|
| Status |
Public on Jul 08, 2024 |
| Title |
WT AIRE 4D6, no Dox ctrl, rep1 |
| Sample type |
SRA |
| |
|
| Source name |
4D6
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: 4D6
cell type: thymic epithelial cells
genotype: WT AIRE
treatment: no Dox ctrl
|
| Treatment protocol |
Dox-inducible AIRE-expressing 4D6 cells were cultured in the absence or presence of 1 µg/mL dox for 24 hrs.
|
| Growth protocol |
4D6 cells were maintained in RPMI supplemented with 10% FBS, 1% L-glutamine
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was immediately extracted by using Direct-zol RNA Miniprep Kit (Zymo Research, R2052) with DNase I digestion.
RNA-seq libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit (New England Biolabs, E7775S) with ribosomal RNA depletion using the NEBNext rRNA Depletion Kit v2 (New England Biolabs, E7405L).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
QC was performed on demultiplexed sequencing files using FASTQC (v0.11.3).
Sequencing reads were trimmed using Trimmomatic (v0.36) and aligned to reference genome (GRCh38 primary assembly, release v43) using STAR (v2.7.0a).
Read counting across genomic features was performed using featureCounts function within the Rsubread R package (v2.12.3).
Differential gene expression analysis was performed using the DEseq2 R package (v1.38.3) and visualized using the ggplot2 R package (v3.4.1).
Assembly: hg38
Supplementary files format and content: tab-delimited txt file includes raw counts
Supplementary files format and content: tab-delimited txt file includes normalized counts
|
| |
|
| Submission date |
Sep 22, 2023 |
| Last update date |
Jul 08, 2024 |
| Contact name |
Qianxia Zhang |
| E-mail(s) |
qianxia.zhang@childrens.harvard.edu
|
| Phone |
9018345955
|
| Organization name |
Boston Children's Hospital
|
| Street address |
3 Blackfan Circle, RM 3117.16
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02115 |
| Country |
USA |
| |
|
| Platform ID |
GPL24676 |
| Series (2) |
| GSE243822 |
Mechanism for controlled assembly of transcriptional condensates by Aire [RNA-seq] |
| GSE243825 |
Mechanism for controlled assembly of transcriptional condensates by Aire |
|
| Relations |
| BioSample |
SAMN37514869 |
| SRA |
SRX21863300 |
