RIOK1 RNA-Seq in K562

General Information


RBP	RIOK1
Cell_Line	K562
Method	CRISPR
Exp_Name	RIOK1-BGKcLV30-K562
ENCODE_series_ID	ENCSR090ZZP
Batch_ID	BGKcLV30
Pool ID	Pool-211117
Local_Set_Name	set50_K
ENCODE_KD_Exp_ID	ENCSR608WYZ
ENCODE_CN_Exp_ID	ENCSR347NKX
Rep1	RIOK1-BGKcLV30-33
Rep2	RIOK1-BGKcLV30-34
CN1	NT-BGKcLV30-1
CN2	NT-BGKcLV30-2
Rep1_qPCR	0.0
Rep2_qPCR	0.0
Rep1_WB	56.7
Rep2_WB	58.9
Antibody Cat#	A302-456A
Antibody Lot#	LOT #1
Antibody DCC ID	ENCAB726SEP
Status	Submitted
Project	ENCODE4
ID	873

Experiment Information (Status: Released)

	BGKcLV30-33	BGKcLV30-33	BGKcLV30-34	BGKcLV30-34
idx	1060	1062	1061	1063
TRCN#_or_BGC#	BGC#0000780	BGC#0000780	BGC#0000780	BGC#0000780
shRNA_or_gRNA_sequence	CCCCGGGCAATTCGACGACG	CCCCGGGCAATTCGACGACG	CCCCGGGCAATTCGACGACG	CCCCGGGCAATTCGACGACG
PAM	CGG	CGG	CGG	CGG
Name	RIOK1_98	RIOK1_98	RIOK1_98	RIOK1_98
Sample_ID	BGKcLV30-33	BGKcLV30-33	BGKcLV30-34	BGKcLV30-34
transduction_Date	8/30/21	8/30/21	8/30/21	8/30/21
days	D6	D6	D6	D6
RBP_name	RIOK1	RIOK1	RIOK1	RIOK1
qPCR_result	0.0	0.0	0.0	0.0
Ave_qPCR	0.0	0.0
RT-qPCR_primer-F	ggtgaaaacttgggcagaaa
RT-qPCR_primer-R	ccgatgaaactcatgacaagaa
protein_conc	1768	1768	2303	2303
WB_result	56.7	52.9	58.9	57.2921974
Ave_WB	57.8	55.1
WB_DONE_date	9/28/21	2/23/22
MW	66KD	66KD
IP
antibody_Cat#	A302-456A	A302-457A	LOT #1	LOT #1
Antibody DCC ID	ENCAB726SEP
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	5198	5200	5199	5201

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

	BGKcLV30-33	BGKcLV30-34
Sample_ID	BGKcLV30-33	BGKcLV30-34
Sample Name
Sample Name	RIOK1-BGKcLV30-33	RIOK1-BGKcLV30-34
RBP	RIOK1	RIOK1
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2022-02-11	2022-02-11
Project	ENCODE4	ENCODE4
Note
ID	10071	10072

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV30-33	BGKcLV30-34
Sample #	61	62
Sample Name	RIOK1-BGKcLV30-33	RIOK1-BGKcLV30-34
Sample_Name_Alias
Index Well Position	A09	B09
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	288	320
Peak_Molarity	35.50	43.30
libSampleQC_DNA_Well	DNA_Library_set50/set2/A11.png	DNA_Library_set50/set2/B11.png
RIN	9.4	9.5
libSample_RNA_Well	RNA_Library_set50/set2/A11.png	RNA_Library_set50/set2/B11.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2021-11-17	2021-11-17
Sample_ID	BGKcLV30-33	BGKcLV30-34
RBP	RIOK1	RIOK1
Batch_ID	BGKcLV30	BGKcLV30
WB_result	56.700	58.900
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	3148	3149

Sequencing Information

	BGKcLV30-33	BGKcLV30-34
Sample_ID	BGKcLV30-33	BGKcLV30-34
Sample Name	RIOK1-BGKcLV30-33	RIOK1-BGKcLV30-34
Pool ID	Pool-211117	Pool-211117
LocalServer_folder	set50_K	set50_K
total_reads	95,180,446	74,046,320
total_aligned_reads	85,247,310	69,686,426
unique_aligned_reads	77,859,776	63,786,518
percent_uniqueAligned	0.81802	0.86144
correlation_replicates	0.993459	0.993459
spikein_reads	24,164	12,882
percent_spikeins	0.00025	0.00017
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	1933	1934

