|
Status |
Public on Jul 26, 2012 |
Title |
CSHL_RnaSeq_GM12878_nucleolus_TAP-Only_shortTotal |
Sample type |
SRA |
|
|
Source name |
GM12878
|
Organism |
Homo sapiens |
Characteristics |
datatype: RnaSeq datatype description: Sequencing analysis of RNA expression rnaextract: shortTotal rnaextract description: Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation biorep: 091NL,092NL,091NL,092NL labexpid: LID47654,LID47653,LID47653,LID47654 labversion: iIDR readtype: 1x101 readtype description: Single 101 nt reads replicate: 3,4 localization: nucleolus localization description: The part of the nucleus where ribosomal RNA is actively transcribed protocol: TAP-Only protocol description: This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned. rnaextract: shortTotal rnaextract description: Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation biorep: 091NL,092NL labexpid: LID47653,LID47654 labversion: iIDR readtype: 1x101 readtype description: Single 101 nt reads
|
Biomaterial provider |
Coriell
|
Growth protocol |
GM12878_protocol.pdf
|
Extracted molecule |
nuclear RNA |
Extraction protocol |
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeCshlShortRnaSeq
|
|
|
Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 2000 |
|
|
Data processing |
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeCshlShortRnaSeq
|
|
|
Submission date |
Jul 26, 2012 |
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 |
GPL11154 |
Series (1) |
GSE24565 |
Small RNA-seq from ENCODE/Cold Spring Harbor Lab |
|
Relations |
SRA |
SRX171107 |
BioSample |
SAMN01095696 |
Named Annotation |
GSM977032_hg19_wgEncodeCshlShortRnaSeqGm12878NucleolusTapMinusRawRep3.bigWig |
Named Annotation |
GSM977032_hg19_wgEncodeCshlShortRnaSeqGm12878NucleolusTapMinusRawRep4.bigWig |
Named Annotation |
GSM977032_hg19_wgEncodeCshlShortRnaSeqGm12878NucleolusTapPlusRawRep3.bigWig |
Named Annotation |
GSM977032_hg19_wgEncodeCshlShortRnaSeqGm12878NucleolusTapPlusRawRep4.bigWig |
Supplementary file |
Size |
Download |
File type/resource |
GSM977032_hg19_wgEncodeCshlShortRnaSeqGm12878NucleolusTapContigs.bedRnaElements.gz |
5.4 Mb |
(ftp)(http) |
BEDRNAELEMENTS |
GSM977032_hg19_wgEncodeCshlShortRnaSeqGm12878NucleolusTapExonsGencV10.gtf.gz |
4.0 Mb |
(ftp)(http) |
GTF |
GSM977032_hg19_wgEncodeCshlShortRnaSeqGm12878NucleolusTapMinusRawRep3.bigWig |
17.3 Mb |
(ftp)(http) |
BIGWIG |
GSM977032_hg19_wgEncodeCshlShortRnaSeqGm12878NucleolusTapMinusRawRep4.bigWig |
15.2 Mb |
(ftp)(http) |
BIGWIG |
GSM977032_hg19_wgEncodeCshlShortRnaSeqGm12878NucleolusTapPlusRawRep3.bigWig |
17.6 Mb |
(ftp)(http) |
BIGWIG |
GSM977032_hg19_wgEncodeCshlShortRnaSeqGm12878NucleolusTapPlusRawRep4.bigWig |
15.5 Mb |
(ftp)(http) |
BIGWIG |
GSM977032_hg19_wgEncodeCshlShortRnaSeqGm12878NucleolusTapProtocolRep3.pdf.gz |
144.2 Kb |
(ftp)(http) |
PDF |
GSM977032_hg19_wgEncodeCshlShortRnaSeqGm12878NucleolusTapProtocolRep4.pdf.gz |
142.3 Kb |
(ftp)(http) |
PDF |
SRA Run Selector |
Raw data are available in SRA |
Processed data provided as supplementary file |