|
| Status |
Public on Aug 07, 2023 |
| Title |
knockout PDH effector T-cell sample 2 |
| Sample type |
SRA |
| |
|
| Source name |
TPdh-/- T-effector
|
| Organism |
Mus musculus |
| Characteristics |
cell line: TPdh-/- T-effector
cell type: effector T-cell
genotype: TPdh-/-
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Tagmented DNA samples were amplified to add single indexed adapters using the Kapa HiFi PCR MasterMix (Roche). The final libraries were twice purified using Ampure XP PCR Purification Beads (Agencourt).
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Raw ATAC-seq data were trimmed to remove residual adapter sequences using Trimmomatic. Adapter seqeunces were supplied by the developed of Trimmomatic in NexteraPE-PE.fa file.
Trimmed reads were mapped to mouse genome reference seqeunce GRCm38 using BWA MEM (v. 0.7.17)
Reads mapping low mappability regions (supplied in ENCFF547MET.bed) were filtered using samtools.
ATAC-seq peaks were identfied using MACS2 software (v. 2.2.7.1)
Assembly: GRCm38
Supplementary files format and content: narrowPeak, bedgraph files
|
| |
|
| Submission date |
May 03, 2023 |
| Last update date |
Aug 07, 2023 |
| Contact name |
Peter McGuire |
| E-mail(s) |
peter.mcguire@nih.gov, payal.banerjee@nih.gov
|
| Organization name |
NHGRI
|
| Street address |
10 Center Dr
|
| City |
Bethesda |
| State/province |
MD |
| ZIP/Postal code |
20892 |
| Country |
USA |
| |
|
| Platform ID |
GPL24247 |
| Series (2) |
| GSE231554 |
Pyruvate dehydrogenase complex integrates the metabolome and epigenome in memory T cell differentiation in vitro [ATAC-Seq] |
| GSE231556 |
Pyruvate dehydrogenase complex integrates the metabolome and epigenome in memory CD8+ T cell differentiation in vitro |
|
| Relations |
| BioSample |
SAMN34566662 |
| SRA |
SRX20204099 |
