|
| Status |
Public on Jul 29, 2011 |
| Title |
CSHL_RnaSeq_GM12878_nucleus_longNonPolyA (superseded by GSE90245) |
| 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: longNonPolyA
rnaextract description: Poly(A)- RNA longer than 200 nt
biorep: 003N,004N,003N,004N
labexpid: LID9197,LID9198,LID9198,LID9197
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: 003N
labexpid: LID9197
readtype: 2x76D
readtype description: Paired 76 n.t. directed reads
replicate: 1
replicate description: tier 1
|
| Biomaterial provider |
Coriell
|
| Growth protocol |
GM12878_protocol.pdf
|
| Extracted molecule |
nuclear 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 |
****************************
GSM767853 record metadata submitted on Jul 27 2011 may be obsolete, up to date experimental metadata was resubmitted by ENCODE DCC and is available at GSE90245
****************************
|
| Data processing |
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeCshlLongRnaSeq
|
| |
|
| Submission date |
Jul 27, 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| Superseded by |
GSE90245 |
| SRA |
SRX085303 |
| BioSample |
SAMN00678396 |
| Named Annotation |
GSM767853_wgEncodeCshlLongRnaSeqGm12878NucleusLongnonpolyaMinusRawSigRep1.bigWig |
| Named Annotation |
GSM767853_wgEncodeCshlLongRnaSeqGm12878NucleusLongnonpolyaMinusRawSigRep2.bigWig |
| Named Annotation |
GSM767853_wgEncodeCshlLongRnaSeqGm12878NucleusLongnonpolyaPlusRawSigRep1.bigWig |
| Named Annotation |
GSM767853_wgEncodeCshlLongRnaSeqGm12878NucleusLongnonpolyaPlusRawSigRep2.bigWig |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM767853_hg19_wgEncodeCshlLongRnaSeqGm12878NucleusPamExonsDeNovo.gff.gz |
12.1 Mb |
(ftp)(http) |
GFF |
| GSM767853_hg19_wgEncodeCshlLongRnaSeqGm12878NucleusPamGeneDeNovoV2.gff.gz |
9.1 Mb |
(ftp)(http) |
GFF |
| GSM767853_hg19_wgEncodeCshlLongRnaSeqGm12878NucleusPamTranscriptDeNovoV2.gtf.gz |
9.7 Mb |
(ftp)(http) |
GTF |
| GSM767853_wgEncodeCshlLongRnaSeqGm12878NucleusLongnonpolyaMinusRawSigRep1.bigWig |
351.3 Mb |
(ftp)(http) |
BIGWIG |
| GSM767853_wgEncodeCshlLongRnaSeqGm12878NucleusLongnonpolyaMinusRawSigRep2.bigWig |
386.7 Mb |
(ftp)(http) |
BIGWIG |
| GSM767853_wgEncodeCshlLongRnaSeqGm12878NucleusLongnonpolyaPlusRawSigRep1.bigWig |
370.0 Mb |
(ftp)(http) |
BIGWIG |
| GSM767853_wgEncodeCshlLongRnaSeqGm12878NucleusLongnonpolyaPlusRawSigRep2.bigWig |
407.3 Mb |
(ftp)(http) |
BIGWIG |
| GSM767853_wgEncodeCshlLongRnaSeqGm12878NucleusPamContigs.bedRnaElements.gz |
15.3 Mb |
(ftp)(http) |
BEDRNAELEMENTS |
| GSM767853_wgEncodeCshlLongRnaSeqGm12878NucleusPamExonsGencV7.gtf.gz |
17.8 Mb |
(ftp)(http) |
GTF |
| GSM767853_wgEncodeCshlLongRnaSeqGm12878NucleusPamGeneDeNovo.gtf.gz |
8.0 Mb |
(ftp)(http) |
GTF |
| GSM767853_wgEncodeCshlLongRnaSeqGm12878NucleusPamGeneGencV7.gtf.gz |
2.0 Mb |
(ftp)(http) |
GTF |
| GSM767853_wgEncodeCshlLongRnaSeqGm12878NucleusPamJunctions.bedRnaElements.gz |
6.3 Mb |
(ftp)(http) |
BEDRNAELEMENTS |
| GSM767853_wgEncodeCshlLongRnaSeqGm12878NucleusPamProtocolRep1.pdf.gz |
432.3 Kb |
(ftp)(http) |
PDF |
| GSM767853_wgEncodeCshlLongRnaSeqGm12878NucleusPamProtocolRep2.pdf.gz |
429.8 Kb |
(ftp)(http) |
PDF |
| GSM767853_wgEncodeCshlLongRnaSeqGm12878NucleusPamSpikeinsRep1.spikeins.bam |
193.3 Mb |
(ftp)(http) |
BAM |
| GSM767853_wgEncodeCshlLongRnaSeqGm12878NucleusPamSpikeinsRep2.spikeins.bam |
122.1 Mb |
(ftp)(http) |
BAM |
| GSM767853_wgEncodeCshlLongRnaSeqGm12878NucleusPamTranscriptDeNovo.gtf.gz |
37.2 Mb |
(ftp)(http) |
GTF |
| GSM767853_wgEncodeCshlLongRnaSeqGm12878NucleusPamTranscriptGencV7.gtf.gz |
4.7 Mb |
(ftp)(http) |
GTF |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
