RIOK2 RNA-Seq in K562

General Information


RBP	RIOK2
Cell_Line	K562
Method	CRISPR
Exp_Name	RIOK2-BGKcLV30-K562
ENCODE_series_ID	ENCSR884KNJ
Batch_ID	BGKcLV30
Pool ID	Pool-211117
Local_Set_Name	set50_K
ENCODE_KD_Exp_ID	ENCSR262ZBE
ENCODE_CN_Exp_ID	ENCSR347NKX
Rep1	RIOK2-BGKcLV30-35
Rep2	RIOK2-BGKcLV30-36
CN1	NT-BGKcLV30-1
CN2	NT-BGKcLV30-2
Rep1_qPCR	36.2
Rep2_qPCR	34.0
Rep1_WB	50.0
Rep2_WB	61.0
Antibody Cat#	A302-449A
Antibody Lot#	LOT #1
Antibody DCC ID	ENCAB828CEY
Status	Submitted
Project	ENCODE4
ID	874

Experiment Information (Status: Released)

	BGKcLV30-35	BGKcLV30-35	BGKcLV30-36	BGKcLV30-36
idx	1064	0	1065	0
TRCN#_or_BGC#	BGC#0000783	BGC#0000783	BGC#0000783	BGC#0000783
shRNA_or_gRNA_sequence	CATTTGTCAACCGATAGCCC	CATTTGTCAACCGATAGCCC	CATTTGTCAACCGATAGCCC	CATTTGTCAACCGATAGCCC
PAM	TGG	TGG	TGG	TGG
Name	RIOK2_96	RIOK2_96	RIOK2_96	RIOK2_96
Sample_ID	BGKcLV30-35	BGKcLV30-35	BGKcLV30-36	BGKcLV30-36
transduction_Date	8/30/21	8/30/21	8/30/21	8/30/21
days	D6	D6	D6	D6
RBP_name	RIOK2	RIOK2	RIOK2	RIOK2
qPCR_result	36.2	36.2	34.0	34.0
Ave_qPCR	35.1	35.1
RT-qPCR_primer-F	gccatgaaggaatttgccta	gccatgaaggaatttgccta
RT-qPCR_primer-R	ttccatgaccactgcatgac	ttccatgaccactgcatgac
protein_conc	1976	1976	2460	2460
WB_result	50.0	64.9	61.0	62.4941
Ave_WB	55.5	63.7
WB_DONE_date	9/10/21	7/6/22	JESS
MW	63KD	63KD
IP
antibody_Cat#	A302-449A	A302-450A	LOT #1	LOT #1
Antibody DCC ID	ENCAB828CEY	ENCAB531RFU
submitted_to_DCC_date
Rep1_TPM	0	0	0	0
Rep2_TPM	0	0	0	0
Action	Ready		Ready
Library_start_date	11/10/21		11/10/21
repeat_library
Note
ID	5202	5204	5203	5205

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
RIOK2	Product_ID: A302-450A Lot_ID: 1 Source: Bethyl Labs Target Name: RIOK2-human

Experiment Status

	BGKcLV30-35	BGKcLV30-36
Sample_ID	BGKcLV30-35	BGKcLV30-36
Sample Name
Sample Name	RIOK2-BGKcLV30-35	RIOK2-BGKcLV30-36
RBP	RIOK2	RIOK2
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2022-02-11	2022-02-11
Project	ENCODE4	ENCODE4
Note
ID	10073	10074

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV30-35	BGKcLV30-36
Sample #	63	64
Sample Name	RIOK2-BGKcLV30-35	RIOK2-BGKcLV30-36
Sample_Name_Alias
Index Well Position	C09	D09
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2021-11-01	2021-11-01
Lib_ID	Lib-211101A	Lib-211101A
Tecan_Location
Tecan
Tecan_date
Size_bp	308	288
Peak_Molarity	63.80	38.90
libSampleQC_DNA_Well	DNA_Library_set50/set2/C11.png	DNA_Library_set50/set2/D11.png
RIN	9.5	9.5
libSample_RNA_Well	RNA_Library_set50/set2/C11.png	RNA_Library_set50/set2/D11.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2021-11-17	2021-11-17
Sample_ID	BGKcLV30-35	BGKcLV30-36
RBP	RIOK2	RIOK2
Batch_ID	BGKcLV30	BGKcLV30
WB_result	50.000	61.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	3150	3151

Sequencing Information

	BGKcLV30-35	BGKcLV30-36
Sample_ID	BGKcLV30-35	BGKcLV30-36
Sample Name	RIOK2-BGKcLV30-35	RIOK2-BGKcLV30-36
Pool ID	Pool-211117	Pool-211117
LocalServer_folder	set50_K	set50_K
total_reads	81,475,162	84,837,040
total_aligned_reads	76,388,734	80,465,338
unique_aligned_reads	69,895,386	73,639,378
percent_uniqueAligned	0.85787	0.86801
correlation_replicates	0.996653	0.996653
spikein_reads	9,446	5,442
percent_spikeins	0.00012	0.00006
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	1935	1936

