Difference between revisions of "User:Karmella Haynes/Notebook/PcTF Genomics/2013/01/06"

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==01/06/13==
 
==01/06/13==
 
<!-- Precede finished items with a checkmark &#x2713; -->
 
<!-- Precede finished items with a checkmark &#x2713; -->
* ChIP seq: run Q-seq alignment on H3K27me3 mock (lane 7)
+
* ChIP seq: run SeqMan NGen alignment on H3K27me3 mock (lane 7)
 
* Expand table from 1/05/13 to include PcTF, PcTF mock, H3K27me3, H3K27me3 mock
 
* Expand table from 1/05/13 to include PcTF, PcTF mock, H3K27me3, H3K27me3 mock
  
 
----
 
----
'''Line item 1'''<br>
 
> Samples
 
  
{| class="wikitable" border="0" cellspacing="3" <!-- Rxn. table -->
+
 
|-valign="top"
+
{| {{table}}
| <u>Reagent</u> || <u>Volume</u>  
+
|-
 +
| Gene || Chromosome || Expected state || H3K27me3<br>max. DOC || H3K27me3 mock<br>max. DOC || PcTF<br>max. DOC || PcTF mock<br>max. DOC
 +
|-
 +
| ALAS1 || chr 3 || active || ~160 || ~100 || ~10 || 
 
|-
 
|-
| reagent 1 || # μL
+
| TBP || chr 6 || active || ~160 || ~275 || ~16 ||
 
|-
 
|-
| reagent 2 || #
+
| ACTB || chr 7 || active || ~180 || ~1 || ~22
 
|-
 
|-
| reagent 3 || #
+
| GUSB || chr 7 || active || ~160 || ~240 || ~16
 
|-
 
|-
| reagent 4 || #
+
| PPIA || chr 7 || active || ~90 || ~480 || ~10
 
|-
 
|-
| dH<sub>2</sub>O || #
+
| GAPDH || chr 12 || active || ~90 || ~240 || ~27
 
|-
 
|-
| &nbsp; || # μL
+
| B2M || chr 15 || active || 0 || ~1 || ~15
 +
|-
 +
| G6PD || chr X (23) || active || ~130 || 0 || ~14
 +
|-
 +
| HPRT1 || chr X (23) || active || ~150 || ~320 || ~11
 +
|-
 +
| PGK1 ||  chr X (23) || active || ~240 || ~475 || ~12
 +
|-
 +
| CDKN2A || chr9 || silent (H3K27me3+) || ~90 || ~650 || ~17
 +
|-
 +
| MMP12 || chr11 || silent (H3K27me3+) || ~18 || ~1 || ~6
 +
|-
 +
| MYT1 || chr20 || silent (H3K27me3+) || '''~270''' || ~525 || ~32
 +
|-
 +
| OLIG1 || chr21 || silent (H3K27me3+) || 0 || 0 || ~5 ||
 +
|-
 +
| OLIG2 || chr21 || silent (H3K27me3+) || ~130 || 0 || 0 ||
 
|}
 
|}
 
--> Reaction conditions
 
 
  
  

Latest revision as of 18:53, 6 January 2013

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01/06/13

  • ChIP seq: run SeqMan NGen alignment on H3K27me3 mock (lane 7)
  • Expand table from 1/05/13 to include PcTF, PcTF mock, H3K27me3, H3K27me3 mock


Gene Chromosome Expected state H3K27me3
max. DOC
H3K27me3 mock
max. DOC
PcTF
max. DOC
PcTF mock
max. DOC
ALAS1 chr 3 active ~160 ~100 ~10
TBP chr 6 active ~160 ~275 ~16
ACTB chr 7 active ~180 ~1 ~22
GUSB chr 7 active ~160 ~240 ~16
PPIA chr 7 active ~90 ~480 ~10
GAPDH chr 12 active ~90 ~240 ~27
B2M chr 15 active 0 ~1 ~15
G6PD chr X (23) active ~130 0 ~14
HPRT1 chr X (23) active ~150 ~320 ~11
PGK1 chr X (23) active ~240 ~475 ~12
CDKN2A chr9 silent (H3K27me3+) ~90 ~650 ~17
MMP12 chr11 silent (H3K27me3+) ~18 ~1 ~6
MYT1 chr20 silent (H3K27me3+) ~270 ~525 ~32
OLIG1 chr21 silent (H3K27me3+) 0 0 ~5
OLIG2 chr21 silent (H3K27me3+) ~130 0 0