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Sample GSM1479568 Query DataSets for GSM1479568
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
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
BioSample SAMN02953963
SRA SRX671566

Supplementary file Size Download File type/resource
GSM1479568_3xFN-Tel-TAL.txt.gz 1.4 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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