|
| Status |
Public on Jul 03, 2019 |
| Title |
Tox∆Ex5 Tim3 +ve P14 T-cells_Day 8 |
| Sample type |
SRA |
| |
|
| Source name |
TOXkoTim3Plus
|
| Organism |
Mus musculus |
| Characteristics |
cell type: P14 T-cells
genotype: ToxKO
infection: LCMV infection
time: day 8
sorted into: Tim-3+ T-cells
|
| Treatment protocol |
N/A
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA was extracted followed by bisulfite treatment for library prepration
Libraries were prepared according to Illumina's instructions accompanying the TruSeq DNA Methylation Kit (Part# EGMK81312). Briefly, Bisulfite converted DNA was annealed with random hexamer with tagging sequence. DNA copy was synthesized using TruSeq DNA Methyl Polymerase. Then Exonuclease I was used to digest excess random primer. The 3’ ends of the strands are then selectively tagged with a second specific sequence tag to generate di-tagged DNA using DNA polymerase. The di-tagged DNA with known sequence tags at both ends was cleaned up by the AMPureXP Beads. The dsDNA library was generated by PCR amplification with Illumina primers for 10 cycles and library fragments of ~350 bp (insert plus adaptor and PCR primer sequences). The library was purified by the AMPureXP Beads. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the HiSeq 2500 following the manufacturer's protocols.
|
| |
|
| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
2-658208
|
| Data processing |
Basecalling was performed using Illumina RealTimeAnalysis software
FASTQ sequences adapter trimmed (trimglore) and mapped to the mm10 genome by BSMAP
CpGs were extracted by the methratio.py in the BSMAP package
Genome_build: mm10
Supplementary_files_format_and_content: methylation ratio are in bed formats that contains methylation ratio for each CpG
|
| |
|
| Submission date |
May 22, 2019 |
| Last update date |
Jul 03, 2019 |
| Contact name |
yiping fan |
| E-mail(s) |
yiping.fan@stjude.org
|
| Phone |
9015955716
|
| Organization name |
st jude children's hospital
|
| Street address |
262 Danny Thomas Place
|
| City |
memphis |
| State/province |
tn |
| ZIP/Postal code |
38105 |
| Country |
USA |
| |
|
| Platform ID |
GPL24247 |
| Series (2) |
| GSE131642 |
Tox reinforces the phenotype and longevity of exhausted T-cells in chronic viral infection [Bisulfite-Seq] |
| GSE131643 |
Tox reinforces the phenotype and longevity of exhausted T-cells in chronic viral infection |
|
| Relations |
| BioSample |
SAMN11830999 |
| SRA |
SRX5883327 |
