|
| Status |
Public on Jul 29, 2011 |
| Title |
CSHL_RnaSeq_SK-N-SH_RA_cell_longNonPolyA (superseded by GSE90251) |
| Sample type |
SRA |
| |
|
| Source name |
SK-N-SH_RA
|
| Organism |
Homo sapiens |
| Characteristics |
datatype: RnaSeq
datatype description: Sequencing analysis of RNA expression
cell description: neuroblastoma cell line, treatment: differentiated with retinoic acid, (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.)
rnaextract: longNonPolyA
rnaextract description: Poly(A)- RNA longer than 200 nt
biorep: 020WC,019WC,020WC,019WC
labexpid: LID9003,LID9011,LID9003,LID9011
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: 019WC
labexpid: LID9003
readtype: 2x76D
readtype description: Paired 76 n.t. directed reads
replicate: 1
replicate description: tier 1
|
| Biomaterial provider |
ATCC
|
| Treatment protocol |
retinoic acid
|
| 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 |
****************************
GSM767845 record metadata submitted on Jul 27 2011 may be obsolete, up to date experimental metadata was resubmitted by ENCODE DCC and is available at GSE90251
****************************
|
| 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| Superseded by |
GSE90251 |
| SRA |
SRX085295 |
| BioSample |
SAMN00678388 |
| Named Annotation |
GSM767845_wgEncodeCshlLongRnaSeqSknshraCellLongnonpolyaMinusRawSigRep1.bigWig |
| Named Annotation |
GSM767845_wgEncodeCshlLongRnaSeqSknshraCellLongnonpolyaMinusRawSigRep2.bigWig |
| Named Annotation |
GSM767845_wgEncodeCshlLongRnaSeqSknshraCellLongnonpolyaPlusRawSigRep1.bigWig |
| Named Annotation |
GSM767845_wgEncodeCshlLongRnaSeqSknshraCellLongnonpolyaPlusRawSigRep2.bigWig |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM767845_hg19_wgEncodeCshlLongRnaSeqSknshraCellPamExonsDeNovo.gff.gz |
12.7 Mb |
(ftp)(http) |
GFF |
| GSM767845_hg19_wgEncodeCshlLongRnaSeqSknshraCellPamGeneDeNovoV2.gff.gz |
7.4 Mb |
(ftp)(http) |
GFF |
| GSM767845_hg19_wgEncodeCshlLongRnaSeqSknshraCellPamTranscriptDeNovoV2.gtf.gz |
8.0 Mb |
(ftp)(http) |
GTF |
| GSM767845_wgEncodeCshlLongRnaSeqSknshraCellLongnonpolyaMinusRawSigRep1.bigWig |
218.6 Mb |
(ftp)(http) |
BIGWIG |
| GSM767845_wgEncodeCshlLongRnaSeqSknshraCellLongnonpolyaMinusRawSigRep2.bigWig |
218.8 Mb |
(ftp)(http) |
BIGWIG |
| GSM767845_wgEncodeCshlLongRnaSeqSknshraCellLongnonpolyaPlusRawSigRep1.bigWig |
222.1 Mb |
(ftp)(http) |
BIGWIG |
| GSM767845_wgEncodeCshlLongRnaSeqSknshraCellLongnonpolyaPlusRawSigRep2.bigWig |
223.0 Mb |
(ftp)(http) |
BIGWIG |
| GSM767845_wgEncodeCshlLongRnaSeqSknshraCellPamContigs.bedRnaElements.gz |
18.9 Mb |
(ftp)(http) |
BEDRNAELEMENTS |
| GSM767845_wgEncodeCshlLongRnaSeqSknshraCellPamExonsGencV7.gtf.gz |
18.2 Mb |
(ftp)(http) |
GTF |
| GSM767845_wgEncodeCshlLongRnaSeqSknshraCellPamGeneDeNovo.gtf.gz |
4.8 Mb |
(ftp)(http) |
GTF |
| GSM767845_wgEncodeCshlLongRnaSeqSknshraCellPamGeneGencV7.gtf.gz |
2.0 Mb |
(ftp)(http) |
GTF |
| GSM767845_wgEncodeCshlLongRnaSeqSknshraCellPamJunctions.bedRnaElements.gz |
5.3 Mb |
(ftp)(http) |
BEDRNAELEMENTS |
| GSM767845_wgEncodeCshlLongRnaSeqSknshraCellPamSpikeinsRep1.spikeins.bam |
597.3 Mb |
(ftp)(http) |
BAM |
| GSM767845_wgEncodeCshlLongRnaSeqSknshraCellPamSpikeinsRep2.spikeins.bam |
814.0 Mb |
(ftp)(http) |
BAM |
| GSM767845_wgEncodeCshlLongRnaSeqSknshraCellPamTranscriptDeNovo.gtf.gz |
23.1 Mb |
(ftp)(http) |
GTF |
| GSM767845_wgEncodeCshlLongRnaSeqSknshraCellPamTranscriptGencV7.gtf.gz |
4.8 Mb |
(ftp)(http) |
GTF |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
