RIOK1 RNA-Seq in HepG2

General Information


RBP	RIOK1
Cell_Line	HepG2
Method	CRISPR
Exp_Name	RIOK1-BGHcLV34-HepG2
ENCODE_series_ID
Batch_ID	BGHcLV34
Pool ID	Pool-220720
Local_Set_Name	set54
ENCODE_KD_Exp_ID
ENCODE_CN_Exp_ID
Rep1	RIOK1-BGHcLV34-33B
Rep2	RIOK1-BGHcLV34-34B
CN1	NT-BGHcLV34-1B
CN2	NT-BGHcLV34-2B
Rep1_qPCR	0.0
Rep2_qPCR	0.0
Rep1_WB	82.3
Rep2_WB	80.6
Antibody Cat#	A302-456A
Antibody Lot#	LOT #1
Antibody DCC ID	ENCAB726SE
Status	Submitted
Project	ENCORE2
ID	949

Experiment Information (Status: Submitting)

	BGHcLV34-33	BGHcLV34-34
idx	1103	1104
TRCN#_or_BGC#	BGC#0000781	BGC#0000781
shRNA_or_gRNA_sequence	CTCCAGTCATGGACTACCGG	CTCCAGTCATGGACTACCGG
PAM	CGG	CGG
Name	RIOK1_98B	RIOK1_98B
Sample_ID	BGHcLV34-33	BGHcLV34-34
transduction_Date	3/24/22	3/24/22
days	D6	D6
RBP_name	RIOK1	RIOK1
qPCR_result	0.0	0.0
Ave_qPCR	0.0
RT-qPCR_primer-F	ggtgaaaacttgggcagaaa
RT-qPCR_primer-R	ccgatgaaactcatgacaagaa
protein_conc	3257	3862
WB_result	82.3	80.6
Ave_WB	81.5
WB_DONE_date	4/18/22
MW	66KD
IP
antibody_Cat#	A302-456A	LOT #1
Antibody DCC ID	ENCAB726SE
submitted_to_DCC_date
Rep1_TPM	0	0
Rep2_TPM	0	0
Action	Ready	Ready
Library_start_date	06/17/22	06/17/22
repeat_library	06/22/22	06/22/22
Note
ID	7282	7283

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
RIOK1	Product_ID: A302-456A Lot_ID: 1 Source: Bethyl Labs Target Name: RIOK1-human

Experiment Status

	BGHcLV34-33	BGHcLV34-34
Sample_ID	BGHcLV34-33	BGHcLV34-34
Sample Name
Sample Name	RIOK1-BGHcLV34-33B	RIOK1-BGHcLV34-34B
RBP	RIOK1	RIOK1
Cell_Line	HepG2	HepG2
Exp UID
Status	Submitting	Submitting
Status_date	2023-04-14	2023-04-14
Project	ENCORE2	ENCORE2
Note
ID	10935	10936

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV34-33	BGHcLV34-33	BGHcLV34-34	BGHcLV34-34
Sample #	13	49	14	50
Sample Name	RIOK1-BGHcLV34-33	RIOK1-BGHcLV34-33B	RIOK1-BGHcLV34-34	RIOK1-BGHcLV34-34B
Sample_Name_Alias
Index Well Position	E02	A07	F02	B07
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2022-06-17	2022-06-21	2022-06-17	2022-06-21
Lib_ID	Lib-220617	Lib-220621	Lib-220617	Lib-220621
Tecan_Location
Tecan
Tecan_date
Size_bp	281	266	288	265
Peak_Molarity	85.00	35.60	7.05	50.70
libSampleQC_DNA_Well		DNA_Library_set54-56/set4/G9.png		DNA_Library_set54-56/set4/H9.png
RIN		9.9		9.7
libSample_RNA_Well		RNA_Library_set54-56/set2/E2.png		RNA_Library_set54-56/set2/F2.png
SampleQC_method		TapeStation_2022		TapeStation_2022
SampleQC_date	2022-06-20	2022-07-20	2022-06-20	2022-07-20
Sample_ID	BGHcLV34-33	BGHcLV34-33	BGHcLV34-34	BGHcLV34-34
RBP	RIOK1	RIOK1	RIOK1	RIOK1
Batch_ID	BGHcLV34	BGHcLV34	BGHcLV34	BGHcLV34
WB_result	82.300	82.300	80.600	80.600
Library Description	TruSeq mRNA	TruSeq mRNA	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix		B		B
Lib_Status	NotToSequence	SendToSequence	NotToSequence	SendToSequence
Project	ENCORE2	ENCORE2	ENCORE2	ENCORE2
ID	3330	3366	3331	3367

