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Sample GSM836189 Query DataSets for GSM836189
Status Public on Dec 05, 2011
Title Total nuclei RNA 5 (20111110_gDNA_vs_nuc120_1_507461-2)
Sample type mixed
 
Channel 1
Source name total nuclei
Organism Caenorhabditis elegans
Characteristics strain: JJ2371
background: unc-120(st364)
age: adult
cell type: whole organism
sample type: total nuclei
Extracted molecule nuclear RNA
Extraction protocol RNA isolation was done with Qiagen RNeasy micro kit. cDNA preparation and amplification were done with the Sigma WTA2 kit. Detailed protocol in supplementary file INTACT_ChIP_protocol.rtf .
Label Cy5
Label protocol Standard NimbleGen protocol using 6 hour labeling reaction rather than 2 hour reaction.
 
Channel 2
Source name Fragmented genomic DNA
Organism Caenorhabditis elegans
Characteristics strain: N2
age: adult
tissue: whole organism
sample type: fragmented genomic DNA
Extracted molecule genomic DNA
Extraction protocol Genomic DNA was fragmented by sonication to
about 400bp.
Label Cy3
Label protocol Standard NimbleGen protocol using 6 hour labeling reaction rather than 2 hour reaction.
 
 
Hybridization protocol Standard NimbleGen protocol.
Scan protocol Standard NimbleGen protocol.
Description Expression profiling of nuclear RNA from total nuclei.
Data processing Standard NimbleGen bi-weight mean adjusted log base 2 ratios (Cy5/Cy3) were converted to standard deviates by subtracting their mean and dividing by their standard deviation. Per-gene expression values in supplementary file Total_nuclei_RNA_5.txt were computed as described in http://nettie.fhcrc.org/labuser/protocols/expression.html: The standardized log ratios for all exonic probes starting with the 20th probe from the 3' ends of WS220 genes were averaged to give a single expression value for each gene.
 
Submission date Nov 18, 2011
Last update date Apr 11, 2012
Contact name Jorja Henikoff
E-mail(s) jorja@fhcrc.org
Phone 206-667-4850
Organization name Fred Hutchinson Cancer Research Center
Department Basic Sciences
Lab Henikoff
Street address 1100 Fairview AV N, A1-162
City Seattle
State/province WA
ZIP/Postal code 98109-1024
Country USA
 
Platform ID GPL7098
Series (1)
GSE31602 Tissue-specific nuclei purification from animal models for genome-wide expression and chromatin profiling.

Data table header descriptions
ID_REF NimbleGen PROBE_ID
VALUE Standard deviate of bi-weight-mean-adjusted log base 2 (Cy5/Cy3)

Data table
ID_REF VALUE
IFS000000001 -0.432
IFS000000047 -0.227
IFS000000093 -0.207
IFS000000139 -0.387
IFS000000185 -0.661
IFS000000231 -0.392
IFS000000277 -0.412
IFS000000323 -0.457
IFS000000369 -0.437
IFS000000415 0.178
IFS000000461 -0.072
IFS000000507 -0.726
IFS000000553 -0.661
IFS000000599 -0.377
IFS000000645 -0.327
IFS000000691 -0.297
IFS000000737 -0.397
IFS000000783 -0.272
IFS000000829 -1.316
IFS000000875 -1.231

Total number of rows: 2143307

Table truncated, full table size 42238 Kbytes.




Supplementary file Size Download File type/resource
GSM836189_Total_nuclei_RNA_5.txt.gz 113.0 Kb (ftp)(http) TXT
GSM836189_Total_nuclei_RNA_5_532.pair.gz 34.0 Mb (ftp)(http) PAIR
GSM836189_Total_nuclei_RNA_5_635.pair.gz 33.6 Mb (ftp)(http) PAIR
GSM836189_Total_nuclei_RNA_5_WS220.bedgraph.gz 16.8 Mb (ftp)(http) BEDGRAPH
GSM836189_Total_nuclei_RNA_5_WS220.gff.gz 25.8 Mb (ftp)(http) GFF
Processed data included within Sample table
Processed data provided as supplementary file

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