|
| Status |
Public on Nov 10, 2023 |
| Title |
U937, SGF29 knockout, IGG [SGFKO_IGG] |
| Sample type |
SRA |
| |
|
| Source name |
U-937
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: U-937
cell type: Monocytes
chip antibody: Normal rabbit IgG (Cell Signaling Technology, Cat. No, 2729)
|
| Treatment protocol |
U937 cells were transduced with FLAG-tagged SGF29-wild-type or SGF29_D196R mutant overexpression constructs for samples: Mutant_F3_Flag, Mutant_H2_Flag, Mutant_H2_input, WT_F7_input, WT_F7_Flag, WT_G2_Flag. For the remaining samples, U937 cells were transduced with sgRNAs expressing a non-targeting control or targeting SGF29.
|
| Growth protocol |
Cells were cultured in RPMI-1640 medium supplemented with 10% heat-inactivated fetal bovine serum, 2mM Glutamine and 100 U/ml penicillin/streptomycin in a humidified atmosphere with 5% CO2 at 37C.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were fixed with 1% formaldehyde and chromatin was sheared using a Bioruptor™ (Diagenode Inc, NJ) in 15 cycles (each one in high-setting for 30 s on and 30 s off), at 4°C. Chromatin was immunoprecipitated using antibodies listed.
Library preparation on eluted DNA was performed using the NEBNext Ultra II DNA library prep kit for Illumina (E7645S and E7600S) as per the manufacturer’s protocol. DNA libraries were sequenced in paired-end 150 bp reads in a NovaSeq600 sequencer (Illumina, San Diego, CA) in Novogene Corporation (Sacramento, CA).
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Reads were trimmed using Cutadapt to remove Illumina Adaptors.
ChIP-seq reads were aligned to the UCSC hg38 genome using Bowtie2. Only uniquely mapping reads with at most two mismatches were retained.
Assembly: hg38
Supplementary files format and content: bigWig
|
| |
|
| Submission date |
Nov 10, 2022 |
| Last update date |
Nov 10, 2023 |
| Contact name |
Karina Ofelia Barbosa Guerra |
| E-mail(s) |
karinabarbosa4@gmail.com, adeshpande@sbpdiscovery.org
|
| Organization name |
Sanford Burnham Prebys Medical Discovery Institute
|
| Department |
Tumor Initiation & Maintenance Program
|
| Lab |
Deshpande
|
| Street address |
10901 North Torrey Pines Rd, Deshpande Lab RM6210B
|
| City |
La Jolla |
| State/province |
CA |
| ZIP/Postal code |
92037 |
| Country |
USA |
| |
|
| Platform ID |
GPL24676 |
| Series (2) |
| GSE217777 |
Mapping of genome-wide histone modifications in SGF29 knockout vs NTC U937 AML cells. Mapping of binding of SGF29 and Tudor-domain mutant SGF29_D196R by FLAG ChIP [ChIP-seq SGF29] |
| GSE217829 |
Epigenetic regulator landscape of HOX/MEIS expression in AML |
|
| Relations |
| BioSample |
SAMN31687162 |
| SRA |
SRX18235723 |
