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Sample GSM6213944 Query DataSets for GSM6213944
Status Public on Jun 30, 2023
Title MEFs, NELFB-AID, EV, +IAA, spike-in, Pol II ChIP-seq, biol rep 2
Sample type SRA
 
Source name Embryos
Organism Mus musculus
Characteristics tissue: Embryos
cell line: Mouse Embryonic Fibroblasts (MEFs)
cell type: Fibroblasts
chip antibody: Pol II (8wg16, Santa Cruz #56767)
genotype: Nelfb -/-; NELFB-AID
treatment: pLenti-NELFB-AID; pCDH-osTIR1-mCherry; Ad-Cre; single clone isolation; pLenti-EV; +IAA; Spike-in; Pol II ChIP
Growth protocol 10% FBS in DMEM
Extracted molecule genomic DNA
Extraction protocol Cells were treated with IAA at 0.5mM for 6 hours, if indicated, and then fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was fragmented with micrococcal nuclease and immunoprecipitated with Pol II or flag antibodies.
ChIP-seq libraries were prepared using the KAPA Hyperprep Library Preparation Kit complemented with Roche SeqCap Adapter Kit A. Post amplification libraries were size selected at 0.7-0.9X using Kapa cleanup beads. Libraries were validated using the Agilent High Sensitivity DNA Kit.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina NextSeq 500
 
Data processing Raw ChIP-seq data in FASTQ format was aligned to mm10 reference genome using bowtie2
The Sequence Alignment Map (SAM) file was converted to a Binary Alignment Map (BAM) file, and then sorted by Samtools. Alignments with MAPQ score smaller than 30 were skipped.
The coverage (the number of reads per bin) track was generated by deepTools. The size of each bin was set at 1bp and the coverage was normalized by Reads Per Kilobase per Million mapped reads (RPKM).
Scores for each gene were calculated by computeMatrix command. The gene bodies were scaled to 3kb and the region between 1kb upstream to TSS and 1.5kb downstream of TES were included in the analysis.
Assembly: mm10
Supplementary files format and content: bigwig
 
Submission date Jun 06, 2022
Last update date Jun 30, 2023
Contact name Haihui Pan
E-mail(s) panh@email.gwu.edu
Organization name George Washington University
Department Biochemistry and Molecular Medicine
Street address 2121 I St NW
City Washington
State/province DC
ZIP/Postal code 20052
Country USA
 
Platform ID GPL19057
Series (1)
GSE205504 Essential Signaling Function of Cytoplasmic NELFB Independent of RNA Polymerase II Pausing [ChIP-seq]
Relations
BioSample SAMN28869516
SRA SRX15596431

Supplementary file Size Download File type/resource
GSM6213944_EV2.bw 207.1 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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