|
| Status |
Public on Apr 16, 2015 |
| Title |
3xFN-Tel-TAL |
| Sample type |
SRA |
| |
|
| Source name |
Immunoprecipitants prepared from Ba/F3 expressing 3xFN-Tel-TAL
|
| Organism |
Mus musculus |
| Characteristics |
cell line: Ba/F3-derived cells
genotype: 3xFN-Tel-TAL
strain: C3H
chip antibody: anti-FLAG M2 Ab (Sigma-Aldrich)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
enChIP-RNA was harvested using Isogen II (Nippon Gene). Illumina TruSeq RNA Sample Prep Kit v2 was used with 60 ng of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina TruSeq RNA Preparation V2 Guide Rev. C.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina MiSeq |
| |
|
| Description |
The chromatin complexes derived from Ba/F3 cells expressing 3xFN-Tel-TAL are immunoprecipitated with anti-FLAG Ab.
|
| Data processing |
Illumina Casava1.8.2 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence using Cutadapt, and mapped to GRCm38/mm10 genes from Ensembl using blast with default parameters.
The genes for mapping contains both cDNA and ncRNA.
Reads per million mapped reads (RPM) were calculated against each gene. The number of reads falling in the genes were counted and normalized by total reads of the samples. The total reads were adjusted to a million.
Genome_build: GRCm38 (mm10)
Supplementary_files_format_and_content: tab-delimited text files include read count and RPM values for 3xFNLDD and 3xFN-Tel-TAL samples.
|
| |
|
| Submission date |
Aug 14, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Daisuke Okuzaki |
| E-mail(s) |
dokuzaki@biken.osaka-u.ac.jp
|
| Phone |
+81-6-6879-4935
|
| Organization name |
Osaka univ.
|
| Department |
Immunology Frontier Research Center
|
| Lab |
Human Immunology （Single Cell Genomics)
|
| Street address |
Yamadaoka 3-1
|
| City |
Suita |
| State/province |
Osaka |
| ZIP/Postal code |
565-0871 |
| Country |
Japan |
| |
|
| Platform ID |
GPL16417 |
| Series (1) |
| GSE60425 |
Identification of RNAs associated with telomeres by enChIP-RNA-Seq |
|
| Relations |
| BioSample |
SAMN02953963 |
| SRA |
SRX671566 |
