|
Status |
Public on Jul 22, 2011 |
Title |
CSHL_RnaSeq_HMEC_cell_longNonPolyA (superseded by GSE78596) |
Sample type |
SRA |
|
|
Source name |
HMEC
|
Organism |
Homo sapiens |
Characteristics |
datatype: RnaSeq datatype description: Sequencing analysis of RNA expression cell description: mammary epithelial cells cell karyotype: normal rnaextract: longNonPolyA rnaextract description: Poly(A)- RNA longer than 200 nt biorep: 036WC labexpid: LID8831 labversion: iIDR readtype: 2x76D readtype description: Paired 76 nt directed reads spikeinpool: Nist14 rnaextract description: Poly(A)- RNA longer than 200 nt biorep: 036WC labexpid: LID8831 readtype: 2x76D readtype description: Paired 76 n.t. directed reads replicate: 1 replicate description: tier 1
|
Biomaterial provider |
Lonza
|
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 |
**************************** GSM765397 record metadata submitted on Jul 21 2011 may be obsolete, up to date experimental metadata was resubmitted by ENCODE DCC and is available at GSE78596 ****************************
|
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Superseded by |
GSE78596 |
SRA |
SRX084675 |
BioSample |
SAMN00672630 |
Named Annotation |
GSM765397_wgEncodeCshlLongRnaSeqHmecCellLongnonpolyaMinusRawSigRep1.bigWig |
Named Annotation |
GSM765397_wgEncodeCshlLongRnaSeqHmecCellLongnonpolyaPlusRawSigRep1.bigWig |
Supplementary file |
Size |
Download |
File type/resource |
GSM765397_hg19_wgEncodeCshlLongRnaSeqHmecCellPamContigsV2.bedRnaElements.gz |
6.2 Mb |
(ftp)(http) |
BEDRNAELEMENTS |
GSM765397_hg19_wgEncodeCshlLongRnaSeqHmecCellPamExonsDeNovo.gff.gz |
1012.3 Kb |
(ftp)(http) |
GFF |
GSM765397_hg19_wgEncodeCshlLongRnaSeqHmecCellPamGeneDeNovoV2.gff.gz |
207.4 Kb |
(ftp)(http) |
GFF |
GSM765397_hg19_wgEncodeCshlLongRnaSeqHmecCellPamTranscriptDeNovoV2.gtf.gz |
264.3 Kb |
(ftp)(http) |
GTF |
GSM765397_wgEncodeCshlLongRnaSeqHmecCellLongnonpolyaMinusRawSigRep1.bigWig |
78.4 Mb |
(ftp)(http) |
BIGWIG |
GSM765397_wgEncodeCshlLongRnaSeqHmecCellLongnonpolyaPlusRawSigRep1.bigWig |
79.7 Mb |
(ftp)(http) |
BIGWIG |
GSM765397_wgEncodeCshlLongRnaSeqHmecCellPamContigs.bedRnaElements.gz |
6.2 Mb |
(ftp)(http) |
BEDRNAELEMENTS |
GSM765397_wgEncodeCshlLongRnaSeqHmecCellPamExonGencV3c.gtf.gz |
12.1 Mb |
(ftp)(http) |
GTF |
GSM765397_wgEncodeCshlLongRnaSeqHmecCellPamGeneDeNovo.gtf.gz |
164.7 Kb |
(ftp)(http) |
GTF |
GSM765397_wgEncodeCshlLongRnaSeqHmecCellPamGeneGencV3c.gtf.gz |
1.5 Mb |
(ftp)(http) |
GTF |
GSM765397_wgEncodeCshlLongRnaSeqHmecCellPamJunctions.bedRnaElements.gz |
1.7 Mb |
(ftp)(http) |
BEDRNAELEMENTS |
GSM765397_wgEncodeCshlLongRnaSeqHmecCellPamProtocolRep1.pdf.gz |
426.2 Kb |
(ftp)(http) |
PDF |
GSM765397_wgEncodeCshlLongRnaSeqHmecCellPamSpikeinsRep1.spikeins.bam |
1.1 Gb |
(ftp)(http) |
BAM |
GSM765397_wgEncodeCshlLongRnaSeqHmecCellPamTranscriptDeNovo.gtf.gz |
906.8 Kb |
(ftp)(http) |
GTF |
GSM765397_wgEncodeCshlLongRnaSeqHmecCellPamTranscriptGencV3c.gtf.gz |
9.7 Mb |
(ftp)(http) |
GTF |
SRA Run Selector |
Raw data are available in SRA |
Processed data provided as supplementary file |