Nov 20, 2014

Protocols-including KDF

#1由 sufang 在 一, 05/18/2015 - 08:50 發表。
Keratinocyte culture method
 
說在前面:
Rheinwald Lab所寄給我們的Human Keratinocyte Culture Methods第一段便比較下面三個廠商來的media, 說請大家用K-sfm來養"low-to-moderate density"的keratinocytes (primary or immortalized)
K-sfmLife Technologiesgrow well from low to moderate density
EpiLifeLife Technologies 
KGM (or MCDB154)Cloneticsvery short replicative lifespan 
 
第二段:
須牢記於心的是, K-sfm的營養成分僅適用於低密度、聚集性的keratinocyte生長, 因此用K-sfm養的細胞, 1/3滿度前就必須passage.
 
第三段: 碰到OSCC的話, 建議與irradiated 3T3 fibroblasts共養、養在DMEM/F12 + 10-20% calf serum + 0.4 ug/ml hydrocortisone.
 
以下是養細胞步驟, Adapt from 宛樺labnotes and Rheinwald Lab.
For a p100 dish (or T75) --> plaing 104 – 105 cells / dish
For a   p60 dish (or T25) --> plaing 103 – 104 cells / dish
Cultures are refed every two days.
5-8 days after plating,  cells are ready for the next passage.
 
–It is important to subculture keratinocytes no more than 8 days after they have been plated, even if they have not reached the desired density (每一繼代不超過8天).
–A healthy, proliferative cell population should contain primarily small cells which have a population doubling time of ~24-30 hours (正常健康的小細胞約24–30小時複製一代)
–It is best practice to count the cells at each subculture and replate at a defined number, avoid the common practice of many labs for serially passaging cell lines of plating 1:4 or 1:10 dilutions (維持每次繼代種入固定細胞數, 不要用1:4, 1:10這種不良繼代習慣).
 
Growing keratinocytes to high density (提高細胞培養密度之培養方法)
–K-sfm medium was not designed to grow cells to high density with retention of viability.  To grow keratinocytes to high density a medium containing higher concentrations of nutrients is needed.  We have found that keratinocytes and SCC cells that have been grown up to ~1/3 confluence in K-sfm can be switched at this time to a 1:1 mixture of K-sfm and a medium we call “DF-K” (note: K-sfm + DF-K -->  KDF medium). 
–SF notes: 請大家漸漸把immortalized keratinocytes 馴服在KDF medium中, 謝謝! These incudes
                  * CGHNK2
                  * OKF4hTERT
                  * NP460hTERT
                  * NP550hTERT
                  * DOK

Recipe for the above Rheinwald lab modification of KSFM:
(GIBCO K-sfm +25 µg/ml BPE +0.4 mM CaCl2 +0.2 ng/ml EGF +pen/strep)
500 ml     K-sfm (Invitrogen/Life Technologies, which comes with 0.1 mM CaCl2)
½ vial       Life Technologies’ tube containing 25 μg Bovine Pituitary Extract (BPE) 
0.5 ml       0.3 M CaCl2 in water (=1000x for 0.3mM)
0.5 ml       0.2 μg/ml EGF in PBS +0.1%BSA (=1000x for 0.2 ng/ml) 
5 ml        Penicillin/Streptomycin (100X conc. solution) (Life Technologies) 
Swirl to mix and then filter-sterilize through a 0.2 μm pore-size sterilization filter.  The medium remains good for at least one month at 4oC. 
Recipe for DF-K medium:
(DMEM + F12 (1:1 v/v) +2 mM L-glutamine +25 µg/ml BPE +0.4 mM CaCl2  + 0.2ng/ml EGF )
250 ml     DMEM (High Glucose, no pyruvate, no glutamine, no calcium (Life Technologies catalog #21068-028)
250 ml     Ham’s F-12 medium (Life Technologies catalog #11765-054)
3.75 ml    200 mM L-Glutamine (=100x for 2 mM) (Invitrogen/Life Technologies)
½ vial      Life Technologies’ tube containing 25 μg Bovine Pituitary Extract (BPE) 
0.42 ml    0.3 mM CaCl2 in water (=1000x for 0.3mM)
0.5 ml      0.2 μg/ml EGF in PBS +0.1%BSA (=1000x for 0.2 ng/ml)
5 ml        Penicillin/Streptomycin (100X conc. solution) (Life Technologies)
 
