|
| Status |
Public on May 01, 2020 |
| Title |
RRBS_R2shp53-CCNE1_SA_replicate1 |
| Sample type |
SRA |
| |
|
| Source name |
Human Mammary Epithelial Cells (HMECs) transduced and selected in Soft Agar
|
| Organism |
Homo sapiens |
| Characteristics |
gender: female
cell type: primary human mammary epithelial cells (HMECs)
transduced with: shP53
transduced with: CCNE1
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA was isolated using the QIAmp DNA Mini kit (Qiagen).
We prepared RRBS libraries as previously described (Auclair G et al, 2014). Briefly, genomic DNA was digested for 5 h with MspI (Thermo Scientific) followed by end-repair, A- tailing (with Klenow fragment, Thermo Scientific) and ligation to paired-end methylated adapters (with T4 DNA ligase, Thermo Scientific) in Tango 1X buffer. We purified fragments between 150 and 400 bp by electrophoresis and performed two rounds of bisulfite conversion with the EpiTect kit (Qiagen). Final RRBS libraries were generated with PfUTurbo Cx hotstart DNA polymerase (Agilent) and indexed PE Illumina primers with 12-15 cycles of PCR. The libraries were purified with AMPure magnetic beads (Beckman Coulter).
|
| |
|
| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
Reduced Representation |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
We cleaned sequencing reads with Trim Galore v0.2.1 using the parameters --rrbs --paired -r1 30 -r2 30 -q 20 --length 20 --retain_unpaired.
We aligned reads to the human genome with BSMAP v2.74 using the parameters -v 2 -w 100 -r 1 -x 400 -m 30 -D C-CGG -n 1.
We extracted methylation percent values with methratio.py from BSMAP v2.74 using the parameters -z -u -g.
We filtered CGs to have a minimum sequencing depth of 8X.
Genome_build: hg19
Supplementary_files_format_and_content: We provide igv files containing methylation scores for all CGs with at least 8X sequencing depth.
|
| |
|
| Submission date |
May 23, 2018 |
| Last update date |
May 01, 2020 |
| Contact name |
stanislas P du manoir |
| E-mail(s) |
stanislas.dumanoir@inserm.fr
|
| Organization name |
IRCM
|
| Lab |
Genetic and phenotypic plasticity of cancer team
|
| Street address |
280 rue des apothicaires
|
| City |
montpellier |
| ZIP/Postal code |
34298 |
| Country |
France |
| |
|
| Platform ID |
GPL11154 |
| Series (2) |
| GSE114807 |
DNA methylation data from Human Mammary Epithelial Cells (HMECs) transduced with shp53, HRASV12, WNT1 and CCNE1 [RRBS-seq] |
| GSE114849 |
DNA methylation and mirRNA/mRNA Expression data from Human Mammary Epithelial Cells (HMECs) transduced with shp53, HRASV12, WNT1 and CCNE1 |
|
| Relations |
| BioSample |
SAMN09241316 |
| SRA |
SRX4116572 |
