|
| Status |
Public on Dec 11, 2015 |
| Title |
HEK-BAHD1 WGBS (replicate 2) |
| Sample type |
SRA |
| |
|
| Source name |
modified HEK293
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: modified HEK293 cell overexpressing BAHD1
|
| Treatment protocol |
EZ DNA Methylation-Gold bisulfite conversion kit (Zymo Research, USA)
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Isolated DNA was reduced into 100-300 bp fragments by sonication and treated with DNA-end repair, 3’-dA overhang and ligation of methylated sequencing adapters. Samples underwent bisulfite treatment with the ZYMO EZ DNA Methylation-Gold kit, with 99.6% bisulfite conversion rate. Desalted, size-selected, PCR amplified fragments were size-selected again.
|
| |
|
| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
bisulfte converted DNA
genome-wide methylated and non-methylated read counts
|
| Data processing |
Qualified libraries were selected for Illumina sequencing by BGI tech. Data filtering includes removing adaptor sequences, contamination and low-quality reads from raw reads. These reads were filtered by custom BGI scripts. Low-quality reads include two types, and reads of the two types were removed: (1) when the ratio of N in whole read was over 10%; (2) when the ratio of base whose quality was less than 20 was over 10%. Observed cytosines on the forward read of each read pair were in silico replaced by thymines, and observed guanines on the reverse read of each read pair were in silico replaced by adenines. The “alignment form” reads were then mapped to the “alignment form” reference genome by SOAP aligner. Every hit with a single placement with minimum numbers of mismatches and a clear strand assignment was defined as unambiguous alignment (uniquely mapped reads) and was used for methyl-cytosine ascertainment. Only the uniquely mapped reads were used to estimate the copy numbers of the local region. Genomic bases with a copy number larger than 1.5 were not used to call methylcytosines and not used in any subsequent analysis to avoid errors caused by misalignment.
Genome_build: hg19
Supplementary_files_format_and_content: chromosome-specific text files including coordinates of CpG positions and counts of methylated reads and coverage at each position.
|
| |
|
| Submission date |
Apr 09, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Helene Bierne |
| E-mail(s) |
helene.bierne@inrae.fr
|
| Phone |
33134652289
|
| Organization name |
INRAE - University PARIS SACLAY
|
| Department |
Micalis Institute
|
| Lab |
Epigenetics and Cellular Microbiology
|
| Street address |
Domaine de Vilvert, bat 442, INRA Micalis
|
| City |
Jouy-en-Josas |
| ZIP/Postal code |
78350 |
| Country |
France |
| |
|
| Platform ID |
GPL16791 |
| Series (2) |
| GSE51867 |
whole-genome bisulfite sequencing (BS-seq) of HEK293 cells (HEK293-CT) and HEK293 cells stably over-expressing the BAHD1 gene (HEK-BAHD1) |
| GSE51868 |
HEK293 cells (HEK293-CT) and HEK293 cells stably over-expressing the BAHD1 gene (HEK-BAHD1) |
|
| Relations |
| BioSample |
SAMN03468605 |
| SRA |
SRX984855 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1654726_TREATED_chr1.cout.txt.gz |
1.2 Gb |
(ftp)(http) |
TXT |
| GSM1654726_TREATED_chr10.cout.txt.gz |
736.1 Mb |
(ftp)(http) |
TXT |
| GSM1654726_TREATED_chr11.cout.txt.gz |
712.0 Mb |
(ftp)(http) |
TXT |
| GSM1654726_TREATED_chr12.cout.txt.gz |
717.3 Mb |
(ftp)(http) |
TXT |
| GSM1654726_TREATED_chr13.cout.txt.gz |
491.7 Mb |
(ftp)(http) |
TXT |
| GSM1654726_TREATED_chr14.cout.txt.gz |
481.9 Mb |
(ftp)(http) |
TXT |
| GSM1654726_TREATED_chr15.cout.txt.gz |
462.2 Mb |
(ftp)(http) |
TXT |
| GSM1654726_TREATED_chr16.cout.txt.gz |
479.0 Mb |
(ftp)(http) |
TXT |
| GSM1654726_TREATED_chr17.cout.txt.gz |
484.5 Mb |
(ftp)(http) |
TXT |
| GSM1654726_TREATED_chr18.cout.txt.gz |
401.0 Mb |
(ftp)(http) |
TXT |
| GSM1654726_TREATED_chr19.cout.txt.gz |
377.5 Mb |
(ftp)(http) |
TXT |
| GSM1654726_TREATED_chr2.cout.txt.gz |
1.2 Gb |
(ftp)(http) |
TXT |
| GSM1654726_TREATED_chr20.cout.txt.gz |
358.0 Mb |
(ftp)(http) |
TXT |
| GSM1654726_TREATED_chr21.cout.txt.gz |
206.6 Mb |
(ftp)(http) |
TXT |
| GSM1654726_TREATED_chr22.cout.txt.gz |
232.7 Mb |
(ftp)(http) |
TXT |
| GSM1654726_TREATED_chr3.cout.txt.gz |
1005.7 Mb |
(ftp)(http) |
TXT |
| GSM1654726_TREATED_chr4.cout.txt.gz |
925.3 Mb |
(ftp)(http) |
TXT |
| GSM1654726_TREATED_chr5.cout.txt.gz |
948.0 Mb |
(ftp)(http) |
TXT |
| GSM1654726_TREATED_chr6.cout.txt.gz |
879.2 Mb |
(ftp)(http) |
TXT |
| GSM1654726_TREATED_chr7.cout.txt.gz |
821.4 Mb |
(ftp)(http) |
TXT |
| GSM1654726_TREATED_chr8.cout.txt.gz |
750.9 Mb |
(ftp)(http) |
TXT |
| GSM1654726_TREATED_chr9.cout.txt.gz |
645.3 Mb |
(ftp)(http) |
TXT |
| GSM1654726_TREATED_chrM.cout.txt.gz |
160.4 Kb |
(ftp)(http) |
TXT |
| GSM1654726_TREATED_chrX.cout.txt.gz |
802.0 Mb |
(ftp)(http) |
TXT |
| GSM1654726_TREATED_chrY.cout.txt.gz |
122.4 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
