|
Status |
Public on Jul 22, 2011 |
Title |
CSHL_RnaSeq_HeLa-S3_nucleus_longPolyA (superseded by GSE90235) |
Sample type |
SRA |
|
|
Source name |
HeLa-S3
|
Organism |
Homo sapiens |
Characteristics |
datatype: RnaSeq datatype description: Sequencing analysis of RNA expression cell lineage: ectoderm rnaextract: longPolyA rnaextract description: Poly(A)+ RNA longer than 200 nt biorep: 011N,012N,012N,011N labexpid: LID8559,LID8560,LID8559,LID8560 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: 011N labexpid: LID8559 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 |
**************************** GSM765403 record metadata submitted on Jul 21 2011 may be obsolete, up to date experimental metadata was resubmitted by ENCODE DCC and is available at GSE90235 ****************************
|
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 (2) |
GSE26284 |
ENCODE Cold Spring Harbor Labs Long RNA-seq |
GSE30567 |
ENCODE Cold Spring Harbor Labs Long RNA-seq (hg19) |
|
Relations |
Superseded by |
GSE90235 |
SRA |
SRX084681 |
BioSample |
SAMN00672636 |
Named Annotation |
GSM765403_wgEncodeCshlLongRnaSeqHelas3NucleusPapMinusRawSigRep1.bigWig |
Named Annotation |
GSM765403_wgEncodeCshlLongRnaSeqHelas3NucleusPapMinusRawSigRep2.bigWig |
Named Annotation |
GSM765403_wgEncodeCshlLongRnaSeqHelas3NucleusPapPlusRawSigRep1.bigWig |
Named Annotation |
GSM765403_wgEncodeCshlLongRnaSeqHelas3NucleusPapPlusRawSigRep2.bigWig |
Supplementary file |
Size |
Download |
File type/resource |
GSM765403_hg19_wgEncodeCshlLongRnaSeqHelas3NucleusPapExonsDeNovo.gff.gz |
8.0 Mb |
(ftp)(http) |
GFF |
GSM765403_hg19_wgEncodeCshlLongRnaSeqHelas3NucleusPapGeneDeNovoV2.gff.gz |
3.3 Mb |
(ftp)(http) |
GFF |
GSM765403_hg19_wgEncodeCshlLongRnaSeqHelas3NucleusPapTranscriptDeNovoV2.gtf.gz |
3.8 Mb |
(ftp)(http) |
GTF |
GSM765403_wgEncodeCshlLongRnaSeqHelas3NucleusPapContigs.bedRnaElements.gz |
14.6 Mb |
(ftp)(http) |
BEDRNAELEMENTS |
GSM765403_wgEncodeCshlLongRnaSeqHelas3NucleusPapExonGencV3c.gtf.gz |
15.0 Mb |
(ftp)(http) |
GTF |
GSM765403_wgEncodeCshlLongRnaSeqHelas3NucleusPapGeneDeNovo.gtf.gz |
2.9 Mb |
(ftp)(http) |
GTF |
GSM765403_wgEncodeCshlLongRnaSeqHelas3NucleusPapGeneGencV3c.gtf.gz |
1.7 Mb |
(ftp)(http) |
GTF |
GSM765403_wgEncodeCshlLongRnaSeqHelas3NucleusPapJunctions.bedRnaElements.gz |
10.6 Mb |
(ftp)(http) |
BEDRNAELEMENTS |
GSM765403_wgEncodeCshlLongRnaSeqHelas3NucleusPapMinusRawSigRep1.bigWig |
642.3 Mb |
(ftp)(http) |
BIGWIG |
GSM765403_wgEncodeCshlLongRnaSeqHelas3NucleusPapMinusRawSigRep2.bigWig |
848.2 Mb |
(ftp)(http) |
BIGWIG |
GSM765403_wgEncodeCshlLongRnaSeqHelas3NucleusPapPlusRawSigRep1.bigWig |
666.1 Mb |
(ftp)(http) |
BIGWIG |
GSM765403_wgEncodeCshlLongRnaSeqHelas3NucleusPapPlusRawSigRep2.bigWig |
881.7 Mb |
(ftp)(http) |
BIGWIG |
GSM765403_wgEncodeCshlLongRnaSeqHelas3NucleusPapProtocolRep1.pdf.gz |
631.1 Kb |
(ftp)(http) |
PDF |
GSM765403_wgEncodeCshlLongRnaSeqHelas3NucleusPapProtocolRep2.pdf.gz |
618.5 Kb |
(ftp)(http) |
PDF |
GSM765403_wgEncodeCshlLongRnaSeqHelas3NucleusPapSpikeinsRep1.spikeins.bam |
135.1 Mb |
(ftp)(http) |
BAM |
GSM765403_wgEncodeCshlLongRnaSeqHelas3NucleusPapSpikeinsRep2.spikeins.bam |
133.2 Mb |
(ftp)(http) |
BAM |
GSM765403_wgEncodeCshlLongRnaSeqHelas3NucleusPapTranscriptDeNovo.gtf.gz |
20.9 Mb |
(ftp)(http) |
GTF |
GSM765403_wgEncodeCshlLongRnaSeqHelas3NucleusPapTranscriptGencV3c.gtf.gz |
11.4 Mb |
(ftp)(http) |
GTF |
SRA Run Selector |
Raw data are available in SRA |
Processed data provided as supplementary file |