|
| Status |
Public on Dec 21, 2015 |
| Title |
G34_DDX5Tko_Th17_ChIPseqDDX5 |
| Sample type |
SRA |
| |
|
| Source name |
In vitro Th17
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
cell type: T cell
age: 6-8wks
genotype: DDX5fl/fl, CD4Cre+
chip antibody: goat anti-DDX5
chip antibody vendor: Abcam
chip antibody cat. #: ab10261
chip antibody lot#: GR101334-5
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Total and IP enriched sonicated chromatin from cultured Th17 cells were harvested using Qiagen PCR purification kit.
ChIP-seq libraries were prepared for sequencing using standard Illumina protocols. 1% PhiX spiked in during the sequencing process and that allows us to calculate QC metrics for each lane and determine if poor performance is library or sequencer related.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using Bowtie
Peaks from the merged datasets were called using MACS.
Genome_build: mm10
Supplementary_files_format_and_content: BED file from MACS peak called.
|
| |
|
| Submission date |
Oct 11, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Wendy Huang |
| E-mail(s) |
Wendy.Huang@med.nyu.edu
|
| Organization name |
NYU School of Medicine
|
| Lab |
Littman Lab
|
| Street address |
540 First Ave Skirball 2-14
|
| City |
New York |
| ZIP/Postal code |
10016 |
| Country |
USA |
| |
|
| Platform ID |
GPL17021 |
| Series (2) |
| GSE70110 |
DDX5 and its associated lncRNA Rmrp modulate Th17 cell effector functions |
| GSE73913 |
Next Generation Sequencing Facilitates Quantitative Analysis of chromatin loci bound by DDX5 in cultured T helper 17 cell [ChIP-Seq] |
|
| Relations |
| SRA |
SRX1328055 |
| BioSample |
SAMN04160357 |
