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Sample GSM777720 Query DataSets for GSM777720
Status Public on Dec 05, 2011
Title Muscle nuclei RNA 1 (20110323_gDNA_vs_PmyoL1_453631)
Sample type mixed
 
Channel 1
Source name INTACT-purified muscle nuclei
Organism Caenorhabditis elegans
Characteristics age: adult
strain: JJ2289
cell type: muscle cell
sample type: INTACT affinity-purified muscle 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 age: adult
strain: N2
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 affinity-purified muscle 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 Muscle_nuclei_RNA_1.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 Aug 12, 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 0.052
IFS000000047 0.158
IFS000000093 0.08
IFS000000139 -0.088
IFS000000185 0.035
IFS000000231 0.03
IFS000000277 0.153
IFS000000323 0.08
IFS000000369 0.097
IFS000000415 0.466
IFS000000461 0.712
IFS000000507 -0.144
IFS000000553 -0.922
IFS000000599 0.024
IFS000000645 -0.155
IFS000000691 0.192
IFS000000737 0.225
IFS000000783 -0.054
IFS000000829 0.242
IFS000000875 -1.106

Total number of rows: 2143307

Table truncated, full table size 41928 Kbytes.




Supplementary file Size Download File type/resource
GSM777720_INTACT_ChIP_protocol.pdf.gz 89.3 Kb (ftp)(http) PDF
GSM777720_Muscle_nuclei_RNA_1.txt.gz 113.8 Kb (ftp)(http) TXT
GSM777720_Muscle_nuclei_RNA_1_532.pair.gz 33.5 Mb (ftp)(http) PAIR
GSM777720_Muscle_nuclei_RNA_1_635.pair.gz 33.2 Mb (ftp)(http) PAIR
GSM777720_Muscle_nuclei_RNA_1_WS220.bedgraph.gz 16.8 Mb (ftp)(http) BEDGRAPH
GSM777720_Muscle_nuclei_RNA_1_WS220.gff.gz 25.7 Mb (ftp)(http) GFF
Processed data provided as supplementary file
Processed data included within Sample table

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