|
| Status |
Public on Jul 22, 2011 |
| Title |
CSHL_RnaSeq_HeLa-S3_cell_longPolyA (superseded by GSE86661) |
| Sample type |
SRA |
| |
|
| Source name |
HeLa-S3
|
| Organism |
Homo sapiens |
| Characteristics |
biomaterial_type: immortalized cell line
line: HeLa-S3
datatype: RnaSeq
datatype description: Sequencing analysis of RNA expression
cell lineage: ectoderm
rnaextract: longPolyA
rnaextract description: Poly(A)+ RNA longer than 200 nt
biorep: 011WC,012WC,012WC,011WC
labexpid: LID16634,LID16633,LID16634,LID16633
labversion: iIDR
readtype: 2x76D
readtype description: Paired 76 nt directed reads
replicate: 1,2
spikeinpool: Nist14
rnaextract description: Poly(A)+ RNA longer than 200 nt
biorep: 011WC
labexpid: LID16633
readtype: 2x76D
readtype description: Paired 76 n.t. directed reads
replicate: 1
replicate description: tier 1
|
| Biomaterial provider |
ATCC
|
| Growth protocol |
HeLa-S3_protocol.pdf
|
| Extracted molecule |
polyA 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 |
****************************
GSM765402 record metadata submitted on Jul 21 2011 may be obsolete, up to date experimental metadata was resubmitted by ENCODE DCC and is available at GSE86661
****************************
|
| Data processing |
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeCshlLongRnaSeq
|
| |
|
| Submission date |
Jul 21, 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 (3) |
| GSE26284 |
ENCODE Cold Spring Harbor Labs Long RNA-seq |
| GSE30567 |
ENCODE Cold Spring Harbor Labs Long RNA-seq (hg19) |
| GSE49417 |
The conserved organization of the human and mouse transcriptomes |
|
| Relations |
| Superseded by |
GSE86661 |
| SRA |
SRX084680 |
| BioSample |
SAMN00672635 |
| Named Annotation |
GSM765402_wgEncodeCshlLongRnaSeqHelas3CellPapMinusRawSigRep1.bigWig |
| Named Annotation |
GSM765402_wgEncodeCshlLongRnaSeqHelas3CellPapMinusRawSigRep2.bigWig |
| Named Annotation |
GSM765402_wgEncodeCshlLongRnaSeqHelas3CellPapPlusRawSigRep1.bigWig |
| Named Annotation |
GSM765402_wgEncodeCshlLongRnaSeqHelas3CellPapPlusRawSigRep2.bigWig |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM765402_hg19_wgEncodeCshlLongRnaSeqHelas3CellPapExonsDeNovo.gff.gz |
6.7 Mb |
(ftp)(http) |
GFF |
| GSM765402_hg19_wgEncodeCshlLongRnaSeqHelas3CellPapGeneDeNovoV2.gff.gz |
1.6 Mb |
(ftp)(http) |
GFF |
| GSM765402_hg19_wgEncodeCshlLongRnaSeqHelas3CellPapTranscriptDeNovoV2.gtf.gz |
2.0 Mb |
(ftp)(http) |
GTF |
| GSM765402_wgEncodeCshlLongRnaSeqHelas3CellPapContigs.bedRnaElements.gz |
12.1 Mb |
(ftp)(http) |
BEDRNAELEMENTS |
| GSM765402_wgEncodeCshlLongRnaSeqHelas3CellPapExonGencV3c.gtf.gz |
14.9 Mb |
(ftp)(http) |
GTF |
| GSM765402_wgEncodeCshlLongRnaSeqHelas3CellPapGeneDeNovo.gtf.gz |
1.6 Mb |
(ftp)(http) |
GTF |
| GSM765402_wgEncodeCshlLongRnaSeqHelas3CellPapGeneGencV3c.gtf.gz |
1.7 Mb |
(ftp)(http) |
GTF |
| GSM765402_wgEncodeCshlLongRnaSeqHelas3CellPapJunctions.bedRnaElements.gz |
9.5 Mb |
(ftp)(http) |
BEDRNAELEMENTS |
| GSM765402_wgEncodeCshlLongRnaSeqHelas3CellPapMinusRawSigRep1.bigWig |
637.8 Mb |
(ftp)(http) |
BIGWIG |
| GSM765402_wgEncodeCshlLongRnaSeqHelas3CellPapMinusRawSigRep2.bigWig |
608.5 Mb |
(ftp)(http) |
BIGWIG |
| GSM765402_wgEncodeCshlLongRnaSeqHelas3CellPapPlusRawSigRep1.bigWig |
666.6 Mb |
(ftp)(http) |
BIGWIG |
| GSM765402_wgEncodeCshlLongRnaSeqHelas3CellPapPlusRawSigRep2.bigWig |
630.3 Mb |
(ftp)(http) |
BIGWIG |
| GSM765402_wgEncodeCshlLongRnaSeqHelas3CellPapProtocolRep1.pdf.gz |
964.7 Kb |
(ftp)(http) |
PDF |
| GSM765402_wgEncodeCshlLongRnaSeqHelas3CellPapProtocolRep2.pdf.gz |
954.8 Kb |
(ftp)(http) |
PDF |
| GSM765402_wgEncodeCshlLongRnaSeqHelas3CellPapSpikeinsRep1.spikeins.bam |
294.3 Mb |
(ftp)(http) |
BAM |
| GSM765402_wgEncodeCshlLongRnaSeqHelas3CellPapSpikeinsRep2.spikeins.bam |
333.2 Mb |
(ftp)(http) |
BAM |
| GSM765402_wgEncodeCshlLongRnaSeqHelas3CellPapTranscriptDeNovo.gtf.gz |
13.7 Mb |
(ftp)(http) |
GTF |
| GSM765402_wgEncodeCshlLongRnaSeqHelas3CellPapTranscriptGencV3c.gtf.gz |
11.3 Mb |
(ftp)(http) |
GTF |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
