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Status |
Public on Feb 19, 2019 |
Title |
CEBPa_ChIP-seq-input |
Sample type |
SRA |
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Source name |
Myeloblast
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Organism |
Homo sapiens |
Characteristics |
cell type: leukemic cell line with an 8;21 chromosome translocation cell line: Kasumi-1 passages: 4-5 passages chip antibody: none
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Growth protocol |
Kasumi-1 cells were cultured in RPMI 1640 Medium (Gibco) supplemented with 10% fetal bovine serum (FBS), 50 U/ml penicillin and 50 μg/ml streptomycin.
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Extracted molecule |
genomic DNA |
Extraction protocol |
At 4 days after retrovirus infection of MIGR1 and CEBPa, GFP+ Kasumi-1 cells were harvested by flow sorting and RNA was extracted with TRIzol Reagent (Invitrogen). (RNA-seq) At 3 days after retrovirus infection of CEBPa, GFP+ Kasumi-1 cells were sorted by BD FACSARIA III through FITC channel. Then they were crosslinked with 1% formaldehyde for 10 mins and then stopped by 125 mM Glycine. After lysis and sonication, 3 μg of HA-Tag (C29F4) Rabbit mAb (CST #3724) was incubated with chromatin sample overnight at 4 ℃, and 20μl protein A/G beads (Smart lifesciences SA032005) were used for immunoprecipitation. Finally, DNA were purified with PCR recovery kit (QIAGEN #28006).(ChIP-seq) Libraries were generated using the TruSeq RNA Sample Preparation Kit (Illumina #RS-122-2001) and sequenced with Illumina HiSeq2500.(RNA-seq) Library preparation was according to the manufacture’s guidelines (KAPA Biosystems KK8503) and sequencing procedures were carried out according to Illumina protocols with minor modifications (Illumina, San Diego).(ChIP-seq)
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Library strategy |
ChIP-Seq |
Library source |
genomic |
Library selection |
ChIP |
Instrument model |
Illumina HiSeq 2500 |
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Description |
ChIP-seq input
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Data processing |
Raw reads were filtered by Seqtk(remove adapters, length less than 25 reads, ribosome RNA, Qual < 20 reads), clean sequenced reads were alignmented to hg38 by TopHat(2.0.9), allow2 mismatches and multihits <=2 per read.(RNA-seq) Aligned reads were extracted by Htseq(0.9.1) with default parameters and normalized with TMM(trimmed mean of M values) method, FPKM were calculated by perl script.(RNA-seq) Raw reads were filtered by Seqtk(remove adapters, length less than 25 reads, Qual < 20 reads), clean reads were alignmented to hg19 by bowtie2(2.2.9) with parameters: -N 1 -p5.(ChIP-seq) Peaks were called by macs2(2.1.1.20160309) callpeaks algorithm with default set. BigWig files were generated by macs2 bdgcmp algorithm with default set.(ChIP-seq) Genome_build: hg19 for ChIP-seq, hg38 for RNA-seq Supplementary_files_format_and_content: FPKM files were calculated by definition.(RNA-seq) Supplementary_files_format_and_content: BigWig files were generated by macs2 bdgcmp algorithm with default set.(ChIP-seq)
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Submission date |
May 18, 2018 |
Last update date |
Feb 19, 2019 |
Contact name |
Chun-hui Xu |
E-mail(s) |
xuch@sibs.ac.cn
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Organization name |
Shanghai Institute of Hematology, Rui Jin Hospital, Shanghai Jiao Tong University School of Medicine
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Department |
State Key Laboratory of Medical Genomics
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Street address |
197 Ruijin Road II
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City |
Shanghai |
State/province |
Shanghai |
ZIP/Postal code |
200025 |
Country |
China |
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Platform ID |
GPL16791 |
Series (1) |
GSE114642 |
Destabilization of AETFC through C/EBPalpha-mediated repression of LYL1 contributes to t(8;21) leukemic cell differentiation |
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Relations |
BioSample |
SAMN09223821 |
SRA |
SRX4099646 |
Supplementary data files not provided |
SRA Run Selector |
Raw data are available in SRA |
Processed data not applicable for this record |
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