RUVBL1 RNA-Seq in HepG2

General Information


RBP	RUVBL1
Cell_Line	HepG2
Method	CRISPR
Exp_Name	RUVBL1-BGHcLV31-HepG2
ENCODE_series_ID	ENCSR312QIX
Batch_ID	BGHcLV31
Pool ID	Pool-220331
Local_Set_Name	set52
ENCODE_KD_Exp_ID	ENCSR785SZL
ENCODE_CN_Exp_ID	ENCSR452TFV
Rep1	RUVBL1-BGHcLV31-19
Rep2	RUVBL1-BGHcLV31-20
CN1	NT-BGHcLV31-1
CN2	NT-BGHcLV31-2
Rep1_qPCR
Rep2_qPCR
Rep1_WB	54.2
Rep2_WB	51.7
Antibody Cat#	A304-716A
Antibody Lot#	LOT #1
Antibody DCC ID	ENCAB336XYM
Status	Submitted
Project	ENCODE4
ID	921

Experiment Information (Status: Released)

	BGHcLV31-19	BGHcLV31-20
idx	935	936
TRCN#_or_BGC#	BGC#0000836	BGC#0000836
shRNA_or_gRNA_sequence	ACTTGGATGTGGCTAATGCG	ACTTGGATGTGGCTAATGCG
PAM	CGG	CGG
Name	RUVBL1_94	RUVBL1_94
Sample_ID	BGHcLV31-19	BGHcLV31-20
transduction_Date	9/23/21	9/23/21
days	D6	D6
RBP_name	RUVBL1	RUVBL1
qPCR_result	xx
Ave_qPCR
RT-qPCR_primer-F
RT-qPCR_primer-R
protein_conc	3744	3722
WB_result	54.2	51.7
Ave_WB	52.9
WB_DONE_date	11/4/21
MW	50kd
IP
antibody_Cat#	A304-716A	LOT #1
Antibody DCC ID	ENCAB336XYM
submitted_to_DCC_date
Rep1_TPM	0	0
Rep2_TPM	0	0
Action	Ready	Ready
Library_start_date	12/16/21	12/16/21
repeat_library
Note
ID	7114	7115

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
RUVBL1	Product_ID: A304-716A Lot_ID: 1 Source: Bethyl Labs Target Name: RUVBL1-human

Experiment Status

	BGHcLV31-19	BGHcLV31-20
Sample_ID	BGHcLV31-19	BGHcLV31-20
Sample Name
Sample Name	RUVBL1-BGHcLV31-19	RUVBL1-BGHcLV31-20
RBP	RUVBL1	RUVBL1
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2022-10-28	2022-10-28
Project	ENCODE4	ENCODE4
Note
ID	10297	10298

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV31-19	BGHcLV31-20
Sample #	11	12
Sample Name	RUVBL1-BGHcLV31-19	RUVBL1-BGHcLV31-20
Sample_Name_Alias
Index Well Position	C02	D02
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	291	293
Peak_Molarity	49.80	62.80
libSampleQC_DNA_Well	DNA_Library_set52/set1/C9.png	DNA_Library_set52/set1/D9.png
RIN	9.6	9.7
libSample_RNA_Well	RNA_Library_set52/set1/C2.png	RNA_Library_set52/set1/D2.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2022-01-04	2022-01-04
Sample_ID	BGHcLV31-19	BGHcLV31-20
RBP	RUVBL1	RUVBL1
Batch_ID	BGHcLV31	BGHcLV31
WB_result	54.200	51.700
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	3188	3189

Sequencing Information

	BGHcLV31-19	BGHcLV31-20
Sample_ID	BGHcLV31-19	BGHcLV31-20
Sample Name	RUVBL1-BGHcLV31-19	RUVBL1-BGHcLV31-20
Pool ID	Pool-220331	Pool-220331
LocalServer_folder	set52	set52
total_reads	99,123,474	84,708,208
total_aligned_reads	87,343,990	75,697,292
unique_aligned_reads	82,279,048	71,209,090
percent_uniqueAligned	0.83007	0.84064
correlation_replicates	0.997815	0.997815
spikein_reads	6,152	3,770
percent_spikeins	0.00006	0.00004
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	1985	1986