Once cultures have grown to ~1/3 confluence in KSFM they either should be subcultured or else subsequently fed daily with a 1:1 mixture of KSFM and DF-K until confluent. Such cultures are suitable for protein, RNA, and DNA extracts or FACS analysis, but may not subculture as well as cells grown to no more than ~1/3 confluence in K-sfm.

Nov 18, 2014

Cloning of colorful CXCL1, 2, 3, IDO1, TDO2

由 sufang 在 二, 11/18/2014 - 15:13 發表 Pre-published CXCL 素菁

ID1234567891011121314151617181920 
CXCL14.895.662.240.910.92.333.672.14.451.179.21.067.181.291.73.572.511.290.58 
                      
ID2122232425262728293031323334353637383940AVE
CXCL10.92.461.892.443.561.82.474.941.952.330.721.26.393.091.320.484.182.592.461.072.64825
                      
IDAC/DOK2ACst/DOK3NNK/DOK1NNKst/DOK3NIC/DOK1 4NQO mo 
CXCL11.481.152.352.060.15 3.82

Entrez Gene:
CXCL1=GRO-a=GMSA (4q21)
CXCL2=GRO-b (4q21)
CXCL3=GRO-c (4q21)
CXCR2 =IL8RB (2q35)


ID1234567891011121314151617181920 
CXCR20.650.360.380.350.650.180.480.210.640.390.760.160.80.620.332.280.430.291.10.4 
                      
ID2122232425262728293031323334353637383940AVE
CXCR20.930.240.420.251.240.540.371.260.890.350.840.21.010.571.810.520.380.740.560.450.63
                      
IDAC/DOK2ACst/DOK3NNK/DOK1NNKst/DOK3NIC/DOK1  4NQO mo 
CXCR20.771.572.030.571.47  1.34 

Nov 14, 2014

MOST104

2014/12/7: Arecoline-induced epigenomic changes in human oral keratinocytes
                  檳榔鹼誘導人類口腔角質細胞中表觀遺傳體改變之研究
--------------------------------
計畫內容(C12-1, C12-2 no more than 23 pages; references no more than 5 pages)
(一)近五年之研究計畫內容與主要研究成果說明。(C12-1)

台灣口腔癌細胞株中八十三個酪氨酸激酶表現剖繪
Expression profiling of 83 protein tyrosine kinases in Taiwanese oral cancer cell lines.
 Figure 1 (DDR1 and collective cancer cell migration) (Eur J Cancer. 2012 48 (Suppl. 6): 167)

以次世代定序方法RNA-Seq分析台灣口腔癌細胞株與不朽化口腔角質細胞株
RNA-Seq analysis of Taiwanese oral cancer cell lines and immortalized keratinocyte lines.
Figure 2 (FGFR3-TACC3 gene fusion) (Cancer Discovery 2013 3: 636 pdf 3670)

參與建立台灣口腔癌與潛在惡性病症生物資料庫
Taiwan OPMD and Oral Cancer bioinformatic Database, TOP-OCD
– RNA-Seq FPKM values for each Taiwanese oral cancer cell lines under the following link (http://molas.iis.sinica.edu.tw/OralCancer)
– 40 Tumor/Normal paired oral cancer tissues (http://molas.iis.sinica.edu.tw/fold1)
– DOK projects (http://molas.iis.sinica.edu.tw/DOK2)
– New data from TOP-OCC (Taiwan OPMD and Oral Cancer Consortium, starts from Jan. 2015)

