|
| Status |
Public on May 04, 2011 |
| Title |
TRF1 monoclonal ChIP BJ fibroblasts |
| Sample type |
SRA |
| |
|
| Source name |
Transformed BJ fibroblasts (SV40 largeT, hTERT, H-ras V12, according to Hahn et.al. Nature 1999)
|
| Organism |
Homo sapiens |
| Characteristics |
culture: confluent, not synchronized cells
chip antibody: TRF1 monoclonal
chip antibody provider: Abcam
chip antibody catalog: ab10579
|
| Growth protocol |
DMEM+10%SVF+Péni/Strepto, 37°C, 5%CO2, ambiant O2
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
ChIP protocol: 1% formaldehyde crosslink, DNA shearing by sonication in 1% SDS buffer, IP on proteinG sepharose beads in 0.1%SDS-1%Triton buffer, DNA purification by phenol-chloroforme extraction
ChIP_protocol_chromatin_amount: 175μg
ChIP_protocol_bead_type: Protein G Sepharose 4 Fast Flow, GE Healthcare
ChIP_protocol_bead_amount 0.25 mL
ChIP_protocol_antibody_amount25μg
Applied Biosystems SOLiD standard fragment library
barcoded fragment libraries were prepared with SOLiD™ Fragment Library Construction Kit using with SOLiD™ Fragment Library Barcoding Kit
Starting material 100 ng ChIP DNA
Libraries were size selected on agarose gels (150 to 200 nucleotides)
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
AB SOLiD System 3.0 |
| |
|
| Description |
TRF1 monoclonal ChIP BJ fibroblasts
bed files : SISSRs v1.4 peaks (pvalue=0.001 and 0.05) ; wig file: density graphs of raw signal (150bp)
|
| Data processing |
Reads matching have been performed using Corona SOLiD matching tool versus hg18 reference genome allowing up to 6 mismatchs. Conversion to .BED files have been done with match2bedFile_converter.pl script from SOLiD ChIP-Seq_Util_1.0.0 tool. Density graphs of raw signal (.wig files) have been generated by computing the start position of the reads in 150bp windows sliding by a 15bp step for uniquely placed reads, no more than 1 read per position for each strand, reads in both strands mixed, normalized to the total number of matched reads; printed if count >2. Peaks identification (.bed files) have been generated with SISSRs v1.4 software with .bed input uniquely aligned reads and parameters: proteinG IP as background, pvalue 0.001 or 0.05, no more than 1 read per position (-a), fragment length 150bp.
|
| |
|
| Submission date |
Dec 10, 2010 |
| Last update date |
May 15, 2019 |
| Contact name |
Kevin Lebrigand |
| Organization name |
IPMC/CNRS
|
| Lab |
Functional Genomics Platform of Nice-Sophia-Antipolis, France.
|
| Street address |
660 route des lucioles
|
| City |
Valbonne - Sophia-Antipolis |
| ZIP/Postal code |
06560 |
| Country |
France |
| |
|
| Platform ID |
GPL9442 |
| Series (1) |
| GSE26005 |
The human TTAGGG Repeat Factors 1 and 2 bind to a subset of interstitial telomeric sequences and satellite repeats |
|
| Relations |
| SRA |
SRX036542 |
| BioSample |
SAMN00188960 |