Data Submission Information

	BGHcLV31-19	BGHcLV31-19	BGHcLV31-19	BGHcLV31-19	BGHcLV31-19	BGHcLV31-19	BGHcLV31-20	BGHcLV31-20	BGHcLV31-20	BGHcLV31-20
ENCODE_alias	brenton-graveley:RUVBL1-BGHcLV31	brenton-graveley:RUVBL1-BGHcLV31-19	brenton-graveley:L-RUVBL1-BGHcLV31-19	brenton-graveley:RUVBL1-BGHcLV31-19_S11_L001_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:RUVBL1-BGHcLV31-19_S11_L001_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:RUVBL1-BGHcLV31-HepG2	brenton-graveley:RUVBL1-BGHcLV31-20	brenton-graveley:L-RUVBL1-BGHcLV31-20	brenton-graveley:RUVBL1-BGHcLV31-20_S12_L001_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:RUVBL1-BGHcLV31-20_S12_L001_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR785SZL	ENCBS332QIZ	ENCLB200COM	ENCFF684MIP	ENCFF971BLV	ENCSR312QIX	ENCBS092QEJ	ENCLB074MTY	ENCFF081SGH	ENCFF868TSO
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	BGHcLV31-19	BGHcLV31-19	BGHcLV31-19	BGHcLV31-19	BGHcLV31-19	BGHcLV31-19	BGHcLV31-20	BGHcLV31-20	BGHcLV31-20	BGHcLV31-20
Sample Name	RUVBL1-BGHcLV31-19	RUVBL1-BGHcLV31-19	RUVBL1-BGHcLV31-19	RUVBL1-BGHcLV31-19	RUVBL1-BGHcLV31-19	RUVBL1-BGHcLV31-19	RUVBL1-BGHcLV31-20	RUVBL1-BGHcLV31-20	RUVBL1-BGHcLV31-20	RUVBL1-BGHcLV31-20
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		RUVBL1-BGHcLV31-19.pdf	L-RUVBL1-BGHcLV31-19.pdf				RUVBL1-BGHcLV31-20.pdf	L-RUVBL1-BGHcLV31-20.pdf
ID	7449	7509	7617	7727	7837	7941	7510	7618	7728	7838

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
RUVBL1-BGHcLV31-19_S11_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set52/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1985	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	6531
RUVBL1-BGHcLV31-19_S11_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set52/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1985	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	6585
RUVBL1-BGHcLV31-19_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set52/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1985					GRCh38	V40	RUVBL1-BGHcLV31-19_S11_L001_R1_001.filtered.trimmed.paired.fastq.gz,RUVBL1-BGHcLV31-19_S11_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18452
RUVBL1-BGHcLV31-19_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	1985					GRCh38	V40	RUVBL1-BGHcLV31-19/Aligned.sortedByCoord.out.bam		ENCORE2	18506
RUVBL1-BGHcLV31-19_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	1985					GRCh38	V40	RUVBL1-BGHcLV31-19/Aligned.sortedByCoord.out.bam		ENCORE2	18560
RUVBL1-BGHcLV31-19_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	1985					GRCh38	V40	RUVBL1-BGHcLV31-19/Aligned.sortedByCoord.out.bam		ENCORE2	18614
RUVBL1-BGHcLV31-19_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	1985					GRCh38	V40	RUVBL1-BGHcLV31-19/Aligned.sortedByCoord.out.bam		ENCORE2	18668
RUVBL1-BGHcLV31-19_quant.sf	ENCODE_DATA/set52/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1985					GRCh38	V40	RUVBL1-BGHcLV31-19_S11_L001_R1_001.filtered.trimmed.paired.fastq.gz,RUVBL1-BGHcLV31-19_S11_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18722
RUVBL1-BGHcLV31-20_S12_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set52/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1986	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	6532
RUVBL1-BGHcLV31-20_S12_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set52/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1986	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	6586
RUVBL1-BGHcLV31-20_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set52/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1986					GRCh38	V40	RUVBL1-BGHcLV31-20_S12_L001_R1_001.filtered.trimmed.paired.fastq.gz,RUVBL1-BGHcLV31-20_S12_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18453
RUVBL1-BGHcLV31-20_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	1986					GRCh38	V40	RUVBL1-BGHcLV31-20/Aligned.sortedByCoord.out.bam		ENCORE2	18507
RUVBL1-BGHcLV31-20_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	1986					GRCh38	V40	RUVBL1-BGHcLV31-20/Aligned.sortedByCoord.out.bam		ENCORE2	18561
RUVBL1-BGHcLV31-20_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	1986					GRCh38	V40	RUVBL1-BGHcLV31-20/Aligned.sortedByCoord.out.bam		ENCORE2	18615
RUVBL1-BGHcLV31-20_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	1986					GRCh38	V40	RUVBL1-BGHcLV31-20/Aligned.sortedByCoord.out.bam		ENCORE2	18669
RUVBL1-BGHcLV31-20_quant.sf	ENCODE_DATA/set52/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1986					GRCh38	V40	RUVBL1-BGHcLV31-20_S12_L001_R1_001.filtered.trimmed.paired.fastq.gz,RUVBL1-BGHcLV31-20_S12_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18723