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Sample GSM5695521 Query DataSets for GSM5695521
Status Public on Oct 02, 2023
Title Z1_shZ1
Sample type SRA
 
Source name HeLa cells
Organism Homo sapiens
Characteristics cell line: HeLa
treatment: shRNA ZFC3H1
passages: 10-25
chip antibody: anti-ZFC3H1 (Bethyl A301-457A)
Treatment protocol Lentiviral particles allowing expression of shRNAs were added to the medium of cells for 5 days.
Growth protocol HeLa cells were routinely cultured in DMEM medium (Sigma-Aldrich) supplemented with FCS 10% and penicillin/streptomycin.
Extracted molecule genomic DNA
Extraction protocol ChIP experiments were performed in HeLa cells using the ChIP IP High Sensitivity (Active Motif 53040).
ChIP-seq libraries were constructed using the Next Gen DNA Library Kit (Active Motif 53216 and 53264).
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina NextSeq 500
 
Description shZ1_IP_Z1
ChIP-seq anti-ZFC3H1 (Bethyl A301-457A)
Data processing Raw reads quality control performed with Fastqc (version 0.11.5).
Reads alignment with BWA (0.7.10) on hg38 human genome version.
Bigwig files were generated using deeptools (3.2.0) bamCompare and normalized by the corresponding input using RPGC normalization.
Genome_build: hg38 (GRCh38)
Supplementary_files_format_and_content: bigwig files containing ChIP-seq coverage for each sample normalized by the corresponding input.
 
Submission date Nov 18, 2021
Last update date Oct 02, 2023
Contact name Rosemary Kiernan
Organization name UMR9002 CNRS-UM
Lab Gene Regulation lab
Street address 141 rue de la cardonille
City Montpellier
ZIP/Postal code 34396
Country France
 
Platform ID GPL18573
Series (1)
GSE189157 PAP-gamma associates with PAXT nuclear exosome to control the abundance of PROMPT ncRNAs
Relations
BioSample SAMN23286571
SRA SRX13169053

Supplementary file Size Download File type/resource
GSM5695521_shZ1_IP_Z1.RPGC.sinorm.bw 1.3 Gb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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