|
| Status |
Public on Sep 08, 2020 |
| Title |
10M-Exp-Spleen-B-RNA |
| Sample type |
SRA |
| |
|
| Source name |
splenic B cells
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
cell type: splenic B cells
genotype: cTKO
Sex: M
|
| Extracted molecule |
total RNA |
| Extraction protocol |
5x10E5 B, and CD4+ and CD8+ T cells were sorted to Trizol by FACS.
paired-end RNA seq libraries were prepared from polyA-enriched RNA by GeneWiz (https://www.genewiz.com/)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
Sequencing and base calling was performed by GeneWiz (https://www.genewiz.com/)
Raw reads were subjected to adapter and quality trimming using bbduk.sh from BBTools.
RNA-seq reads were aligned to the mm10 genome assembly using STAR with default parameters
Aligned bam files were processed in R/Bioconductor using SummarizeOverlaps to summarize the bam for the intervals in TxDb.Mmusculus.UCSC.mm10.knownGene (exons by gene) generating a "summarized experiment".
The "summarized experiment" was analyzed using deseq2 with default parameters. Deseq2 results summary was used to generate a CSV of base mean expression, fold change and p-value comparing wildtype and h1cTKO;vav-iCre expression which was exported as a CSV.
Genome_build: mm10 (GENCODE Release M20 (GRCm38.p6))
Supplementary_files_format_and_content: Results of differential expression between WT and cTKO cells from DESeq2 in comma-separated file format
|
| |
|
| Submission date |
Nov 29, 2019 |
| Last update date |
Sep 08, 2020 |
| Contact name |
Boris Bartholdy |
| Organization name |
Albert Einstein College of Medicine
|
| Department |
Cell Biology
|
| Street address |
1300 Morris Park Ave
|
| City |
Bronx |
| State/province |
NY |
| ZIP/Postal code |
10461 |
| Country |
USA |
| |
|
| Platform ID |
GPL21103 |
| Series (2) |
| GSE141186 |
H1 linker histones regulate the balance of repressive and active chromatin domains via localized genomic compaction [RNA-seq] |
| GSE141187 |
H1 linker histones regulate the balance of repressive and active chromatin domains via localized genomic compaction |
|
| Relations |
| BioSample |
SAMN13429259 |
| SRA |
SRX7241815 |