Nov 7, 2014

DDR1 manuscript 相關

DDR1 manuscript 相關

 
2015/05/08 (Thu)  MS submitted to Research Topic "Oral Oncology"
2015/05/30 (Sat)   MS returned, interactive reviews activated:
Editor: Rui Amaral Mendes Catholic University of Portugal; Editor of J Carcinogenesis and Mutagenesis; Adhuant Prof at CWRU
2015/08/28 rejected... by Specialty Chief Editor Jean­Pascal Machiels

Reviewer#1:
加上morphology圖於Fig 1B
band quantitation
spheroid invasion
Reviewer#2:
移入IHC圖於Fig 5E
補上shRNA sequences and offtarget exp result 於Fig S1B

TOP-OCC and TOP-OCD

2014/11/12 OPMD IRB:
基因檢測是以單核苷酸多態性(single nucleotide polymorphism, SNP)為主,特別是會影響酵素功能的功能性(functional)SNP與在亞洲人當中比較重要的SNP。SNP的檢測將採用Taqman allele discrimination的方式1。
首先,把DNA的濃度標準化為15ng/µL。然後,在96孔盤裡分別加入84位不同研究對象的DNA與試劑的混合液(2µL=30ng DNA in a 25µL reaction)、8個陽性對照及4個陰性對照,預計共需要24個96孔盤來完成所有研究對象(N=2000)每一個SNP的檢測。接著,把96孔盤放置在Applied Biosystem 7500 real time PCR(Foster City, CA)進行資料的讀取。每一個SNP的檢測將會經過幾個步驟的品質管制:
a.    以對照組的檢測資料來評估Hardy-Weinberg disequilibrium,p值<0.01的SNP將被排除。
b.    Allele 的頻率將與the International Hapmap Project(www.hapmap.org)2 的中國人的基因資料來做比較。
c.    偵測頻率(call rate)< 95%的SNP將被排除。
d.    10%的DNA樣本將被重覆檢測來評估檢測的準確度。
1.    de Kok JB, Wiegerinck ET, Giesendorf BA, Swinkels DW. Rapid genotyping of single nucleotide polymorphisms using novel minor groove binding DNA oligonucleotides (MGB probes). Hum Mutat. 2002;19:554-559.
2.    The International HapMap Consortium. (2003) The International HapMap Project. Nature;426:789-796.

Genetic variants in one-carbon metabolism genes and breast


Nov 4, 2014

Epigenetic Talks Bing Ren

Dear All,
I like to invite you to join two exciting Epigenetic Talks by the world leading scientists Yi Zhang and Bing Ren on Oct 23 and Nov 4, respectively, at Academia Sinica.

Bing Ren
UCSD
Regulation of the 3D Genome
11 am, Nov 4, 2014
B1 Auditorium, IMB, Academia Sinica
Dr. Bing Ren, Member of Ludwig Institute for Cancer Research San Diego Branch and Professor at Department of Cellular and Molecular Medicine UCSD School of Medicine, is one of the top scientists worldwide in deep sequencing in both biology study and innovative technology development and one of the World’s Most Influential Scientific Minds in 2014 selected by Thomas Reuters.  We strongly believe that his visit will advance our view towards this explosive field and may very likely stimulate significant progress of our local genome-wide study and international collaboration. 
Representative publications: 
Jin F, Li Y, Dixon JR, Selvaraj S, Ye Z, Lee AY, Yen CA, Schmitt AD, Espinoza CA, Ren B.
Nature. 2013 Nov 14;503(7475):290-4. doi: 10.1038/nature12644. Epub 2013 Oct 20.

Nov 2, 2014

Tak Wah Mak

由 sufang 在 日, 11/02/2014 - 11:09 發表 Pre-published Cancer Metabolism Notes

Genomic alterations in cancers
mutations (300,000; > 20,000 genes)
epithelial : 50-100; leukemia: 20
amplifications (3000)
deletions (thousands)
translocations (fusions: 7000)
epigenetic changes (extensive)
Drivers : hundred, 90% loss of functions
Inter-and intra-tumor heterogeneity (Charles Sweton)
< 1/2 mutated or amplified genes expressed