RUVBL2 RNA-Seq in HepG2

General Information


RBP	RUVBL2
Cell_Line	HepG2
Method	CRISPR
Exp_Name	RUVBL2-BGHcLV31-HepG2
ENCODE_series_ID	ENCSR636LSV
Batch_ID	BGHcLV31
Pool ID	Pool-220331
Local_Set_Name	set52
ENCODE_KD_Exp_ID	ENCSR153WFE
ENCODE_CN_Exp_ID	ENCSR452TFV
Rep1	RUVBL2-BGHcLV31-21
Rep2	RUVBL2-BGHcLV31-22
CN1	NT-BGHcLV31-1
CN2	NT-BGHcLV31-2
Rep1_qPCR
Rep2_qPCR
Rep1_WB	68.5
Rep2_WB	61.9
Antibody Cat#	A302-536A
Antibody Lot#	LOT #1
Antibody DCC ID	NO ID
Status	Submitted
Project	ENCODE4
ID	922

Experiment Information (Status: Released)

	BGHcLV31-21	BGHcLV31-21	BGHcLV31-22	BGHcLV31-22
idx	937	939	938	940
TRCN#_or_BGC#	BGC#0000838	BGC#0000838	BGC#0000838	BGC#0000838
shRNA_or_gRNA_sequence	TTACTTGATGCGAACGCCGA	TTACTTGATGCGAACGCCGA	TTACTTGATGCGAACGCCGA	TTACTTGATGCGAACGCCGA
PAM	TGG	TGG	TGG	TGG
Name	RUVBL2_99	RUVBL2_99	RUVBL2_99	RUVBL2_99
Sample_ID	BGHcLV31-21	BGHcLV31-21	BGHcLV31-22	BGHcLV31-22
transduction_Date	9/23/21	9/23/21	9/23/21	9/23/21
days	D6	D6	D6	D6
RBP_name	RUVBL2	RUVBL2	RUVBL2	RUVBL2
qPCR_result	xx
Ave_qPCR
RT-qPCR_primer-F
RT-qPCR_primer-R
protein_conc	3877	3877	3816	3816
WB_result	68.5	63.4	61.9	68.9
Ave_WB	65.2	66.2
WB_DONE_date	11/4/21	2/23/22
MW	51kd	51kd
IP
antibody_Cat#	A302-536A	A302-537A	LOT #1	LOT #1
Antibody DCC ID	NO ID
submitted_to_DCC_date
Rep1_TPM	0	0	0	0
Rep2_TPM	0	0	0	0
Action	Ready		Ready
Library_start_date	12/16/21		12/16/21
repeat_library
Note
ID	9164	9166	9165	9167

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
RUVBL2	Product_ID: A302-536A Lot_ID: 1 Source: Bethyl Labs Target Name: RUVBL2-human

Experiment Status

	BGHcLV31-21	BGHcLV31-22
Sample_ID	BGHcLV31-21	BGHcLV31-22
Sample Name
Sample Name	RUVBL2-BGHcLV31-21	RUVBL2-BGHcLV31-22
RBP	RUVBL2	RUVBL2
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2022-10-28	2022-10-28
Project	ENCODE4	ENCODE4
Note
ID	10299	10300

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV31-21	BGHcLV31-22
Sample #	13	14
Sample Name	RUVBL2-BGHcLV31-21	RUVBL2-BGHcLV31-22
Sample_Name_Alias
Index Well Position	E02	F02
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2021-12-16	2021-12-16
Lib_ID	Lib-211216	Lib-211216
Tecan_Location
Tecan
Tecan_date
Size_bp	288	309
Peak_Molarity	79.10	74.50
libSampleQC_DNA_Well	DNA_Library_set52/set1/E9.png	DNA_Library_set52/set1/F9.png
RIN	9.7	9.6
libSample_RNA_Well	RNA_Library_set52/set1/E2.png	RNA_Library_set52/set1/F2.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2022-01-04	2022-01-04
Sample_ID	BGHcLV31-21	BGHcLV31-22
RBP	RUVBL2	RUVBL2
Batch_ID	BGHcLV31	BGHcLV31
WB_result	68.500	61.900
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	3190	3191

Sequencing Information

	BGHcLV31-21	BGHcLV31-22
Sample_ID	BGHcLV31-21	BGHcLV31-22
Sample Name	RUVBL2-BGHcLV31-21	RUVBL2-BGHcLV31-22
Pool ID	Pool-220331	Pool-220331
LocalServer_folder	set52	set52
total_reads	109,163,078	63,449,926
total_aligned_reads	96,971,628	56,308,384
unique_aligned_reads	91,126,682	53,040,538
percent_uniqueAligned	0.83478	0.83594
correlation_replicates	0.998988	0.998988
spikein_reads	6,294	4,604
percent_spikeins	0.00006	0.00007
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	1987	1988

