|
| Status |
Public on Feb 23, 2021 |
| Title |
CTCF.Halo_24h_ChIPseq_Rep1 |
| Sample type |
SRA |
| |
|
| Source name |
CTCF-AID-HaloTag+TIR
|
| Organism |
Mus musculus |
| Characteristics |
cell type: ES-derived erythroid progenitor cells
strain: C57BL/6
chip antibody: Millipore 07-729
treatment: 24h auxin
|
| Treatment protocol |
Cells were treated with either auxin (1mM), Triptolide (1uMx5h) or DRB (75uMx7h). See Description column for Samples.
|
| Growth protocol |
G1E-ER4 (Weiss et al., 1997) derived single-cell clones were grown in IMDM+15% FBS, penicillin/streptomycin, kit ligand, monothioglycerol and Epoetin alpha in a standard tissue culture incubator at 37 degrees with 5% CO2 (as described in Weiss et al., 1997).
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Lysates were prepared from sonicated nuclei and histone-DNA complexes were isolated with indicated antibodies.
ChIP-seq libraries were prepared using Illumina’s TruSeq ChIP sample preparation kit (Illumina, catalog no. IP-202-1012) according to manufacturer’s specifications, with the addition of size selection (left side at 0.9x, right side at 0.6x) using SPRIselect beads (Beckman Coulter, catalog no. B23318). Library size was determined (average 351 bp, range 333-372 bp) using the Agilent Bioanalyzer 2100, followed by quantitation using real-time PCR using the KAPA Library Quant Kit for Illumina (KAPA Biosystems catalog no. KK4835). Libraries were then pooled and sequenced (1x75bp) on the Illumina NextSeq 500 platform according to manufacturer’s instructions. Bclfastq2 v 2.15.04 (default parameters) was used to convert reads to fastq.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
2786
|
| Data processing |
Bowtie 1.1.0 was used to align sequences (Langmead and Salzberg, 2012) to the mm9 reference genome. Reads with more than one mismatch or multiple alignments were excluded.
Significantly enriched regions were called using MACS2 version 2.1.0 (Y. Zhang et al., 2008) with the following parameters: P = 10−5, extsize = 300 and local lambda = 100,000 using whole-cell extract input controls.
Reads for the bigwigs were RPM normalized.
Genome_build: mm9
|
| |
|
| Submission date |
May 12, 2020 |
| Last update date |
Feb 24, 2021 |
| Contact name |
Jing Luan |
| E-mail(s) |
jluan@pennmedicine.upenn.edu
|
| Organization name |
University of Pennsylvania
|
| Street address |
3615 Civic Center Blvd, ARC 315
|
| City |
Philadelphia |
| ZIP/Postal code |
19103 |
| Country |
USA |
| |
|
| Platform ID |
GPL19057 |
| Series (2) |
| GSE150415 |
Distinct properties and functions of CTCF revealed by a rapidly inducible degron system [ChIP-Seq] |
| GSE150418 |
Distinct properties and functions of CTCF revealed by a rapidly inducible degron system |
|
| Relations |
| BioSample |
SAMN14905779 |
| SRA |
SRX8332843 |
