|
| Status |
Public on Oct 08, 2010 |
| Title |
CSHL_RnaSeq_GM12878_cell_TAP-Only_shortTotal |
| Sample type |
SRA |
| |
|
| Source name |
GM12878
|
| Organism |
Homo sapiens |
| Characteristics |
biomaterial_type: immortalized cell line
line: GM12878
datatype: RnaSeq
datatype description: Sequencing analysis of RNA expression
cell description: B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus
rnaextract: shortTotal
rnaextract description: Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation
biorep: 003WC,003WC,004WC,gen0101WC,004WC
labexpid: LID20902,LID20899,crg-2,LID20899,LID20902
labversion: Produced by Hannon Lab,iIDR
readtype: 1x36
readtype description: Single 36 nt reads
replicate: 1,2
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: 003WC
labexpid: LID20899
readtype: 1x36
readtype description: Single 36 nt reads
replicate: 1
|
| Biomaterial provider |
Coriell
|
| Growth protocol |
GM12878_protocol.pdf
|
| Extracted molecule |
total RNA |
| Extraction protocol |
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeCshlShortRnaSeq
hg19: For extraction protocol details see: 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 |
Oct 06, 2010 |
| 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 |
SRX028001 |
| BioSample |
SAMN00115096 |
| Named Annotation |
GSM605625_hg19_wgEncodeCshlShortRnaSeqGm12878CellShortMinusRaw.bigWig |
| Named Annotation |
GSM605625_hg19_wgEncodeCshlShortRnaSeqGm12878CellShortPlusRaw.bigWig |
| Named Annotation |
GSM605625_hg19_wgEncodeCshlShortRnaSeqGm12878CellShorttotalTapMinusRawRep1.bigWig |
| Named Annotation |
GSM605625_hg19_wgEncodeCshlShortRnaSeqGm12878CellShorttotalTapMinusRawRep2.bigWig |
| Named Annotation |
GSM605625_hg19_wgEncodeCshlShortRnaSeqGm12878CellShorttotalTapPlusRawRep1.bigWig |
| Named Annotation |
GSM605625_hg19_wgEncodeCshlShortRnaSeqGm12878CellShorttotalTapPlusRawRep2.bigWig |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM605625_hg18_wgEncodeCshlShortRnaSeqAlignmentsGm12878CellShort.tagAlign.txt.gz |
28.2 Mb |
(ftp)(http) |
TXT |
| GSM605625_hg18_wgEncodeCshlShortRnaSeqTransfragsGm12878CellShort.broadPeak.txt.gz |
7.0 Mb |
(ftp)(http) |
TXT |
| GSM605625_hg19_wgEncodeCshlShortRnaSeqGm12878CellShortAln.bam |
52.3 Mb |
(ftp)(http) |
BAM |
| GSM605625_hg19_wgEncodeCshlShortRnaSeqGm12878CellShortMinusRaw.bigWig |
23.9 Mb |
(ftp)(http) |
BIGWIG |
| GSM605625_hg19_wgEncodeCshlShortRnaSeqGm12878CellShortPlusRaw.bigWig |
23.9 Mb |
(ftp)(http) |
BIGWIG |
| GSM605625_hg19_wgEncodeCshlShortRnaSeqGm12878CellShortTransfrags.shortFrags.txt.gz |
4.1 Mb |
(ftp)(http) |
TXT |
| GSM605625_hg19_wgEncodeCshlShortRnaSeqGm12878CellShorttotalTapContigs.bedRnaElements.gz |
584.0 Kb |
(ftp)(http) |
BEDRNAELEMENTS |
| GSM605625_hg19_wgEncodeCshlShortRnaSeqGm12878CellShorttotalTapExonsGencV7.gtf.gz |
1.2 Mb |
(ftp)(http) |
GTF |
| GSM605625_hg19_wgEncodeCshlShortRnaSeqGm12878CellShorttotalTapMinusRawRep1.bigWig |
4.9 Mb |
(ftp)(http) |
BIGWIG |
| GSM605625_hg19_wgEncodeCshlShortRnaSeqGm12878CellShorttotalTapMinusRawRep2.bigWig |
5.1 Mb |
(ftp)(http) |
BIGWIG |
| GSM605625_hg19_wgEncodeCshlShortRnaSeqGm12878CellShorttotalTapPlusRawRep1.bigWig |
4.8 Mb |
(ftp)(http) |
BIGWIG |
| GSM605625_hg19_wgEncodeCshlShortRnaSeqGm12878CellShorttotalTapPlusRawRep2.bigWig |
5.0 Mb |
(ftp)(http) |
BIGWIG |
| GSM605625_hg19_wgEncodeCshlShortRnaSeqGm12878CellShorttotalTapProtocolRep1.pdf.gz |
293.3 Kb |
(ftp)(http) |
PDF |
| GSM605625_hg19_wgEncodeCshlShortRnaSeqGm12878CellShorttotalTapProtocolRep2.pdf.gz |
306.4 Kb |
(ftp)(http) |
PDF |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
