harokopos@fleming.gr
14022022

Hi Martin,

Indeed the the samples id is VK3R26_272-2_Ctrl tr. From what I can see this sample shouldn't be included in the analysis since it gave almost no reads during sequence.

V

#@
10022022
Dear Vangelis,

in the analysis of Vasso's samples (see https://genomics-lab.fleming.gr/fleming/VKlab/run514/metaseqR2_run514b/index.html)
there is a problematic sample "26 - 272.2" that was not in the tables sent by Michalis. Can you please verify its identity?

The info you sent was:
"
The Sample ids are
VK3R25 - 261.2
26 - 272.2
27 - 283.2
28 - 285/288.1pool
29 - 261.5
30 - 272.3
31 - 343.4
32 - 343.5
33 - 348.3
Run ID ION514 (211207)
"

An argument against 272-2 can be seen from the RNA-Seq reads noise plot,
where 100% of its reads contribute to less than 10% of the features.
Also its location in the MDS plot suggests its status as an outlier.

BW
Martin

#@
Vasiliki Koliaraki
	
Feb 10, 2022, 3:25 PM (6 days ago)
	
to me, Michalis
Dear Martin,

Thank you very much!
I had a brief look at the data and saw that sample 272-2_CNTR_tr performed really badly in quality-control tests and PCA analysis. Looking at the actual counts, I noticed that for too many genes it had the value 74.
I believe we have to exclude it from our analysis.
What do you think?

Regards,
Vasso


Vasiliki Koliaraki, PhD
Group Leader - Researcher C
Institute for Fundamental Biomedical Research (IFBR)
Biomedical Sciences Research Center "Alexander Fleming"
34 Fleming Street, 16672, Vari, Greece
Tel: +30-210-9656310 (ext. 206)


#@
Hi Martin,

Sorry for the late reply, never saw or forgot your first mail probably.

The Sample ids are
VK3R25 - 261.2
26 - 272.2
27 - 283.2
28 - 285/288.1pool
29 - 261.5
30 - 272.3
31 - 343.4
32 - 343.5
33 - 348.3
Run ID ION514 (211207)

Thanks & sorry again
V

#@
31012022
Vasso:
The analysis between the groups is:

- CNTR untreated vs CNTR treated
- CNTR untreated vs Cre treated
- CNTR treated vs Cre treated

This is the main analysis that we need for these samples. 
We will have a look at the results and let you know if the "Preliminary analysis" or the exclusion of any sample will be necessary.

Group Name
for Analysis 1	Sample/prep name BIOLOGICAL REPLICATE	mouse genotype			treatment
CNTR treated	261.2	                                Igf1 lox/lox			BBN
                283.2	                                Igf1 lox/lox			BBN
                285.6+288.1 pool                   	Igf1 lox/lox			BBN
Cre treated	261.5	                                Twist2Cre +/- Igf1 lox/lox	BBN
                272.3	                                Twist2Cre +/- Igf1 lox/lox	BBN
CNTR untreated	343.4	                                Igf1 lox/lox             	Untreated
                343.5	                                Twist2Cre +/- Igf1 lox/lox	Untreated
                348.3	                                Twist2Cre +/- Igf1 lox/lox	Untreated