RUVBL1 RNA-Seq in K562

General Information


RBP	RUVBL1
Cell_Line	K562
Method	CRISPR
Exp_Name	RUVBL1-BGKcLV33-K562
ENCODE_series_ID	ENCSR031YNO
Batch_ID	BGKcLV33
Pool ID	Pool-220418
Local_Set_Name	set53
ENCODE_KD_Exp_ID	ENCSR119PLU
ENCODE_CN_Exp_ID	ENCSR271ZAB
Rep1	RUVBL1-BGKcLV33-23
Rep2	RUVBL1-BGKcLV33-24
CN1	NT-BGKcLV33-1
CN2	NT-BGKcLV33-2
Rep1_qPCR
Rep2_qPCR
Rep1_WB	23.9
Rep2_WB	25.7
Antibody Cat#	A302-832A
Antibody Lot#	LOT #1
Antibody DCC ID
Status	Submitted
Project	ENCODE4
ID	897

Experiment Information (Status: Released)

	BGKcLV33-17	BGKcLV33-17	BGKcLV33-17	BGKcLV33-18	BGKcLV33-18	BGKcLV33-18
idx	1119	1194	1196	1120	1195	1197
TRCN#_or_BGC#	BGC#0000836	BGC#0000829	BGC#0000829	BGC#0000836	BGC#0000829	BGC#0000829
shRNA_or_gRNA_sequence	ACTTGGATGTGGCTAATGCG	TGACGCTGGTGGCGACGCGA	TGACGCTGGTGGCGACGCGA	ACTTGGATGTGGCTAATGCG	TGACGCTGGTGGCGACGCGA	TGACGCTGGTGGCGACGCGA
PAM	CGG	AGG	AGG	CGG	AGG	AGG
Name	RUVBL1_94	RPUSD2_97	RPUSD2_97	RUVBL1_94	RPUSD2_97	RPUSD2_97
Sample_ID	BGKcLV33-17	BGKcLV33-17	BGKcLV33-17	BGKcLV33-18	BGKcLV33-18	BGKcLV33-18
transduction_Date	12/7/21	2/22/22	2/22/22	12/7/21	2/22/22	2/22/22
days	D6	D6	D6	D6	D6	D6
RBP_name	RUVBL1	RPUSD2	RPUSD2	RUVBL1	RPUSD2	RPUSD2
qPCR_result		xx	xx		xx	xx
Ave_qPCR
RT-qPCR_primer-F
RT-qPCR_primer-R
protein_conc	430	2379	2379	464	1748	1748
WB_result	0.0	85.8	86.9	0.0	83.7	87.2
Ave_WB	0.0	84.7	87.0
WB_DONE_date	1/19/22	3/7/22	3/2/22
MW	50kd	61kd	61kd
IP
antibody_Cat#	A304-716A	A305-210A	A305-209A	LOT #1	LOT #1	LOT #1
Antibody DCC ID		ENCAB939JYD	ENCAB305MHJ		8/4/22	8/4/22
submitted_to_DCC_date			8/16/22
Rep1_TPM	0	0	0	0	0	0
Rep2_TPM	0	0	0	0	0	0
Action			Ready			Ready
Library_start_date			04/13/22			04/13/22
repeat_library
Note
ID	5259	5334	5336	5260	5335	5337

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
RPUSD2	Product_ID: A305-209A Lot_ID: 1 Source: Bethyl Labs Target Name: RPUSD2-human
RPUSD2	Product_ID: A305-210A Lot_ID: 1 Source: Bethyl Labs Target Name: RPUSD2-human

Experiment Status

	BGKcLV33-17	BGKcLV33-17	BGKcLV33-17	BGKcLV33-18	BGKcLV33-18	BGKcLV33-18
Sample_ID	BGKcLV33-17	BGKcLV33-17	BGKcLV33-17	BGKcLV33-18	BGKcLV33-18	BGKcLV33-18
Sample Name
Sample Name	RPUSD2-BGKcLV33-17			RPUSD2-BGKcLV33-18
RBP	RPUSD2	RUVBL1	RPUSD2	RPUSD2	RUVBL1	RPUSD2
Cell_Line	K562	K562	K562	K562	K562	K562
Exp UID
Status	Released	NotSatisfied	NotSatisfied	Released	NotSatisfied	NotSatisfied
Status_date	2022-10-28	2022-03-30	2022-03-30	2022-10-28	2022-03-30	2022-03-30
Project	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4
Note
ID	10645	10703	10763	10646	10704	10764