Sequencing Information

	BGHcLV34-33	BGHcLV34-34
Sample_ID	BGHcLV34-33	BGHcLV34-34
Sample Name	RIOK1-BGHcLV34-33B	RIOK1-BGHcLV34-34B
Pool ID	Pool-220720	Pool-220720
LocalServer_folder	set54	set54
total_reads	39,683,824	47,370,582
total_aligned_reads	31,038,280	38,344,020
unique_aligned_reads	29,324,292	36,227,024
percent_uniqueAligned	0.73895	0.76476
correlation_replicates	0.998908	0.998908
spikein_reads	14,058	8,812
percent_spikeins	0.00035	0.00019
original_ReadLength	101	101
QC_Status	Submitting	Submitting
ID	2213	2214

Data Submission Information DCC submission information was not avaliable

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
RIOK1-BGHcLV34-33B_S19_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set54/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2213	NovaSeq6000	100	paired-ended	1				NT-BGHcLV34-1B_S23_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV34-2B_S24_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8508
RIOK1-BGHcLV34-33B_S19_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set54/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2213	NovaSeq6000	100	paired-ended	2				NT-BGHcLV34-1B_S23_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV34-2B_S24_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8558
RIOK1-BGHcLV34-33B_Signal.Unique.strand+.bw	ENCODE_DATA/set54/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2213					GRCh38	V40	RIOK1-BGHcLV34-33B/Aligned.sortedByCoord.out.bam		ENCORE2	17754
RIOK1-BGHcLV34-33B_Signal.Unique.strand-.bw	ENCODE_DATA/set54/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2213					GRCh38	V40	RIOK1-BGHcLV34-33B/Aligned.sortedByCoord.out.bam		ENCORE2	17804
RIOK1-BGHcLV34-33B_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set54/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2213					GRCh38	V40	RIOK1-BGHcLV34-33B/Aligned.sortedByCoord.out.bam		ENCORE2	17854
RIOK1-BGHcLV34-33B_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set54/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2213					GRCh38	V40	RIOK1-BGHcLV34-33B/Aligned.sortedByCoord.out.bam		ENCORE2	17904
RIOK1-BGHcLV34-33B_quant.sf	ENCODE_DATA/set54/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2213					GRCh38	V40	RIOK1-BGHcLV34-33B_S19_R1_001.filtered.trimmed.paired.fastq.gz,RIOK1-BGHcLV34-33B_S19_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	17954
RIOK1-BGHcLV34-33B_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set54/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2213					GRCh38	V40	RIOK1-BGHcLV34-33B_S19_R1_001.filtered.trimmed.paired.fastq.gz,RIOK1-BGHcLV34-33B_S19_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	29295
RIOK1-BGHcLV34-34B_S20_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set54/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2214	NovaSeq6000	100	paired-ended	1				NT-BGHcLV34-1B_S23_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV34-2B_S24_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8509
RIOK1-BGHcLV34-34B_S20_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set54/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2214	NovaSeq6000	100	paired-ended	2				NT-BGHcLV34-1B_S23_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV34-2B_S24_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8559
RIOK1-BGHcLV34-34B_Signal.Unique.strand+.bw	ENCODE_DATA/set54/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2214					GRCh38	V40	RIOK1-BGHcLV34-34B/Aligned.sortedByCoord.out.bam		ENCORE2	17755
RIOK1-BGHcLV34-34B_Signal.Unique.strand-.bw	ENCODE_DATA/set54/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2214					GRCh38	V40	RIOK1-BGHcLV34-34B/Aligned.sortedByCoord.out.bam		ENCORE2	17805
RIOK1-BGHcLV34-34B_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set54/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2214					GRCh38	V40	RIOK1-BGHcLV34-34B/Aligned.sortedByCoord.out.bam		ENCORE2	17855
RIOK1-BGHcLV34-34B_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set54/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2214					GRCh38	V40	RIOK1-BGHcLV34-34B/Aligned.sortedByCoord.out.bam		ENCORE2	17905
RIOK1-BGHcLV34-34B_quant.sf	ENCODE_DATA/set54/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2214					GRCh38	V40	RIOK1-BGHcLV34-34B_S20_R1_001.filtered.trimmed.paired.fastq.gz,RIOK1-BGHcLV34-34B_S20_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	17955
RIOK1-BGHcLV34-34B_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set54/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2214					GRCh38	V40	RIOK1-BGHcLV34-34B_S20_R1_001.filtered.trimmed.paired.fastq.gz,RIOK1-BGHcLV34-34B_S20_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	29296