |
4.9 Mb |
(ftp)(http) |
GTF |
| GSM758560_wgEncodeCshlLongRnaSeqGm12878CytosolPapContigs.bedRnaElements.gz |
11.2 Mb |
(ftp)(http) |
BEDRNAELEMENTS |
| GSM758560_wgEncodeCshlLongRnaSeqGm12878CytosolPapExonGencV3c.gtf.gz |
15.0 Mb |
(ftp)(http) |
GTF |
| GSM758560_wgEncodeCshlLongRnaSeqGm12878CytosolPapGeneDeNovo.gtf.gz |
1.2 Mb |
(ftp)(http) |
GTF |
| GSM758560_wgEncodeCshlLongRnaSeqGm12878CytosolPapGeneGencV3c.gtf.gz |
1.7 Mb |
(ftp)(http) |
GTF |
| GSM758560_wgEncodeCshlLongRnaSeqGm12878CytosolPapJunctions.bedRnaElements.gz |
9.2 Mb |
(ftp)(http) |
BEDRNAELEMENTS |
| GSM758560_wgEncodeCshlLongRnaSeqGm12878CytosolPapMinusRawSigRep1.bigWig |
444.2 Mb |
(ftp)(http) |
BIGWIG |
| GSM758560_wgEncodeCshlLongRnaSeqGm12878CytosolPapMinusRawSigRep2.bigWig |
425.0 Mb |
(ftp)(http) |
BIGWIG |
| GSM758560_wgEncodeCshlLongRnaSeqGm12878CytosolPapPlusRawSigRep1.bigWig |
456.9 Mb |
(ftp)(http) |
BIGWIG |
| GSM758560_wgEncodeCshlLongRnaSeqGm12878CytosolPapPlusRawSigRep2.bigWig |
437.0 Mb |
(ftp)(http) |
BIGWIG |
| GSM758560_wgEncodeCshlLongRnaSeqGm12878CytosolPapProtocolRep1.pdf.gz |
953.0 Kb |
(ftp)(http) |
PDF |
| GSM758560_wgEncodeCshlLongRnaSeqGm12878CytosolPapProtocolRep2.pdf.gz |
959.3 Kb |
(ftp)(http) |
PDF |
| GSM758560_wgEncodeCshlLongRnaSeqGm12878CytosolPapSpikeinsRep1.spikeins.bam |
78.0 Mb |
(ftp)(http) |
BAM |
| GSM758560_wgEncodeCshlLongRnaSeqGm12878CytosolPapSpikeinsRep2.spikeins.bam |
42.4 Mb |
(ftp)(http) |
BAM |
| GSM758560_wgEncodeCshlLongRnaSeqGm12878CytosolPapTranscriptDeNovo.gtf.gz |
13.7 Mb |
(ftp)(http) |
GTF |
| GSM758560_wgEncodeCshlLongRnaSeqGm12878CytosolPapTranscriptGencV3c.gtf.gz |
11.4 Mb |
(ftp)(http) |
GTF |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
