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Sample GSM6783623 Query DataSets for GSM6783623
Status Public on Dec 04, 2022
Title CRISPR RNA-seq from K562 (ENCLB633OCK)
Sample type SRA
 
Source name Homo sapiens K562 cell line genetically modified (deletion) using CRISPR targeting H. sapiens DDX18
Organism Homo sapiens
Characteristics antibody: DDX18
line: K562
biomaterial_type: cell line
description: RNA-seq on K562 cells treated with a CRISPR gRNA against DDX18. (DDX18-BGKcLV28-72)
biosample encode accession: ENCBS515ZUG (SAMN31998231)
organism: Homo sapiens
Sex: female
health state: chronic myelogenous leukemia (CML)
dev stage: adult
age: 53 year
donor_id: ENCDO000AAD
lab: Brenton Graveley, UConn
source: ATCC
link: ENCBS515ZUG at ENCODE; https://www.encodeproject.org/ENCBS515ZUG/
link: Derived from ENCODE donor ENCDO000AAD; https://www.encodeproject.org/ENCDO000AAD/
Extracted molecule total RNA
Extraction protocol extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/19a43854-2f20-471f-8977-74f8f5dd8ca2/@@download/attachment/L-DDX18-BGKcLV28-72.pdf
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Description https://www.encodeproject.org/experiments/ENCSR300LXO/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against DDX18. (DDX18-BGKcLV28)
experiment encode accession: ENCSR300LXO
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR220DTX
encode release date: 2021-11-19
lab: Brenton Graveley, UConn
library encode accession: ENCLB633OCK
fragmentation methods: chemical (Illumina TruSeq)
size range: >200
spikeins used: Ambion mix 1 spike-ins
Data processing See GSM*_README.txt supplementary file linked below
 
Submission date Dec 03, 2022
Last update date Jan 20, 2023
Contact name ENCODE DCC
E-mail(s) encode-help@lists.stanford.edu
Organization name ENCODE DCC
Street address 300 Pasteur Dr
City Stanford
State/province CA
ZIP/Postal code 94305-5120
Country USA
 
Platform ID GPL24676
Series (1)
GSE220014 CRISPR RNA-seq from K562 (ENCSR300LXO)
Relations
BioSample SAMN31998231
SRA SRX18486483
Named Annotation GSM6783623_ENCFF915VWU_minus_strand_signal_of_all_reads_GRCh38.bigWig
Named Annotation GSM6783623_ENCFF447HDL_plus_strand_signal_of_all_reads_GRCh38.bigWig
Named Annotation GSM6783623_ENCFF665WUW_plus_strand_signal_of_unique_reads_GRCh38.bigWig
Named Annotation GSM6783623_ENCFF709LER_minus_strand_signal_of_unique_reads_GRCh38.bigWig

Supplementary file Size Download File type/resource
GSM6783623_ENCFF404MXR_transcript_quantifications_GRCh38.tsv.gz 6.3 Mb (ftp)(http) TSV
GSM6783623_ENCFF447HDL_plus_strand_signal_of_all_reads_GRCh38.bigWig 133.1 Mb (ftp)(http) BIGWIG
GSM6783623_ENCFF515MXL_gene_quantifications_GRCh38.tsv.gz 3.1 Mb (ftp)(http) TSV
GSM6783623_ENCFF665WUW_plus_strand_signal_of_unique_reads_GRCh38.bigWig 121.1 Mb (ftp)(http) BIGWIG
GSM6783623_ENCFF684AXS_transcript_quantifications_GRCh38.tsv.gz 9.8 Mb (ftp)(http) TSV
GSM6783623_ENCFF709LER_minus_strand_signal_of_unique_reads_GRCh38.bigWig 117.6 Mb (ftp)(http) BIGWIG
GSM6783623_ENCFF915VWU_minus_strand_signal_of_all_reads_GRCh38.bigWig 130.4 Mb (ftp)(http) BIGWIG
GSM6783623_ENCLB633OCK_README.txt.gz 825 b (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
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