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

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|style="background-color: #EEE"|[[Image:owwnotebook_icon.png|128px]]<span style="font-size:22px;">Pc-TF Genomics</span>
|style="background-color: #EEE"|[[Image:owwnotebook_icon.png|128px]]<span style="font-size:22px;">Pc-TF Genomics</span>
|style="background-color: #F2F2F2" align="center"|<html><img src="/images/9/94/Report.png" border="0" /></html> [[{{#sub:{{FULLPAGENAME}}|0|-11}}|Main project page]]<br />{{#if:{{#lnpreventry:{{FULLPAGENAME}}}}|<html><img src="/images/c/c3/Resultset_previous.png" border="0" /></html>[[{{#lnpreventry:{{FULLPAGENAME}}}}{{!}}Previous entry]]<html>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</html>}}{{#if:{{#lnnextentry:{{FULLPAGENAME}}}}|[[{{#lnnextentry:{{FULLPAGENAME}}}}{{!}}Next entry]]<html><img src="/images/5/5c/Resultset_next.png" border="0" /></html>}}
|style="background-color: #F2F2F2" align="center"|[[File:Report.png|frameless|link={{#sub:{{FULLPAGENAME}}|0|-11}}]][[{{#sub:{{FULLPAGENAME}}|0|-11}}|Main project page]]<br />{{#if:{{#lnpreventry:{{FULLPAGENAME}}}}|[[File:Resultset_previous.png|frameless|link={{#lnpreventry:{{FULLPAGENAME}}}}]][[{{#lnpreventry:{{FULLPAGENAME}}}}{{!}}Previous entry]]&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;}}{{#if:{{#lnnextentry:{{FULLPAGENAME}}}}|[[{{#lnnextentry:{{FULLPAGENAME}}}}{{!}}Next entry]][[File:Resultset_next.png|frameless|link={{#lnnextentry:{{FULLPAGENAME}}}}]]}}
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==mm/dd/yy==
==01/06/13==
<!-- Precede finished items with a checkmark &#x2713; -->
<!-- Precede finished items with a checkmark &#x2713; -->
* Line item 1
* 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


----
----
'''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 22:20, 26 September 2017

Pc-TF Genomics Main project page
Previous entry      Next entry


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



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