|
| Status |
Public on Jul 22, 2011 |
| Title |
CSHL_RnaSeq_MCF-7_cell_longPolyA (superseded by GSE90237) |
| Sample type |
SRA |
| |
|
| Source name |
MCF-7
|
| Organism |
Homo sapiens |
| Characteristics |
biomaterial_type: immortalized cell line
line: MCF-7
datatype: RnaSeq
datatype description: Sequencing analysis of RNA expression
cell description: mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis
rnaextract: longPolyA
rnaextract description: Poly(A)+ RNA longer than 200 nt
biorep: 015WC,016WC,015WC,016WC
labexpid: LID8686,LID8687,LID8686,LID8687
labversion: iIDR
readtype: 2x76D
readtype description: Paired 76 nt directed reads
replicate: 1,2
spikeinpool: Nist14
rnaextract: longPolyA
rnaextract description: Poly(A)+ RNA longer than 200 nt
biorep: 015WC
labexpid: LID8686
readtype: 2x76D
readtype description: Paired 76 n.t. directed reads
replicate: 1
replicate description: tier 1
|
| Biomaterial provider |
ATCC
|
| 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 |
****************************
GSM765388 record metadata submitted on Jul 21 2011 may be obsolete, up to date experimental metadata was resubmitted by ENCODE DCC and is available at GSE90237
****************************
|
| 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| Superseded by |
GSE90237 |
| SRA |
SRX084666 |
| BioSample |
SAMN00672621 |
| Named Annotation |
GSM765388_wgEncodeCshlLongRnaSeqMcf7CellPapMinusRawSigRep1.bigWig |
| Named Annotation |
GSM765388_wgEncodeCshlLongRnaSeqMcf7CellPapMinusRawSigRep2.bigWig |
| Named Annotation |
GSM765388_wgEncodeCshlLongRnaSeqMcf7CellPapPlusRawSigRep1.bigWig |
| Named Annotation |
GSM765388_wgEncodeCshlLongRnaSeqMcf7CellPapPlusRawSigRep2.bigWig |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM765388_hg19_wgEncodeCshlLongRnaSeqMcf7CellPapExonsDeNovo.gff.gz |
7.3 Mb |
(ftp)(http) |
GFF |
| GSM765388_hg19_wgEncodeCshlLongRnaSeqMcf7CellPapGeneDeNovoV2.gff.gz |
1.7 Mb |
(ftp)(http) |
GFF |
| GSM765388_hg19_wgEncodeCshlLongRnaSeqMcf7CellPapTranscriptDeNovoV2.gtf.gz |
2.2 Mb |
(ftp)(http) |
GTF |
| GSM765388_wgEncodeCshlLongRnaSeqMcf7CellPapContigs.bedRnaElements.gz |
18.4 Mb |
(ftp)(http) |
BEDRNAELEMENTS |
| GSM765388_wgEncodeCshlLongRnaSeqMcf7CellPapExonGencV3c.gtf.gz |
15.2 Mb |
(ftp)(http) |
GTF |
| GSM765388_wgEncodeCshlLongRnaSeqMcf7CellPapGeneDeNovo.gtf.gz |
2.0 Mb |
(ftp)(http) |
GTF |
| GSM765388_wgEncodeCshlLongRnaSeqMcf7CellPapGeneGencV3c.gtf.gz |
1.7 Mb |
(ftp)(http) |
GTF |
| GSM765388_wgEncodeCshlLongRnaSeqMcf7CellPapJunctions.bedRnaElements.gz |
11.1 Mb |
(ftp)(http) |
BEDRNAELEMENTS |
| GSM765388_wgEncodeCshlLongRnaSeqMcf7CellPapMinusRawSigRep1.bigWig |
887.4 Mb |
(ftp)(http) |
BIGWIG |
| GSM765388_wgEncodeCshlLongRnaSeqMcf7CellPapMinusRawSigRep2.bigWig |
824.3 Mb |
(ftp)(http) |
BIGWIG |
| GSM765388_wgEncodeCshlLongRnaSeqMcf7CellPapPlusRawSigRep1.bigWig |
928.5 Mb |
(ftp)(http) |
BIGWIG |
| GSM765388_wgEncodeCshlLongRnaSeqMcf7CellPapPlusRawSigRep2.bigWig |
866.5 Mb |
(ftp)(http) |
BIGWIG |
| GSM765388_wgEncodeCshlLongRnaSeqMcf7CellPapProtocolRep1.pdf.gz |
612.9 Kb |
(ftp)(http) |
PDF |
| GSM765388_wgEncodeCshlLongRnaSeqMcf7CellPapProtocolRep2.pdf.gz |
614.6 Kb |
(ftp)(http) |
PDF |
| GSM765388_wgEncodeCshlLongRnaSeqMcf7CellPapSpikeinsRep1.spikeins.bam |
153.5 Mb |
(ftp)(http) |
BAM |
| GSM765388_wgEncodeCshlLongRnaSeqMcf7CellPapSpikeinsRep2.spikeins.bam |
238.9 Mb |
(ftp)(http) |
BAM |
| GSM765388_wgEncodeCshlLongRnaSeqMcf7CellPapTranscriptDeNovo.gtf.gz |
18.5 Mb |
(ftp)(http) |
GTF |
| GSM765388_wgEncodeCshlLongRnaSeqMcf7CellPapTranscriptGencV3c.gtf.gz |
11.5 Mb |
(ftp)(http) |
GTF |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