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV33-17	BGKcLV33-18
Sample #	15	16
Sample Name	RPUSD2-BGKcLV33-17	RPUSD2-BGKcLV33-18
Sample_Name_Alias
Index Well Position	G02	H02
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2022-04-06	2022-04-06
Lib_ID	Lib-220406	Lib-220406
Tecan_Location
Tecan
Tecan_date
Size_bp	300	307
Peak_Molarity	50.00	59.40
libSampleQC_DNA_Well	DNA_Library_set53/set1/G6.png	DNA_Library_set53/set1/H6.png
RIN	9.8	9.8
libSample_RNA_Well	RNA_Library_set53/set1/G2.png	RNA_Library_set53/set1/H2.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2022-04-18	2022-04-18
Sample_ID	BGKcLV33-17	BGKcLV33-18
RBP	RPUSD2	RPUSD2
Batch_ID	BGKcLV33	BGKcLV33
WB_result	86.900	87.200
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	3276	3277

Sequencing Information

	BGKcLV33-17	BGKcLV33-18
Sample_ID	BGKcLV33-17	BGKcLV33-18
Sample Name	RPUSD2-BGKcLV33-17	RPUSD2-BGKcLV33-18
Pool ID	Pool-220418	Pool-220418
LocalServer_folder	set53	set53
total_reads	78,736,262	75,133,716
total_aligned_reads	70,183,076	66,146,848
unique_aligned_reads	64,162,574	60,328,314
percent_uniqueAligned	0.81491	0.80295
correlation_replicates	0.996577	0.996577
spikein_reads	8,198	8,288
percent_spikeins	0.00010	0.00011
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	2043	2044

Data Submission Information

	BGKcLV33-17	BGKcLV33-17	BGKcLV33-17	BGKcLV33-17	BGKcLV33-17	BGKcLV33-17	BGKcLV33-18	BGKcLV33-18	BGKcLV33-18	BGKcLV33-18
ENCODE_alias	brenton-graveley:RPUSD2-BGKcLV33	brenton-graveley:RPUSD2-BGKcLV33-17	brenton-graveley:L-RPUSD2-BGKcLV33-17	brenton-graveley:RPUSD2-BGKcLV33-17_S69_L002_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:RPUSD2-BGKcLV33-17_S69_L002_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:RPUSD2-BGKcLV33-K562	brenton-graveley:RPUSD2-BGKcLV33-18	brenton-graveley:L-RPUSD2-BGKcLV33-18	brenton-graveley:RPUSD2-BGKcLV33-18_S70_L002_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:RPUSD2-BGKcLV33-18_S70_L002_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR563QCQ	ENCBS556WPL	ENCLB101GCF	ENCFF538BGJ	ENCFF654YHO	ENCSR705LEY	ENCBS013NVH	ENCLB696WVQ	ENCFF710WLH	ENCFF901SNL
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	BGKcLV33-17	BGKcLV33-17	BGKcLV33-17	BGKcLV33-17	BGKcLV33-17	BGKcLV33-17	BGKcLV33-18	BGKcLV33-18	BGKcLV33-18	BGKcLV33-18
Sample Name	RPUSD2-BGKcLV33-17	RPUSD2-BGKcLV33-17	RPUSD2-BGKcLV33-17	RPUSD2-BGKcLV33-17	RPUSD2-BGKcLV33-17	RPUSD2-BGKcLV33-17	RPUSD2-BGKcLV33-18	RPUSD2-BGKcLV33-18	RPUSD2-BGKcLV33-18	RPUSD2-BGKcLV33-18
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
		LV53_biosample_protocol	LV53_library_protocol				LV53_biosample_protocol	LV53_library_protocol
protocol_URL		RPUSD2-BGKcLV33-17.pdf	L-RPUSD2-BGKcLV33-17.pdf				RPUSD2-BGKcLV33-18.pdf	L-RPUSD2-BGKcLV33-18.pdf
ID	7478	7565	7675	7785	7895	7967	7566	7676	7786	7896

