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Sample GSM1058711 Query DataSets for GSM1058711
Status Public on Aug 05, 2013
Title KG1-undifferentiated
Sample type SAGE
Anchor NlaIII
Tag Count 74795
Tag Length 17
 
Source name Acute mylogenous lukemia KG-1 cell line (Catalog No.CCL-246)
Organism Homo sapiens
Characteristics cell line: KG1
cell type: Acute mylogenous lukemia
status: Undifferentiated
Treatment protocol HL60 cells were differentiated with 1.3% DMSO (Sigma catalog No. D4540) in complete media for 6-8 days with media change every 3rd day. KG60 cells were differentiated with PMA (100ng/ml) for 5 days.
Growth protocol HL60 and KG1 cell were maintained in complete Iscoves Modified Medium (ATCC catalog No.30-2005) supplemented with 10% fetal bovine serum (ATCC catalog No. 30-2020), penicillin (100U/ml), and streptomycin (100µg/ml), at 37 degrees C and 5% CO2. Neutrophiles were maintained in Krebs-HEPES + BSA.
Extracted molecule polyA RNA
Extraction protocol Total cellular RNA was isolated from differentiated and from undifferentiated cell lines and human naïve neutrophils using tri-Reagent (MRC, Cincinati, OH) following manufacturer’s instructions. RNA integrity was routinely checked using 500 ng/ml of RNA on 1% denaturing agarose gel. SAGE was performed according to the Serial Analysis of Gene Expression detailed Protocol Version C, with Nla III as the digestion enzyme, Mme as the tagging enzyme.
 
Data processing Transformants were analyzed by colony PCR. Approximately 4000-5000 clones for each library were cycle sequenced using M13 forward primer and analyzed on Applied Biosystems DNA Sequencer. Approximately 20-25 individual tags were produced per clone. Sequences were analyzed using SAGE analysis software version 4.5 (Johns Hopkins University, Baltimore, MD, USA) and annotated using the downloadable reference sequence database SAGEmap.
 
Submission date Dec 31, 2012
Last update date Aug 05, 2013
Contact name Anason Halees
E-mail(s) ahalees@kfshrc.edu.sa
Organization name King Faisal Specialist Hospital & Research Centre
Department Research Center
Lab Cell Biology
Street address P.O.Box 3354
City Riaydh
ZIP/Postal code 11211
Country Saudi Arabia
 
Platform ID GPL1485
Series (1)
GSE43211 Differentiated vs. undifferentiated promyelocytic cell lines (HL-60 and KG-1) and Neutrophiles

Data table header descriptions
TAG sequence
COUNT tag count
TPM tags per million

Data table
TAG COUNT TPM
AAAAAAAAAAAAAAAAA 55 735.34
AAAAAAAAAAAAAAAAC 2 26.74
AAAAAAAAAAAAAAAAG 3 40.11
AAAAAAAAAAAAAAAAT 2 26.74
AAAAAAAAAAAAAAACA 1 13.37
AAAAAAAAAAAAAAACT 1 13.37
AAAAAAAAAAAAACTAT 1 13.37
AAAAAAAAAAAAGAAAA 1 13.37
AAAAAAAAAAACAAAAA 1 13.37
AAAAAAAAAACAATTTT 1 13.37
AAAAAAAAAACCACAAA 1 13.37
AAAAAAAAAATTTTTTT 1 13.37
AAAAAAAAAGAAAAAAA 2 26.74
AAAAAAAAAGAAGAAAA 1 13.37
AAAAAAAAAGAAGTTTT 1 13.37
AAAAAAAAAGGTTCCAT 1 13.37
AAAAAAAAATCCAAATT 1 13.37
AAAAAAAAATGAAAAAC 1 13.37
AAAAAAAAATGAAGTAG 1 13.37
AAAAAAAAATTGTAGGT 1 13.37

Total number of rows: 32906

Table truncated, full table size 837 Kbytes.




Supplementary data files not provided

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