RUVBL2 RNA-Seq in K562

General Information


RBP	RUVBL2
Cell_Line	K562
Method	CRISPR
Exp_Name	RUVBL2-BGKcLV46-K562
ENCODE_series_ID
Batch_ID	BGKcLV46
Pool ID	Pool-250312
Local_Set_Name	set77
ENCODE_KD_Exp_ID
ENCODE_CN_Exp_ID
Rep1	RUVBL2-BGKcLV46-87
Rep2	RUVBL2-BGKcLV46-88
CN1	NT-BGKcLV46-1
CN2	NT-BGKcLV46-2
Rep1_qPCR	xx
Rep2_qPCR	xx
Rep1_WB	83.3
Rep2_WB	86.7
Antibody Cat#	A302-536A
Antibody Lot#	lot# 1
Antibody DCC ID
Status	Submitted
Project	ENCORE2
ID	1653

Experiment Information (Status: Submitting)

	BGKcLV46-87	BGKcLV46-87	BGKcLV46-88	BGKcLV46-88
idx	0	0	0	0
TRCN#_or_BGC#	BGC#0001269	BGC#0001269	BGC#0001269	BGC#0001269
shRNA_or_gRNA_sequence	TTACTTGATGCGAACGCCGA	TTACTTGATGCGAACGCCGA	TTACTTGATGCGAACGCCGA	TTACTTGATGCGAACGCCGA
PAM	TGG	TGG	TGG	TGG
Name	RUVBL2_99	RUVBL2_99	RUVBL2_99	RUVBL2_99
Sample_ID	BGKcLV46-87	BGKcLV46-87	BGKcLV46-88	BGKcLV46-88
transduction_Date	12/20/24	12/20/24	12/20/24	12/20/24
days	D6	D6	D6	D6
RBP_name	RUVBL2	RUVBL2	RUVBL2	RUVBL2
qPCR_result	xx	xx	xx	xx
Ave_qPCR
RT-qPCR_primer-F
RT-qPCR_primer-R
protein_conc	4960	4960	5263	5263
WB_result	83.3	81.6	86.7	86.4449
Ave_WB
WB_DONE_date	1/15/25	4/15/25
MW		51kd		actin
IP
antibody_Cat#	A302-536A	A302-537A	lot# 1	lot# 1
Antibody DCC ID
submitted_to_DCC_date
Rep1_TPM	0	0	0	0
Rep2_TPM	0	0	0	0
Action	Ready		Ready
Library_start_date
repeat_library
Note
ID	6100	6102	6101	6103

Western Blot Western Blot info was not avaliable

Experiment Status

	BGKcLV46-87	BGKcLV46-88
Sample_ID	BGKcLV46-87	BGKcLV46-88
Sample Name
Sample Name	RUVBL2-BGKcLV46-87	RUVBL2-BGKcLV46-88
RBP	RUVBL2	RUVBL2
Cell_Line	K562	K562
Exp UID
Status	Submitting	Submitting
Status_date	2025-04-21	2025-04-21
Project	ENCORE2	ENCORE2
Note
ID	14062	14063

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV46-87	BGKcLV46-88
Sample #	41	42
Sample Name	RUVBL2-BGKcLV46-87	RUVBL2-BGKcLV46-88
Sample_Name_Alias
Index Well Position	A06	B06
Index_table	IDT_UniqueDualIndex_96_V2	IDT_UniqueDualIndex_96_V2
LibPrep_date	2025-02-20	2025-02-20
Lib_ID	Lib-250220	Lib-250220
Tecan_Location
Tecan
Tecan_date
Size_bp	308	316
Peak_Molarity	77.70	72.60
libSampleQC_DNA_Well	DNA_Library_set77/set1/A12.png	DNA_Library_set77/set1/B12.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_set77/set1/A6.png	RNA_Library_set77/set1/B6.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2025-02-28	2025-02-28
Sample_ID	BGKcLV46-87	BGKcLV46-88
RBP	RUVBL2	RUVBL2
Batch_ID	BGKcLV46	BGKcLV46
WB_result	83.300	86.700
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	4700	4701

