|
| Status |
Public on Jul 29, 2011 |
| Title |
CSHL_RnaSeq_A549_cell_longNonPolyA (superseded by GSE90242) |
| Sample type |
SRA |
| |
|
| Source name |
A549
|
| Organism |
Homo sapiens |
| Characteristics |
datatype: RnaSeq
datatype description: Sequencing analysis of RNA expression
cell description: epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis
rnaextract: longNonPolyA
rnaextract description: Poly(A)- RNA longer than 200 nt
biorep: 021WC,021WC,022WC,022WC
labexpid: LID9005,LID9006,LID9006,LID9005
labversion: iIDR
readtype: 2x76D
readtype description: Paired 76 nt directed reads
replicate: 1,2
spikeinpool: Nist14
rnaextract: longNonPolyA
rnaextract description: Poly(A)- RNA longer than 200 nt
biorep: 021WC
labexpid: LID9005
readtype: 2x76D
readtype description: Paired 76 n.t. directed reads
replicate: 1
replicate description: tier 1
|
| Biomaterial provider |
ATCC
|
| 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 |
****************************
GSM767854 record metadata submitted on Jul 27 2011 may be obsolete, up to date experimental metadata was resubmitted by ENCODE DCC and is available at GSE90242
****************************
|
| Data processing |
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeCshlLongRnaSeq
|
| |
|
| Submission date |
Jul 27, 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| Superseded by |
GSE90242 |
| SRA |
SRX085304 |
| BioSample |
SAMN00678397 |
| Named Annotation |
GSM767854_wgEncodeCshlLongRnaSeqA549CellLongnonpolyaMinusRawSigRep1.bigWig |
| Named Annotation |
GSM767854_wgEncodeCshlLongRnaSeqA549CellLongnonpolyaMinusRawSigRep2.bigWig |
| Named Annotation |
GSM767854_wgEncodeCshlLongRnaSeqA549CellLongnonpolyaPlusRawSigRep1.bigWig |
| Named Annotation |
GSM767854_wgEncodeCshlLongRnaSeqA549CellLongnonpolyaPlusRawSigRep2.bigWig |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM767854_hg19_wgEncodeCshlLongRnaSeqA549CellPamExonsDeNovo.gff.gz |
10.5 Mb |
(ftp)(http) |
GFF |
| GSM767854_hg19_wgEncodeCshlLongRnaSeqA549CellPamGeneDeNovoV2.gff.gz |
5.5 Mb |
(ftp)(http) |
GFF |
| GSM767854_hg19_wgEncodeCshlLongRnaSeqA549CellPamTranscriptDeNovoV2.gtf.gz |
6.0 Mb |
(ftp)(http) |
GTF |
| GSM767854_wgEncodeCshlLongRnaSeqA549CellLongnonpolyaMinusRawSigRep1.bigWig |
168.6 Mb |
(ftp)(http) |
BIGWIG |
| GSM767854_wgEncodeCshlLongRnaSeqA549CellLongnonpolyaMinusRawSigRep2.bigWig |
163.1 Mb |
(ftp)(http) |
BIGWIG |
| GSM767854_wgEncodeCshlLongRnaSeqA549CellLongnonpolyaPlusRawSigRep1.bigWig |
172.5 Mb |
(ftp)(http) |
BIGWIG |
| GSM767854_wgEncodeCshlLongRnaSeqA549CellLongnonpolyaPlusRawSigRep2.bigWig |
167.6 Mb |
(ftp)(http) |
BIGWIG |
| GSM767854_wgEncodeCshlLongRnaSeqA549CellPamContigs.bedRnaElements.gz |
16.0 Mb |
(ftp)(http) |
BEDRNAELEMENTS |
| GSM767854_wgEncodeCshlLongRnaSeqA549CellPamExonsGencV7.gtf.gz |
18.1 Mb |
(ftp)(http) |
GTF |
| GSM767854_wgEncodeCshlLongRnaSeqA549CellPamGeneDeNovo.gtf.gz |
3.5 Mb |
(ftp)(http) |
GTF |
| GSM767854_wgEncodeCshlLongRnaSeqA549CellPamGeneGencV7.gtf.gz |
2.0 Mb |
(ftp)(http) |
GTF |
| GSM767854_wgEncodeCshlLongRnaSeqA549CellPamJunctions.bedRnaElements.gz |
5.1 Mb |
(ftp)(http) |
BEDRNAELEMENTS |
| GSM767854_wgEncodeCshlLongRnaSeqA549CellPamSpikeinsRep1.spikeins.bam |
528.6 Mb |
(ftp)(http) |
BAM |
| GSM767854_wgEncodeCshlLongRnaSeqA549CellPamSpikeinsRep2.spikeins.bam |
419.0 Mb |
(ftp)(http) |
BAM |
| GSM767854_wgEncodeCshlLongRnaSeqA549CellPamTranscriptDeNovo.gtf.gz |
17.9 Mb |
(ftp)(http) |
GTF |
| GSM767854_wgEncodeCshlLongRnaSeqA549CellPamTranscriptGencV7.gtf.gz |
4.8 Mb |
(ftp)(http) |
GTF |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
