|
| Status |
Public on Jan 01, 2017 |
| Title |
TenenLab_U937_ChIPseq_input |
| Sample type |
SRA |
| |
|
| Source name |
U937
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: U937
chip antibody: no antibody (input)
|
| Treatment protocol |
8.5x106 U937 cells were harvested, washed with ice-cold PBS and cross-linked with 1% formaldehyde (Sigma) for ten minutes at room temperature with gentle agitation. 2M glycine was added to quench the reaction. Cell pellets were obtained by 10 minutes of cold centrifugation at 2,000 rpm and lysed (50 mM HEPES pH7.5, 150 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate, 0.1% SDS + protease inhibitors (Complete mini catalog # 04693139001, Roche)). The solution was incubated at 4°C for 30 minutes. Cell pellets were collected by 10 minutes of centrifugation at 2,000 rpm at 4°C, resuspended in lysis buffer and sonicated in a Bioruptor Next Gen water bath sonicator (Diagenode) to 200-500bp. Further steps were all performed by Peconic LLC (USA).
|
| Growth protocol |
U937 cells were maintained in RPMI-1640 medium supplemented with 10% fetal bovine serum (FBS)
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Library contruction and sequencign were performed by Peconic LLC (USA)
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Data processing |
Images obtained from high throughput sequencing were processed using the Illumina pipeline to generate raw sequence files.
Mapping: reads were mapped on the human hg19 genome using bowtie2 (parameters: --very-sensitive)
Filtering: reads mapping multiple loci were removed by filtering out reads with MAPQ < 10 (using samtools view -q10)
Visualisation: reads pileup were computed and bigwig files were produced using HOMER (program makeUCSCfile, dewfault parameters)
Removing duplicated reads: for input sequencign, dulicated reads (ie possible pcr amplificatino artifact) were removed using samtools rmdup -s ; this was not done for ChIPexo, as we expect reads to stack at the exact locus of the crosslinking after exonuclease treatment
Genome_build: hg19
Supplementary_files_format_and_content: USCS bigwig format (binary track of pile up signal)
|
| |
|
| Submission date |
Jan 21, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
samuel Collombet |
| E-mail(s) |
samuelcollombet@gmail.com
|
| Organization name |
Ecole Normale Superieure
|
| Department |
Biology
|
| Lab |
Thieffry
|
| Street address |
46 rue d'Ulm
|
| City |
Paris |
| ZIP/Postal code |
75005 |
| Country |
France |
| |
|
| Platform ID |
GPL10999 |
| Series (1) |
| GSE65130 |
Znf143 binding sites in U937 cells by ChIPexo |
|
| Relations |
| BioSample |
SAMN03288892 |
| SRA |
SRX849030 |