Sequencing Information

	BGKcLV46-87	BGKcLV46-88
Sample_ID	BGKcLV46-87	BGKcLV46-88
Sample Name	RUVBL2-BGKcLV46-87	RUVBL2-BGKcLV46-88
Pool ID	Pool-250312	Pool-250312
LocalServer_folder	set77	set77
total_reads	55,817,381	50,692,938
total_aligned_reads	50,588,344	44,479,457
unique_aligned_reads	46,633,539	41,148,066
percent_uniqueAligned	0.83547	0.81171
correlation_replicates	0.996749	0.996749
spikein_reads	100,108	55,900
percent_spikeins	0.00179	0.00110
original_ReadLength	101	101
QC_Status	Submitting	Submitting
ID	3403	3404

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
RUVBL2-BGKcLV46-87_S39_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set77/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3403	NovaSeq6000	100	paired-ended	1				NT-BGKcLV46-1_S1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV46-2_S2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	32190
RUVBL2-BGKcLV46-87_S39_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set77/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3403	NovaSeq6000	100	paired-ended	2				NT-BGKcLV46-1_S1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV46-2_S2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	32240
RUVBL2-BGKcLV46-87_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set77/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3403					GRCh38	V40	RUVBL2-BGKcLV46-87_S39_L001_R1_001.filtered.trimmed.paired.fastq.gz,RUVBL2-BGKcLV46-87_S39_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	32290
RUVBL2-BGKcLV46-87_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set77/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3403					GRCh38	V40	RUVBL2-BGKcLV46-87_Aligned.sortedByCoord.out.bam		ENCORE2	32340
RUVBL2-BGKcLV46-87_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set77/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3403					GRCh38	V40	RUVBL2-BGKcLV46-87_Aligned.sortedByCoord.out.bam		ENCORE2	32390
RUVBL2-BGKcLV46-87_Signal.Unique.strand-.bw	ENCODE_DATA/set77/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3403					GRCh38	V40	RUVBL2-BGKcLV46-87_Aligned.sortedByCoord.out.bam		ENCORE2	32440
RUVBL2-BGKcLV46-87_Signal.Unique.strand+.bw	ENCODE_DATA/set77/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3403					GRCh38	V40	RUVBL2-BGKcLV46-87_Aligned.sortedByCoord.out.bam		ENCORE2	32490
RUVBL2-BGKcLV46-87_quant.sf	ENCODE_DATA/set77/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3403					GRCh38	V40	RUVBL2-BGKcLV46-87_S39_L001_R1_001.filtered.trimmed.paired.fastq.gz,RUVBL2-BGKcLV46-87_S39_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	32540
RUVBL2-BGKcLV46-88_S40_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set77/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3404	NovaSeq6000	100	paired-ended	1				NT-BGKcLV46-1_S1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV46-2_S2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	32191
RUVBL2-BGKcLV46-88_S40_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set77/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3404	NovaSeq6000	100	paired-ended	2				NT-BGKcLV46-1_S1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV46-2_S2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	32241
RUVBL2-BGKcLV46-88_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set77/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3404					GRCh38	V40	RUVBL2-BGKcLV46-88_S40_L001_R1_001.filtered.trimmed.paired.fastq.gz,RUVBL2-BGKcLV46-88_S40_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	32291
RUVBL2-BGKcLV46-88_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set77/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3404					GRCh38	V40	RUVBL2-BGKcLV46-88_Aligned.sortedByCoord.out.bam		ENCORE2	32341
RUVBL2-BGKcLV46-88_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set77/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3404					GRCh38	V40	RUVBL2-BGKcLV46-88_Aligned.sortedByCoord.out.bam		ENCORE2	32391
RUVBL2-BGKcLV46-88_Signal.Unique.strand-.bw	ENCODE_DATA/set77/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3404					GRCh38	V40	RUVBL2-BGKcLV46-88_Aligned.sortedByCoord.out.bam		ENCORE2	32441
RUVBL2-BGKcLV46-88_Signal.Unique.strand+.bw	ENCODE_DATA/set77/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3404					GRCh38	V40	RUVBL2-BGKcLV46-88_Aligned.sortedByCoord.out.bam		ENCORE2	32491
RUVBL2-BGKcLV46-88_quant.sf	ENCODE_DATA/set77/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3404					GRCh38	V40	RUVBL2-BGKcLV46-88_S40_L001_R1_001.filtered.trimmed.paired.fastq.gz,RUVBL2-BGKcLV46-88_S40_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	32541