Atelier génomique (AMU SBBCU22L - AG)

Funding and acknowledgments

We would like to thank all the people that were involved in the preparation of this practical session especially:

  • Jean Imbert (TAGC/CoReBio PACA).
  • Bertrand Jordan (CoReBio PACA).
  • Christian Reil (CoReBio PACA).
  • Anne Chorazewiez (ex CoReBio PACA).
  • Aurélie Glowacz (AMU).
  • and Myriam Ramadour (PGM).

We would like to gratefully acknowledge CoReBio Paca which provided us with the funding to set up this practical session.


Year

2015-2016

Attendees

6 students from the Master BBSG II (Bioinformatique, biochimie structurale et génomique).


Trainers

  • Denis Puthier, TAGC
  • Lydie Pradel, TAGC
  • Beatrice Loriod, TAGC/TGML
  • Nicolas Fernandez, TAGC/TGML

About

The aim of this practical session is to provide students with the basic concepts and skills needed to perform Chromatin Immunoprecipitation and Sequencing (ChIP-Seq). Chromatine extracts will be prepared from control and activated cell line. Next, a multiplexed ChIP-Seq library will be produced using the Microplex Library Preparation kit (Diagenode) and validated at each step. Finally, the subsequent library will be sequenced using a NextSeq 500 Illumina sequencer.

After inspecting carefully the reports from the sequencer, downstream analyses are performed using a Galaxy instance deployed on our own server (pedagogix). Reads are quality checked, trimmed and mapped to the reference genome.


Schedule of the course 2015-2016

The practical session will take place from October 12 through October 16, 2015 at the TGML platform hosted in the TAGC laboratory.


Protocols

Name link
Chromatin preparation and immunoprecipitation protocole.doc.zip
Diagenode Microplex Library Preparation kit MicroPlex-Libary-Prep-Kit-v2-manual.pdf
Agilent BioAnalyzer 6000 RNA_Nano 0_Agilent_BioAnalyzer_6000_RNA_Nano.pdf

Tools and files for analysis

  • Galaxy server: an open source, web-based platform for data intensive biomedical research.
  • Integrative Genomics Viewer (IGV): a high-performance visualization tool for interactive exploration of large, integrated genomic datasets.
  • FastQC: A quality control tool for high throughput sequence data;
  • sickle - Trimming tool for FASTQ files using quality.
  • Bowtie - Read aligner.
  • Deeptools - A set of tools to handle bigWigs.
  • R: a freely available language and environment for statistical computing and graphics
  • RStudio: An interface to R.

Results and additional data

  • Lab (2015)
Type link
Chromatin check (fragment size #1) Bioanalyzer report
Chromatin check (fragment size #2) Bioanalyzer report

H3K27Ac-Control_sorted.bw

  • Sequencing results (2015)
Type link
Unstimulated H3K27Ac (fastqc trimmed R1) H3K27Ac_Control_R1_trim_fastqc.zip
Unstimulated H3K27Ac (fastqc trimmed R2) H3K27Ac_Control_R2_trim_fastqc.zip
Stimulated H3K27Ac (fastqc trimmed R1) H3K27Ac_Treated_R1_trim_fastqc.zip
Stimulated H3K27Ac (fastqc trimmed R2) H3K27Ac_Treated_R2_trim_fastqc.zip
Unstimulated H3K27Me3 (fastqc trimmed R1) H3K27Me3-Contr_R1_trim_fastqc.zip
Unstimulated H3K27Me3 (fastqc trimmed R2) H3K27Me3-Contr_R2_trim_fastqc.zip
Stimulated H3K27Me3 (fastqc trimmed R1) H3K27Me3_Treated_R1_trim_fastqc.zip
Stimulated H3K27Me3 (fastqc trimmed R2) H3K27Me3_Treated_R2_trim_fastqc.zip
Unstimulated H3K27Ac (bigwig) H3K27Ac-Control_sorted_2015.bw.zip
Stimulated H3K27Ac (bigwig) H3K27Ac_Treated_sorted_2015.bw.zip
Unstimulated H3K27me3 (bigwig) H3K27Me3-Contr_sorted_2015.bw.zip
Stimulated H3K27me3 (bigwig) H3K27Me3_Treated_sorted_2015.bw.zip
Unstimulated H3K27Ac (signal around promoters) H3K27Ac-Control_prom1k1k_2015.txt.zip
Stimulated H3K27Ac (signal around promoters) H3K27Ac_Treated_prom1k1k_2015.txt.zip
Unstimulated H3K27Me3 (signal around promoters) H3K27Me3-Contr_prom1k1k_2015.txt.zip
Stimulated H3K27Me3 (signal around promoters) H3K27Me3_Treated_prom1k1k_2015.txt.zip
Unstimulated H3K27Ac (peaks bed format) H3K27Ac_Control_peaks.bed.zip
Unstimulated H3K27Ac (peaks xls format) H3K27Ac_Control_peaks.xls.zip
Stimulated H3K27Ac (peaks bed format) H3K27Ac_Treated_peaks.bed.zip
Stimulated H3K27Ac (peaks xls format) H3K27Ac_Treated_peaks.xls.zip
Unstimulated H3K27me3 (peaks bed format) H3K27Me3_Control__peaks.bed.zip
Unstimulated H3K27me3 (peaks xls format) H3K27Me3_Control__peaks.xls.zip
Stimulated H3K27me3 (peaks bed format) H3K27Me3_Treated_peaks.bed.zip
Unstimulated H3K27me3 (peaks xls format) H3K27Me3_Treated_peaks.xls.zip
  • Sequencing results (2014)
Type link
Input (bigwig) NS-S_Input.bw.zip
Unstimulated H3K27Ac (bigwig) NS_H3K27Ac.bw
Unstimulated H3K27Ac(signal around promoters) NS_H3K27Ac_prom1k1k.txt
Unstimulated H3K4me3 (bigwig) NS_H3K4me3.bw
Unstimulated H3K4me3(signal around promoters) NS_H3K4me3_prom1k1k.txt
Stimulated H3K4me3 (bigwig) S_H3K4me3.bw
Stimulated H3K4me3(signal around promoters) S_H3K4me3_prom1k1k.txt
Unstimulated H3K27Ac (peaks) NS_H3K27Ac_peaks.bed
Unstimulated H3K4me3 (peaks) NS_H3K4me3_peaks.bed
Stimulated H3K4me3 (peaks) S_H3K4me3_peaks.bed
Unstimulated H3K27Ac (bam index chr19) NS_H3K27Ac_chr19.bam.bai
Unstimulated H3K27Ac (bam chr19) NS_H3K27Ac_chr19.bam.bai
  • Sequencing results (others)
Type link
RNA-Seq (counts, gene) counts.txt
RNA-Seq (counts, transcript) counts.txt
Unstimulated H3K4me1 (bigwig) NS_H3K4me1.bw
Unstimulated H3K4me2 (bigwig) NS_H3K4me2.bw
Unstimulated PolII (bigwig) NS_PolII.bw
Unstimulated RNA-Seq (bigwig minus strand) NS_RNA_min.bw
Unstimulated RNA-Seq (bigwig plus strand) NS_RNA_plus.bw
Stimulated H3K4me3 (signal around promoters) H3K4me3-S_prom1k1k.tsv
Stimulated RNA-Seq (bigwig minus strand) S_RNA_min.bw
Stimulated RNA-Seq (bigwig plus strand) S_RNA_plus.bw