|
| Status |
Public on Feb 14, 2018 |
| Title |
PITX1_ChIPseq_Rep1 |
| Sample type |
SRA |
| |
|
| Source name |
embryonic hindlimb tissue
|
| Organism |
Anolis carolinensis |
| Characteristics |
developmental stage: stage 6-7
antibody: Pitx1(Santa Cruz, sc-18922X, Lot G0105)
tissue: hindlimb
|
| Growth protocol |
Hindlimbs were collected from stage 6-7 Anolis carolinensis embryos.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Lysates were clarified from sonicated hindlimb tissues and PITX1-DNA complexes were isolated with antibody.
Libraries were prepared according to instructions accompanying the NEBNext Ultra DNA Library Prep Kit (NEB #E6240S/L). Libraries were sequenced on the HiSeq platform.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Sequencing read quality was evaluated using FastQC (version 0.5.1)
ChIP-seq reads were aligned to the Anolis carolinensis genome (anoCar2) using bowtie (version 0.12.8)
Peaks were identified using MACS2 with default parameters except for the effective genome size set for lizard (anoCar2)
Genome_build: anoCar2
Supplementary_files_format_and_content: Bigwig files were converted from bedGraph files generated by MACS2
|
| |
|
| Submission date |
Sep 29, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Jialiang Wang |
| E-mail(s) |
jialiang.wang@utsouthwestern.edu
|
| Organization name |
University of Texas Southwestern Medical Center
|
| Street address |
5323 Harry Hines Blvd
|
| City |
Dallas |
| State/province |
TX |
| ZIP/Postal code |
75390 |
| Country |
USA |
| |
|
| Platform ID |
GPL15001 |
| Series (2) |
| GSE104457 |
PITX1 Promotes Chondrogenesis and Myogenesis in Mouse Hindlimbs Through Conserved Regulatory Targets [ChIP-Seq] |
| GSE104460 |
PITX1 Promotes Chondrogenesis and Myogenesis in Mouse Hindlimbs Through Conserved Regulatory Targets |
|
| Relations |
| BioSample |
SAMN07722630 |
| SRA |
SRX3234604 |
