Commit e689649d authored by Balog's avatar Balog
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Update intake_meeting_notes.md

parent 027c57a4
......@@ -5,37 +5,38 @@ Please fill in more details or N/A if not applicable for the following questions
### Project setup
* What is your research question?
I want to find DE genes after LRIF1 depletion on total RNA.
* Please describe your study design.
We generated 12 samples, 6 controls and 6 LRIF1 depleted sample (by shRNAs)
and NGS was performed on total RNA after rRNA depletion.
* How many samples? Do the subjects have family members can be sequenced as well?
12 samples, 4 different cell lines.
* What type of data and experiment (e.g., DNA, RNA, captured exomes, etc) are you interested in?
Total RNA seq
* For cancer project, do you have tumor normal pairs? If not, why?
NA
* For RNAseq project, please provide sample sheet (ref to other files in /doc)?
Will be created later by Sander.
* Is this project part of a larger study? How do you compare with other similar project if any?
We want to compare it to 092, but 092 was only polyA RNA. Alignment should be done to hg19.
* What's your publication plan?
### If you already have generated sequencing data or have decided your sequencing protocol, please answer the following questions:
* What is the species you study? Any specific genomics modification?
Human
* Please describe your sequencing platform (the consistency in platforms), coverage, sequenced region (e.g, fullgenome, exome, targeted)
HiSeq 2500, paired end, 125bp
* For RNAseq, is it a strand-specific library and how was the RNA captured (e.g., polyA or rRNA depletion)?
rRNA depletion
* Was it single-end, paired-end, mate-pair or a combination?
paired end
* What is/are the average insert size(s)?
300-400 bp
* Which adapter-ligation protocol was used (TruSeq, Nextera, ...)? Please provide a list of used adaptors if possible.
NEBNext Ultra Directional Kit
* Did anyone already perform data analysis on the sequencing data (e.g., by the sequencing center)? If yes, what is the conclusion?
No
### If you are going to do sequencing, please answer the following questions
* Did you already find a sequencing center (e.g. LGTC, BGI) to do sequencing?
......@@ -43,9 +44,9 @@ Please fill in more details or N/A if not applicable for the following questions
### Expected deliverables:
* What kind of output datasets do you need and in which format?
count table in Excel, DE
* What kind of documents do you need? E.g. QC report, description of the pipelines.
* If your goal is to perform differential gene expression analysis, please specify your research question by providing which sample sets should be compared to each other. If samples are paired, please indicate in sample sheet.
6 control samples (labelled 002 or 004) should be compared to the 6 depleted samples (labelled with HB2 or HB3).
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