|
| Status |
Public on Aug 14, 2012 |
| Title |
CSHL_RnaSeq_HMEpC_cell_total (superseded by GSE78616) |
| Sample type |
SRA |
| |
|
| Source name |
HMEpC
|
| Organism |
Homo sapiens |
| Characteristics |
datatype: RnaSeq
datatype description: Sequencing analysis of RNA expression
rnaextract: total
rnaextract description: Total RNA extract (longer than 200 nt)
biorep: 063WC
labexpid: LID47096
labversion: iIDR
readtype: 2x101D
readtype description: Paired 101 nt directed reads
replicate: 1
spikeinpool: Nist13
localization description: Whole cell
rnaextract: total
rnaextract description: Total RNA extract (longer than 200 nt)
biorep: 063WC
labexpid: LID47096
labversion: iIDR
readtype: 2x101D
readtype description: Paired 101 nt directed reads
spikeinpool: Nist13
|
| Biomaterial provider |
PromoCell
|
| Growth protocol |
HMEpC_Gingeras_protocol.pdf
|
| 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 HiSeq 2000 |
| |
|
| Description |
****************************
GSM984621 record metadata submitted on Aug 13 2012 may be obsolete, up to date experimental metadata was resubmitted by ENCODE DCC and is available at GSE78616
****************************
|
| Data processing |
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeCshlLongRnaSeq
|
| |
|
| Submission date |
Aug 13, 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 |
GPL11154 |
| Series (1) |
| GSE30567 |
ENCODE Cold Spring Harbor Labs Long RNA-seq (hg19) |
|
| Relations |
| Superseded by |
GSE78616 |
| SRA |
SRX179446 |
| BioSample |
SAMN01121040 |
| Named Annotation |
GSM984621_hg19_wgEncodeCshlLongRnaSeqHmepcCellTotalMinusRep1.bigWig |
| Named Annotation |
GSM984621_hg19_wgEncodeCshlLongRnaSeqHmepcCellTotalPlusRep1.bigWig |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM984621_hg19_wgEncodeCshlLongRnaSeqHmepcCellTotalContigs.bedRnaElements.gz |
52.3 Mb |
(ftp)(http) |
BEDRNAELEMENTS |
| GSM984621_hg19_wgEncodeCshlLongRnaSeqHmepcCellTotalExonsDeNovo.gff.gz |
12.2 Mb |
(ftp)(http) |
GFF |
| GSM984621_hg19_wgEncodeCshlLongRnaSeqHmepcCellTotalExonsGencV10.gtf.gz |
17.5 Mb |
(ftp)(http) |
GTF |
| GSM984621_hg19_wgEncodeCshlLongRnaSeqHmepcCellTotalGeneDeNovo.gff.gz |
3.3 Mb |
(ftp)(http) |
GFF |
| GSM984621_hg19_wgEncodeCshlLongRnaSeqHmepcCellTotalGeneGencV10.gtf.gz |
1.6 Mb |
(ftp)(http) |
GTF |
| GSM984621_hg19_wgEncodeCshlLongRnaSeqHmepcCellTotalJunctions.bedRnaElements.gz |
6.6 Mb |
(ftp)(http) |
BEDRNAELEMENTS |
| GSM984621_hg19_wgEncodeCshlLongRnaSeqHmepcCellTotalMinusRep1.bigWig |
259.4 Mb |
(ftp)(http) |
BIGWIG |
| GSM984621_hg19_wgEncodeCshlLongRnaSeqHmepcCellTotalPlusRep1.bigWig |
266.4 Mb |
(ftp)(http) |
BIGWIG |
| GSM984621_hg19_wgEncodeCshlLongRnaSeqHmepcCellTotalProtocolRep1.pdf.gz |
255.0 Kb |
(ftp)(http) |
PDF |
| GSM984621_hg19_wgEncodeCshlLongRnaSeqHmepcCellTotalSpikeinsRep1.spikeins.bam |
228.6 Mb |
(ftp)(http) |
BAM |
| GSM984621_hg19_wgEncodeCshlLongRnaSeqHmepcCellTotalTranscriptDeNovo.gtf.gz |
4.0 Mb |
(ftp)(http) |
GTF |
| GSM984621_hg19_wgEncodeCshlLongRnaSeqHmepcCellTotalTranscriptGencV10.gtf.gz |
4.3 Mb |
(ftp)(http) |
GTF |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
