NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM1955372 Query DataSets for GSM1955372
Status Public on Jun 01, 2016
Title Lockd knockout, rep 1
Sample type RNA
 
Source name G1E_Lockd deletion
Organism Mus musculus
Characteristics cell line background: G1E
cell type: erythroid cell line
genotype/variation: Lockd deletion
Treatment protocol CRISPR/Cas9 was used to delete Lockd
Growth protocol Cells were grown in G1E media as described previously (Weiss et al, MCB 1997)
Extracted molecule total RNA
Extraction protocol RNA was isolated from cultured cells using the Qiagen Rneasy kit
Label biotin
Label protocol Single-stranded cDNA was generated from the amplified cRNA with the WT cDNA Synthesis Kit (Affymetrix) and then fragmented and labeled with the WT Terminal Labeling Kit (Affymetrix).
 
Hybridization protocol Samples were hybridized with GeneChip Mogene 2.0 ST Arrays (Affymetrix) and scanned at the University of Pennsylvania Molecular Profiling Facility
Scan protocol Array scanning was performed according to the manufacturer's instruction (Affymetrix)
Description KO.U.2
Data processing Raw data were normalized useing RMA algorithm (rma-gene-full option). Data analysis and statistical evaluations were performed with customized Matlab scripts (R2012b)
affymetrix-algorithm-name = rma-gene-full
affymetrix-algorithm-version = 1.0
program-name = Expression Console
program-version = 1.3.1.187
 
Submission date Nov 27, 2015
Last update date Jun 01, 2016
Contact name Vikram Paralkar
E-mail(s) vikram.paralkar@uphs.upenn.edu
Phone 215-590-0558
Organization name University of Pennsylvania
Street address 3400 Civic Center Boulevard, Perelman Center, 7th Floor, South Pavilion Extension
City Philadelphia
State/province PA
ZIP/Postal code 19104
Country USA
 
Platform ID GPL16570
Series (2)
GSE75449 Unlinking a lncRNA from its associated cis element [gene expression]
GSE75881 Unlinking a lncRNA from its associated cis element

Data table header descriptions
ID_REF
VALUE normalized

Data table
ID_REF VALUE
17200001 7.01233
17200003 6.43636
17200005 5.00563
17200007 4.49219
17200009 6.5502
17200011 4.78983
17200013 5.75866
17200015 6.06134
17200017 4.825
17200019 4.53866
17200021 5.42569
17200023 6.56554
17200025 6.17925
17200027 6.83054
17200029 5.26218
17200031 4.21297
17200033 4.16516
17200035 3.50914
17200037 5.82044
17200039 3.37258

Total number of rows: 41345

Table truncated, full table size 682 Kbytes.




Supplementary file Size Download File type/resource
GSM1955372_5078_55651_KO2U_MoGene2.0ST.CEL.gz 9.5 Mb (ftp)(http) CEL
GSM1955372_5078_55651_KO2U_MoGene2.0ST.rma-gene-full.chp.gz 254.4 Kb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap