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Sample GSM6783626 Query DataSets for GSM6783626
Status Public on Dec 04, 2022
Title CRISPR RNA-seq from K562 (ENCLB230CRI)
Sample type SRA
 
Source name Homo sapiens K562 cell line genetically modified (deletion) using CRISPR targeting H. sapiens RPUSD2
Organism Homo sapiens
Characteristics antibody: SKIV2L2
line: K562
biomaterial_type: cell line
description: RNA-seq on K562 cells treated with a CRISPR gRNA against SKIV2L2. (SKIV2L2-BGKcLV33-9)
biosample encode accession: ENCBS383XHL (SAMN31998094)
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: ENCBS383XHL at ENCODE; https://www.encodeproject.org/ENCBS383XHL/
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/35af20d5-0e82-4f0b-81f5-176ba4ea0952/@@download/attachment/L-SKIV2L2-BGKcLV33-9.pdf
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Description https://www.encodeproject.org/experiments/ENCSR300UBK/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with a CRISPR gRNA against SKIV2L2. (SKIV2L2-BGKcLV33)
experiment encode accession: ENCSR300UBK
assay title: CRISPR RNA-seq
assembly: GRCh38
possible controls: ENCSR271ZAB
encode release date: 2022-10-27
lab: Brenton Graveley, UConn
library encode accession: ENCLB230CRI
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)
GSE220015 CRISPR RNA-seq from K562 (ENCSR300UBK)
Relations
BioSample SAMN31998094
SRA SRX18486486
Named Annotation GSM6783626_ENCFF741UQM_plus_strand_signal_of_all_reads_GRCh38.bigWig
Named Annotation GSM6783626_ENCFF802EJA_minus_strand_signal_of_unique_reads_GRCh38.bigWig
Named Annotation GSM6783626_ENCFF720AZQ_minus_strand_signal_of_all_reads_GRCh38.bigWig
Named Annotation GSM6783626_ENCFF157OWJ_plus_strand_signal_of_unique_reads_GRCh38.bigWig

Supplementary file Size Download File type/resource
GSM6783626_ENCFF157OWJ_plus_strand_signal_of_unique_reads_GRCh38.bigWig 147.7 Mb (ftp)(http) BIGWIG
GSM6783626_ENCFF620YRH_gene_quantifications_GRCh38.tsv.gz 3.1 Mb (ftp)(http) TSV
GSM6783626_ENCFF720AZQ_minus_strand_signal_of_all_reads_GRCh38.bigWig 161.0 Mb (ftp)(http) BIGWIG
GSM6783626_ENCFF741UQM_plus_strand_signal_of_all_reads_GRCh38.bigWig 163.5 Mb (ftp)(http) BIGWIG
GSM6783626_ENCFF749ZNK_transcript_quantifications_GRCh38.tsv.gz 6.3 Mb (ftp)(http) TSV
GSM6783626_ENCFF802EJA_minus_strand_signal_of_unique_reads_GRCh38.bigWig 144.1 Mb (ftp)(http) BIGWIG
GSM6783626_ENCFF860KZW_transcript_quantifications_GRCh38.tsv.gz 9.8 Mb (ftp)(http) TSV
GSM6783626_ENCLB230CRI_README.txt.gz 824 b (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
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