Data Submission Information

	BGKcLV30-35	BGKcLV30-35	BGKcLV30-35	BGKcLV30-35	BGKcLV30-35	BGKcLV30-35	BGKcLV30-36	BGKcLV30-36	BGKcLV30-36	BGKcLV30-36
ENCODE_alias	brenton-graveley:RIOK2-BGKcLV30	brenton-graveley:RIOK2-BGKcLV30-35	brenton-graveley:L-RIOK2-BGKcLV30-35	brenton-graveley:RIOK2-BGKcLV30-35_S65_L001_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:RIOK2-BGKcLV30-35_S65_L001_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:RIOK2-BGKcLV30-K562	brenton-graveley:RIOK2-BGKcLV30-36	brenton-graveley:L-RIOK2-BGKcLV30-36	brenton-graveley:RIOK2-BGKcLV30-36_S66_L001_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:RIOK2-BGKcLV30-36_S66_L001_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR262ZBE	ENCBS262WNW	ENCLB747WRZ	ENCFF798QBI	ENCFF811OBO	ENCSR884KNJ	ENCBS255XED	ENCLB369KFL	ENCFF437WRC	ENCFF646VIQ
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	BGKcLV30-35	BGKcLV30-35	BGKcLV30-35	BGKcLV30-35	BGKcLV30-35	BGKcLV30-35	BGKcLV30-36	BGKcLV30-36	BGKcLV30-36	BGKcLV30-36
Sample Name	RIOK2-BGKcLV30-35	RIOK2-BGKcLV30-35	RIOK2-BGKcLV30-35	RIOK2-BGKcLV30-35	RIOK2-BGKcLV30-35	RIOK2-BGKcLV30-35	RIOK2-BGKcLV30-36	RIOK2-BGKcLV30-36	RIOK2-BGKcLV30-36	RIOK2-BGKcLV30-36
Selected	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes
Status	Released	Released	Released	Released	Released	Released	Released	Released	Released	Released
Status_Date	2022-02-11	2022-02-11	2022-02-11	2022-02-11	2022-02-11	2022-02-11	2022-02-11	2022-02-11	2022-02-11	2022-02-11
Project	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4
		LV50K_biosample_protocol	LV50K_library_protocol				LV50K_biosample_protocol	LV50K_library_protocol
protocol_URL		RIOK2-BGKcLV30-35.pdf	L-RIOK2-BGKcLV30-35.pdf				RIOK2-BGKcLV30-36.pdf	L-RIOK2-BGKcLV30-36.pdf
ID	5873	5939	6011	6083	6155	6195	5940	6012	6084	6156

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-BGKcLV30-35_S65_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set50_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1935	NovaSeq6000	100	paired-ended	1				NT-BGKcLV30-1_S47_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV30-2_S48_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	5863
RIOK2-BGKcLV30-35_S65_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set50_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1935	NovaSeq6000	100	paired-ended	2				NT-BGKcLV30-1_S47_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV30-2_S48_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	5893
RIOK2-BGKcLV30-35_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set50_K/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1935					GRCh38	V40	RIOK2-BGKcLV30-35_S65_L001_R1_001.filtered.trimmed.paired.fastq.gz,RIOK2-BGKcLV30-35_S65_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18764
RIOK2-BGKcLV30-35_Signal.Unique.strand+.bw	ENCODE_DATA/set50_K/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1935					GRCh38	V40	RIOK2-BGKcLV30-35/Aligned.sortedByCoord.out.bam		ENCORE2	18794
RIOK2-BGKcLV30-35_Signal.Unique.strand-.bw	ENCODE_DATA/set50_K/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1935					GRCh38	V40	RIOK2-BGKcLV30-35/Aligned.sortedByCoord.out.bam		ENCORE2	18824
RIOK2-BGKcLV30-35_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set50_K/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1935					GRCh38	V40	RIOK2-BGKcLV30-35/Aligned.sortedByCoord.out.bam		ENCORE2	18854
RIOK2-BGKcLV30-35_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set50_K/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1935					GRCh38	V40	RIOK2-BGKcLV30-35/Aligned.sortedByCoord.out.bam		ENCORE2	18884
RIOK2-BGKcLV30-35_quant.sf	ENCODE_DATA/set50_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1935					GRCh38	V40	RIOK2-BGKcLV30-35_S65_L001_R1_001.filtered.trimmed.paired.fastq.gz,RIOK2-BGKcLV30-35_S65_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18914
RIOK2-BGKcLV30-36_S66_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set50_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1936	NovaSeq6000	100	paired-ended	1				NT-BGKcLV30-1_S47_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV30-2_S48_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	5864
RIOK2-BGKcLV30-36_S66_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set50_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1936	NovaSeq6000	100	paired-ended	2				NT-BGKcLV30-1_S47_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV30-2_S48_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	5894
RIOK2-BGKcLV30-36_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set50_K/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1936					GRCh38	V40	RIOK2-BGKcLV30-36_S66_L001_R1_001.filtered.trimmed.paired.fastq.gz,RIOK2-BGKcLV30-36_S66_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18765
RIOK2-BGKcLV30-36_Signal.Unique.strand+.bw	ENCODE_DATA/set50_K/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1936					GRCh38	V40	RIOK2-BGKcLV30-36/Aligned.sortedByCoord.out.bam		ENCORE2	18795
RIOK2-BGKcLV30-36_Signal.Unique.strand-.bw	ENCODE_DATA/set50_K/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1936					GRCh38	V40	RIOK2-BGKcLV30-36/Aligned.sortedByCoord.out.bam		ENCORE2	18825
RIOK2-BGKcLV30-36_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set50_K/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1936					GRCh38	V40	RIOK2-BGKcLV30-36/Aligned.sortedByCoord.out.bam		ENCORE2	18855
RIOK2-BGKcLV30-36_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set50_K/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1936					GRCh38	V40	RIOK2-BGKcLV30-36/Aligned.sortedByCoord.out.bam		ENCORE2	18885
RIOK2-BGKcLV30-36_quant.sf	ENCODE_DATA/set50_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1936					GRCh38	V40	RIOK2-BGKcLV30-36_S66_L001_R1_001.filtered.trimmed.paired.fastq.gz,RIOK2-BGKcLV30-36_S66_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18915