|
| Status |
Public on Dec 21, 2012 |
| Title |
CENP-A ChIPSeq_JT15 |
| Sample type |
SRA |
| |
|
| Source name |
C.albicans strain J191, IP
|
| Organism |
Candida albicans |
| Characteristics |
strain: J191
growth conditions: Log phase grown C. albicans cells
media: YPDU
protein: CENP-A/Cse4
chip antibody: Polyclonal anti-Cse4 antibodies (Sanyal K & Carbon J PNAS 99, 12969 - 12974 (2002))
|
| Treatment protocol |
None
|
| Growth protocol |
C. albicans cells were grown to log phase at 30oC
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Lysates were clarified from sonicated nuclei and CENPA-DNA complexes were isolated with antibody.
Libraries for multiplex ChIP Sequencing were constructed using NEXTflex™ ChIP-Seq Sample Preparation Kitprotocol outlined in “Preparing Samples for ChIP Sequencing of DNA” (BIOO Scientific# IP-5143-01). Briefly, DNA was subjected to a series of enzymatic reactions that repair frayed ends and phosphorylate the fragments. The end repaired fragments were subjected to two rounds of SPRI clean up with Agencourt AMPURE XP beads (Beckman Coulter #A63881) for size selection of DNA inserts between 300 to 400bp. The size selected fragments were adenylated with a single nucleotide 3'dATP overhang (BIOO Scientific# IP-5143-01) and adaptors were ligated (NEXT Flex adapters). The fragments with ligated adapters were enriched with 18 cycles of PCR. The prepared libraries were quantified using Qubit and validated for quality by running an aliquot on a High Sensitivity Bioanalyzer Chip (Agilent). Libraries were sequenced on the Illumina Genome Analyzer IIx (GAIIx) following the manufacturer's protocols.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Data processing |
Basecalls performed using OLB version 1.9.3, Demultiplexing and FASTQ conversion performed using CASAVA 1.7.0.
Raw data QC and adapter filtering performed using SeqQC_V2.1 internal software.
Chip Seq reads were aligned to C.albicans Assembly version 21 using bowtie-0.12.8 with the following parameters (-v(mismatch) 3 –best(best alignment) -m(Number of alignment) 1 ).
Alignment file to binary sorted alignment file performed using samtools-0.1.7a.
Binary alignment file to bed file conversion using BEDTools-Version-2.12.0. Bed to Peak calling performed using Homer v3.8.1 with the default parameters().
Genome_build: C.albicans Assembly version 21
Supplementary_files_format_and_content: .bed peak file generated using Homer v3.8.1.
|
| |
|
| Submission date |
Dec 13, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Kaustuv Sanyal |
| E-mail(s) |
sanyal@jncasr.ac.in
|
| Phone |
918022082878
|
| Organization name |
Jawaharlal Nehru Centre for Advanced Scientific Research
|
| Department |
Molecular Biology and Genetics Unit
|
| Lab |
Molecular Mycology Laboratory,
|
| Street address |
Jakkur
|
| City |
Bangalore |
| State/province |
Karnataka |
| ZIP/Postal code |
560064 |
| Country |
India |
| |
|
| Platform ID |
GPL15149 |
| Series (1) |
| GSE42907 |
To detect CENP-A enrichment on Chromosome 1,5 &7 in C. albicans centromere deleted clones |
|
| Relations |
| SRA |
SRX209808 |
| BioSample |
SAMN01831167 |