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
RPUSD2-BGKcLV33-17_S69_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set53/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2043	NovaSeq6000	100	paired-ended	1				NT-BGKcLV33-1_S55_L002_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV33-2_S56_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	6621
RPUSD2-BGKcLV33-17_S69_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set53/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2043	NovaSeq6000	100	paired-ended	2				NT-BGKcLV33-1_S55_L002_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV33-2_S56_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	6677
RPUSD2-BGKcLV33-17_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set53/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2043					GRCh38	V40	RPUSD2-BGKcLV33-17_S69_L002_R1_001.filtered.trimmed.paired.fastq.gz,RPUSD2-BGKcLV33-17_S69_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18098
RPUSD2-BGKcLV33-17_Signal.Unique.strand+.bw	ENCODE_DATA/set53/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2043					GRCh38	V40	RPUSD2-BGKcLV33-17/Aligned.sortedByCoord.out.bam		ENCORE2	18154
RPUSD2-BGKcLV33-17_Signal.Unique.strand-.bw	ENCODE_DATA/set53/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2043					GRCh38	V40	RPUSD2-BGKcLV33-17/Aligned.sortedByCoord.out.bam		ENCORE2	18210
RPUSD2-BGKcLV33-17_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set53/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2043					GRCh38	V40	RPUSD2-BGKcLV33-17/Aligned.sortedByCoord.out.bam		ENCORE2	18266
RPUSD2-BGKcLV33-17_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set53/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2043					GRCh38	V40	RPUSD2-BGKcLV33-17/Aligned.sortedByCoord.out.bam		ENCORE2	18322
RPUSD2-BGKcLV33-17_quant.sf	ENCODE_DATA/set53/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2043					GRCh38	V40	RPUSD2-BGKcLV33-17_S69_L002_R1_001.filtered.trimmed.paired.fastq.gz,RPUSD2-BGKcLV33-17_S69_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18378
RPUSD2-BGKcLV33-18_S70_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set53/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2044	NovaSeq6000	100	paired-ended	1				NT-BGKcLV33-1_S55_L002_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV33-2_S56_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	6622
RPUSD2-BGKcLV33-18_S70_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set53/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2044	NovaSeq6000	100	paired-ended	2				NT-BGKcLV33-1_S55_L002_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV33-2_S56_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	6678
RPUSD2-BGKcLV33-18_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set53/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2044					GRCh38	V40	RPUSD2-BGKcLV33-18_S70_L002_R1_001.filtered.trimmed.paired.fastq.gz,RPUSD2-BGKcLV33-18_S70_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18099
RPUSD2-BGKcLV33-18_Signal.Unique.strand+.bw	ENCODE_DATA/set53/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2044					GRCh38	V40	RPUSD2-BGKcLV33-18/Aligned.sortedByCoord.out.bam		ENCORE2	18155
RPUSD2-BGKcLV33-18_Signal.Unique.strand-.bw	ENCODE_DATA/set53/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2044					GRCh38	V40	RPUSD2-BGKcLV33-18/Aligned.sortedByCoord.out.bam		ENCORE2	18211
RPUSD2-BGKcLV33-18_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set53/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2044					GRCh38	V40	RPUSD2-BGKcLV33-18/Aligned.sortedByCoord.out.bam		ENCORE2	18267
RPUSD2-BGKcLV33-18_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set53/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2044					GRCh38	V40	RPUSD2-BGKcLV33-18/Aligned.sortedByCoord.out.bam		ENCORE2	18323
RPUSD2-BGKcLV33-18_quant.sf	ENCODE_DATA/set53/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2044					GRCh38	V40	RPUSD2-BGKcLV33-18_S70_L002_R1_001.filtered.trimmed.paired.fastq.gz,RPUSD2-BGKcLV33-18_S70_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18379