|
| Status |
Public on Nov 11, 2015 |
| Title |
MLXWT-H4AC1 |
| Sample type |
SRA |
| |
|
| Source name |
C2C12_MLXWT-H4AC
|
| Organism |
Mus musculus |
| Characteristics |
cell line: C2C12
cell type: myoblasts
transduced with: MLX WT
chip antibody: Rabbit Anti-acetyl-histone H4
chip antibody vendor: Millipore
chip antibody cat. #: 06-866
chip antibody lot #: 2586451
|
| Growth protocol |
C2C12 myoblasts were transducted by lentivirus constructs containing MLX-WT, MLX-DN sequence with empty vector (EV) and non-targetting shRNA controls.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
For ChIP-sequencing, libraries were prepared from 10 ng DNA using the NEB Next ChIP-Seq Library Prep Reagent Set for Illumina with NEB Next High-Fidelity 2x PCR Master Mix according to the manufacturer’s instructions (New England Biolabs) with the following modifications: a second 1:1 Ampure cleanup was added after adaptor ligation; the Ampure size selection step prior to PCR was eliminated; the 72C extension step of the PCR was lengthened to 45 s.
Completed libraries were analyzed for insert size distribution on a 2100 BioAnalyzer High Sensitivity kit (Agilent Technologies) or Caliper LabChip GX DNA High Sensitivity Reagent Kit (PerkinElmer) Libraries were quantified using the Quant-iT PicoGreen dsDNA assay (Life Technologies) and Kapa Library Quantificaiton kit (Kapa Biosystems) or low pass sequencing on a MiSeq nano kit (Illumina). Fifty cycle single end sequencing was performed on an Illumlina HiSeq 2500 for DNA obtained from MLX-WT and MLX-DN samples immunoprecipitated for acetylated histone H4 with three replicates for each sample including input chromatin as control.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer |
| |
|
| Description |
Histone H4 Acetylation mark in MLX WT sample
|
| Data processing |
Basecalls performed using CASAVA
BWA (version 0.5.9-r26-dev, default parameter) to align the reads to mouse genome mm9 (MGSCv37 from Sanger).
marked duplicated reads with Picard (version 1.65(1160)) with only non-duplicated reads kept by samtools (parameter “-q 1 -F 1024” version 0.1.18 (r982:295))
To quality control (QC) the data and estimate the fragment size, the non-duplicated version of SPP (version 1.11) has been used to draw cross-correlation with support of R (version 2.14.0) using the packages caTools (version 1.17) and bitops (version 1.0-6). All our data passed QC following ENCODE criterion. MACS2 ( version 2.0.9 20111102, nomodel with extsize defined as fragment size estimated above ) have been used to call peaks.
Genome_build: mm9
Supplementary_files_format_and_content: peak call files from MACS
|
| |
|
| Submission date |
Nov 04, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
David Finkelstein |
| E-mail(s) |
[email protected]
|
| Phone |
9014953931
|
| Organization name |
St Jude Children's Research Hospital
|
| Department |
Computational Biology
|
| Street address |
332 N. Lauderdale St.
|
| City |
Memphis |
| State/province |
TN |
| ZIP/Postal code |
38105 |
| Country |
USA |
| |
|
| Platform ID |
GPL9185 |
| Series (1) |
| GSE74678 |
The glucose-sensing transcription factor MLX promotes myogenesis via myokine signaling |
|
| Relations |
| BioSample |
SAMN04240364 |
| SRA |
SRX1418066 |
