|
| Status |
Public on Jun 12, 2017 |
| Title |
MEF_NT_K4d_BrUTP_1 |
| Sample type |
SRA |
| |
|
| Source name |
MEF transplanted to Xenopus oocyte injected with K4d and with BrUTP
|
| Organisms |
Xenopus laevis; Mus musculus |
| Characteristics |
pairing of samples: Group1
transferred nucleus/sample type: p53minus_ MEF
starting material: pool of 16 oocytes
developmental stage/condition: stage 5-6 xenopus Nuclear transfer oocytes
antibody: anti-BrdUTP (Sc32323AC, Santa Cruz Biotechnology Inc)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA extractions were performed using Qiagen RNeasy Mini kit (Qiagen, 74106) according to the manufacturer's protocol including the on column DNAse step. Illumina TruSeq RNA sample prep kit for RNA-seq.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
immunoprecipitated RNA
|
| Data processing |
fastq file processed by filering out low quality reads (<Q20) and llow quality bases (<Q20) with sickle. Adaptors were removed with cutadapt 1.0.
RNA-seq data have been aligned to mus musculus mm9 and X. Laevis genome 6.1 background genome using TopHat 2.0.6
ChIP-seq data have been aligned to X. Laevis genome 6.1 mus musculus mm9 and X. Laevis genome 6.1 background genome using BWA 0.6.2 with default options. Duplicate reads were then removed
Differential analysis was conducted using EdgeR package
Genome_build: mus musculus mm9 and X. Laevis genome 6.1
Supplementary_files_format_and_content: text files contain RPKMs
Supplementary_files_format_and_content: bw files contain coverage across genome binned in 50bp windows
|
| |
|
| Submission date |
Oct 12, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Charles Bradshaw |
| Organization name |
University of Cambridge
|
| Department |
Gurdon Institute
|
| Street address |
Tennis Court Road
|
| City |
Cambridge |
| ZIP/Postal code |
CB2 1QN |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL22553 |
| Series (1) |
| GSE87872 |
Gene resistance to transcriptional reprogramming following nuclear transfer is directly mediated by multiple chromatin repressive pathways |
|
| Relations |
| BioSample |
SAMN05900868 |
| SRA |
SRX2240132 |
