RIOK2 RNA-Seq in HepG2

General Information


RBP	RIOK2
Cell_Line	HepG2
Method	CRISPR
Exp_Name	RIOK2-BGHcLV32-HepG2
ENCODE_series_ID	ENCSR666QHG
Batch_ID	BGHcLV32
Pool ID	Pool-220331
Local_Set_Name	set52
ENCODE_KD_Exp_ID	ENCSR485ZHW
ENCODE_CN_Exp_ID	ENCSR911CLD
Rep1	RIOK2-BGHcLV32-33B
Rep2	RIOK2-BGHcLV32-34B
CN1	NT-BGHcLV32-1B
CN2	NT-BGHcLV32-2B
Rep1_qPCR	25.9
Rep2_qPCR	23.7
Rep1_WB	87.0
Rep2_WB	75.7
Antibody Cat#	A302-449A
Antibody Lot#	LOT #1
Antibody DCC ID	ENCAB828CEY
Status	Submitted
Project	ENCODE4
ID	940

Experiment Information (Status: Released)

	BGHcLV32-33	BGHcLV32-34
idx	1032	1033
TRCN#_or_BGC#	BGC#0000783	BGC#0000783
shRNA_or_gRNA_sequence	CATTTGTCAACCGATAGCCC	CATTTGTCAACCGATAGCCC
PAM	TGG	TGG
Name	RIOK2_96	RIOK2_96
Sample_ID	BGHcLV32-33	BGHcLV32-34
transduction_Date	10/28/21	10/28/21
days	D6	D6
RBP_name	RIOK2	RIOK2
qPCR_result	25.9	23.7
Ave_qPCR	24.8
RT-qPCR_primer-F	gccatgaaggaatttgccta
RT-qPCR_primer-R	ttccatgaccactgcatgac
protein_conc	3996	3988
WB_result	87.0	75.7
Ave_WB	81.4
WB_DONE_date	11/15/21	JESS
MW	63KD
IP
antibody_Cat#	A302-449A	LOT #1
Antibody DCC ID	ENCAB828CEY	8/4/22
submitted_to_DCC_date
Rep1_TPM	0	0
Rep2_TPM	0	0
Action	Ready	Ready
Library_start_date	2/9/22	2/9/22
repeat_library	02/14/22	02/14/22
Note
ID	7211	7212

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
RIOK2	Product_ID: A302-449A Lot_ID: 1 Source: Bethyl Labs Target Name: RIOK2-human

Experiment Status

	BGHcLV32-33	BGHcLV32-34
Sample_ID	BGHcLV32-33	BGHcLV32-34
Sample Name
Sample Name	RIOK2-BGHcLV32-33B	RIOK2-BGHcLV32-34B
RBP	RIOK2	RIOK2
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2022-10-28	2022-10-28
Project	ENCODE4	ENCODE4
Note
ID	10365	10366

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV32-33	BGHcLV32-33	BGHcLV32-34	BGHcLV32-34
Sample #	39	53	40	54
Sample Name	RIOK2-BGHcLV32-33	RIOK2-BGHcLV32-33B	RIOK2-BGHcLV32-34	RIOK2-BGHcLV32-34B
Sample_Name_Alias
Index Well Position	G05	E07	H05	F07
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2022-02-01	2022-02-15	2022-02-01	2022-02-15
Lib_ID	Lib-220201	Lib-220215	Lib-220201	Lib-220215
Tecan_Location
Tecan
Tecan_date
Size_bp		301		296
Peak_Molarity		70.30		62.80
libSampleQC_DNA_Well		DNA_Library_set52/set3/E12.png		DNA_Library_set52/set3/F12.png
RIN		9.7		9.8
libSample_RNA_Well		RNA_Library_set52/set2/C8.png		RNA_Library_set52/set2/D8.png
SampleQC_method		TapeStation_2022		TapeStation_2022
SampleQC_date		2022-02-16		2022-02-16
Sample_ID	BGHcLV32-33	BGHcLV32-33	BGHcLV32-34	BGHcLV32-34
RBP	RIOK2	RIOK2	RIOK2	RIOK2
Batch_ID	BGHcLV32	BGHcLV32	BGHcLV32	BGHcLV32
WB_result	87.000	87.000	75.700	75.700
Library Description	TruSeq mRNA	TruSeq mRNA	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix		B		B
Lib_Status	NotToSequence	SendToSequence	NotToSequence	SendToSequence
Project	ENCODE4	ENCODE4	ENCODE4	ENCODE4
ID	3216	3230	3217	3231

