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| Status |
Public on Nov 15, 2016 |
| Title |
HCAFIS03_13S |
| Sample type |
SRA |
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| Source name |
EM_Methylated_13
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| Organism |
Homo sapiens |
| Characteristics |
tissue: Blood
subset: EM
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| Growth protocol |
CD8+ T cell subsets were isolated from peripheral blood by fluorescence-activated cell sorting (FACS)
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
After sonication (Bioruptor, Diagenode), chromatin was immunoprecipitated with an iDeal ChIP-seq Kit (Diagenode)
TruSeq® ChIP Sample Preparation (Illumina Inc.)
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiScanSQ |
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| Data processing |
Basecalls performed using CASAVA version 1.8.2
Individual FASTQ files for each sample were merged prior to the quality control & filtering steps
Quality control of the reads was carried out using FASTQC software (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
Reads were filtered from the adapter sequences and their quality score using trim_galore software. (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) and only are retained those with at least 20 phred quality score.
Reads were mapped to hg19 (Homo sapiens) reference genome using Bowtie2 for paired end read alignments, allowing two mismatches (n = 2).
Resulting SAM aligment files were converted to BED format to be used in as input for peak calling software SPP v1.10 and further analyses were conducted via Diffbind and ChIPpeakAnno BioconductoR packages (https://bioconductor.org/packages/release/bioc/html/DiffBind.html; https://bioconductor.org/packages/release/bioc/html/ChIPpeakAnno.html ).
Genome_build: hg19
Supplementary_files_format_and_content: Peak calling results, obtained from SPP in encodePeak format. These tables are in tab separated plain text format.
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| Submission date |
Jun 09, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Jose Luis Lavin |
| E-mail(s) |
joluito@gmail.com
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| Organization name |
CIC bioGUNE
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| Street address |
Parque Tecnológico de Bizkaia Building 502, Floor 0
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| City |
Derio |
| State/province |
Bizkaia |
| ZIP/Postal code |
48160 |
| Country |
Spain |
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| Platform ID |
GPL15456 |
| Series (2) |
| GSE83155 |
Epigenetic regulation of the transcriptional program in memory and terminally differentiated CD8+ T cells [HCAFIS_03_ChIPseq] |
| GSE83159 |
Epigenetic regulation of the transcriptional program in memory and terminally differentiated CD8+ T cells |
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| Relations |
| BioSample |
SAMN05223288 |
| SRA |
SRX1835676 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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