|
| Status |
Public on Jul 12, 2012 |
| Title |
Caltech_RnaSeq_HCT-116_2x75_200 |
| Sample type |
SRA |
| |
|
| Source name |
HCT-116
|
| Organism |
Homo sapiens |
| Characteristics |
biomaterial_type: immortalized cell line
line: HCT-116
datatype: RnaSeq
datatype description: Sequencing analysis of RNA expression
readtype: 2x75
readtype description: Paired 75 nt reads
insertlength: 200
insertlength description: insert length of 200nt
labexpid: 12097,12096
mapalgorithm: TH1014
mapalgorithm description: TopHat v1.0.14
readtype: 2x75
readtype description: Paired 75 nt reads
replicate: 1,2
insertlength: 200
insertlength description: insert length of 200nt
treatment: None
treatment description: No special treatment or protocol applies
labexpid: 12096
mapalgorithm: TH1014
mapalgorithm description: TopHat v1.0.14
readtype: 2x75
readtype description: Paired 75 nt reads
replicate: 1
|
| Biomaterial provider |
ATCC
|
| Treatment protocol |
None
|
| Growth protocol |
HCT-116_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=wgEncodeCaltechRnaSeq
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer |
| |
|
| Data processing |
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeCaltechRnaSeq
|
| |
|
| Submission date |
Jul 10, 2012 |
| 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 |
GPL9052 |
| Series (1) |
|
| Relations |
| Reanalyzed by |
GSE80793 |
| SRA |
SRX159835 |
| BioSample |
SAMN01087963 |
| Named Annotation |
GSM958749_hg19_wgEncodeCaltechRnaSeqHct116R2x75Th1014Il200SigRep1V4.bigWig |
| Named Annotation |
GSM958749_hg19_wgEncodeCaltechRnaSeqHct116R2x75Th1014Il200SigRep2V4.bigWig |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM958749_hg19_wgEncodeCaltechRnaSeqHct116R2x75Il200ExonsGencV3cRep1V3.gtf.gz |
7.8 Mb |
(ftp)(http) |
GTF |
| GSM958749_hg19_wgEncodeCaltechRnaSeqHct116R2x75Il200ExonsGencV3cRep2V3.gtf.gz |
7.8 Mb |
(ftp)(http) |
GTF |
| GSM958749_hg19_wgEncodeCaltechRnaSeqHct116R2x75Il200GeneDeNovoRep1V3.gtf.gz |
1.4 Mb |
(ftp)(http) |
GTF |
| GSM958749_hg19_wgEncodeCaltechRnaSeqHct116R2x75Il200GeneDeNovoRep2V3.gtf.gz |
1.3 Mb |
(ftp)(http) |
GTF |
| GSM958749_hg19_wgEncodeCaltechRnaSeqHct116R2x75Il200GeneGencV3cRep1V3.gtf.gz |
1.9 Mb |
(ftp)(http) |
GTF |
| GSM958749_hg19_wgEncodeCaltechRnaSeqHct116R2x75Il200GeneGencV3cRep2V3.gtf.gz |
1.9 Mb |
(ftp)(http) |
GTF |
| GSM958749_hg19_wgEncodeCaltechRnaSeqHct116R2x75Il200JunctionsRep1V3.bigBed |
5.8 Mb |
(ftp)(http) |
BIGBED |
| GSM958749_hg19_wgEncodeCaltechRnaSeqHct116R2x75Il200JunctionsRep2V3.bigBed |
6.2 Mb |
(ftp)(http) |
BIGBED |
| GSM958749_hg19_wgEncodeCaltechRnaSeqHct116R2x75Il200SplicesRep1V2.bam |
1.7 Gb |
(ftp)(http) |
BAM |
| GSM958749_hg19_wgEncodeCaltechRnaSeqHct116R2x75Il200SplicesRep1V2.bam.bai.gz |
744.4 Kb |
(ftp)(http) |
BAI |
| GSM958749_hg19_wgEncodeCaltechRnaSeqHct116R2x75Il200SplicesRep2V2.bam |
1.7 Gb |
(ftp)(http) |
BAM |
| GSM958749_hg19_wgEncodeCaltechRnaSeqHct116R2x75Il200SplicesRep2V2.bam.bai.gz |
783.7 Kb |
(ftp)(http) |
BAI |
| GSM958749_hg19_wgEncodeCaltechRnaSeqHct116R2x75Il200TSSRep1V3.gtf.gz |
3.1 Mb |
(ftp)(http) |
GTF |
| GSM958749_hg19_wgEncodeCaltechRnaSeqHct116R2x75Il200TSSRep2V3.gtf.gz |
3.2 Mb |
(ftp)(http) |
GTF |
| GSM958749_hg19_wgEncodeCaltechRnaSeqHct116R2x75Il200TranscriptDeNovoRep1V3.gtf.gz |
5.1 Mb |
(ftp)(http) |
GTF |
| GSM958749_hg19_wgEncodeCaltechRnaSeqHct116R2x75Il200TranscriptDeNovoRep2V3.gtf.gz |
5.1 Mb |
(ftp)(http) |
GTF |
| GSM958749_hg19_wgEncodeCaltechRnaSeqHct116R2x75Il200TranscriptGencV3cRep1V3.gtf.gz |
13.2 Mb |
(ftp)(http) |
GTF |
| GSM958749_hg19_wgEncodeCaltechRnaSeqHct116R2x75Il200TranscriptGencV3cRep2V3.gtf.gz |
13.2 Mb |
(ftp)(http) |
GTF |
| GSM958749_hg19_wgEncodeCaltechRnaSeqHct116R2x75Th1014Il200SigRep1V4.bigWig |
186.1 Mb |
(ftp)(http) |
BIGWIG |
| GSM958749_hg19_wgEncodeCaltechRnaSeqHct116R2x75Th1014Il200SigRep2V4.bigWig |
225.8 Mb |
(ftp)(http) |
BIGWIG |
SRA Run Selector |
| Processed data provided as supplementary file |
| Raw data are available in SRA |