Sequencing Information

	BGHcLV32-33	BGHcLV32-34
Sample_ID	BGHcLV32-33	BGHcLV32-34
Sample Name	RIOK2-BGHcLV32-33B	RIOK2-BGHcLV32-34B
Pool ID	Pool-220331	Pool-220331
LocalServer_folder	set52	set52
total_reads	114,650,144	107,815,412
total_aligned_reads	102,537,458	93,743,350
unique_aligned_reads	96,519,690	88,170,320
percent_uniqueAligned	0.84186	0.81779
correlation_replicates	0.997501	0.997501
spikein_reads	21,478	12,842
percent_spikeins	0.00019	0.00012
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	2025	2026

Data Submission Information

	BGHcLV32-33	BGHcLV32-33	BGHcLV32-33	BGHcLV32-33	BGHcLV32-33	BGHcLV32-33	BGHcLV32-34	BGHcLV32-34	BGHcLV32-34	BGHcLV32-34
ENCODE_alias	brenton-graveley:RIOK2-BGHcLV32-B	brenton-graveley:RIOK2-BGHcLV32-33B	brenton-graveley:L-RIOK2-BGHcLV32-33B	brenton-graveley:RIOK2-BGHcLV32-33B_S51_L001_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:RIOK2-BGHcLV32-33B_S51_L001_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:RIOK2-BGHcLV32-HepG2	brenton-graveley:RIOK2-BGHcLV32-34B	brenton-graveley:L-RIOK2-BGHcLV32-34B	brenton-graveley:RIOK2-BGHcLV32-34B_S52_L001_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:RIOK2-BGHcLV32-34B_S52_L001_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR485ZHW	ENCBS188GNU	ENCLB319QXP	ENCFF219UFG	ENCFF193LZY	ENCSR666QHG	ENCBS628VDP	ENCLB241JQK	ENCFF844HDZ	ENCFF990QJB
object_type	experiment	biosample	library	file_fastq1	file_fastq2	gene_silencing_series	biosample	library	file_fastq1	file_fastq2
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHcLV32-33	BGHcLV32-33	BGHcLV32-33	BGHcLV32-33	BGHcLV32-33	BGHcLV32-33	BGHcLV32-34	BGHcLV32-34	BGHcLV32-34	BGHcLV32-34
Sample Name	RIOK2-BGHcLV32-33B	RIOK2-BGHcLV32-33B	RIOK2-BGHcLV32-33B	RIOK2-BGHcLV32-33B	RIOK2-BGHcLV32-33B	RIOK2-BGHcLV32-33B	RIOK2-BGHcLV32-34B	RIOK2-BGHcLV32-34B	RIOK2-BGHcLV32-34B	RIOK2-BGHcLV32-34B
Selected	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes
Status	Released	Released	Released	Released	Released	Released	Released	Released	Released	Released
Status_Date	2022-10-28	2022-10-28	2022-10-28	2022-10-28	2022-10-28	2022-10-28	2022-10-28	2022-10-28	2022-10-28	2022-10-28
Project	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4
		LV52_biosample_protocol	LV52_library_protocol				LV52_biosample_protocol	LV52_library_protocol
protocol_URL		RIOK2-BGHcLV32-33B.pdf	L-RIOK2-BGHcLV32-33B.pdf				RIOK2-BGHcLV32-34B.pdf	L-RIOK2-BGHcLV32-34B.pdf
ID	7469	7545	7657	7769	7879	7960	7546	7658	7770	7880

