|
| 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CSHL_RnaSeq_HMEC_cell_longNonPolyA (superseded by GSE78596) |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| Superseded by |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 |
