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Sample GSM1100724 Query DataSets for GSM1100724
Status Public on Apr 11, 2013
Title TA_1 [lncRNA Array]
Sample type RNA
 
Source name Mouse Brain_transit amplifying cells (TA)
Organism Mus musculus
Characteristics strain background: C57BL/6
cell type: FACS isolated transit amplifying cells
Treatment protocol For FACS isolated cells, total SVZ was dissected and subjected to the FACS protocol detailed in Pastrana, et al 2009
Growth protocol SVZ cells were grown in monolayer in proliferation media. At passage 5-7, cells were switched to media without growth factors for indicated timepoints (1,2,4 days)
Extracted molecule total RNA
Extraction protocol Total RNA was isolated with trizol reagent and amplified with Whole Transcriptome Amplification Kit (Thermo).
Label Cy3
Label protocol Labeling was performed according to standard Nimblegen Protocols
 
Hybridization protocol Hybridization was perfomed on a Maui Hybridization System
Scan protocol Scanning was done on a GenePix 4000B scanner according to standard Nimblegen protocols
Description SAMPLE 3
Data processing The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249) as implemented in the DEVA package, version 1.2.1
Sample data table contains RMA-normalized, averaged gene-level signal intensity (i.e. values in the 'EXPRS' column in processed data *RMA.calls file)
 
Submission date Mar 19, 2013
Last update date Jan 01, 2019
Contact name Abhinav Nellore
E-mail(s) abhinav.nellore@ucsf.edu
Phone 4439101925
Organization name UCSF
Street address 513 Parnassus Avenue
City San Francisco
State/province CA
ZIP/Postal code 94143-0794
Country USA
 
Platform ID GPL16745
Series (2)
GSE45281 Integration of genome-wide approaches identifies lncRNAs of adult neural stem cells and their progeny in vivo [lncRNA Array]
GSE45282 Integration of genome-wide approaches identifies lncRNAs of adult neural stem cells and their progeny in vivo

Data table header descriptions
ID_REF
VALUE RMA-normalized, averaged gene-level signal intensity (EXPRS)

Data table
ID_REF VALUE
AK005028_CONTROL_SEQS 3704.9166
AK010953_CONTROL_SEQS 2525.3830
AK039117_CONTROL_SEQS 3251.0459
AK128971_CONTROL_SEQS 12564.2868
AK129421_CONTROL_SEQS 8454.5834
AK140151_CONTROL_SEQS 263.6495
AK143943_CONTROL_SEQS 48.3803
AY971958_CONTROL_SEQS 6192.7409
BC001994_CONTROL_SEQS 12165.7409
BC003772_CONTROL_SEQS 17293.9329
BC003833_CONTROL_SEQS 31653.5051
BC007135_CONTROL_SEQS 1672.4198
BC007466_CONTROL_SEQS 861.9909
BC011310_CONTROL_SEQS 299.1123
BC012966_CONTROL_SEQS 4851.6033
BC016421_CONTROL_SEQS 82.1753
BC023729_CONTROL_SEQS 7620.6856
BC023796_CONTROL_SEQS 3383.0437
BC025073_CONTROL_SEQS 930.6595
BC028816_CONTROL_SEQS 9822.0468

Total number of rows: 17664

Table truncated, full table size 898 Kbytes.




Supplementary file Size Download File type/resource
GSM1100724_521989A03_custom_2012-04-04T154234_532.pair.gz 2.1 Mb (ftp)(http) PAIR
GSM1100724_521989A03_custom_532_RMA.calls.gz 252.9 Kb (ftp)(http) CALLS
Processed data included within Sample table
Processed data provided as supplementary file

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