|
| Status |
Public on Mar 06, 2017 |
| Title |
CD34- cells-replicate 2-control |
| Sample type |
SRA |
| |
|
| Source name |
thymus
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: CD34-
replicate: 2
chip antibody: Isotype control
|
| Treatment protocol |
CD34+ and CD34- cells were isolated from human thymuses using the magnetic activated cell sorting (MACS) system. The CD34+ fraction showed >85% purity for CD34+ cells when measured by FACS. Two biological replicates were sequenced for each cell type. One replicate was derived from cells pooled from two thymuses. The other replicate was derived from cells from a separate thymus.
|
| Growth protocol |
CD34+ and CD34- cells were isolated from human thymuses using the magnetic activated cell sorting (MACS) system. The CD34+ fraction showed >85% purity for CD34+ cells when measured by FACS. Two biological replicates were sequenced for each cell type. One replicate was derived from cells pooled from two thymuses. The other replicate was derived from cells from a separate thymus.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
CD34+ (19-29×106 cells) or CD34- (60×106 cells) cells were treated with 1% formaldehyde for 10 minutes, which was followed by chromatin shearing with micrococcal nuclease to an average size of 150 base pairs. An aliquot of precleared chromatin was incubated with 1µg of anti-Bcl11b (IP) or 1µg of isotype control (control) antibody (antibodies from Cell Signaling) followed by hybridization to 30μl of Protein G Magnetic Beads for 3 hours. The protein-DNA complexes were eluted, and incubated with proteinase K to digest protein. The eluate was reverse crosslinked by incubation at 65°C for 2 hours. DNA was purified with a DNA purification kit (Cell Signaling).
Libraries were made with the Next Ultra™ DNA Library Prep Kit (NEB) (input=5 ng of ChIP DNA)
Libraries were sequenced on Illumina Nextseq500 (paired end 75 base pair sequencing)
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Read alignment: Bowtie2 (version 2.2.6) was used to align reads to the human genome (hg 19).
Peak calling: MACS2 version 2.1.0 (BAMPE mode, default q value cutoff of 0.01 ), peaks for each IP sample called relative to its corresponding control. Reads with a mapping quality below 30 were removed prior to inputting reads into MACS2
Genome_build: hg19
Supplementary_files_format_and_content: peak
|
| |
|
| Submission date |
Jul 21, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
chintan parekh |
| E-mail(s) |
cparekh@chla.usc.edu
|
| Organization name |
Children's Hospital Los Angeles
|
| Department |
Pediatrics
|
| Street address |
4650 sunset blvd, mail stop 54
|
| City |
Los Angeles |
| State/province |
California |
| ZIP/Postal code |
90027 |
| Country |
USA |
| |
|
| Platform ID |
GPL18573 |
| Series (2) |
| GSE84677 |
BCL11B DNA binding sites in progenitor and differentiated populations in the human thymus |
| GSE84678 |
BCL11B |
|
| Relations |
| BioSample |
SAMN05426692 |
| SRA |
SRX1968079 |
