|
| Status |
Public on Jul 29, 2016 |
| Title |
mut 2 |
| Sample type |
SRA |
| |
|
| Source name |
CD34+ hematopoietic stem cells
|
| Organism |
Homo sapiens |
| Characteristics |
source: peripheral blood mobilized stem cells
passages: primary stem cells cultured for 14 days
antibody: anti-FLAG M2 (Sigma-Aldrich, Catalog no. F3165)
transduction: lentivirus expressing FLAG-tagged mutant BCL11B and GFP
|
| Treatment protocol |
Transduced with lentivirus
|
| Growth protocol |
Grown in X-vivo 15 medium, supplemented with human SCF, Flt3L, TPO and IL-3 for 14 days
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Diagenode ChIP-seq kit
University of California, Davis Genomics Core
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
Mut2_vs_GFP2.bed
|
| Data processing |
FASTQC (check quality) 0.63
FAST groomer 1.04
BWA for illumina (MAP the reads to the genome) 1.2.3
MACS2 callpeak (Peak identification: Enrichement fold 2.5, FDR:0.05) 2.1.0.20151222.0
IDR (To identified peaks between replicates, FDR:0.05) 2012
Genome_build: hg38, Dec 2013
|
| |
|
| Submission date |
Jul 28, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Divya Punwani |
| E-mail(s) |
divya.punwani@ucsf.edu
|
| Phone |
4154763674
|
| Organization name |
University of California San Francisco
|
| Department |
Pediatrics
|
| Street address |
555 Mission bay blvd south
|
| City |
San Francisco |
| State/province |
CA |
| ZIP/Postal code |
94158 |
| Country |
USA |
| |
|
| Platform ID |
GPL20301 |
| Series (1) |
| GSE84941 |
Bcl11b defect in a human severe combined immunodeficiency with multisystem anomalies |
|
| Relations |
| BioSample |
SAMN05461987 |
| SRA |
SRX1986464 |
