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[CHIP-seq] MeDIP-seq,ChIP-seq,RNA-seq结合起来分析,你就算合格了

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发表于 2017-2-15 14:38:09 | 显示全部楼层 |阅读模式
最近看了一篇文章,可以算是纯粹的数据分析文章了,是国内表观大牛朱冰实验室出品的。
发表在cell molecular上面,第一张图是实验,最后一张图是提出模型,中间5张图都是自己的数据的生物信息学分析!
数据在;https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE57700

就是对mouse的ESC进行各种测序,各种指定的突变前后的各种测序看看peaks和表达的变化。首先是34个ChIP-seq,数据:
GSM1386970SALL1-ChIPSeq-TT2
GSM1386971input-of-ChIPSeq-TT2
GSM1386972Tet1-ChIPSeq-WT-TT2
GSM1386991SALL4A-ChIPSeq-in-Sall4-het
GSM1386992input-of-ChIPSeq-in-sall4-het
GSM1386997SALL4A-ChIPSeq-in-sall4-KO
GSM1386998input-of-ChIPSeq-in-sall4-KO
GSM2065691bio-Tet2-ChIP-in-CloneE1
GSM2065692input-of-bioTet2-ChIP-in-CloneE1
GSM2065693Sall1-ChIP-in-WT-of-Sall-DKO
GSM2065694Sall4-ChIP-in-WT-of-Sall-DKO
GSM2065695input-for-ChIP-in-WT-of-Sall-DKO
GSM2065700Sall4-ChIP-in-Sall4KO+WT
GSM2065701input-of-ChIP-in-Sall4KO+WT
GSM2065702Sall4-ChIP-in-Sall4KO+Mutant
GSM2065703input-of-ChIP-in-Sall4KO+Mutant
GSM2065704TET1-ChIP-in-Sall4het
GSM2065705TET1-ChIP-in-Sall4KO
GSM2065706SALL1-ChIP-in-Sall4het
GSM2065707SALL1-ChIP-in-Sall4KO
GSM2065708H3K27ac-ChIP-in-Sall4het
GSM2065709H3K27ac-ChIP-in-Sall4KO
GSM2065710bio-Tet2-ChIP-in-Sall4het-BirA
GSM2065711input-of-ChIP-in-Sall4het-BirA
GSM2065712bio-Tet2-ChIP-in-Sall4KO-BirA
GSM2065713input-of-ChIP-in-Sall4KO-BirA
GSM2290354Sall4-ChIP-in-TT2-shScr-2nd
GSM2290355input-of-Sall4-ChIP-in-TT2-shScr-2nd
GSM2290356Sall4-ChIP-in-TT2-shTet2
GSM2290357input-of-Sall4-ChIP-in-TT2-shTet2
GSM1386979SALL4A-in-shScr-TT2
GSM1386981input-of-shScr-TT2
GSM1386982SALL4A-shTet1-TT2
GSM1386984input-shTet1-TT2


然后是34个MeDIP-seq,数据:

GSM1386973hmedip-in-TT2
GSM1386974input-of-DIP-in-TT2
GSM1386975caC-DIPSeq-in-shScr-TT2
GSM1386976input-of-DIPSeq-in-shScr-TT2
GSM1386977caC-DIPSeq-in-shTdg-TT2
GSM1386978input-of-DIPSeq-in-shTdg-TT2
GSM1386985hmedip-in-WT-of-sall1-sall4-DKO
GSM1386986medip-in-WT-of-sall1-sall4-DKO
GSM1386987input-of-DIPSeq-in-WT-of-sall1-sall4-DKO
GSM1386988hmedip-in-sall1-sall4-DKO
GSM1386989medip-in-sall1-sall4-DKO
GSM1386990input-of-DIPSeq-in-sall1-sall4-DKO
GSM1386993hmedip-in-sall4-het
GSM1386994input-of-DIP-in-sall4-het
GSM1386995hmedip-in-sall4-KO
GSM1386996input-of-DIPSeq-in-sall4-KO
GSM1386999hmedip-in-sall4ko-plus-WT
GSM1387000input-of-DIPSeq-in-sall4ko-plus-WT
GSM1387001hmedip-in-sall4KO-plus-mutant
GSM1387002input-of-DIPSeq-in-sall4ko-plus-mutant
GSM1387017hmedip_in_s1het
GSM1387018hmedip_in_s1ko
GSM1387019input_of_DIP_in_s1het
GSM1387020input_of_DIP_in_s1ko
GSM2065696caC-DIP-in-sall4het-shTdg
GSM2065697input-of-DIP-in-sall4het-shTdg
GSM2065698caC-DIP-in-sall4KO-shTdg
GSM2065699input-of-DIP-in-sall4KO-shTdg
GSM2065714hMeDIP-in-TT2-shScr
GSM2065715input-of-DIP-in-TT2-shScr
GSM2065716hMeDIP-in-TT2-shTet1
GSM2065717input-of-DIP-in-TT2-shTet1
GSM2065718hMeDIP-in-TT2-shTet2
GSM2065719input-of-DIP-in-TT2-shTet2


最后是12个RNA-seq的数据:
GSM1387011RNASeq-s4het.rep1
GSM1387012RNASeq-s4ko.rep1
GSM1387013RNASeq_SALL_DKO
GSM1387014RNASeq_WT_of_SALL_DKO
GSM1387015RNASeq_s1_het
GSM1387016RNASeq_s1_ko
GSM1387025RNASeq_s4ko_mut_rescue.rep1
GSM1387026RNASeq_s4ko_wt_rescue
GSM2065687RNASeq-WT-TT2
GSM2065688RNASeq-s4het.rep2
GSM2065689RNASeq-s4ko.rep2
GSM2065690RNASeq_s4ko_mut_rescue.rep2


这3种数据的分析套路大家都很清楚了,不会的再去我博客看看!
一个RNA-seq实战-超级简单-2小时搞定!
一个ChIP-seq实战-超级简单-2小时搞定!
一个MeDIP-seq实战-超级简单-2小时搞定!

现在考验大家的时候到了,组成一个学习班,把这个数据分析一遍!
有兴趣的联系我微信 !


需要有一定NGS数据分析功底的朋友,不要随便什么人,就加了,浪费我时间,我不是来教学的!
这5张图还是有一定难度的!
图1:

图2:

图3:

图4:

图5:





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