|
| Status |
Public on Dec 22, 2022 |
| Title |
CD4+ T cell, neonatal, DMSO treated control, rep1 |
| Sample type |
SRA |
| |
|
| Source name |
lung
|
| Organism |
Mus musculus |
| Characteristics |
tissue: lung
developmental stage: P4
cell type: CD4+ T cell
genotype: C57BL/6NJ
treatment: Control
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Mouse lungs were minced and dissociated into a single-cell suspension. CD4+ cells were selected by MACS. CD4+ T cells were then sorted from the CD45+ population by FACS before lysis and mRNA extraction.
Bulk mRRBS libraries prepared using QIAGEN AllPrep DNA/RNA micro kit, disgested with the endonuclease MspI, size-selected using SPRI beads, and subjected to bisulfite conversion using the Zymo Research EZ DNA Methylation-Lightning kit. Libraries were constructed with the Zymo Research Pico Methyl-Seq Library Prep Kit with Illumina TruSeq DNA methylation indices.
|
| |
|
| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
Reduced Representation |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
CD4_DME1
|
| Data processing |
Reads demultiplexed to fastq using BCL2FASTQ v2.17.1.14 with default parameters
Reads were trimmed and filtered using TrimGalore! v0.4.3
Reads were aligned to the mm10 genome and methylation status was extracted using Bismark v0.16.3
Statistical analysis of differential methylation was performed using the R package DSS
Assembly: mm10
Supplementary files format and content: bismark.cov.gz files, methylation calling output from Bismark after alignment, used as direct input to DSS
Supplementary files format and content: DMLtest files, CSV files containing the results of the DMLtest function from DSS, filtered by FDR and annotated with HOMER
|
| |
|
| Submission date |
Sep 29, 2022 |
| Last update date |
Dec 22, 2022 |
| Contact name |
Sylvia N Michki |
| E-mail(s) |
michkin@chop.edu
|
| Organization name |
Children's Hospital of Philadelphia
|
| Department |
Pulmonary & Sleep Medicine
|
| Street address |
3615 Civic Center Blvd
|
| City |
Philadelphia |
| State/province |
PA |
| ZIP/Postal code |
19104 |
| Country |
USA |
| |
|
| Platform ID |
GPL19057 |
| Series (2) |
| GSE214488 |
DNA methyltransferase inhibition induces dynamic gene expression changes in lung CD4+ T cells of neonatal mice with E. coli pneumonia [RRBS] |
| GSE214490 |
DNA methyltransferase inhibition induces dynamic gene expression changes in lung CD4+ T cells of neonatal mice with E. coli pneumonia |
|
| Relations |
| BioSample |
SAMN31097705 |
| SRA |
SRX17757623 |
