|
| Status |
Public on Jun 22, 2020 |
| Title |
RNA-seq_rsc_siCtcf_1 |
| Sample type |
SRA |
| |
|
| Source name |
rat Schwann cell
|
| Organism |
Rattus norvegicus |
| Characteristics |
tissue: Schwann cell
genotype: siCtcf
developmental stage: differentiation for 9h
|
| Growth protocol |
RNA from control and Ctcf mutant sciatic nerves were extracted using TRIZOL (Life Technologies) followed by purification using an RNeasy Mini Kit (Qiagen).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA: RNA from control and Ctcf deficient sciatic nerves or rat Schwann cells were extracted using TRIZOL (Life Technologies) followed by purification using an RNeasy Mini Kit (Qiagen).
RNA-seq libraries were prepared using Illumina RNA-Seq Preparation Kit.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
siCtcf vs siControl gene_rep_matix_anno_diff.txt.gz
|
| Data processing |
Illumina Casava software used for basecalling.
Sequenced reads were trimmed for adaptor sequence.
RNA-seq: Reads mapped to mm10 or rn5 whole genome by Tophat with default options.
RNA-seq for mouse nerve: DESeq2 was used to generate normalized read counts, and to identify differentially expressed genes between the different comparison groups; RNA-seq for RSCs: Fragment Per Kilobase of exon per Megabase of library size (FPKM) were calculated using Cufflinks with default options. Outputs from Cufflinks are provided as supplementary files as a tab-delimited text file.
Genome_build: RNA-seq for mouse nerve: mm10; RNA-seq for RSCs: rn5
Supplementary_files_format_and_content: tab-delimited text file, contain the estimated expression values produced by Cufflinks and Deseq;
|
| |
|
| Submission date |
Sep 30, 2019 |
| Last update date |
Jun 22, 2020 |
| Contact name |
Richard Lu |
| Organization name |
Cincinnati Children's Hospital Medical Center
|
| Department |
CBDI
|
| Lab |
Lu Lab,T6.525
|
| Street address |
3333 Burnet Ave
|
| City |
Cincinnati |
| State/province |
OH |
| ZIP/Postal code |
45229 |
| Country |
USA |
| |
|
| Platform ID |
GPL18694 |
| Series (1) |
| GSE138117 |
CTCF-dependent chromatin architecture and SUZ12/PRC2 complex recruitment are required for peripheral myelination and repair |
|
| Relations |
| BioSample |
SAMN12873009 |
| SRA |
SRX6922970 |
