|
| Status |
Public on Mar 16, 2012 |
| Title |
CSHL_RnaSeq_NHEK_cell_TAP-Only_shortTotal |
| Sample type |
SRA |
| |
|
| Source name |
NHEK
|
| Organism |
Homo sapiens |
| Characteristics |
biomaterial_type: primary cell
cell_type: keratinocyte
donor_id: ENCDO268AAA
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: 007WC,008WC,007WC,008WC
labexpid: LID21000,LID20999,LID21000,LID20999
labversion: iIDR
readtype: 1x36
readtype description: Single 36 nt reads
replicate: 1,2
localization: cell
localization description: Whole cell
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: 007WC
labexpid: LID20999
readtype: 1x36
readtype description: Single 36 nt reads
replicate: 1
|
| Biomaterial provider |
Lonza
|
| Growth protocol |
Keratinocyte_protocol.pdf
|
| Extracted molecule |
total 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 Genome Analyzer IIx |
| |
|
| Data processing |
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeCshlShortRnaSeq
|
| |
|
| Submission date |
Mar 16, 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 |
GPL10999 |
| Series (1) |
| GSE24565 |
Small RNA-seq from ENCODE/Cold Spring Harbor Lab |
|
| Relations |
| SRA |
SRX130237 |
| BioSample |
SAMN00829023 |
| Named Annotation |
GSM897086_hg19_wgEncodeCshlShortRnaSeqNhekCellShorttotalTapMinusRawRep1.bigWig |
| Named Annotation |
GSM897086_hg19_wgEncodeCshlShortRnaSeqNhekCellShorttotalTapMinusRawRep2.bigWig |
| Named Annotation |
GSM897086_hg19_wgEncodeCshlShortRnaSeqNhekCellShorttotalTapPlusRawRep1.bigWig |
| Named Annotation |
GSM897086_hg19_wgEncodeCshlShortRnaSeqNhekCellShorttotalTapPlusRawRep2.bigWig |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM897086_hg19_wgEncodeCshlShortRnaSeqNhekCellShorttotalTapContigs.bedRnaElements.gz |
559.8 Kb |
(ftp)(http) |
BEDRNAELEMENTS |
| GSM897086_hg19_wgEncodeCshlShortRnaSeqNhekCellShorttotalTapExonsGencV7.gtf.gz |
1.5 Mb |
(ftp)(http) |
GTF |
| GSM897086_hg19_wgEncodeCshlShortRnaSeqNhekCellShorttotalTapMinusRawRep1.bigWig |
4.6 Mb |
(ftp)(http) |
BIGWIG |
| GSM897086_hg19_wgEncodeCshlShortRnaSeqNhekCellShorttotalTapMinusRawRep2.bigWig |
4.5 Mb |
(ftp)(http) |
BIGWIG |
| GSM897086_hg19_wgEncodeCshlShortRnaSeqNhekCellShorttotalTapPlusRawRep1.bigWig |
4.5 Mb |
(ftp)(http) |
BIGWIG |
| GSM897086_hg19_wgEncodeCshlShortRnaSeqNhekCellShorttotalTapPlusRawRep2.bigWig |
4.4 Mb |
(ftp)(http) |
BIGWIG |
| GSM897086_hg19_wgEncodeCshlShortRnaSeqNhekCellShorttotalTapProtocolRep1.pdf.gz |
294.9 Kb |
(ftp)(http) |
PDF |
| GSM897086_hg19_wgEncodeCshlShortRnaSeqNhekCellShorttotalTapProtocolRep2.pdf.gz |
291.4 Kb |
(ftp)(http) |
PDF |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
