|
| Status |
Public on Nov 22, 2022 |
| Title |
EBF1-dTAG_N, 0h, rep3 |
| Sample type |
SRA |
| |
|
| Source name |
A-MuLV transformed pro-B cells
|
| Organism |
Mus musculus |
| Characteristics |
cell type: A-MuLV transformed pro-B cells
genotype: EBF1-dTAG_N
treatment: DMSO 6h
|
| Treatment protocol |
Cells were treated with dTAG-13 (final concentration 0.5 uM) or DMSO for 6 hours.
|
| Growth protocol |
Production of A-MuLV transformed cells with the replacement of endogenous EBF1 by exogenous modified genes was described in Boller et al. 2016. A-MuLV transformed cells were cultured in the RPMI 1640 medium with 10% FCS; 1x Penicillin-Streptomycin-Glutamine; 0.06 mM β-mercaptoethanol.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using the RNeasy Micro Kit (Qiagen) according to the manufacturer's instructions.
Illumina Stranded Total RNA Prep with Ribo-Zero Plus kit was used for library preparation according to the manufacturer's protocol.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
EBF1-dTAG_N_0h_rep3
exon_counts.tsv
gene_counts.tsv
DESeq2_results_Ex_In.csv
|
| Data processing |
Quality control and read mapping was done using snakePipes (v2.5.1), an automatic pipeline for analysis of deep sequencing data.
Reads were mapped to the mouse genome (GRCm38 – mm10) using STAR (v2.7.4a).
Reads were sorted and indexed using samtools (v1.10) and duplicates were removed by sambamba_markdup.
Coverage bigwig files were created using bamCoverage from deeptools (v3.3.2) with RPKM normalization.
The expression level of the annotated genes (GRCm38.p4) was calculated by featureCounts (subread v2.0.0). The exon_count.tsv was obtained using default settings, and the gene_count.tsv was obtained using "-O" and "-t" options. Intron counts were calculated as the difference between gene counts and exon counts for each gene.
The differential gene expression was analyzed using the DESeq2 package, for exons and introns separately. Genes with a q-value < 0.05 were considered significantly differentially expressed.
Assembly: mm10
Supplementary files format and content: Two raw count matrices (for exons and entire genes) obtained from featureCounts are provided in tab-delimited format (.tsv).
Supplementary files format and content: Two separate bigwig files (.bw) for forward and reverse strand are provided for each sample.
Supplementary files format and content: One table (.csv) with combined DESeq2 results for exons and introns.
|
| |
|
| Submission date |
Apr 20, 2022 |
| Last update date |
Nov 22, 2022 |
| Contact name |
Nikolay Zolotarev |
| E-mail(s) |
zolotarev@ie-freiburg.mpg.de
|
| Organization name |
Max Planck Institute of Immunobiology and Epigenetics
|
| Department |
Cellular and Molecular Immunology
|
| Lab |
Laboratory Rudolf Grosschedl
|
| Street address |
Stübeweg, 51
|
| City |
Freiburg |
| ZIP/Postal code |
79108 |
| Country |
Germany |
| |
|
| Platform ID |
GPL24247 |
| Series (2) |
| GSE201143 |
Changes in gene expression after EBF1 degradation |
| GSE201144 |
EBF1 degradation in B Cells |
|
| Relations |
| BioSample |
SAMN27671787 |
| SRA |
SRX14935584 |