File Information

file_name	file_path	file_format	output_type	assay_type	lab	Sample ID	platform	read_length	run_type	paired_end	assembly	genome_annotation	derived_from	controlled_by	Project	FILE_ID
RIOK2-BGHcLV32-33B_S51_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set52/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2025	NovaSeq6000	100	paired-ended	1				NT-BGHcLV32-1B_S53_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV32-2B_S54_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	6511
RIOK2-BGHcLV32-33B_S51_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set52/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2025	NovaSeq6000	100	paired-ended	2				NT-BGHcLV32-1B_S53_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV32-2B_S54_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	6565
RIOK2-BGHcLV32-33B_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set52/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2025					GRCh38	V40	RIOK2-BGHcLV32-33B_S51_L001_R1_001.filtered.trimmed.paired.fastq.gz,RIOK2-BGHcLV32-33B_S51_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18432
RIOK2-BGHcLV32-33B_Signal.Unique.strand+.bw	ENCODE_DATA/set52/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2025					GRCh38	V40	RIOK2-BGHcLV32-33B/Aligned.sortedByCoord.out.bam		ENCORE2	18486
RIOK2-BGHcLV32-33B_Signal.Unique.strand-.bw	ENCODE_DATA/set52/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2025					GRCh38	V40	RIOK2-BGHcLV32-33B/Aligned.sortedByCoord.out.bam		ENCORE2	18540
RIOK2-BGHcLV32-33B_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set52/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2025					GRCh38	V40	RIOK2-BGHcLV32-33B/Aligned.sortedByCoord.out.bam		ENCORE2	18594
RIOK2-BGHcLV32-33B_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set52/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2025					GRCh38	V40	RIOK2-BGHcLV32-33B/Aligned.sortedByCoord.out.bam		ENCORE2	18648
RIOK2-BGHcLV32-33B_quant.sf	ENCODE_DATA/set52/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2025					GRCh38	V40	RIOK2-BGHcLV32-33B_S51_L001_R1_001.filtered.trimmed.paired.fastq.gz,RIOK2-BGHcLV32-33B_S51_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18702
RIOK2-BGHcLV32-34B_S52_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set52/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2026	NovaSeq6000	100	paired-ended	1				NT-BGHcLV32-1B_S53_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV32-2B_S54_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	6512
RIOK2-BGHcLV32-34B_S52_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set52/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2026	NovaSeq6000	100	paired-ended	2				NT-BGHcLV32-1B_S53_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV32-2B_S54_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	6566
RIOK2-BGHcLV32-34B_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set52/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2026					GRCh38	V40	RIOK2-BGHcLV32-34B_S52_L001_R1_001.filtered.trimmed.paired.fastq.gz,RIOK2-BGHcLV32-34B_S52_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18433
RIOK2-BGHcLV32-34B_Signal.Unique.strand+.bw	ENCODE_DATA/set52/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2026					GRCh38	V40	RIOK2-BGHcLV32-34B/Aligned.sortedByCoord.out.bam		ENCORE2	18487
RIOK2-BGHcLV32-34B_Signal.Unique.strand-.bw	ENCODE_DATA/set52/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2026					GRCh38	V40	RIOK2-BGHcLV32-34B/Aligned.sortedByCoord.out.bam		ENCORE2	18541
RIOK2-BGHcLV32-34B_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set52/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2026					GRCh38	V40	RIOK2-BGHcLV32-34B/Aligned.sortedByCoord.out.bam		ENCORE2	18595
RIOK2-BGHcLV32-34B_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set52/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2026					GRCh38	V40	RIOK2-BGHcLV32-34B/Aligned.sortedByCoord.out.bam		ENCORE2	18649
RIOK2-BGHcLV32-34B_quant.sf	ENCODE_DATA/set52/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2026					GRCh38	V40	RIOK2-BGHcLV32-34B_S52_L001_R1_001.filtered.trimmed.paired.fastq.gz,RIOK2-BGHcLV32-34B_S52_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18703