Data Submission Information

	BGHcLV31-21	BGHcLV31-21	BGHcLV31-21	BGHcLV31-21	BGHcLV31-21	BGHcLV31-21	BGHcLV31-22	BGHcLV31-22	BGHcLV31-22	BGHcLV31-22
ENCODE_alias	brenton-graveley:RUVBL2-BGHcLV31	brenton-graveley:RUVBL2-BGHcLV31-21	brenton-graveley:L-RUVBL2-BGHcLV31-21	brenton-graveley:RUVBL2-BGHcLV31-21_S13_L001_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:RUVBL2-BGHcLV31-21_S13_L001_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:RUVBL2-BGHcLV31-HepG2	brenton-graveley:RUVBL2-BGHcLV31-22	brenton-graveley:L-RUVBL2-BGHcLV31-22	brenton-graveley:RUVBL2-BGHcLV31-22_S14_L001_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:RUVBL2-BGHcLV31-22_S14_L001_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR153WFE	ENCBS841DKK	ENCLB386NQP	ENCFF324XEQ	ENCFF375JFU	ENCSR636LSV	ENCBS050QUI	ENCLB135XBK	ENCFF555AIK	ENCFF483MTR
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	BGHcLV31-21	BGHcLV31-21	BGHcLV31-21	BGHcLV31-21	BGHcLV31-21	BGHcLV31-21	BGHcLV31-22	BGHcLV31-22	BGHcLV31-22	BGHcLV31-22
Sample Name	RUVBL2-BGHcLV31-21	RUVBL2-BGHcLV31-21	RUVBL2-BGHcLV31-21	RUVBL2-BGHcLV31-21	RUVBL2-BGHcLV31-21	RUVBL2-BGHcLV31-21	RUVBL2-BGHcLV31-22	RUVBL2-BGHcLV31-22	RUVBL2-BGHcLV31-22	RUVBL2-BGHcLV31-22
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		RUVBL2-BGHcLV31-21.pdf	L-RUVBL2-BGHcLV31-21.pdf				RUVBL2-BGHcLV31-22.pdf	L-RUVBL2-BGHcLV31-22.pdf
ID	7450	7511	7619	7729	7839	7942	7512	7620	7730	7840

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-BGHcLV31-21_S13_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set52/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1987	NovaSeq6000	100	paired-ended	1				NT-BGHcLV31-1_S1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV31-2_S2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	6533
RUVBL2-BGHcLV31-21_S13_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set52/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1987	NovaSeq6000	100	paired-ended	2				NT-BGHcLV31-1_S1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV31-2_S2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	6587
RUVBL2-BGHcLV31-21_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set52/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1987					GRCh38	V40	RUVBL2-BGHcLV31-21_S13_L001_R1_001.filtered.trimmed.paired.fastq.gz,RUVBL2-BGHcLV31-21_S13_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18454
RUVBL2-BGHcLV31-21_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	1987					GRCh38	V40	RUVBL2-BGHcLV31-21/Aligned.sortedByCoord.out.bam		ENCORE2	18508
RUVBL2-BGHcLV31-21_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	1987					GRCh38	V40	RUVBL2-BGHcLV31-21/Aligned.sortedByCoord.out.bam		ENCORE2	18562
RUVBL2-BGHcLV31-21_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	1987					GRCh38	V40	RUVBL2-BGHcLV31-21/Aligned.sortedByCoord.out.bam		ENCORE2	18616
RUVBL2-BGHcLV31-21_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	1987					GRCh38	V40	RUVBL2-BGHcLV31-21/Aligned.sortedByCoord.out.bam		ENCORE2	18670
RUVBL2-BGHcLV31-21_quant.sf	ENCODE_DATA/set52/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1987					GRCh38	V40	RUVBL2-BGHcLV31-21_S13_L001_R1_001.filtered.trimmed.paired.fastq.gz,RUVBL2-BGHcLV31-21_S13_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18724
RUVBL2-BGHcLV31-22_S14_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set52/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1988	NovaSeq6000	100	paired-ended	1				NT-BGHcLV31-1_S1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV31-2_S2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	6534
RUVBL2-BGHcLV31-22_S14_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set52/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1988	NovaSeq6000	100	paired-ended	2				NT-BGHcLV31-1_S1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV31-2_S2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	6588
RUVBL2-BGHcLV31-22_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set52/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1988					GRCh38	V40	RUVBL2-BGHcLV31-22_S14_L001_R1_001.filtered.trimmed.paired.fastq.gz,RUVBL2-BGHcLV31-22_S14_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18455
RUVBL2-BGHcLV31-22_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	1988					GRCh38	V40	RUVBL2-BGHcLV31-22/Aligned.sortedByCoord.out.bam		ENCORE2	18509
RUVBL2-BGHcLV31-22_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	1988					GRCh38	V40	RUVBL2-BGHcLV31-22/Aligned.sortedByCoord.out.bam		ENCORE2	18563
RUVBL2-BGHcLV31-22_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	1988					GRCh38	V40	RUVBL2-BGHcLV31-22/Aligned.sortedByCoord.out.bam		ENCORE2	18617
RUVBL2-BGHcLV31-22_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	1988					GRCh38	V40	RUVBL2-BGHcLV31-22/Aligned.sortedByCoord.out.bam		ENCORE2	18671
RUVBL2-BGHcLV31-22_quant.sf	ENCODE_DATA/set52/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1988					GRCh38	V40	RUVBL2-BGHcLV31-22_S14_L001_R1_001.filtered.trimmed.paired.fastq.gz,RUVBL2-BGHcLV31-22_S14_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18725