|
| Status |
Public on Apr 24, 2022 |
| Title |
Ctr1_rep2_LCL_Runx3 |
| Sample type |
SRA |
| |
|
| Source name |
human lymphoblastoid cell line
|
| Organism |
Homo sapiens |
| Characteristics |
phenotype: unaffected
antibody: Runx3 (39301Active motif + 653604 BioLegend)
crosslinking: two steps cross-linking
|
| Growth protocol |
LCLs derived from ATR-X patients and healthy controls were incubated with RPMI medium supplemented with 15% FCS, 1% PenStrep and 1% glutamine at 37°C and 5% CO2.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
108 cells were crosslinked with 2 mM EGS for 45 minuntes and 1% FA for 20 minutes (ATRX) or 2mM DSG for 30 minutes and 1% FA for 30 minutes (Runx3). Cells were lysed and sonicated on the Covaris to give fragments of 100-300bp. Immunoprecipitation was performed by incubation of diluted chromatin overnight.
NEBNext Ultra II DNA Library Prep kit for Illumina (New England Biolabs).
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
Genome-wide library of Immunoprecipitated fragments
|
| Data processing |
Mapping : bowtie2, hg19
For un-mapping reads : trimming adaptors trim_galore, combining overlapping R1-R2 reads : flash
Combining trimmed+flashed and originally mapped reads, mapping again with bowtie2, hg19
Removing read pairs overlapping Blacklisted regions
Removing duplicates : samtools rmdup
Reconstructing sequenced fragments from R1+R2 read pairs ( bedtools bedpe | cut -f 1,2,6) - for visualisation
Pileup of fragments (bedtools genomecov -counts)
Generating bigwig tracks
Genome_build: hg19
Supplementary_files_format_and_content: bigWig of filtered fragments
|
| |
|
| Submission date |
Jan 09, 2022 |
| Last update date |
Apr 24, 2022 |
| Contact name |
Julia Truch |
| Organization name |
University of Oxford
|
| Department |
RDM - WIMM
|
| Lab |
GIBBONS/HIGGS
|
| Street address |
John Radcliffe Hospital, Headley Way, Headington
|
| City |
Oxford |
| ZIP/Postal code |
Oxford OX3 9DS |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL18573 |
| Series (1) |
| GSE193310 |
Two steps cross-linking LCL ChIP-seq |
|
| Relations |
| BioSample |
SAMN24776450 |
| SRA |
SRX13681306 |
