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Sample GSM1100733 Query DataSets for GSM1100733
Status Public on Apr 11, 2013
Title 4d_diff [lncRNA Array]
Sample type RNA
Source name cell culture
Organism Mus musculus
Characteristics strain background: C57BL/6
cell type: SVZ-NSCs four day in differentiation media
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 12
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
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
VALUE RMA-normalized, averaged gene-level signal intensity (EXPRS)

Data table
AK005028_CONTROL_SEQS 2449.5957
AK010953_CONTROL_SEQS 1420.8526
AK039117_CONTROL_SEQS 341.2787
AK128971_CONTROL_SEQS 12255.1109
AK129421_CONTROL_SEQS 4028.4726
AK140151_CONTROL_SEQS 1445.8968
AK143943_CONTROL_SEQS 71.2620
AY971958_CONTROL_SEQS 64.2918
BC001994_CONTROL_SEQS 969.0743
BC003772_CONTROL_SEQS 3303.9053
BC003833_CONTROL_SEQS 14116.4090
BC007135_CONTROL_SEQS 660.9176
BC007466_CONTROL_SEQS 422.0652
BC011310_CONTROL_SEQS 406.7777
BC012966_CONTROL_SEQS 2990.0092
BC016421_CONTROL_SEQS 51.0266
BC023729_CONTROL_SEQS 200.9348
BC023796_CONTROL_SEQS 6535.5368
BC025073_CONTROL_SEQS 244.0835
BC028816_CONTROL_SEQS 12529.9518

Total number of rows: 17664

Table truncated, full table size 899 Kbytes.

Supplementary file Size Download File type/resource
GSM1100733_521989A12_custom_2012-04-04T154254_532.pair.gz 2.1 Mb (ftp)(http) PAIR
GSM1100733_521989A12_custom_532_RMA.calls.gz 253.1 Kb (ftp)(http) CALLS
Processed data included within Sample table
Processed data provided as supplementary file

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