Data Submission Information

	BGKcLV30-33	BGKcLV30-33	BGKcLV30-33	BGKcLV30-33	BGKcLV30-33	BGKcLV30-33	BGKcLV30-34	BGKcLV30-34	BGKcLV30-34	BGKcLV30-34
ENCODE_alias	brenton-graveley:RIOK1-BGKcLV30	brenton-graveley:RIOK1-BGKcLV30-33	brenton-graveley:L-RIOK1-BGKcLV30-33	brenton-graveley:RIOK1-BGKcLV30-33_S63_L001_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:RIOK1-BGKcLV30-33_S63_L001_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:RIOK1-BGKcLV30-K562	brenton-graveley:RIOK1-BGKcLV30-34	brenton-graveley:L-RIOK1-BGKcLV30-34	brenton-graveley:RIOK1-BGKcLV30-34_S64_L001_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:RIOK1-BGKcLV30-34_S64_L001_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR608WYZ	ENCBS394BIN	ENCLB003ECN	ENCFF546OBV	ENCFF107BNL	ENCSR090ZZP	ENCBS862EQG	ENCLB543PEV	ENCFF608BCE	ENCFF361HRU
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	BGKcLV30-33	BGKcLV30-33	BGKcLV30-33	BGKcLV30-33	BGKcLV30-33	BGKcLV30-33	BGKcLV30-34	BGKcLV30-34	BGKcLV30-34	BGKcLV30-34
Sample Name	RIOK1-BGKcLV30-33	RIOK1-BGKcLV30-33	RIOK1-BGKcLV30-33	RIOK1-BGKcLV30-33	RIOK1-BGKcLV30-33	RIOK1-BGKcLV30-33	RIOK1-BGKcLV30-34	RIOK1-BGKcLV30-34	RIOK1-BGKcLV30-34	RIOK1-BGKcLV30-34
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		RIOK1-BGKcLV30-33.pdf	L-RIOK1-BGKcLV30-33.pdf				RIOK1-BGKcLV30-34.pdf	L-RIOK1-BGKcLV30-34.pdf
ID	5872	5937	6009	6081	6153	6194	5938	6010	6082	6154

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-BGKcLV30-33_S63_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set50_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1933	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	5861
RIOK1-BGKcLV30-33_S63_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set50_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1933	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	5891
RIOK1-BGKcLV30-33_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set50_K/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1933					GRCh38	V40	RIOK1-BGKcLV30-33_S63_L001_R1_001.filtered.trimmed.paired.fastq.gz,RIOK1-BGKcLV30-33_S63_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18762
RIOK1-BGKcLV30-33_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	1933					GRCh38	V40	RIOK1-BGKcLV30-33/Aligned.sortedByCoord.out.bam		ENCORE2	18792
RIOK1-BGKcLV30-33_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	1933					GRCh38	V40	RIOK1-BGKcLV30-33/Aligned.sortedByCoord.out.bam		ENCORE2	18822
RIOK1-BGKcLV30-33_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	1933					GRCh38	V40	RIOK1-BGKcLV30-33/Aligned.sortedByCoord.out.bam		ENCORE2	18852
RIOK1-BGKcLV30-33_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	1933					GRCh38	V40	RIOK1-BGKcLV30-33/Aligned.sortedByCoord.out.bam		ENCORE2	18882
RIOK1-BGKcLV30-33_quant.sf	ENCODE_DATA/set50_K/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1933					GRCh38	V40	RIOK1-BGKcLV30-33_S63_L001_R1_001.filtered.trimmed.paired.fastq.gz,RIOK1-BGKcLV30-33_S63_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18912
RIOK1-BGKcLV30-34_S64_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set50_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1934	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	5862
RIOK1-BGKcLV30-34_S64_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set50_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1934	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	5892
RIOK1-BGKcLV30-34_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set50_K/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1934					GRCh38	V40	RIOK1-BGKcLV30-34_S64_L001_R1_001.filtered.trimmed.paired.fastq.gz,RIOK1-BGKcLV30-34_S64_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18763
RIOK1-BGKcLV30-34_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	1934					GRCh38	V40	RIOK1-BGKcLV30-34/Aligned.sortedByCoord.out.bam		ENCORE2	18793
RIOK1-BGKcLV30-34_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	1934					GRCh38	V40	RIOK1-BGKcLV30-34/Aligned.sortedByCoord.out.bam		ENCORE2	18823
RIOK1-BGKcLV30-34_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	1934					GRCh38	V40	RIOK1-BGKcLV30-34/Aligned.sortedByCoord.out.bam		ENCORE2	18853
RIOK1-BGKcLV30-34_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	1934					GRCh38	V40	RIOK1-BGKcLV30-34/Aligned.sortedByCoord.out.bam		ENCORE2	18883
RIOK1-BGKcLV30-34_quant.sf	ENCODE_DATA/set50_K/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1934					GRCh38	V40	RIOK1-BGKcLV30-34_S64_L001_R1_001.filtered.trimmed.paired.fastq.gz,RIOK1-BGKcLV30-34_S64_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18913